Targeting pax2 for the induction of defb1-mediated tumor immunity and cancer therapy

Description of equivalent WO 2007047512 A2

TARGETING PAX2 FOR THE INDUCTION OF DEFB1-MEDIATED TUMOR IMMUNITY AND CANCER THERAPY

Brief Description of Invention

Current anticancer chemotherapies that are based on alkylating agents, antimetabolites and natural products are heterogeneous in their mechanism of action. Consequently, most of them also act against normal cells resulting in severe side effects and toxicity to the patient. Disclosed herein is a method for the treatment of advanced prostate cancer using human beta defensin-1 (DEFBl), which is a naturally component of the innate immune system, to induce prostate cancer tumor immunity. This is accomplished through endogenously added DEFBl, ectopically expressed DEFBl or de novo expression of DEFBl by inhibiting the transcriptional repressor PAX2 by a variety of mechanisms or agents. Inhibiting PAX2 expression by siRNA therapy turns on DEFBl expression and generates DEFBl -mediated cell death in prostate cancer. With this, the technology described here is used for the design of small molecules to specifically block PAX2 expression. Alternatively provided are molecules containing the CCTTG (SEQ ID NO:1) recognition sequence (in either forward of reverse orientation) that to bind to the DNA- binding domain of PAX2 preventing its binding to the DEFBl promoter through competitive inhibition. This permits DEFBl expression, triggering both an innate and adaptive immune response, and resulting in the killing of prostate cancer cells and the suppression of prostate tumor formation. In conclusion, these modulators of innate tumor immunity, PAX2 and DEFBl, and the molecular therapies based on them provide for the treatment of prostate cancer with little toxicity to the patient.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings illustrate one or more embodiments of the invention and, together with the written description, serve to explain the principles of the invention. Wherever possible, the same reference numbers are used throughout the drawings to refer to the same or like elements of an embodiment.

Figure 1. QRT-PCR analysis of DEFBl Expression. In order to verify induction of DEFBl expression, QRT-PCR was performed. A, DEFBl relative expression levels were compared in clinical samples from 6 patients that underwent radical prostatectomies. B, DEFBl relative expression levels were compared in benign and malignant prostatic clinical samples, hPrEC cells and in prostate cancer cell lines before and after DEFBl induction. C, DEFBl relative expression levels were analyzed in benign tissue, malignant tissue and PIN in a single tissue section. D, DEFBl expression in benign tissue, malignant tissue and PIN in one patient was compared to the average DEFBl expression level found in benign tissue.

Figure 2. Microscopic analysis of DEFBl induced changes in membrane integrity and cell morphology. Cell morphology of DU145, PC3 and LNCaP was analyzed by phase contrast microscopy after 48 hours of DEFBl induction. Membrane ruffling is indicated by black arrows and apoptotic bodies are indicated white arrows.

Figure 3. Analysis of DEFBl Cytotoxicity in Prostate Cancer Cells. The prostate cell lines DU145, PC3 and LNCaP were treated with PonA to induce DEFBl expression for 1-3 days after which MTT assay was performed to determine cell viability. Results represent mean ± s.d., n=9.

Figure 4. Induction of cell death in DU145 and PC3 cells by DEFBl. DEFBl expression was induced in prostate cancer cell lines DUl 45 (A) and PC3 (B) and then subjected to annexin V/FITC/propidium iodide staining and flow cytometric analysis. Cells positive for propidium iodide and annexin V were considered apoptotic. Times of induction are shown under each panel. Numbers next to the boxes for each time point represent the percentages of propidium iodide (PI)^" annexin V⁺ cells (lower right quadrant), and Pl⁺ annexin V⁺ cells (upper right quadrant). The data are from a single experiment that is representative of three separate experiments.

Figure 5. Pan-caspase analysis following DEFBl induction. DU145 and PC3 cells were stained with FAM-VAD-FMK-labeled fluoromethyl ketone to detect caspase activity. Cells were visible under DIC for each condition. Confocal microscopic analysis revealed no caspase staining in control DU145 (B), PC3 cells (F) and LNCaP (J). Cells treated with PonA for 24 hours to induce DEFBl revealed caspase activity in DU145 (D) and PC3 (H). No caspase activity was detected in LNCaP (L). Figure 6. Silencing of PAX2 Protein Expression Following PAX2 siRNA Treatment.

(a) Western blot analysis of PC3 and DUl 45 cells transfected with PAX2 siRNA duplex at day zero (lane 1), day two (lane 2), and day four (lane 3). (b) Western blot analysis of PC3 and DU145 cells transfected with PAX2 siRNA duplex at day zero (lane 1), day two (lane 2), day four (lane 3) and day 6 (lane 4). PAX2 protein was undetectable as early as after four days of treatment (lane 3) in DU145 cells and after six days of treatment in PC3. Blots were stripped and re-probed for /?-actin as an internal control.

Figure 7. Analysis of Prostate Cancer Cells Growth after Treatment with Pax 2 siRNA. Phase contrast microscopic analysis of DU145, PC3 and LNCaP at 6 days in the presence of normal growth media. Treatment with negative control siRNA had no effect on the cells. However, there was a significant reduction in cell number in all three lines following treatment with PAX2 siRNA.

Figure 8. Analysis of Cell Death Following siRNA Silencing of PAX2. Prostate cancer cell lines PC3, DU145, and LNCaP were treated with 0.5 μg of a pool of four PAX2 siRNA's or four non-specific control siRNA's for 2, 4 or 6 days after which MTT assay was done to determine cell viability. Results represent mean ± s.d., n=9.

Figure 9. Analysis of Caspase Activity. DU145, PC3 and LNCaP cells were stained with carboxyfluorescein-labeled fluoromethyl ketone to detected caspase activity following treatment with PAX2 siRNA. Confocal microscopic analysis of untreated and treated cells show cells were visible with DIC. Analysis under fluorescence revealed no caspase staining in control DUl 45 (B), PC3 cells (F) and LNCaP cells (J). However, cell treated with PAX2 siRNA induced caspase activity in DU145 (D), PC3 (H) and LNCaP (L).

Figure 10. Analysis of Apoptotic Factors Following PAX2 siRNA Treatment. Changes in expression of pro-apoptotic factors were compared in untreated control cells and in cells treated for six days with PAX2 siRNA. A, BAX expression levels increased in DU145, PC3 and LNCaP. B, BID expression increased in DUl 45 and LNCaP, but change in PC3. C, BAD expression levels increased in all three cell lines. Figure 11. Model of PAX2 Binding to DNA Recognition Sequence. The PAX2 transcriptional repressor binds to a CCTTG (SEQ ID NO.l) recognition site immediately adjacent to the DEFBl TATA box preventing transcription and DEFBl protein expression. Inhibition of PAX2 protein expression allows normal DEFBl expression.

Figure 12. Illustration of the DEFBl Reporter Construct. The DEFBl promoter consisting of the first 160 bases upstream of the mRNA start site was PCR amplified from DU145 cell and ligated into the pGL3 luciferase reporter plasmid.

Figure 13. Inhibition of PAX2 Results in DEFBl Expression. DU145, PC3, LNCaP and HPrEC were treated for 48 hours with PAX2 siRNA. QRT-PCR analysis before treatment showed no DEFBl expression in DU145, PC3 and LNCaP. However, DEFBl expression was restored following treatment in all lines. There was no change in DEFBl expression following siRNA treatment of PAX2-null HprEC.

Figure 14. Inhibition of PAX2 Results in Increased DEFBl Promoter Activity. PC3 promoter/pGL3 and DU145 promoter/pGL3 construct were generated and were transfected into PC3 and DUl 45 cells, respectively. Promoter activity was compared before and after PAX2 inhibition by siRNA treatment. DEFBl promoter activity increased 2.65-fold in DU145 and 3.78 fold in PC3 following treatment.

Figure 15. DEFBl Causes Loss of Membrane Integrity. Membrane integrity of PC3 and DU145 cells was analyzed by confocal laser microscopy following the induction of DEFBl expression for 48 hours. Green staining was indicative of the localization of AO, and red staining represents EtBr. Yellow staining represents the co-localization of both AO and EtBr in the nucleus.

Figure 16. PAX2 Inhibition Results in Loss of Membrane Integrity. Cells were treated for 48 hours with PAX2 siRNA and membrane integrity was analyzed by confocal laser microscopy.

Figure 17. ChIP Analysis of PAX2 binding to DEFBl Promoter. CbJP analysis was performed on DUl 45 and PC3 cells. Following immunoprecipitation with an anti-PAX2 antibody, PCR was performed to detect the DEFBl promoter region containing the GTTCC PAX2 recognition site. This demonstrates that the PAX2 transcriptional repressor is bound to the DEFBl promoter in prostate cancer cell lines.

Figure 18. Predicted Structure of the PrdPD and PrdHD with DNA. The coordinates of the structures of the PrdPD bound to DNA (Xu et aL, 1995 and the PrdHD bound to DNA (Wilson et al., 1995) were used to construct a model of the two domains as they bound to a PHO site. The individual binding sites are abutted next to each other with a specific orientation as indicated. The PAI binding site is in red, the HD binding site is in blue, and the corresponding PAI domain is in turquoise, and HD is in yellow. The RED domain is oriented based on the PrdPD crystal structure.

Figure 19. Comparison of Consensus Sequences of Different Paired Domains. At the top of the Figure is drawn a schematic representation of protein±DNA contacts described in the crystallographic analysis of the Prd-paired-domain±DNA complex [9J. Empty boxes indicate a-helices, shaded boxes indicates b-sheets and a thick line indicate a b-turn. Contacting amino acids are shown by single-letter code. Only direct amino acid±base contacts are shown. Empty circles indicate major groove contacts while red arrows indicate minor groove contacts. This scheme is aligned to all known consensus sequences for paired- domain proteins (top strands only are shown). Vertical lines between consensus sequences indicate conserved base-pairs. Numbering of the positions is shown at the bottom of the Figure and it is the same as that used in [9 J.

DETAILED DESCRIPTION OF THE INVENTION

As shown herein, PAX2 inhibits expression of DEFBl, and DEFBl is shown to have tumor cell killing activity. Thus, provided is a method of treating cancer in a subject by inhibiting expression of PAX2. An example of a cancer treated by the present method is prostate cancer. The present methods are particularly effective for treatment of late stage prostate cancer.

In the cancer treatment methods disclosed, the method of inhibiting expression of PAX 2 can be by administration of a nucleic acid encoding a siRNA for PAX 2. Dharmachon is a commercial source for such siRNAs. The siRNA for use in the methods can be selected from the group consisting of: AUAGACUCGACUUGACUUCUU (SEQ ID NO:2) AUCUUCAUCACGUUUCCUCUU (SEQ ID NO-A) GUAUUCAGCAAUCUUGUCCUU (SEQ ID NO:6) GAUUUGAUGUGCUCUGAUGUU (SEQ ID NO:8)

The following table illustrates the above antisense sequences and their corresponding sense sequences.

Sense (5'-3') Antisense (5'-3')

Sequence A 5'- GAAGUCAAGUCGAGUCUAUUU-S' δ'-AUAGACUCGACUUGACUUCUU-S'

Sequence B 5'-GAGGAAACGUGAUGAAGAUUU-S' δ'-AUCUUCAUCACGUUUCCUCUU-S'

Sequence C 5'-GGACAAGAUUGCUGAAUACUU-3^■ δ'-GUAUUCAGCAAUCUUGUCCUU-S'

Sequence D δ'-CAUCAGAGCA-CAUCAAAUCUU-S' δ'-GAUUUGAUGUGCUCUGAUGUU-S'

Further examples of molecules that inhibit PAX2 include: #1 ACCCGACTATGTTCGCCTGG (SEQID NO:XXX), #2 AAGCTCTGGATCGAGTCTTTG (SEQ ID NO:XXX), and #4 ATGTGTCAGGCACACAGACG (SEQ ID NO:XXX). #4 was shown to inhibit PAX2 (Davies et al., Hum. MoI. Gen Jan. 15, 13 (2); 235).

Another paper (Muratovska et al., Paired-Box genes, are frequently expressed in cancer and often required for cancer cell survival Oncogene (2003) 22, 7989-7997) discloses the following siRNAs: GUCGAGUCUAUCUGCAUCCTT (SEQ ID NO:xxx) and GGAUGCAGAUAGACUCGACTT (SEQ ID NO:XXX).

To down-regulate Pax2 expression, Fonsato et al. transfected tumor-derived endothelial cells with an anti-sense PAX2 vector. See Fonsato V. et al (Expression of Pax2 in human renal tumor-derived endothelial cells sustains apoptosis resistance and angiogenesis, Am J Pathol. 2006 Feb;168(2):706-l), incorporated herein by referene for its description of this molecule. Similarly, Hueber et al. teach that PAX2 antisense cDNA and PAX2-small interfering RNA (100 nM) reduce endogenous PAX2 protein. See Hueber et al. PAX2 inactivation enhances cisplatin-induced apoptosis in renal carcinoma cells, Kidney Int. 2006 Apr;69(7):l 139-45 incorporated herein for its teaching of PAX2 antisense and PAX2 siRNA.

Additional inhibitors of PAX2 expression or the binding of PAX2 to the DEFBl promoter are provided to increase DEFBl expression in the presently disclosed methods. For example, small molecules and antibodies are designed based on the present studies to interfere with or inhibit the binding of PAX2 to the DEFBl promoter.

As shown herein, PAX2 inhibits expression of DEFBl, and DEFBl is shown to have tumor cell killing activity. Thus, a method of treating cancer in a subject by administering DEFBl is also provided. An example of a cancer treated by the present method is prostate cancer.

Similarly, provided is a method of treating cancer in a subject by increasing expression of DEFBl in the subject. The present methods of administering or increasing the expression of DEFBl are particularly effective for treatment of late stage prostate cancer. m one embodiment of the methods of the invention for treating cancer by administering DEFBl or increasing DEFBl expression (e.g., by inhibiting expression or binding of PAX2), the subject is a subject diagnosed with prostate cancer. In a further embodiment of the methods of the invention for treating cancer by administering DEFBl or increasing DEFBl expression (e.g., by inhibiting expression or binding of PAX2), the subject is a subject diagnosed with advanced (late stage) prostate cancer. hi the method wherein the expression of DEFBl is increased, it can be increased by blocking the binding of PAX2 to the DEFBl promoter. The blocking of binding of PAX2 to the DEFBl promoter can be by administration of an oligonucleotide containing the PAX2 DNA binding site of DEFBl. This oligonucleotide can be complementary to the sequence of PAX2 that binds to the DEFBl promoter. Alternatively, the oligonucleotide can interact with the PAX2 in a way that inhibits binding to DEFBl . This interaction can be based on three-dimensional structure rather than primary nucleotide sequence.

PAX proteins are a family of transcription factors conserved during evolution and able to bind specific DNA sequences through a domains called a "paired domain" and a "homeodomain". The paired domain (PD) is a consensus sequence shared by certain PAX proteins (e.g., PAX2 and PAX6). The PD directs DNA binding of amino acids located in the o3-helix forming a DNA-Protein complex. For PAX2, the amino acids in the HD recognize and interact specifically with a CCTTG DNA core sequence. Therefore, the critical region for PAX2 binding to DEFBl would be AAGTTCACCCTTGACTGTG. Oligonucleotides up to and exceeding 64 bases in length, which include this sequence or its complement are expected to be inhibitors. The DNA-binding specificity of the PAX-8 paired domain was investigated. Site selection experiments indicate that PAX-8 binds to a consensus sequence similar to those bound by PAX-2 and PAX-5. When consensus sequences of various paired domains are observed in light of recent structural studies describing paired-domain-DNA interaction [Xu, Rould, Jun, Desplan and Pabo (1995) Cell 80, 639-650], it appears that base-pairs contacted in the minor groove are conserved, while most of the base-pairs contacted in the major groove are not. Therefore a network of specific minor groove contacts is a common characteristic of paired-domain-DNA interactions. The functional importance of such a network can be successfully tested by analyzing the effect of consensus-based mutations on the PAX2 binding site of the DEFBl promoter.

The PAX2 DNA binding site of DEFBl can comprise SEQ ID NO:1 (CCTTG).

The oligonucleotide comprising, to the PAX2 DNA binding site of DEFBl is selected from the group consisting of

X₁ CCTTG (SEQ ID NO: I)X₂, wherein X₁ is from 1 to 35 contiguous flanking nucleotides of DEFBl and X₂ is from 1 to 35 nucleotides. The nucleotides can be contiguous nucleotides that normally flank the PAX2 DNA binding site of DEFBl. Alternatively, they can be unrelated to DEFBl, and selected routinely to avoid interference with the recognition sequence.

For example, the inhibitory oligonucleotides can be selected from the group consisting of:

CTCCCTTCAGTTCCGTCGAC (SEQIDNO:9) CTCCCTTCACCTTGGTCGAC (SEQ IDNO:10)

ACTGTGGCACCTCCCTTCAGTTCCGTCGACGAGGTTGTGC (SEQ IDNO:12) ACTGTGGCACCTCCCTTCACCTTGGTCGACGAGGTTGTGC (SEQIDNO:13)

The disclosed compositions can be used to treat any disease where uncontrolled cellular proliferation occurs such as cancers. A non-limiting list of different types of cancers is as follows: lymphomas (Hodgkins and non-Hodgkins), leukemias, carcinomas, carcinomas of solid tissues, squamous cell carcinomas, adenocarcinomas, sarcomas, gliomas, high grade gliomas, blastomas, neuroblastomas, plasmacytomas, histiocytomas, melanomas, adenomas, hypoxic tumors, myelomas, ADDS-related lymphomas or sarcomas, metastatic cancers, or cancers in general.

A representative but non-limiting list of cancers that the disclosed compositions can be used to treat is the following: lymphoma, B cell lymphoma, T cell lymphoma, mycosis fungoides, Hodgkin's Disease, myeloid leukemia, bladder cancer, brain cancer, nervous system cancer, head and neck cancer, squamous cell carcinoma of head and neck, kidney cancer, lung cancers such as small cell lung cancer and non-small cell lung cancer, neuroblastoma/glioblastoma, ovarian cancer, pancreatic cancer, prostate cancer, skin cancer, liver cancer, melanoma, squamous cell carcinomas of the mouth, throat, larynx, and lung, colon cancer, cervical cancer, cervical carcinoma, breast cancer, and epithelial cancer, renal cancer, genitourinary cancer, pulmonary cancer, esophageal carcinoma, head and neck carcinoma, large bowel cancer, hematopoietic cancers; testicular cancer; colon and rectal cancers, prostatic cancer, or pancreatic cancer. Compounds disclosed herein may also be used for the treatment of precancer conditions such as cervical and anal dysplasias, other dysplasias, severe dysplasias, hyperplasias, atypical hyperplasias, and neoplasias. Further, a number of diseases stemming from chronic inflammation, e.g., prostatitis and Benign Prostatic Hypertrophy (BPH), as well as various cancers of the prostate, can be impacted by the present methods and compounds.

DEFBl's gene locus (8p23.3) is a hotspot for deletions and has been linked to patients with poorer prognosis. Thus, DEFBl (and perhaps PAX2) can be used as a biomarker, e.g., in a screening for the early detection of prostate cancer. Furthermore, data presented here indicate that its loss may occur as early as PIN (or even before), and may be a major contributing factor to the onset of prostate cancer.

Nucleic Acid Homology/Identity/Similarity

It is understood that as discussed herein the use of the terms homology and identity mean the same thing as similarity. Thus, for example, if the use of the word homology is used between two non-natural sequences it is understood that this is not necessarily indicating an evolutionary relationship between these two sequences, but rather is looking at the similarity or relatedness between their nucleic acid sequences. Many of the methods for determining homology between two evolutionarily related molecules are routinely applied to any two or more nucleic acids or proteins for the purpose of measuring sequence similarity regardless of whether they are evolutionarily related or not.

In general, it is understood that one way to define any known variants and derivatives or those that might arise, of the disclosed genes and proteins herein, is through defining the variants and derivatives in terms of homology to specific known sequences.

This identity of particular sequences disclosed herein is also discussed elsewhere herein. In general, variants of genes and proteins herein disclosed typically have at least, about 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 91, 98, or 99 percent homology to the stated sequence or the native sequence. Those of skill in the art readily understand how to determine the homology of two proteins or nucleic acids, such as genes. For example, the homology can be calculated after aligning the two sequences so that the homology is at its highest level.

Another way of calculating homology can be performed by published algorithms. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Adv. Appl. Math. 2: 482 (1981), by the homology alignment algorithm of Needleman and Wunsch, J. MoL Biol. 48: 443 (1970), by the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by inspection.

The same types of homology can be obtained for nucleic acids by for example the algorithms disclosed in Zuker, M. Science 244:48-52, 1989, Jaeger et al. Proc. Natl. Acad. Sci. USA 86:7706-7710, 1989, Jaeger et al. Methods Enzymol. 183:281-306, 1989 which are herein incorporated by reference for at least material related to nucleic acid alignment. It is understood that any of the methods typically can be used and that in certain instances the results of these various methods may differ, but the skilled artisan understands if identity is found with at least one of these methods, the sequences would be said to have the stated identity, and be disclosed herein.

For example, as used herein, a sequence recited as having a particular percent homology to another sequence refers to sequences that have the recited homology as calculated by any one or more of the calculation methods described above. For example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using the Zuker calculation method even if the first sequence does not have 80 percent homology to the second sequence as calculated by any of the other calculation methods. As another example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using both the Zuker calculation method and the Pearson and Lipman calculation method even if the first sequence does not have 80 percent homology to the second sequence as calculated by the Smith and Waterman calculation method, the Needleman and Wunsch calculation method, the Jaeger calculation methods, or any of the other calculation methods. As yet another example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using each of calculation methods (although, in practice, the different calculation methods will often result in different calculated homology percentages). Hybridization/selective hybridization

The term hybridization typically means a sequence driven interaction between at least two nucleic acid molecules, such as an oligonucleotide inhibitor, a primer or a probe and a gene. Sequence driven interaction means an interaction that occurs between two nucleotides or nucleotide analogs or nucleotide derivatives in a nucleotide specific manner. For example, G interacting with C or A interacting with T are sequence driven interactions. Typically sequence driven interactions occur on the Watson-Crick face or Hoogsteen face of the nucleotide. The hybridization of two nucleic acids is affected by a number of conditions and parameters known to those of skill in the art. For example, the salt concentrations, pH, and temperature of the reaction all affect whether two nucleic acid molecules will hybridize.

Parameters for selective hybridization between two nucleic acid molecules are well known to those of skill in the art. For example, in some embodiments selective hybridization conditions can be defined as stringent hybridization conditions. For example, stringency of hybridization is controlled by both temperature and salt concentration of either or both of the hybridization and washing steps. For example, the conditions of hybridization to achieve selective hybridization may involve hybridization in high ionic strength solution (6X SSC or 6X SSPE) at a temperature that is about 12-25°C below the Tm (the melting temperature at which half of the molecules dissociate from their hybridization partners) followed by washing at a combination of temperature and salt concentration chosen so that the washing temperature is about 5°C to 20°C below the Tm. The temperature and salt conditions are readily determined empirically in preliminary experiments in which samples of reference DNA immobilized on filters are hybridized to a labeled nucleic acid of interest and then washed under conditions of different stringencies. Hybridization temperatures are typically higher for DNA-RNA and RNA-RNA hybridizations. The conditions can be used as described above to achieve stringency, or as is known in the art. (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1989; Kunkel et al. Methods Enzymol. 1987:154:367, 1987 which is herein incorporated by reference for material at least related to hybridization of nucleic acids). A preferable stringent hybridization condition for a DNA:DNA hybridization can be at about 68°C (in aqueous solution) in 6X SSC or 6X SSPE followed by washing at 68°C. Stringency of hybridization and washing, if desired, can be reduced accordingly as the degree of complementarity desired is decreased, and further, depending upon the G-C or A-T richness of any area wherein variability is searched for. Likewise, stringency of hybridization and washing, if desired, can be increased accordingly as homology desired is increased, and further, depending upon the G-C or A-T richness of any area wherein high homology is desired, all as known in the art.

Another way to define selective hybridization is by looking at the amount (percentage) of one of the nucleic acids bound to the other nucleic acid. For example, in some embodiments selective hybridization conditions would be when at least about, 60, 65, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 percent of the limiting nucleic acid is bound to the non-limiting nucleic acid. Typically, the non-limiting nucleic acid is in for example, 10 or 100 or 1000 fold excess. This type of assay can be performed at under conditions where both the limiting and non-limiting nucleic acid are foF example, 10 fold or 100 fold or 1000 fold below their k_d, or where only one of the nucleic acid molecules is 10 fold or 100 fold or 1000 fold or where one or both nucleic acid molecules are above their k_d.

Another way to define selective hybridization is by looking at the percentage of nucleic acid that gets enzymatically manipulated under conditions where hybridization is required to promote the desired enzymatic manipulation, e.g., for primers. For example, in some embodiments selective hybridization conditions would be when at least about, 60, 65, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 percent of the primer is enzymatically manipulated under conditions which promote the enzymatic manipulation, for example if the enzymatic manipulation is DNA extension, then selective hybridization conditions would be when at least about 60, 65, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 percent of the primer molecules are extended. Preferred conditions also include those suggested by the manufacturer or indicated in the art as being appropriate for the enzyme performing the manipulation. Just as with homology, it is understood that there are a variety of methods herein disclosed for determining the level of hybridization between two nucleic acid molecules. It is understood that these methods and conditions may provide different percentages of hybridization between two nucleic acid molecules, but unless otherwise indicated meeting the parameters of any of the methods would be sufficient. For example if 80% hybridization was required and as long as hybridization occurs within the required parameters in any one of these methods it is considered disclosed herein.

It is understood that those of skill in the art understand that if a composition or method meets any one of these criteria for determining, hybridization either collectively or singly it is a composition or method that is disclosed herein.

Nucleotides and related molecules

A nucleotide is a molecule that contains a base moiety, a sugar moiety and a phosphate moiety. Nucleotides can be linked together through their phosphate moieties and sugar moieties creating an internucleoside linkage. The base moiety of a nucleotide can be adenin-9-yl (A), cytosin-1-yl (C), guanin-9-yl (G), uracil-1-yl (U), and thymin-1-yl (T). The sugar moiety of a nucleotide is a ribose or a deoxyribose. The phosphate moiety of a nucleotide is pentavalent phosphate. A non-limiting example of a nucleotide would be 3'-AMP (3'-adenosine monophosphate) or 5'-GMP (5'-guanosine monophosphate).

A nucleotide analog is a nucleotide which contains some type of modification to any of the base, sugar, or phosphate moieties. Modifications to the base moiety would include natural and synthetic modifications of A, C, G, and TYU as well as different purine or pyrimidine bases, such as uracil-5-yl (.psi.), hypoxanthin-9-yl (T), and 2-aminoadenin-9-yl. A modified base includes but is not limited to 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and

2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine. Additional base modifications can be found for example in U.S. Pat. No. 3,687,808, Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613, and Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B. ed., CRC Press, 1993. Certain nucleotide analogs, such as 5 -substituted pyrimidines, 6-azapyrimidines andN-2, N-6 and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine can increase the stability of duplex formation. Often time base modifications can be combined with for example a sugar modification, such as T- O-methoxyethyl, to achieve unique properties such as increased duplex stability. There are numerous United States patents such as 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121, 5,596,091; 5,614,617; and 5,681,941, which detail and describe a range of base modifications. Each of these patents is herein incorporated by reference.

Nucleotide analogs can also include modifications of the sugar moiety. Modifications to the sugar moiety would include natural modifications of the ribose and deoxyribose as well as synthetic modifications. Sugar modifications include but are not limited to the following modifications at the 2' position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-0-alkyl, wherein the alkyl, alkenyl and alkynyl maybe substituted or unsubstituted Ci to C_1O, alkyl or C₂ to C₁₀ alkenyl and alkynyl. 2' sugar modifications also include but are not limited to -O[(CH₂)_n O]_m CH₃, - O(CH₂)_n OCH₃, -O(CH₂)_n NH₂, -O(CH₂)_n CH₃, -O(CH₂)_n -ONH₂, and -O(CH₂)_nON[(CH₂)_n CH₃)J₂, where n and m are from 1 to about 10.

Other modifications at the 2' position include but are not limited to: C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH₃, OCN, Cl, Br, CN, CF₃, OCF₃, SOCH₃, SO₂ CH₃, ONO₂, NO₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties. Similar modifications may also be made at other positions on the sugar, particularly the 3' position of the sugar on the 3' terminal nucleotide or in 2'-5' linked oligonucleotides and the 5' position of 5' terminal nucleotide. Modified sugars would also include those that contain modifications at the bridging ring oxygen, such as CH₂ and S. Nucleotide sugar analogs may also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar. There are numerous United States patents that teach the preparation of such modified sugar structures such as 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; and 5,700,920, each of which is herein incorporated by reference in its entirety.

Nucleotide analogs can also be modified at the phosphate moiety. Modified phosphate moieties include but are not limited to those that can be modified so that the linkage between two nucleotides contains a phosphorothioate, chiral phosphorothioate, phosphorodithioate, phosphotriester, aminoalkylphosphotriester, methyl and other alkyl phosphonates including 3'-alkylene phosphonate and chiral phosphonates, phosphinates, phosphoramidates including 3 '-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates. It is understood that these phosphate or modified phosphate linkage between two nucleotides can be through a 3'-5' linkage or a 2'-5' linkage, and the linkage can contain inverted polarity such as 3'-5' to 5'-3' or 2'-5' to 5'-2\ Various salts, mixed salts and free acid forms are also included. Numerous United States patents teach how to make and use nucleotides containing modified phosphates and include but are not limited to, 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799; 5,587,361; and 5,625,050, each of which is herein incorporated by reference.

It is understood that nucleotide analogs need only contain a single modification, but may also contain multiple modifications within one of the moieties or between different moieties.

Nucleotide substitutes are molecules having similar functional properties to nucleotides, but which do not contain a phosphate moiety, such as peptide nucleic acid (PNA). Nucleotide substitutes are molecules that will recognize nucleic acids in a Watson- Crick or Hoogsteen manner, but which are linked together through a moiety other than a phosphate moiety. Nucleotide substitutes are able to conform to a double helix type structure when interacting with the appropriate target nucleic acid.

Nucleotide substitutes are nucleotides or nucleotide analogs that have had the phosphate moiety and/or sugar moieties replaced. Nucleotide substitutes do not contain a standard phosphorus atom. Substitutes for the phosphate can be for example, short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones;formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH₂ component parts. Numerous United States patents disclose how to make and use these types of phosphate replacements and include but are not limited to 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and 5,677,439, each of which is herein incorporated by reference.

It is also understood in a nucleotide substitute that both the sugar and the phosphate moieties of the nucleotide can be replaced, by for example an amide type linkage (aminoethylglycine) (PNA). United States patents 5,539,082; 5,714,331;and 5,719,262 teach how to make and use PNA molecules, each of which is herein incorporated by reference. (See also Nielsen et al., Science, 1991, 254, 1497-1500).

It is also possible to link other types of molecules (conjugates) to nucleotides or nucleotide analogs to enhance for example, cellular uptake. Conjugates can be chemically linked to the nucleotide or nucleotide analogs. Such conjugates include but are not limited to lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989,

86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Let., 1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N. Y. Acad. Sci.,

1992, 660, 306-309; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538), an aliphatic chain, e.g., dodecandiol or undecyl residues (Saison-Behmoaras et al., EMBO J., 1991, 10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259, 327-330; Svinarchuk et al., Biochimie,

1993, 75, 49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium l^-di-O-hexadecyl-rac-glycero-S-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids Res., 1990, 18, 3777-3783), apolyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14,

969-973), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654), apalmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277, 923-937. Numerous United States patents teach the preparation of such conjugates and include, but are not limited to U.S. Pat. Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730; 5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124; 5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737; 4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830; 5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022; 5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371; 5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941, each of which is herein incorporated by reference.

A Watson-Crick interaction is at least one interaction with the Watson-Crick face of a nucleotide, nucleotide analog, or nucleotide substitute. The Watson-Crick face of a nucleotide, nucleotide analog, or nucleotide substitute includes the C2, Nl, and C6 positions of a purine based nucleotide, nucleotide analog, or nucleotide substitute and the C2, N3, C4 positions of a pyrimidine based nucleotide, nucleotide analog, or nucleotide substitute.

A Hoogsteen interaction is the interaction that takes place on the Hoogsteen face of a nucleotide or nucleotide analog, which is exposed in the major groove of duplex DNA. The Hoogsteen face includes the N7 position and reactive groups (NH2 or O) at the C6 position of purine nucleotides.

Sequences

There are a variety of sequences related to the DEFBl gene and to the PAX2 transcriptional factor, respectively, having the following GenBank Accession Numbers: U50930 and NM_003989.1. These sequences and others are herein incorporated by reference in their entireties as well as for individual subsequences contained therein.

The one particular sequence set forth in SEQ ID NO: xxx and having GenBank accession number U50930 is used herein as an example to exemplify a source for the disclosed DEFBl nucleic acids. The one particular sequence set forth in SEQ ID NO:xxx and having GenBank accession number NM_003989 (see Appendix A).l is used herein as an example, to exemplify a source for the disclosed PAX2 nucleic acids. Other examples of PAX2 sequences, based on alternative splicing are also found in GenBank. These are variants a-e, shown in Appendices B-F. It is understood that the description related to this sequence is applicable to any sequence related to unless specifically indicated otherwise. Those of skill in the art understand how to resolve sequence discrepancies and differences and to adjust the compositions and methods relating to a particular sequence to other related sequences. siRNA molecules, competitive inhibitors of DEFBl promoter-PAX2, and primers and/or probes can be designed for any DEFBl or PAX2 sequence given the information disclosed herein and known in the art. Nucleic acid synthesis

The nucleic acids, such as, the oligonucleotides to be used as inhibitors can be made using standard chemical synthesis methods or can be produced using enzymatic methods or any other known method. Such methods can range from standard enzymatic digestion followed by nucleotide fragment isolation (see for example, Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Edition (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y., 1989) Chapters 5, 6) to purely synthetic methods, for example, by the cyanoethyl phosphoramidite method using a Milligen or Beckman System lPlus DNA synthesizer (for example, Model 8700 automated synthesizer of Milligen-Biosearch, Burlington, MA or ABI Model 380B). Synthetic methods useful for making oligonucleotides are also described by Ikuta et al., Ann. Rev. Biochem. 53:323-356 (1984), (phosphotriester and phosphite-triester methods), and Narang et al., Methods Enzymol., 65:610-620 (1980), (phosphotriester method). Protein nucleic acid molecules can be made using known methods such as those described by Nielsen et ah, Bioconjug. Chem. 5:3-7 (1994).

Primers and probes

Disclosed are compositions including primers and probes, which are capable of interacting with the DEFBl gene as disclosed herein. In certain embodiments the primers are used to support DNA amplification reactions. Typically the primers will be capable of being extended in a sequence specific manner. Extension of a primer in a sequence specific manner includes any methods wherein the sequence and/or composition of the nucleic acid molecule to which the primer is hybridized or otherwise associated directs or influences the composition or sequence of the product produced by the extension of the primer. Extension of the primer in a sequence specific manner therefore includes, but is not limited to, PCR, DNA sequencing, DNA extension, DNA polymerization, RNA transcription, or reverse transcription. Techniques and conditions that amplify the primer in a sequence specific manner are preferred. In certain embodiments the primers are used for the DNA amplification reactions, such as PCR or direct sequencing. It is understood that in certain embodiments the primers can also be extended using non-enzymatic techniques, where for example, the nucleotides or oligonucleotides used to extend the primer are modified such that they will chemically react to extend the primer in a sequence specific manner.

The size of the primers or probes for interaction with the DEFBl or PAX2 gene in certain embodiments can be any size that supports the desired enzymatic manipulation of the primer, such as DNA amplification or the simple hybridization of the probe or primer. A typical primer or probe would be at least 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 61, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3500, or 4000 nucleotides long.

In other embodiments a primer or probe can be less than or equal to 6, 7, 8, 9, 10, 11, 12 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3500, or 4000 nucleotides long.

The primers for the DEFBl or PAX2 gene typically will be used to produce an amplified DNA product that contains the region of the DEFBl gene to which PAX2 binds, hi general, typically the size of the product will be such that the size can be accurately determined to within 3, or 2 or 1 nucleotides.

In certain embodiments this product is at least 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 61, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3500, or 4000 nucleotides long.

In other embodiments the product is less than or equal to 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 61, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3500, or 4000 nucleotides long.

Functional Nucleic Acids

RNAi

It is also understood that the disclosed nucleic acids can be used for RNAi or RNA interference. It is thought that RNAi involves a two-step mechanism for RNA interference (RNAi): an initiation step and an effector step. For example, in the first step, input double- stranded (ds) RNA (siRNA) is processed into small fragments, such as 21-23-nucleotide 'guide sequences'. RNA amplification occurs in whole animals. Typically then, the guide RNAs can be incorporated into a protein RNA complex which is capable of degrading RNA, the nuclease complex, which has been called the RNA-induced silencing complex (RISC). This RISC complex acts in the second effector step to destroy mRNAs that are recognized by the guide RNAs through base-pairing interactions. RNAi involves the introduction by any means of double stranded RNA into the cell which triggers events that cause the degradation of a target RNA. RNAi is a form of post-transcriptional gene silencing, hi addition to the siRNAs disclosed herein, disclosed are RNA hairpins that can act in RNAi. For description of making and using RNAi molecules see, e.g., Hammond et al., Nature Rev Gen 2: 110-119 (2001); Sharp, Genes Dev 15: 485-490 (2001), Waterhouse et al., Proc. Natl. Acad. Sci. USA 95(23): 13959-13964 (1998) all of which are incorporated herein by reference in their entireties and at least form material related to delivery and making of RNAi molecules.

RNAi has been shown to work in many types of cells, including mammalian cells. For work in mammalian cells it is preferred that the RNA molecules which will be used as targeting sequences within the RISC complex are shorter. For example, less than or equal to 50 or 40 or 30 or 29, 28, 27, 26, 25, 24, 23, ,22, 21, 20, 19, 18, 17, 16 , 15, 14, 13 , 12, 11, or 10 nucleotides in length. These RNA molecules can also have overhangs on the 3' or 5' ends relative to the target RNA which is to be cleaved. These overhangs can be at least or less than or equal to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20 nucleotides long. RNAi works in mammalian stem cells, such as mouse ES cells. Examples of siRNAs can be found in Table 4.

Functional nucleic acids are nucleic acid molecules that have a specific function, such as binding a target molecule or catalyzing a specific reaction. Functional nucleic acid molecules can be divided into the following categories, which are not meant to be limiting. For example, functional nucleic acids include antisense molecules, aptamers, ribozymes, triplex forming molecules, and external guide sequences. The functional nucleic acid molecules can act as effectors, inhibitors, modulators, and stimulators of a specific activity possessed by a target molecule, or the functional nucleic acid molecules can possess a de novo activity independent of any other molecules. ₍

Functional nucleic acid molecules can interact with any macromolecule, such as DNA, RNA, polypeptides, or carbohydrate chains. Thus, functional nucleic acids can interact with mRNA or the genomic DNA of PAX2. Often functional nucleic acids are designed to interact with other nucleic acids based on sequence homology between the target molecule and the functional nucleic acid molecule. In other situations, the specific recognition between the functional nucleic acid molecule and the target molecule is not based on sequence homology between the functional nucleic acid molecule and the target molecule, but rather is based on the formation of tertiary structure that allows specific recognition to take place.

Antisense molecules are designed to interact with a target nucleic acid molecule through either canonical or non-canonical base pairing. The interaction of the antisense molecule and the target molecule is designed to promote the destruction of the target molecule through, for example, RNAseH mediated RNA-DNA hybrid degradation. Alternatively the antisense molecule is designed to interrupt a processing function that normally would take place on the target molecule, such as transcription or replication. Antisense molecules can be designed based on the sequence of the target molecule. Numerous methods for optimization of antisense efficiency by finding the most accessible regions of the target molecule exist. Exemplary methods would be in vitro selection experiments and DNA modification studies using DMS and DEPC. It is preferred that antisense molecules bind the target molecule with a dissociation constant (k_d)less than or equal to 10^"δ, 10^'8, 10^"10, or 10^"12. A representative sample of methods and techniques which aid in the design and use of antisense molecules can be found in the following non-limiting list of United States patents: 5,135,917, 5,294,533, 5,627,158, 5,641,754, 5,691,317, 5,780,607, 5,786,138, 5,849,903, 5,856,103, 5,919,772, 5,955,590, 5,990,088, 5,994,320, 5,998,602, 6,005,095, 6,007,995, 6,013,522, 6,017,898, 6,018,042, 6,025,198, 6,033,910, 6,040,296, 6,046,004, 6,046,319, and 6,057,437.

Aptamers are molecules that interact with a target molecule, preferably in a specific way. Typically aptamers are small nucleic acids ranging from 15-50 bases in length that fold into defined secondary and tertiary structures, such as stem-loops or G-quartets. Aptamers can bind small molecules, such as ATP (United States patent 5,631,146) and theophiline (United States patent 5,580,737), as well as large molecules, such as reverse transcriptase (United States patent 5,786,462) and thrombin (United States patent 5,543,293). Aptamers can bind very tightly with kas from the target molecule of less than 10^"12 M. It is preferred that the aptamers bind the target molecule with a k_d less than 10^"6, 10^~8, 10^"10, or 10^"12. Aptamers can bind the target molecule with a very high degree of specificity. For example, aptamers have been isolated that have greater than a 10000 fold difference in binding affinities between the target molecule and another molecule that differ at only a single position on the molecule (United States patent 5,543,293). It is preferred that the aptamer have a ka with the target molecule at least 10, 100, 1000, 10,000, or 100,000 fold lower than the kd with a background binding molecule. Representative examples of how to make and use aptamers to bind a variety of different target molecules can be found in the following non-limiting list of United States patents: 5,476,766, 5,503,978, 5,631,146, 5,731,424 , 5,780,228, 5,792,613, 5,795,721, 5,846,713, 5,858,660 , 5,861,254, 5,864,026, 5,869,641, 5,958,691, 6,001,988, 6,011,020, 6,013,443, 6,020,130, 6,028,186, 6,030,776, and 6,051,698.

Ribozymes are nucleic acid molecules that are capable of catalyzing a chemical reaction, either intramolecularly or intermolecularry. Ribozymes are thus catalytic nucleic acid. It is preferred that the ribozymes catalyze intermolecular reactions. There are a number of different types of ribozymes that catalyze nuclease or nucleic acid polymerase type reactions which are based on ribozymes found in natural systems, such as hammerhead ribozymes, (for example, but not limited to the following United States patents: 5,334,711,

5,436,330, 5,616,466, 5,633,133, 5,646,020, 5,652,094, 5,712,384, 5,770,715, 5,856,463, 5,861,288, 5,891,683, 5,891,684, 5,985,621, 5,989,908, 5,998,193, 5,998,203, WO 9858058 by Ludwig and Sproat, WO 9858057 by Ludwig and Sproat, and WO 9718312 by Ludwig and Sproat) hairpin ribozymes (for example, but not limited to the following United States patents: 5,631,115, 5,646,031, 5,683,902, 5,712,384, 5,856,188, 5,866,701, 5,869,339, and 6,022,962), and tetrahymena ribozymes (for example, but not limited to the following United States patents: 5,595,873 and 5,652,107). There are also a number of ribozymes that are not found in natural systems, but which have been engineered to catalyze specific reactions de novo (for example, but not limited to the following United States patents: 5,580,967, 5,688,670, 5,807,718, and 5,910,408). Preferred ribozymes cleave RNA or DNA substrates, and more preferably cleave RNA substrates. Ribozymes typically cleave nucleic acid substrates through recognition and binding of the target substrate with subsequent cleavage. This recognition is often based mostly on canonical or non-canonical base pair interactions. This property makes ribozymes particularly good candidates for target specific cleavage of nucleic acids because recognition of the target substrate is based on the target substrates sequence. Representative examples of how to make and use ribozymes to catalyze a variety of different reactions can be found in the following non- limiting list of United States patents: 5,646,042, 5,693,535, 5,731,295, 5,811,300, 5,837,855, 5,869,253, 5,877,021, 5,877,022, 5,972,699, 5,972,704, 5,989,906, and 6,017,756.

Triplex forming functional nucleic acid molecules are molecules that can interact with either double-stranded or single-stranded nucleic acid. When triplex molecules interact with a target region, a structure called a triplex is formed, in which there three strands of DNA are forming a complex dependant on both Watson-Crick and Hoogsteen base-pairing. Triplex molecules are preferred because they can bind target regions with high affinity and specificity. It is preferred that the triplex forming molecules bind the target molecule with a k_d less than 10^"6, 10^'8, 10^"10, or 10^"12. Representative examples of how to make and use triplex forming molecules to bind a variety of different target molecules can be found in the following non-limiting list of United States patents: 5,176,996, 5,645,985, 5,650,316, 5,683,874, 5,693,773, 5,834,185, 5,869,246, 5,874,566, and 5,962,426.

External guide sequences (EGSs) are molecules that bind a target nucleic acid molecule forming a complex, and this complex is recognized by RNase P, which cleaves the target molecule. EGSs can be designed to specifically target a RNA molecule of choice. RNAse P aids in processing transfer RNA (tRNA) within a cell. Bacterial RNAse P can be recruited to cleave virtually any RNA sequence by using an EGS that causes the target RNArEGS complex to mimic the natural tRNA substrate. (WO 92/03566 by Yale, and Forster and Airman, Science 238:407-409 (1990)).

Similarly, eukaryotic EGS/RNAse P-directed cleavage of RNA can be utilized to cleave desired targets within eukaryotic cells. (Yuan et al., Proc. Natl. Acad. Sci. USA 89:8006-8010 (1992); WO 93/22434 by Yale; WO 95/24489 by Yale; Yuan and Airman, EMBO J 14:159-168 (1995), and Carrara et al.. Proc. Natl. Acad. Sci. OJSA) 92:2627-2631 (1995)). Representative examples of how to make and use EGS molecules to facilitate cleavage of a variety of different target molecules be found in the following non-limiting list of United States patents: 5,168,053, 5,624,824, 5,683,873, 5,728,521, 5,869,248, and 5,877,162.

Delivery of the compositions to cells

There are a number of compositions and methods which can be used to deliver nucleic acids to cells, either in vitro or in vivo. These methods and compositions can largely be broken down into two classes: viral based delivery systems and non-viral based delivery systems. For example, the nucleic acids can be delivered through a number of direct delivery systems such as, electroporation, lipofection, calcium phosphate precipitation, plasmids, viral vectors, viral nucleic acids, phage nucleic acids, phages, . cosmids, or via transfer of genetic material in cells or carriers such as cationic liposomes. Appropriate means for transfection, including viral vectors, chemical transfectants, or physico-mechanical methods such as electroporation and direct diffusion of DNA, are described by, for example, Wolff, J. A., et al., Science, 247, 1465-1468, (1990); and Wolff, J. A. Nature, 352, 815-818, (1991)Such methods are well known in the art and readily adaptable for use with the compositions and methods described herein. In certain cases, the methods will be modified to specifically function with large DNA molecules. Further, these methods can be used to target certain diseases and cell populations by using the targeting characteristics of the carrier.

Nucleic acid based delivery systems

Transfer vectors can be any nucleotide construction used to deliver genes into cells (e.g., a plasmid), or as part of a general strategy to deliver genes, e.g., as part of recombinant retrovirus or adenovirus (Ram et al. Cancer Res. 53:83-88, (1993)). As used herein, plasmid or viral vectors are agents that transport the disclosed nucleic acids, such as DEFBl coding sequences, PAX2 siRNAs or other antisense molecules into the cell without degradation and include a promoter yielding expression of the gene in the cells into which it is delivered. Viral vectors are, for example, Adenovirus, Adeno-associated virus, Herpes virus, Vaccinia virus, Polio virus, ADDS virus, neuronal trophic virus, Sindbis and other RNA viruses, including these viruses with the HIV backbone. Also preferred are any viral families which share the properties of these viruses which make them suitable for use as vectors. Retroviruses include Murine Maloney Leukemia virus, MMLV, and retroviruses that express the desirable properties of MMLV as a vector. Retroviral vectors are able to carry a larger genetic payload, i.e., a transgene or marker gene, than other viral vectors, and for this reason are a commonly used vector. However, they are not as useful in non-proliferating cells. Adenovirus vectors are relatively stable and easy to work with, have high titers, and can be delivered in aerosol formulation, and can transfect non-dividing cells. Pox viral vectors are large and have several sites for inserting genes, they are thermostable and can be stored at room temperature. A preferred embodiment is a viral vector which has been engineered so as to suppress the immune response of the host organism, elicited by the viral antigens. Preferred vectors of this type will carry coding regions for Interleukin 8 or 10.

Viral vectors can have higher transaction (ability to introduce genes) abilities than chemical or physical methods to introduce genes into cells. Typically, viral vectors contain, nonstructural early genes, structural late genes, an RNA polymerase III transcript, inverted terminal repeats necessary for replication and encapsidation, and promoters to control the transcription and replication of the viral genome. When engineered as vectors, viruses typically have one or more of the early genes removed and a gene or gene/promotor cassette is inserted into the viral genome in place of the removed viral DNA. Constructs of this type can carry up to about 8 kb of foreign genetic material. The necessary functions of the removed early genes are typically supplied by cell lines which have been engineered to express the gene products of the early genes in trans.

Retroviral Vectors

A retrovirus is an animal virus belonging to the virus family of Retroviridae, including any types, subfamilies, genus, or tropisms. Retroviral vectors, in general, are described by Verma, I.M., Retroviral vectors for gene transfer. In Microbiology- 1985,

American Society for Microbiology, pp. 229-232, Washington, (1985), which is incorporated by reference herein. Examples of methods for using retroviral vectors for gene therapy are described in U.S. Patent Nos. 4,868,116 and 4,980,286; PCT applications WO 90/02806 and WO 89/07136; and Mulligan, (Science 260:926-932 (1993)); the teachings of which are incorporated herein by reference.

A retrovirus is essentially a package which has packed into it nucleic acid cargo. The nucleic acid cargo carries with it a packaging signal, which ensures that the replicated daughter molecules will be efficiently packaged within the package coat. In addition to the package signal, there are a number of molecules which are needed in cis, for the replication, and packaging of the replicated virus. Typically a retroviral genome, contains the gag, pol, and env genes which are involved in the making of the protein coat. It is the gag, pol, and env genes which are typically replaced by the foreign DNA that it is to be transferred to the target cell. Retrovirus vectors typically contain a packaging signal for incorporation into the package coat, a sequence which signals the start of the gag transcription unit, elements necessary for reverse transcription, including a primer binding site to bind the tRNA primer of reverse transcription, terminal repeat sequences that guide the switch of RNA strands during DNA synthesis, a purine rich sequence 5' to the 3' LTR that serve as the priming site for the synthesis of the second strand of DNA synthesis, and specific sequences near the ends of the LTRs that enable the insertion of the DNA state of the retrovirus to insert into the host genome. The removal of the gag, pol, and env genes allows for about 8 kb of foreign sequence to be inserted into the viral genome, become reverse transcribed, and upon replication be packaged into a new retroviral particle. This amount of nucleic acid is sufficient for the delivery of a one to many genes depending on the size of each transcript. It is preferable to include either positive or negative selectable markers along with other genes in the insert.

Since the replication machinery and packaging proteins in most retroviral vectors have been removed (gag, pol, and env), the vectors are typically generated by placing them into a packaging cell line. A packaging cell line is a cell line which has been transfected or transformed with a retrovirus that contains the replication and packaging machinery, but lacks any packaging signal. When the vector carrying the DNA of choice is transfected into these cell lines, the vector containing the gene of interest is replicated and packaged into new retroviral particles, by the machinery provided in cis by the helper cell. The genomes for the machinery are not packaged because they lack the necessary signals. Adenoviral Vectors

The construction of replication-defective adenoviruses has been described (Berkner et al., J. Virology 61:1213-1220 (1987); Massie et al., MoI. Cell. Biol. 6:2872-2883 (1986); Haj-Ahmad et al., J. Virology 51:261-21 A (1986); Davidson et al., J. Virology 61:1226-1239 (1987); Zhang "Generation and identification of recombinant adenovirus by liposome-mediated transfection and PCR analysis" BioTechniques 15:868-872 (1993)). The benefit of the use of these viruses as vectors is that they are limited in the extent to which they can spread to other cell types, since they can replicate within an initial infected cell, but are unable to form new infectious viral particles. Recombinant adenoviruses have been shown to achieve high efficiency gene transfer after direct, in vivo delivery to airway epithelium, hepatocytes, vascular endothelium, CNS parenchyma and a number of other tissue sites (Morsy, J. Clin. Invest. 92:1580-1586 (1993); Kirshenbaum, J. Clin. Invest. 92:381-387 (1993); Roessler, J. Clin. Invest. 92:1085-1092 (1993); Moullier, Nature Genetics 4:154-159^{^}(1993); La Salle, Science 259:988-990 (1993); Gomez-Foix, J. Biol. Chem. 267:25129-25134 (1992); Rich, Human Gene Therapy 4:461-476 (1993); Zabner, Nature Genetics 6:75-83 (1994); Guzman, Circulation Research 73:1201-1207 (1993); Bout, Human Gene Therapy 5:3-10 (1994); Zabner, Cell 75:207-216 (1993); Caillaud, Eur. J. Neuroscience 5:1287-1291 (1993); and Ragot, J. Gen. Virology 74:501-507 (1993)). Recombinant adenoviruses achieve gene transduction by binding to specific cell surface receptors, after which the virus is internalized by receptor-mediated endocytosis, in the same manner as wild type or replication-defective adenovirus (Chardonnet and Dales, Virology 40:462-477 (1970); Brown and Burlingham, J. Virology 12:386-396 (1973); Svensson and Persson, J. Virology 55:442-449 (1985); Seth, et al., J. Virol. 51:650-655 (1984); Seth, et al., MoI. Cell. Biol. 4:1528-1533 (1984); Varga et al., J. Virology 65:6061-6070 (1991); Wickham et al., Cell 73:309-319 (1993)).

A viral vector can be one based on an adenovirus which has had the El gene removed and these virions are generated in a cell line such as the human 293 cell line. Li another preferred embodiment both the El and E3 genes are removed from the adenovirus genome.

Adeno-associated viral vectors

Another type of viral vector is based on an adeno-associated virus (AAV). This defective parvovirus is a preferred vector because it can infect many cell types and is nonpathogenic to humans. AAV type vectors can transport about 4 to 5 kb and wild type AAV is known to stably insert into chromosome 19. Vectors which contain this site specific integration property are preferred. An especially preferred embodiment of this type of vector is the P4.1 C vector produced by Avigen, San Francisco, CA, which can contain the herpes simplex virus thymidine kinase gene, HSV-tk, and/or a marker gene, such as the gene encoding the green fluorescent protein, GFP.

In another type of AAV virus, the AAV contains a pair of inverted terminal repeats (ITRs) which flank at least one cassette containing a promoter which directs cell-specific expression operably linked to a heterologous gene. Heterologous in this context refers to any nucleotide sequence or gene which is not native to the AAV or B19 parvovirus.

Typically the AAV and B19 coding regions have been deleted, resulting in a safe, noncytotoxic vector. The AAV ITRs, or modifications thereof, confer infectivity and site- specific integration, but not cytotoxicity, and the promoter directs cell-specific expression. United states Patent No. 6,261,834 is herein incorporated by reference for material related to the AAV vector.

1. The disclosed vectors thus provide DNA molecules which are capable of integration into a mammalian chromosome without substantial toxicity.

2. The inserted genes in viral and retroviral usually contain promoters, and/or enhancers to help control the expression of the desired gene product. A promoter is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site. A promoter contains core elements required for basic interaction of RNA polymerase and transcription factors, and may contain upstream elements and response elements.

Large payload viral vectors

Molecular genetic experiments with large human herpes viruses have provided a means whereby large heterologous DNA fragments can be cloned, propagated and established in cells permissive for infection with herpes viruses (Sun et al., Nature genetics 8: 33-41, 1994; Cotter and Robertson, Curr Opin Mol Ther 5: 633-644, 1999). These large DNA viruses (herpes simplex virus (HSV) and Epstein-Barr virus (EBV), have the potential to deliver fragments of human heterologous DNA > 150 kb to specific cells. EBV recombinants can maintain large pieces of DNA in the infected B-cells as episomal DNA. Individual clones carried human genomic inserts up to 330 kb appeared genetically stable

The maintenance of these episomes requires a specific EBV nuclear protein, EBNAl, constitutively expressed during infection with EBV. Additionally, these vectors can be used for transfection, where large amounts of protein can be generated transiently in vitro. Herpesvirus amplicon systems are also being used to package pieces of DNA > 220 kb and to infect cells that can stably maintain DNA as episomes.

Other useful systems include, for example, replicating and host-restricted non- replicating vaccinia virus vectors.

Non-nucleic acid based systems

The disclosed compositions can be delivered to the target cells in a variety of ways. For example, the compositions can be delivered through electroporation, or through lipofection, or through calcium phosphate precipitation. The delivery mechanism chosen will depend in part on the type of cell targeted and whether the delivery is occurring for example in vivo or in vitro.

Thus, the compositions can comprise, in addition to the disclosed vectors for example, lipids such as liposomes, such as cationic liposomes (e.g., DOTMA, DOPE, and DC-cholesterol) or anionic liposomes. Liposomes can further comprise proteins to facilitate targeting a particular cell, if desired. Administration of a composition comprising a compound and a cationic liposome can be administered to the blood afferent to a target organ or inhaled into the respiratory tract to target cells of the respiratory tract. Regarding liposomes, see, e.g., Brigham et al. Am. J. Resp. Cell. MoI Biol. 1:95-100 (1989); Feigner et al. Proc. Natl. Acad. Sci USA 84:7413-7417 (1987); U.S. Pat. No.4,897,355. Furthermore, the compound can be administered as a component of a microcapsule that can be targeted to specific cell types, such as macrophages, or where the diffusion of the compound or delivery of the compound from the microcapsule is designed for a specific rate or dosage. hi the methods described above which include the administration and uptake of exogenous DNA into the cells of a subject (i.e., gene transduction or transfection), delivery of the compositions to cells can be via a variety of mechanisms. As one example, delivery can be via a liposome, using commercially available liposome preparations such as LIPOFECTIN, LIPOFECTAMINE (GIBCO-BRL, Inc., Gaithersburg, MD), SUPERFECT (Qiagen, Inc. Hilden, Germany) and TRANSFECTAM (Promega Biotec, Inc., Madison, WI), as well as other liposomes developed according to procedures standard in the art. In addition, the disclosed nucleic acid or vector can be delivered in vivo by electroporation, the technology for which is available from Genetronics, Inc. (San Diego, CA) as well as by means of a SONOPORATION machine (ImaRx Pharmaceutical Corp., Tucson, AZ).

The materials may be in solution, suspension (for example, incorporated into microparticles, liposomes, or cells). These may be targeted to a particular cell type via antibodies, receptors, or receptor ligands. The following references are examples of the use of this technology to target specific proteins to tumor tissue (Senter, et al., Bioconjugate Chem.. 2:447-451, (1991); Bagshawe, K.D., Br. J. Cancer, 60:275-281, (1989); Bagshawe, et al., Br. J. Cancer, 58:700-703, (1988); Senter, et al., Bioconiugate Chem.. 4:3-9, (1993); Battelli, et al., Cancer Immunol. Immunother., 35:421-425, (1992); Pietersz and McKenzie, Immunolog. Reviews, 129:57-80, (1992); and Roffler, et al., Biochem. Pharmacol, 42:2062-2065, (1991)). These techniques can be used for a variety of other specific cell types. Vehicles such as "stealth" and other antibody conjugated liposomes (including lipid mediated drug targeting to colonic carcinoma), receptor mediated targeting of DNA through cell specific ligands, lymphocyte directed tumor targeting, and highly specific therapeutic retroviral targeting of murine glioma cells in vivo. The following references are examples of the use of this technology to target specific proteins to tumor tissue (Hughes et al., Cancer Research, 49:6214-6220, (1989); and Litzinger and Huang, Biochimica et Biophysica Acta, 1104:179-187, (1992)). In general, receptors are involved in pathways of endocytosis, either constitutive or ligand induced. These receptors cluster in clathrin-coated pits, enter the cell via clathrin-coated vesicles, pass through an acidified endosome in which the receptors are sorted, and then either recycle to the cell surface, become stored intracellular, or are degraded in lysosomes. The internalization pathways serve a variety of functions, such as nutrient uptake, removal of activated proteins, clearance of macromolecules, opportunistic entry of viruses and toxins, dissociation and degradation of ligand, and receptor-level regulation. Many receptors follow more than one intracellular pathway, depending on the cell type, receptor concentration, type of ligand, ligand valency, and ligand concentration. Molecular and cellular mechanisms of receptor-mediated endocytosis has been reviewed (Brown and Greene, DNA and Cell Biology 10:6, 399-409 (1991)).

Nucleic acids that are delivered to cells which are to be integrated into the host cell genome, typically contain integration sequences. These sequences are often viral related sequences, particularly when viral based systems are used. These viral integration systems can also be incorporated into nucleic acids which are to be delivered using a non-nucleic acid based system of deliver, such as a liposome, so that the nucleic acid contained in the delivery system can be come integrated into the host genome.

Other general techniques for integration into the host genome include, for example, systems designed to promote homologous recombination with the host genome. These systems typically rely on sequence flanking the nucleic acid to be expressed that has enough homology with a target sequence within the host cell genome that recombination between the vector nucleic acid and the target nucleic acid takes place, causing the delivered nucleic acid to be integrated into the host genome. These systems and the methods necessary to promote homologous recombination are known to those of skill in the art.

In vivo/ex vivo

As described herein, the compositions can be administered in a pharmaceutically acceptable carrier and can be delivered to the subject's cells in vivo and/or ex vivo by a variety of mechanisms well known in the art (e.g., uptake of naked DNA, liposome fusion, intramuscular injection of DNA via a gene gun, endocytosis and the like).

If ex vivo methods are employed, cells or tissues can be removed and maintained outside the body according to standard protocols well known in the art. The compositions can be introduced into the cells via any gene transfer mechanism, such as, for example, calcium phosphate mediated gene delivery, electroporation, microinjection or proteoliposomes. The transduced cells can then be infused (e.g., in a pharmaceutically acceptable carrier) or homotopically transplanted back into the subject per standard methods for the cell or tissue type. Standard methods are known for transplantation or infusion of various cells into a subject.

Expression systems

The nucleic acids that are delivered to cells typically contain expression controlling systems. For example, the inserted genes in viral and retroviral systems usually contain promoters, and/or enhancers to help control the expression of the desired gene product. A promoter is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site. A promoter contains core elements required for basic interaction of RNA polymerase and transcription factors, and may contain upstream elements and response elements. Viral Promoters and Enhancers

Preferred promoters controlling transcription from vectors in mammalian host cells may be obtained from various sources, for example, the genomes of viruses such as: polyoma, Simian Virus 40 (S V40), adenovirus, retroviruses, hepatitis-B virus and most preferably cytomegalovirus, or from heterologous mammalian promoters, e.g. beta actin promoter. The early and late promoters of the SV40 virus are conveniently obtained as an SV40 restriction fragment which also contains the SV40 viral origin of replication (Fiers et al., Nature.273: 113 (1978)). The immediate early promoter of the human cytomegalovirus is conveniently obtained as a HindIII E restriction fragment (Greenway, PJ. et al., Gene 18: 355-360 (1982)). Of course, promoters from the host cell or related species also are useful herein.

Enhancer generally refers to a sequence of DNA that functions at no fixed distance from the transcription start site and can be either 5' (Laimins, L. et al., Proc. Natl. Acad. ScL 78: 993 (1981)) or 3' (Lusky, MX., et al., MoL Cell Bio. 3: 1108 (1983)) to the transcription unit. Furthermore, enhancers can be within an intron (Banerji, J.L. et al., Cell 33: 729 (1983)) as well as within the coding sequence itself (Osborne, T.F., et al., MoI. Cell Bio. 4: 1293 (1984)). They are usually between 10 and 300 bp in length, and they function in cis. Enhancers function to increase transcription from nearby promoters. Enhancers also often contain response elements that mediate the regulation of transcription. Promoters can also contain response elements that mediate the regulation of transcription. Enhancers often determine the regulation of expression of a gene. While many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, -fetoprotein and insulin), typically one will use an enhancer from a eukaryotic cell virus for general expression. Preferred examples are the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.

The promotor and/or enhancer may be specifically activated either by light or specific chemical events which trigger their function. Systems can be regulated by reagents such as tetracycline and dexamethasone. There are also ways to enhance viral vector gene expression by exposure to irradiation, such as gamma irradiation, or alkylating chemotherapy drugs. In certain embodiments the promoter and/or enhancer region can act as a constitutive promoter and/or enhancer to maximize expression of the region of the transcription unit to be transcribed. In certain constructs the promoter and/or enhancer region be active in all eukaryotic cell types, even if it is only expressed in a particular type of cell at a particular time. A preferred promoter of this type is the CMV promoter (650 bases). Other preferred promoters are SV40 promoters, cytomegalovirus (full length promoter), and retroviral vector LTR.

It has been shown that all specific regulatory elements can be cloned and used to construct expression vectors that are selectively expressed in specific cell types such as melanoma cells. The glial fibrillary acetic protein (GFAP) promoter has been used to selectively express genes in cells of glial origin.

Expression vectors used in eukaryotic host cells (yeast, fungi, insect, plant, animal, human or nucleated cells) may also contain sequences necessary for the termination of transcription which may affect mRNA expression. These regions are transcribed as polyadenylated segments in the untranslated portion of the mRNA encoding tissue factor protein. The 3' untranslated regions also include transcription termination sites. It is preferred that the transcription unit also contain a polyadenylation region. One benefit of this region is that it increases the likelihood that the transcribed unit will be processed and transported like mRNA. The identification and use of polyadenylation signals in expression constructs is well established. It is preferred that homologous polyadenylation signals be used in the transgene constructs. In certain transcription units, the polyadenylation region is derived from the S V40 early polyadenylation signal and consists of about 400 bases. It is also preferred that the transcribed units contain other standard sequences alone or in combination with the above sequences improve expression from, or stability of, the construct. Proteins

Protein variants

Variants of the DEFBl protein are provided. Derivatives of the DEFBl protein function in the disclosed methods and compositions. Protein variants and derivatives are well understood to those of skill in the art and in can involve amino acid sequence modifications. For example, amino acid sequence modifications typically fall into one or more of three classes: substitutional, insertional or deletional variants. Insertions include amino and/or carboxyl terminal fusions as well as intrasequence insertions of single or multiple amino acid residues. Insertions ordinarily will be smaller insertions than those of amino or carboxyl terminal fusions, for example, on the order of one to four residues. Immunogenic fusion protein derivatives, such as those described in the examples, are made by fusing a polypeptide sufficiently large to confer immunogenicity to the target sequence by cross-linking in vitro or by recombinant cell culture transformed with DNA encoding the fusion. Deletions are characterized by the removal of one or more amino acid residues from the protein sequence. Typically, no more than about from 2 to 6 residues are deleted at any one site within the protein molecule. These variants ordinarily are prepared by site specific mutagenesis of nucleotides in the DNA encoding the protein, thereby producing DNA encoding the variant, and thereafter expressing the DNA in recombinant cell culture. Techniques for making substitution mutations at predetermined sites in DNA having a known sequence are well known, for example Ml 3 primer mutagenesis and PCR mutagenesis. Amino acid substitutions are typically of single residues, but can occur at a number of different locations at once; insertions usually will be on the order of about from 1 to 10 amino acid residues; and deletions will range about from 1 to 30 residues. Deletions or insertions preferably are made in adjacent pairs, i.e. a deletion of 2 residues or insertion of 2 residues. Substitutions, deletions, insertions or any combination thereof may be combined to arrive at a final construct. The mutations must not place the sequence out of reading frame and preferably will not create complementary regions that could produce secondary mRNA structure. Substitutional variants are those in which at least one residue has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the following Tables 1 and 2 and are referred to as conservative substitutions.

TABLE 1: Amino Acid Abbreviations

<img file="WO2007047512A2_D0001.tif" /><img file="WO2007047512A2_D0002.tif" />

TABLE 2: Amino Acid Substitutions

Original Residue Exemplary Conservative Substitutions, others are known in the art.

Alaser

Arglys, gin

Asngln; his

Aspglu

Cysser

Glnasn, lys

Gluasp

Glypro

Hisasn;gln

Ileleu; val

Leuile; val

Lysarg; gin;

MetLeu; ile

Phemet; leu; tyr

Serthr

Thrser

Trptyr

Tyrtrp; phe

Value; leu

Substantial changes in function or immunological identity are made by selecting substitutions that are less conservative than those in Table 2, i.e., selecting residues that differ more significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site or (c) the bulk of the side chain. The substitutions which in general are expected to produce the greatest changes in the protein properties will be those in which (a) a hydrophilic residue, e.g. seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g. leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histidyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine, in this case, (e) by increasing the number of sites for sulfation and/or glycosylation.

For example, the replacement of one amino acid residue with another that is biologically and/or chemically similar is known to those skilled in the art as a conservative substitution. For example, a conservative substitution would be replacing one hydrophobic residue for another, or one polar residue for another. The substitutions include combinations such as, for example, GIy, Ala; VaI, He, Leu; Asp, GIu; Asn, GIn; Ser, Thr; Lys, Arg; and Phe, Tyr. Such conservatively substituted variations of each explicitly disclosed sequence are included within the mosaic polypeptides provided herein.

Substitutional or deletional mutagenesis can be employed to insert sites for N- glycosylation (Asn-X-Thr/Ser) or O-glycosylation (Ser or Thr). Deletions of cysteine or other labile residues also may be desirable. Deletions or substitutions of potential proteolysis sites, e.g. Arg, is accomplished for example by deleting one of the basic residues or substituting one by glutaminy.l or histidyl residues.

Certain post-translational derivatizations are the result of the action of recombinant host cells on the expressed polypeptide. Glutaminyl and asparaginyl residues are frequently post-translationally deamidated to the corresponding glutamyl and asparyl residues. Alternatively, these residues are deamidated under mildly acidic conditions. Other post- translational modifications include hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl or threonyl residues, methylation of the o-amino groups of lysine, arginine, and histidine side chains (T.E. Creighton, Proteins: Structure and Molecular Properties, W. H. Freeman &amp; Co., San Francisco pp 79-86 [1983J), acetylation of the N- terminal amine and, in some instances, amidation of the C-terminal carboxyl.

It is understood that one way to define the variants and derivatives of the disclosed proteins herein is through defining the variants and derivatives in terms of homology/identity to specific known sequences. For example, SEQ ID N0:xxx sets forth a particular sequence of DEFBl and SEQ ID NO:xxx sets forth a particular sequence of PAX2. Specifically disclosed are variants of these and other proteins herein disclosed which have at least, 70% or 75% or 80% or 85% or 90% or 95% homology to the stated sequence. Those of skill in the art readily understand how to determine the homology of two proteins. For example, the homology can be calculated after aligning the two sequences so that the homology is at its highest level.

Another way of calculating homology can be performed by published algorithms. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Adv. Appl. Math. 2: 482 (1981), by the homology alignment algorithm of Needleman and Wunsch, J. MoL Biol. 48: 443 (1970), by the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85: 2444

(1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by inspection.

The same types of homology can be obtained for nucleic acids by for example the algorithms disclosed in Zuker, M. Science 244:48-52, 1989, Jaeger et al. Proc. Natl. Acad. Sd. USA 86:7706-7710, 1989, Jaeger Qt ύ. Methods Enzymol. 183:281-306, 1989 which are herein incorporated by reference for at least material related to nucleic acid alignment.

It is understood that the description of conservative mutations and homology can be combined together in any combination, such as embodiments that have at least 70% homology to a particular sequence wherein the variants are conservative mutations.

As this specification discusses various proteins and protein sequences it is understood that the nucleic acids that can encode those protein sequences are also disclosed. This would include all degenerate sequences related to a specific protein sequence, i.e. all nucleic acids having a sequence that encodes one particular protein sequence as well as all nucleic acids, including degenerate nucleic acids, encoding the disclosed variants and derivatives pf the protein sequences. Thus, while each particular nucleic acid sequence may not be written out herein, it is understood that each and every sequence is in fact disclosed and described herein through the disclosed protein sequence. For example, one of the many nucleic acid sequences that can encode the DEFBl protein sequence set forth in SEQ ID NO:xxx is set forth in SEQ JX) N0:xxx. It is also understood that while no amino acid sequence indicates what particular DNA sequence encodes that protein within an organism, where particular variants of a disclosed protein are disclosed herein, the known nucleic acid sequence that encodes that protein in the particular DEFBl from which that protein arises is also known and herein disclosed and described.

It is understood that there are numerous amino acid and peptide analogs which can be incorporated into the disclosed compositions. For example, there are numerous D amino acids or amino acids which have a different functional substituent then the amino acids shown in Table 1 and Table 2. The opposite stereo isomers of naturally occurring peptides are disclosed, as well as the stereo isomers of peptide analogs. These amino acids can readily be incorporated into polypeptide chains by charging tRNA molecules with the amino acid of choice and engineering genetic constructs that utilize, for example, amber codons, to insert the analog amino acid into a peptide chain in a site specific way (Thorson et al., Methods in Molec. Biol. 77:43-73 (1991), Zoller, Current Opinion in Biotechnology,

3:348-354 (1992); Ibba, Biotechnology &amp; Genetic Enginerring Reviews 13:197-216 (1995), CaMIl et al., TffiS, 14(10):400-403 (1989); Benner, TIB Tech, 12:158-163 (1994); Ibba and Hennecke, Bio/technology, 12:678-682 (1994) all of which are herein incorporated by reference at least for material related to amino acid analogs).

Molecules can be produced that resemble peptides, but which are not connected via a natural peptide linkage. For example, linkages for amino acids or amino acid analogs can include CH₂NH-, -CH₂S-, -CH₂-CH₂ --, -CH=CH-- (cis and trans), -COCH₂ --, - CH(OH)CH₂-, and -CHH₂SO- (These and others can be found in Spatola, A. F. in Chemistry and Biochemistry of Amino Acids, Peptides, and Proteins, B. Weinstein, eds., Marcel Dekker, New York, p. 267 (1983); Spatola, A. F., Vega Data (March 1983), Vol. 1, Issue 3, Peptide Backbone Modifications (general review); Morley, Trends Pharm Sci (1980) pp. 463-468; Hudson, D. et al., lot J Pept Prot Res 14:177-185 (1979) (-CH₂NH-, CH₂CH₂-); Spatola et al. Life Sci 38:1243-1249 (1986) (-CH H₂-S); Hann J. Chem. Soc Perkin Trans. 1307-314 (1982) (--CH-CH-, cis and trans); Almquist et al. J. Med. Chem. 23:1392-1398 (1980) (-COCH₂-); Jennings-White et al. Tetrahedron Lett 23:2533 (1982) (-COCH₂-); Szelke et al. European Appln, EP 45665 CA (1982): 97:39405 (1982) (- CH(OH)CH₂-); Holladay et al. Tetrahedron. Lett 24:4401-4404 (1983) (-C(OH)CH₂-); and Hruby Life Sci 31:189-199 (1982) (-CH₂-S-); each of which is incorporated herein by reference. A particularly preferred non-peptide linkage is --CH₂NH-. It is understood that peptide analogs can have more than one atom between the bond atoms, such as b-alanine, g- aminobutyric acid, and the like.

Amino acid analogs and analogs and peptide analogs often have enhanced or desirable properties, such as, more economical production, greater chemical stability, enhanced pharmacological properties (half-life, absorption, potency, efficacy, etc.), altered specificity (e.g., a broad-spectrum of biological activities), reduced antigenicity, and others.

D-amino acids can be used to generate more stable peptides, because D amino acids are not recognized by peptidases and such. Systematic substitution of one or more amino acids of a consensus sequence with a D-amino acid of the same type (e.g., D-lysine in place of L-lysine) can be used to generate more stable peptides. Cysteine residues can be used to cyclize or attach two or more peptides together. This can be beneficial to constrain peptides into particular conformations. (Rizo and Gierasch Ann. Rev. Biochem. 61:387 (1992), incorporated herein by reference). Pharmaceutical carriers/Delivery of pharmaceutical products

As described above, the compositions can also be administered in vivo in a pharmaceutically acceptable carrier. By "pharmaceutically acceptable" is meant a material that is not biologically or otherwise undesirable, i.e., the material may be administered to a subject, along with the nucleic acid or vector, without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained. The carrier would naturally be selected to minimize any degradation of the active ingredient and to minimize any adverse side effects in the subject, as would be well known to one of skill in the art.

The compositions may be administered orally, parenterally (e.g., intravenously), by intramuscular injection, by intraperitoneal injection, transdermally, extracorporeally, topically or the like, including topical intranasal administration or administration by inhalant. As used herein, "topical intranasal administration" means delivery of the compositions into the nose and nasal passages through one or both of the nares and can comprise delivery by a spraying mechanism or droplet mechanism, or through aerosolization of the nucleic acid or vector. Administration of the compositions by inhalant can be through the nose or mouth via delivery by a spraying or droplet mechanism. Delivery can also be directly to any area of the respiratory system (e.g., lungs) via intubation. The exact amount of the compositions required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity of the allergic disorder being treated, the particular nucleic acid or vector used, its mode of administration and the like. Thus, it is not possible to specify an exact amount for every composition. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein.

Parenteral administration of the composition, if used, is generally characterized by injection. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions. A more recently revised approach for parenteral administration involves use of a slow release or sustained release system such that a constant dosage is maintained. See, e.g., U.S. Patent No. 3,610,795, which is incorporated by reference herein.

The materials may be in solution, suspension (for example, incorporated into microparticles, liposomes, or cells). These may be targeted to a particular cell type via antibodies, receptors, or receptor ligands. The following references are examples of the use of this technology to target specific proteins to tumor tissue (Senter, et al., Biocom^'ugate Chem.. 2:447-451, (1991); Bagshawe, K.D., Br. J. Cancer. 60:275-281, (1989); Bagshawe, et al., Br. J. Cancer. 58:700-703, (1988); Senter, et al., Bioconiugate Chem.. 4:3-9, (1993); Battelli, et al., Cancer Immunol. Immunother., 35:421-425, (1992); Pietersz and McKenzie, Immunolog. Reviews. 129:57-80, (1992); and Roffler, et al., Biochem. Pharmacol. 42:2062- 2065, (1991)). Vehicles such as "stealth" and other antibody conjugated liposomes (including lipid mediated drug targeting to colonic carcinoma), receptor mediated targeting of DNA through cell specific ligands, lymphocyte directed tumor targeting, and highly specific therapeutic retroviral targeting of murine glioma cells in vivo. The following references are examples of the use of this technology to target specific proteins to tumor tissue (Hughes et al., Cancer Research, 49:6214-6220, (1989); and Litzinger and Huang, Biochimica et Biophysica Acta. 1104:179-187, (1992)). In general, receptors are involved in pathways of endocytosis, either constitutive or ligand induced. These receptors cluster in clathrin-coated pits, enter the cell via clathrin-coated vesicles, pass through an acidified endosome in which the receptors are sorted, and then either recycle to the cell surface, become stored intracellularly, or are degraded in lysosomes. The internalization pathways serve a variety of functions, such as nutrient uptake, removal of activated proteins, clearance of macromolecules, opportunistic entry of viruses and toxins, dissociation and degradation of ligand, and receptor-level regulation. Many receptors follow more than one intracellular pathway, depending on the cell type, receptor concentration, type of ligand, ligand valency, and ligand concentration. Molecular and cellular mechanisms of receptor- mediated endocytosis has been reviewed (Brown and Greene, DNA and Cell Biology 10:6, 399-409 (1991)).

Pharmaceutically Acceptable Carriers

The compositions, including DEFBl, DEFBl -encoding nucleic acids, oligonucleotide inhibitors of PAX2 binding, can be used therapeutically in combination with a pharmaceutically acceptable carrier.

Suitable carriers and their formulations are described in Remington: The Science and Practice of Pharmacy (19th ed.) ed. A.R. Gennaro, Mack Publishing Company, Easton, PA 1,995. Typically, an appropriate amount of a pharmaceutically-acceptable salt is used in the formulation to render the formulation isotonic. Examples of the pharmaceutically- acceptable carrier include, but are not limited to, saline, Ringer's solution and dextrose solution. The pH of the solution is preferably from about 5 to about 8, and more preferably from about 7 to about 7.5. Further carriers include sustained release preparations such as semipermeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shaped articles, e.g., films, liposomes or microparticles. It will be apparent to those persons skilled in the art that certain carriers may be more preferable depending upon, for instance, the route of administration and concentration of composition being administered.

Pharmaceutical carriers are known to those skilled in the art. These most typically would be standard carriers for administration of drugs to humans, including solutions such as sterile water, saline, and buffered solutions at physiological pH. The compositions can be administered intramuscularly or subcutaneously. Other compounds will be administered according to standard procedures used by those skilled in the art.

Pharmaceutical compositions may include carriers, thickeners, diluents, buffers, preservatives, surface active agents and the like in addition to the molecule of choice. Pharmaceutical compositions may also include one or more active ingredients such as antimicrobial agents, antiinflammatory agents, anesthetics, and the like.

The pharmaceutical composition maybe administered in a number of ways depending on whether local or systemic treatment is desired, and on the area to be treated. Administration may be topically (including ophthalmically, vaginally, rectally, intranasally), orally, by inhalation, or parenterally, for example by intravenous drip, subcutaneous, intraperitoneal or intramuscular injection. The disclosed antibodies can be administered intravenously, intraperitoneally, intramuscularly, subcutaneously, intracavity, or transdermally.

Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl- oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like. Formulations for topical administration may include ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.

Compositions for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets, or tablets. Thickeners, flavorings, diluents, emulsifiers, dispersing aids or binders may be desirable..

Some of the compositions may potentially be administered as a pharmaceutically acceptable acid- or base- addition salt, formed by reaction with inorganic acids such as hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, and phosphoric acid, and organic acids such as formic acid, acetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid, malonic acid, succinic acid, maleic acid, and fumaric acid, or by reaction with an inorganic base such as sodium hydroxide, ammonium hydroxide, potassium hydroxide, and organic bases such as mono-, di-, trialkyl and aryl amines and substituted ethanolamines. Therapeutic Uses

Effective dosages and schedules for administering the compositions may be determined empirically, and making such determinations is within the skill in the art. The dosage ranges for the administration of the compositions are those large enough to produce the desired effect in which the symptoms disorder are effected. The dosage should not be so large as to cause adverse side effects, such as unwanted cross-reactions, anaphylactic reactions, and the like. Generally, the dosage will vary with the age, condition, sex and extent of the disease in the patient, route of administration, or whether other drugs are included in the regimen, and can be determined by one of skill in the art. The dosage can be adjusted by the individual physician in the event of any counterindications. Dosage can vary, and can be administered in one or more dose administrations daily, for one or several days. Guidance can be found in the literature for appropriate dosages for given classes of pharmaceutical products. For example, guidance in selecting appropriate doses for antibodies can be found in the literature on therapeutic uses of antibodies, e.g., Handbook of Monoclonal Antibodies, Ferrone et al., eds., Noges Publications, Park Ridge, NJ., (1985) ch. 22 and pp. 303-357; Smith et al., Antibodies in Human Diagnosis and Therapy, Haber et al., eds., Raven Press, New York (1977) pp. 365-389. A typical daily dosage of the oligonucleotide used alone might range from about 1 μg/kg to up to 100 mg/kg of body weight or more per day, depending on the factors mentioned above. In a more specific example, 5 to 7 mg/kg/day can be used. This is appropriate for i.v. administration and higher dosages, up to about 150mg/m²/day s.c. are appropriate. This can be administered daily for a week in from 1 to 24 courses. See for example A Phase I Pharmacokinetic and Biological Correlative Study of Oblimersen Sodium (Genasense, G3139), an Antisense Oligonucleotide to the Bcl-2 mRNA, and of Docetaxel in Patients with Hormone-Refractory Prostate Cancer, Clinical Cancer Research, Vol. 10, 5048-5057, August 1, 2004, incorporated herein for it's teaching of dosages for oligonucleotides.

Following administration of a disclosed composition for treating cancer, the efficacy of the therapeutic composition can be assessed in various ways well known to the skilled practitioner. For instance, one of ordinary skill in the art will understand that a composition, DEFBl, DEFBl -encoding nucleic acid, inhibitor of PAX2, disclosed herein is efficacious in treating cancer in a subject by observing that the composition reduces tumor load or prevents a further increase in tumor load. Methods of assessing tumor load are known in the art

The compositions that inhibit the interactions between PAX2 and the DEFBl promoter can be administered prophylactically to patients or subjects who are at risk for cancer.

Other molecules that interact with PAX2 to inhibit its interaction with the DEFBl promoter can be delivered in ways similar to those described for the pharmaceutical products.

The disclosed compositions and methods can also be used for example as tools to isolate and test new drug candidates for a variety of related diseases. Thus, a method of identifying inhibitors of the binding of PAX2 to the DEFBl promoter is provided. The method can comprise contacting a system that expresses DEFBl with a putative inhibitor in the presence and/or absence of PAX2 to determine whether there is an inhibitory effect on this interaction.

Compositions identified by screening with disclosed compositions / combinatorial chemistry

Combinatorial chemistry

The disclosed compositions can be used as targets for any combinatorial technique to identify molecules or macromolecular molecules that interact with the disclosed compositions in a desired way. Also disclosed are the compositions that are identified through combinatorial techniques or screening techniques in which the compositions disclosed as the PAX2 sequence or portions thereof (e.g., PAX2 DNA-binding domain), are used as the target in a combinatorial or screening protocol.

It is understood that when using the disclosed compositions in combinatorial techniques or screening methods, molecules, such as niacromolecular molecules, will be identified that have particular desired properties such as inhibition or stimulation or the target molecule's function. The molecules identified and isolated when using the disclosed compositions, such as, DEFBl or PAX2, are also disclosed. Thus, the products produced using the combinatorial or screening approaches that involve the disclosed compositions are also considered herein disclosed.

It is understood that the disclosed methods for identifying molecules that inhibit the interactions between, for example, DEFBl promoter and PAX2 can be performed using high through put means. For example, putative inhibitors can be identified using Fluorescence Resonance Energy Transfer (FRET) to quickly identify interactions. The underlying theory of the techniques is that when two molecules are close in space, ie, interacting at a level beyond background, a signal is produced or a signal can be quenched. Then, a variety of experiments can be performed, including, for example, adding in a putative inhibitor. If the inhibitor competes with the interaction between the two signaling molecules, the signals will be removed from each other in space, and this will cause a decrease or an increase in the signal, depending on the type of signal used. This decrease or increasing signal can be correlated to the presence or absence of the putative inhibitor. Any signaling means can be used. For example, disclosed are methods of identifying an inhibitor of the interaction between any two of the disclosed molecules comprising, contacting a first molecule and a second molecule together in the presence of a putative inhibitor, wherein the first molecule or second molecule comprises a fluorescence donor, wherein the first or second molecule, typically the molecule not comprising the donor, comprises a fluorescence acceptor; and measuring Fluorescence Resonance Energy Transfer (FRET), in the presence of the putative inhibitor and the in absence of the putative inhibitor, wherein a decrease in FRET in the presence of the putative inhibitor as compared to FRET measurement in its absence indicates the putative inhibitor inhibits binding between the two molecules. This type of method can be performed with a cell system as well. Combinatorial chemistry includes but is not limited to all methods for isolating small molecules or macromolecules that are capable of binding either a small molecule or another macromolecule, typically in an iterative process. Proteins, oligonucleotides, and sugars are examples of macromolecules. For example, oligonucleotide molecules with a given function, catalytic or ligand-binding, can be isolated from a complex mixture of random oligonucleotides in what has been referred to as "in vitro genetics" (Szostak, TIBS 19:89, 1992). One synthesizes a large pool of molecules bearing random and defined sequences and subjects that complex mixture, for example, approximately 10¹⁵ individual sequences in 100 μg of a 100 nucleotide RNA, to some selection and enrichment process. Through repeated cycles of affinity chromatography and PCR amplification of the molecules bound to the ligand on the column, Ellington and Szostak (1990) estimated that 1 in 10¹⁰ RNA molecules folded in such a way as to bind a small molecule dyes. DNA molecules with such ligand-binding behavior have been isolated as well (Ellington and Szostak, 1992; Bock et al, 1992). Techniques aimed at similar goals exist for small organic molecules, proteins, antibodies and other macromolecules known to those of skill in the art. Screening sets of molecules for a desired activity whether based on small organic libraries, oligonucleotides, or antibodies is broadly referred to as combinatorial chemistry. Combinatorial techniques are particularly suited for defining binding interactions between molecules and for isolating molecules that have a specific binding activity, often called aptamers when the macromolecules are nucleic acids.

There are a number of methods for isolating proteins which either have de novo activity or a modified activity. For example, phage display libraries have been used to isolate numerous peptides that interact with a specific target. (See for example, United States Patent No. 6,031,071; 5,824,520; 5,596,079; and 5,565,332 which are herein incorporated by reference at least for their material related to phage display and methods relate to combinatorial chemistry)

A preferred method for isolating proteins that have a given function is described by Roberts and Szostak (Roberts R. W. and Szostak J. W. Proc. Natl. Acad. Sci. USA, 94(23)12997-302 (1997). This combinatorial chemistry method couples the functional power of proteins and the genetic power of nucleic acids. An RNA molecule is generated in which a puromycin molecule is covalently attached to the 3 '-end of the RNA molecule. An in vitro translation of this modified RNA molecule causes the correct protein, encoded by the RNA to be translated. In addition, because of the attachment of the puromycin, a peptdyl acceptor which cannot be extended, the growing peptide chain is attached to the puromycin which is attached to the RNA. Thus, the protein molecule is attached to the genetic material that encodes it. Normal in vitro selection procedures can now be done to isolate functional peptides. Once the selection procedure for peptide function is complete traditional nucleic acid manipulation procedures are performed to amplify the nucleic acid that codes for the selected functional peptides. After amplification of the genetic material, new RNA is transcribed with puromycin at the 3 '-end, new peptide is translated and another functional round of selection is performed. Thus, protein selection can be performed in an iterative manner just like nucleic acid selection techniques. The peptide which is translated is controlled by the sequence of the RNA attached to the puromycin. This sequence can be anything from a random sequence engineered for optimum translation (i.e. no stop codons etc.) or it can be a degenerate sequence of a known RNA molecule to look for improved or altered function of a known peptide. The conditions for nucleic acid amplification and in vitro translation are well known to those of ordinary skill in the art and are preferably performed as in Roberts and Szostak (Roberts R. W. and Szostak J. W. Proc. Natl. Acad. Sci. USA, 94(23)12997-302 (1997)).

Another preferred method for combinatorial methods designed to isolate peptides is described in Cohen et al. (Cohen B.A.,et al., Proc. Natl. Acad. Sci. USA 95(24): 14272-7 (1998)). This method utilizes and modifies two-hybrid technology. Yeast two-hybrid systems are useful for the detection and analysis of proteinrprotein interactions. The two-hybrid system, initially described in the yeast Saccharomyces cerevisiae, is a powerful molecular genetic technique for identifying new regulatory molecules, specific to the protein of interest (Fields and Song, Nature 340:245-6 (1989)). Cohen et al., modified this technology so that novel interactions between synthetic or engineered peptide sequences could be identified which bind a molecule of choice. The benefit of this type of technology is that the selection is done in an intracellular environment. The method utilizes a library of peptide molecules that attached to an acidic activation domain.

Using methodology well known to those of skill in the art, in combination with various combinatorial libraries, one can isolate and characterize those small molecules or macromolecules, which bind to or interact with the desired target. The relative binding affinity of these compounds can be compared and optimum compounds identified using competitive binding studies, which are well known to those of skill in the art. Techniques for making combinatorial libraries and screening combinatorial libraries to isolate molecules which bind a desired target are well known to those of skill in the art. Representative techniques and methods can be found in but are not limited to United States patents 5,084,824, 5,288,514, 5,449,754, 5,506,337, 5,539,083, 5,545,568, 5,556,762, 5,565,324, 5,565,332, 5,573,905, 5,618,825, 5,619,680, 5,627,210, 5,646,285, 5,663,046, 5,670,326, 5,677,195, 5,683,899, 5,688,696, 5,688,997, 5,698,685, 5,712,146, 5,721,099, 5,723,598, 5,741,713, 5,792,431, 5,807,683, 5,807,754, 5,821,130, 5,831,014, 5,834,195, 5,834,318, 5,834,588, 5,840,500, 5,847,150, 5,856,107, 5,856,496, 5,859,190, 5,864,010, 5,874,443, 5,877,214, 5,880,972, 5,886,126, 5,886,127, 5,891,737, 5,916,899, 5,919,955, 5,925,527, 5,939,268, 5,942,387, 5,945,070, 5,948,696, 5,958,702, 5,958,792, 5,962,337, 5,965,719, 5,972,719, 5,976,894, 5,980,704, 5,985,356, 5,999,086, 6,001,579, 6,004,617, 6,008,321, 6,017,768, 6,025,371, 6,030,917, 6,040,193, 6,045,671, 6,045,755, 6,060,596, and 6,061,636.

Combinatorial libraries can be made from a wide array of molecules using a number of different synthetic techniques. For example, libraries containing fused 2,4- pyrimidinediones (United States patent 6,025,371) dihydrobenzopyrans (United States Patent 6,017,768and 5,821,130), amide alcohols (United States Patent 5,976,894), hydroxy- amino acid amides (United States Patent 5,972,719) carbohydrates (United States patent 5,965,719), l,4-benzodiazepin-2,5-diones (United States patent 5,962,337), cyclics (United States patent 5,958,792), biaryl amino acid amides (United States patent 5,948,696), thiophenes (United States patent 5,942,387), tricyclic Tetrahydroquinolines (United States patent 5,925,527), benzofurans (United States patent 5,919,955), isoquinolines (United States patent 5,916,899), hydantoin and thiohydantoin (United States patent 5,859,190), indoles (United States patent 5,856,496), imidazol-pyrido-indole and imidazol-pyrido- benzothiophenes (United States patent 5,856,107) substituted 2-methylene-2, 3- dihydrothiazoles (United States patent 5,847,150), quinolines (United States patent 5,840,500), PNA (United States patent 5,831,014), containing tags (United States patent 5,721,099), polyketides (United States patent 5,712,146), morpholino-subunits (United States patent 5,698,685 and 5,506,337), sulfamides (United States patent 5,618,825), and benzodiazepines (United States patent 5,288,514).

Screening molecules similar to the disclosed siRNA molecules for inhibition of PAX2 suppression of DEFBl expresson is a method of isolating desired compounds. Molecules isolated which can either be competitive inhibitors or non-competitive inhibitors.

In another embodiment the inhibitors are non-competitive inhibitors. One type of non-competitive inhibitor will cause allosteric rearrangements.

As used herein combinatorial methods and libraries included traditional screening methods and libraries as well as methods and libraries used in iterative processes.

Computer assisted drug design

The disclosed compositions can be used as targets for any molecular modeling technique to identify either the structure of the disclosed compositions or to identify potential or actual molecules, such as small molecules, which interact in a desired way with the disclosed compositions. The nucleic acids, peptides, and related molecules disclosed herein can be used as targets in any molecular modeling program or approach.

It is understood that when using the disclosed compositions in modeling techniques, molecules, such as macromolecular molecules, will be identified that have particular desired properties such as inhibition or stimulation of the target molecule's function. The molecules identified and isolated when using the disclosed compositions, such as, SEQ ID NO: 1, are also disclosed. Thus, the products produced using the molecular modeling approaches that involve the disclosed compositions, such as, SEQ ID NO:1, are also considered herein disclosed.

Thus, one way to isolate molecules that bind a molecule of choice is through rational design. This is achieved through structural information and computer modeling. Computer modeling technology allows visualization of the three-dimensional atomic structure of a selected molecule and the rational design of new compounds that will interact with the molecule. The three-dimensional construct typically depends on data from x-ray crystallographic analyses or NMR imaging of the selected molecule. The molecular dynamics require force field data. The computer graphics systems enable prediction of how a new compound will link to the target molecule and allow experimental manipulation of the structures of the compound and target molecule to perfect binding specificity. Prediction of what the molecule-compound interaction will be when small changes are made in one or both requires molecular mechanics software and computationally intensive computers, usually coupled with user-friendly, menu-driven interfaces between the molecular design program and the user. Examples of molecular modeling systems are the CHARMm and QUANTA programs, Polygen Corporation, Waltham, MA. CHARMm performs the energy minimization and molecular dynamics functions. QUANTA performs the construction, graphic modeling and analysis of molecular structure. QUANTA allows interactive construction, modification, visualization, and analysis of the behavior of molecules with each other.

A number of articles review computer modeling of drugs interactive with specific proteins, such as Rotivinen, et al., 1988 Acta Pharmaceutica Fennica 97, 159-166; Ripka, New Scientist 54-57 (June 16, 1988); McKinaly and Rossmann, 1989 Annu. Rev. Pharmacol. Toxiciol. 29, 111-122; Perry and Davies, OSAR: Quantitative Structure- Activity Relationships in Drug Design pp. 189-193 (Alan R. Liss, Inc. 1989); Lewis and Dean, 1989 Proc. R. Soc. Lond. 236, 125-140 and 141-162; and, with respect to a model enzyme for nucleic acid components, Askew, et al., 1989 J. Am. Chem. Soc. Ill, 1082- 1090. Other computer programs that screen and graphically depict chemicals are available from companies such as BioDesign, Inc., Pasadena, CA., Allelix, ftic, Mississauga, Ontario, Canada, and Hypercube, Inc., Cambridge, Ontario. Although these are primarily designed for application to drugs specific to particular proteins, they can be adapted to design of molecules specifically interacting with specific regions of DNA or RNA, once that region is identified.

Although described above with reference to design and generation of compounds which could alter binding, one could also screen libraries of known compounds, including natural products or synthetic chemicals, and biologically active materials, including proteins, for compounds which alter substrate binding or enzymatic activity. Computer readable mediums

It is understood that the disclosed nucleic acids and proteins can be represented as a sequence consisting of the nucleotides of amino acids. There are a variety of ways to display these sequences, for example the nucleotide guanosine can be represented by G or g. Likewise the amino acid valine can be represented by VaI or V. Those of skill in the art understand how to display and express any nucleic acid or protein sequence in any of the variety of ways that exist, each of which is considered herein disclosed. Specifically contemplated herein is the display of these sequences on computer readable mediums, such as, commercially available floppy disks, tapes, chips, hard drives, compact disks, and video disks, or other computer readable mediums. Also disclosed are the binary code representations of the disclosed sequences. Those of skill in the art understand what computer readable mediums. Thus, computer readable mediums on which the nucleic acids or protein sequences are recorded, stored, or saved.

Disclosed are computer readable mediums comprising the sequences and information regarding the sequences set forth herein. Also disclosed are computer readable mediums comprising the sequences and information regarding the sequences set forth.

The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how the compounds, compositions, articles, devices and/or methods claimed herein are made and evaluated, and are intended to be purely exemplary and are not intended to limit the disclosure. Efforts have been made to ensure accuracy with respect to numbers (e.g., amounts, temperature, etc.), but some errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, temperature is in ⁰C or is at ambient temperature, and pressure is at or near atmospheric.

The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how the compounds, compositions, articles, devices and/or methods claimed herein are made and evaluated, and are intended to be purely exemplary of the invention and are not intended to limit the scope of what the inventors regard as their invention. Efforts have been made to ensure accuracy with respect to numbers (e.g., amounts, temperature, etc.), but some errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, temperature is in C or is at ambient temperature, and pressure is at or near atmospheric.

Example I

Human Beta Defensin-1 is Cytotoxic to Late-Stage Prostate Cancer and Plays a Role in Prostate Cancer Tumor Immunity

Abstract

DEFBl was cloned into an inducible expression system to examine what effect it had on normal prostate epithelial cells, as well as androgen receptor positive (AR⁺) and androgen receptor negative (AR^") prostate cancer cell lines. Induction of DEFBl expression resulted in a decrease in cellular growth in AR^' cells DU145 and PC3, but had no effect on the growth of the AR⁺ prostate cancer cells LNCaP. DEFBl also caused rapid induction of caspase-mediated apoptosis. Data presented here are the first to provide evidence of its role in innate tumor immunity and indicate that its loss contributes to tumor progression in prostate cancer.

Materials and Methods

Cell Lines

The cell lines DU145 were cultured in DMEM medium, PC3 were grown in F12 medium, and LNCaP were grown in RPMI medium (Life Technologies, Inc., Grand Island, NY). Growth media for all three lines was supplemented with 10% (v/v) fetal bovine serum (Life Technologies). The hPrEC cells were cultured in prostate epithelium basal media (Cambrex Bio Science, Inc., Walkersville, MD). All cell lines were maintained at 37°C and 5% CO₂.

Tissue Samples and Laser Capture Microdissection

Prostate tissues obtained from consented patients that underwent radical prostatectomy were acquired through the Hollings Cancer Center tumor bank in accordance with an Institutional Review Board-approved protocol. This included guidelines for the processing, sectioning, histological characterization, RNA purification and PCR amplification of samples. Following pathologic examination of frozen tissue sections, laser capture microdissection (LCM) was performed to ensure that the tissue samples assayed consisted of pure populations of benign prostate cells. For each tissue section analyzed, LCM was performed at three different regions containing benign tissue and the cells collected were then pooled.

Cloning of DEFBl Gene

DEFBl cDNA was generated from RNA by reverse transcription-PCR. The PCR primers were designed to contain CIaI and Kpnl restriction sites. DEFBl PCR products were restriction digested with CM and Kpnl and ligated into a TA cloning vector. The TA/DEFBl vector was then transfected into E. coli by heat shock and individual clones were selected and expanded. Plasmids were isolated by Cell Culture DNA Midiprep (Qiagen, Valencia, CA) and sequence integrity verified by automated sequencing. The

DEFBl gene fragment was then ligated into the pTRE2 digested with CIaI and Kpnl, which served as an intermediate vector for orientation purposes. Then the pTRE2/DEFBl construct was digested with Apal and Kpnl to excise the DEFBl insert, which was ligated into pEMD vector of the Ecdysone Inducible Expression System (Invitrogen, Carlsbad, CA) also double digested with Apal and Kpnl. The construct was again transfected into E. coli and individual clones were selected and expanded. Plasmids were isolated and sequence integrity of pIND/DEFBl was again verified by automated sequencing.

Transfection

Cells (1 x 10⁶) were seeded onto 100-mm Petri dishes and grown overnight. Then the cells were co-transfected using Lipofectamine 2000 (Invitrogen, Carlsbad, CA) with lμg of p VgRXR plasmid, which expresses the heterodimeric ecdysone receptor, and lμg of the pIND/DEFBl vector construct or empty pDSTD control vector in Opti-MEM media (Life Technologies, Inc., Grand Island, NY).

SNA Isolation and Quantitative RT-PCR

In order to verify DEFBl protein expression in the cells transfected with DEFBl construct, RNA was collected after a 24 hour induction period with Ponasterone A (Pon A). Briefly, total RNA was isolated using the SV Total RNA Isolation System (Promega, Madison, WI) from approximately 1 x 10⁶ cells harvested by trypsinizing. Here, cells were lysed and total RNA was isolated by centrifugation through spin columns. For cells collected by LCM, total RNA was isolated using the PicoPure RNA Isolation Kit (Arcturus Biosciences, Mt. View, CA) following the manufacturer's protocol. Total RNA (0.5 μg per reaction) from both sources was reverse transcribed into cDNA utilizing random primers (Promega). AMV Reverse Transcriptase II enzyme (500 units per reaction; Promega) was used for first strand synthesis and TfI DNA Polymerase for second strand synthesis (500 units per reaction; Promega) as per the manufacturer's protocol. In each case, 50 pg of cDNA was used per ensuing PCR reaction. Two-step QRT-PCR was performed on cDNA generated using the MultiScribe Reverse Transcripatase from the TaqMan Reverse Transcription System and the SYBR Green PCR Master Mix (Applied Biosystems).

The primer pair for DEFBl (Table 3) was generated from the published DEFBl sequence (GenBank Accession No. U50930)¹⁰. Forty cycles of PCR were performed under standard conditions using an annealing temperature of 56⁰C. In addition, /3-actin (Table 3) was amplified as a housekeeping gene to normalize the initial content of total cDNA. DEFBl expression was calculated as the relative expression ratio between DEFBl and β- actin and was compared in cells lines induced and uninduced for DEFBl expression, as well as LCM benign prostatic tissue. As a negative control, QRT-PCR reactions without cDNA template were also performed. All reactions were run three times in triplicate.

MTTCeIl Viability Assay

To examine the effects of DEFBl on cell growth, metabolic 3-[4,5-dimethylthiazol- 2yl]-2,5 diphenyl tetrazolium bromide (MTT) assays were performed. PC3, DU145 and LNCaP cells co-transfected with pVgRXR plasmid and pIND/DEFBl construct or empty pEMD vector were seeded onto a 96-well plate at 1-5 xl O³ cells per well. Twenty- four hours after seeding, fresh growth medium was added containing 10 μM Ponasterone A daily to induce DEFBl expression for 24-, 48- and 72 hours after which the MTT assay was performed according to the manufacturer's instructions (Promega). Reactions were performed three times in triplicate.

Flow Cytometry

PC3 and DU145 cells co-transfected with the DEFBl expression system were grown in 60-mm dishes and induced for 12, 24, and 48 hours with 10 μM Ponasterone A. Following each incubation period, the medium was collected from the plates (to retain any detached cells) and combined with PBS used to wash the plates. The remaining attached cells were harvested by trypsinization and combined with the detached cells and PBS. The cells were then pelleted at 4⁰C (500 x g) for 5 min, washed twice in PBS, and resuspended in lOOul of Ix Annexin binding buffer (0.1 M Hepes/NaOH at pH 7.4, 1.4 M NaCl, 25 mM CaCl₂) containing 5 μl of Annexin V-FITC and 5 μl of PI. The cells were incubated at RT for 15 min in the dark, then diluted with 400 μl of Ix Annexin binding buffer and analyzed by FACscan (Becton Dickinson, San Jose, CA). All reactions were performed three times.

Microscopic Analysis

Cell morphology was analyzed by phase contrast microscopy. DUl 45, PC3 and LNCaP cells containing no vector, empty plasmid or DEFBl plasmid were seeded onto 6 well culture plates (BD Falcon, USA). The following day plasmid-containing cells were induced for a period of 48h with media containing 10 μM Ponasterone A, while control cells received fresh media. The cells were then viewed under an inverted Zeiss IM 35 microscope (Carl Zeiss, Germany). Phase contrast pictures of a field of cells were obtained using the SPOT Insight Mosaic 4.2 camera (Diagnostic Instruments, USA). Cells were examined by phase contrast microscopy under 32X magnification and digital images were stored as uncompressed TIFF files and exported into Photoshop CS software (Adobe Systems, San Jose, CA) for image processing and hard copy presentation.

Caspase Detection

Detection of caspase activity in the prostate cancer cell lines was performed using

APO LOGDT™ Carboxyfϊuorescin Caspase detection kit (Cell Technology, Mountain View, CA). Active caspases were detected through the use of a FAM-VAD-FMK inhibitor that irreversibly binds to active caspases. Briefly, DU145 and PC3 cells (1.5-3 XlO^) containing the DEFBl expression system were plated in 35 mm glass bottom micro well dishes (Matek, Ashland, MA) and treated for 24 hours with media only or with media containing PonA as previously described. Next, 10 μl of a 3OX working dilution of carboxyfluorescein labeled peptide fluoromethyl ketone (FAM-VAD-FMK) was added to 300μl of media and added to each 35 mm dish. Cells were then incubated for 1 hour at 37⁰C under 5% CO2. Then, the medium was aspirated and the cells were washed twice with 2 ml of a IX Working dilution Wash Buffer. Cells were viewed under differential interference contrast (DIC) or under laser excitation at 488nm. The fluorescent signal was analyzed using a confocal microscope (Zeiss LSM 5 Pascal) and a 63X DIC oil lens with a Vario 2 RGB Laser Scanning Module.

Statistical Analysis

Statistical differences were evaluated using the Student's t-test for unpaired values. P values were determined by a two-sided calculation, and a P value of less than 0.05 was considered statistically significant.

Results

DEFBl Expression in Prostate Tissue and Cell Lines

DEFBl expression levels were measured by QRT-PCR in benign and malignant prostatic tissue, hPrEC prostate epithelial cells and DUl 45, PC3 and LNCaP prostate cancer cells. DEFBl expression was detected in all of the benign clinical samples. The average amount of DEFBl relative expression was 0.0073. In addition, DEFBl relative expression in hPrEC cells was 0.0089. There was no statistical difference in DEFBl expression detected in the benign prostatic tissue samples and hPrEC (Figure IA). Analysis of the relative DEFBl expression levels in the prostate cancer cell lines revealed significantly lower levels in DU145, PC3 and LNCaP. As a further point of reference, relative DEFBl expression was measured in the adjacent malignant section of prostatic tissue from patient #1215. There were no significant differences in the level of DEFBl expression observed in the three prostate cancer lines compared to malignant prostatic tissue from patient #1215 (Figure IB), m addition, expression levels in all four samples were close to the no template negative controls which confirmed little to no endogenous DEFBl expression (data not shown). QRT-PCR was also performed on the prostate cancer cell lines transfected with the DEFBl expression system. Following a 24 hour induction period, relative expression levels were 0.01360 in DU145, 0.01503 in PC3 and 0.138 in LNCaP. Amplification products were verified by gel electrophoresis.

QRT-PCR was performed on LCM tissues regions containing benign, PIN and cancer. DEFBl relative expression was 0.0146 in the benign region compared to 0.0009 in the malignant region (Figure 1C). This represents a 94% decrease which again demonstrates a significant down-regulation of expression. Furthermore, analysis of PIN revealed that DEFBl expression level was 0.044 which was a 70% decrease. Comparing expression in patient #1457 to the average expression level found in benign regions of six other patients (Figure 1 A.) revealed a ratio of 1.997 representing almost twice as much expression (Figure ID.). However, the expression ratio was 0.0595 in PIN and was 0.125 in malignant tissue compared to average expression levels in benign tissue.

DEFBl Causes Cell Membrane Permeability and Ruffling

Induction of DEFBl in the prostate cancer cell lines resulted in a significant reduction in cell number in DUl 45 and PC3, but had no effect on cell proliferation in LNCaP (Figure 2). As a negative control, cell proliferation was monitored in all three lines containing empty plasmid. There were no observable changes in cell morphology in DU145, PC3 or LNCaP cells following the addition of PonA. In addition, DEFBl induction resulted in morphological changes in both DUl 45 and PC3. Here cells appeared more rounded and exhibited membrane ruffling indicative of cell death. Apoptotic bodies were also present in both lines.

Expression of DEFBl Results in Decreased Cell Viability

The MTT assay showed a reduction in cell viability by DEFBl in PC3 and DUl 45 cells, but no significant effect on LNCaP cells (Figure 3). After 24 hours, relative cell viability was 72% in DUl 45 and 56% in PC3. Analysis 48 hours after induction revealed 49% cell viability in DU145 and 37% cell viability in PC3. After 72 hours of DEFBl expression resulted in 44% and 29% relative cell viability in DUl 45 and PC3 cells, respectively.

DEFBl Causes Rapid Caspase-mediated Apoptosis in Late-stage Prostate Cancer Cells

In order to determine whether the effects of DEFBl on PC3 and DUl 45 were cytostatic or cytotoxic, FACS analysis was performed. Under normal growth conditions, more than 90% of PC3 and DUl 45 cultures were viable and non-apoptotic (lower left quadrant) and did not stain with annexin V or PI (Figure 4). After inducing DEFBl expression in PC3 cells, the number of apoptotic cells (lower and upper right quadrants) totaled 10% at 12 hours, 20% at 24 hours, and 44% at 48 hours. For DU145 cells, the number of apoptotic cells totaled 12% after 12 hours, 34% at 24 hours, and 59% after 48 hours of induction. There was no increase in apoptosis observed in cells containing empty plasmid following induction with PonA (data not shown).

Caspase activity was determined by confocal laser microscopic analysis (Figure 5). DUl 45 and PC3 cell were induced for DEFBl expression and activity was monitored based on the binding of green fluoresing FAM-VAD-FMK to caspases in cells actively undergoing apoptosis. Analysis of cells under DIC showed the presence of viable control DUl 45 (A), PC3 (E) and LNCaP (T) cells at 0 hours. Excitation by the confocal laser at 488 nm produced no detectable green staining which indicates no caspase activity in DUl 45 (B), PC3 (F) or LNCaP (J). Following induction for 24 hours, DU145 (C), PC3 (G) and LNCaP (K) cells were again visible under DIC. Confocal analysis under fluorescence revealed green staining in DUl 45 (D) and PC3 (H) cell indicating caspase activity. However, there was no green staining in LNCaP (L), indicating no induction of apoptosis by DEFBl. siRNA Silencing ofPAX2

In order to achieve efficient gene silencing, a pool of four complementary short interfering ribonucleotides (siRNAs) targeting human PAX2 mRNA (Accession No. NM_003989.1), were synthesized (Dharmacon Research, Lafayette, CO, USA). A second pool of four siRNAs were used as an internal control to test for the specificity of PAX2 siRNAs. Two of the sequences synthesized target the GL2 luciferase mRNA (Accession No. X65324), and two were non-sequence-specific (Table 4). For annealing of siRNAs, 35 M of single strands were incubated in annealing buffer (100 mM potassium acetate, 30 mM HEPES-KOH at pH 7.4, 2 mM magnesium acetate) for 1 min at 90°C followed by 1 h incubation at 37°C.

Western Analysis

Briefly, cells were harvested by trypsinization and washed twice with PBS. Lysis buffer was prepared according to the manufacturer's instructions (Sigma), and was then added to the cells. Following a 15 minute incubation period at 4⁰C on an orbital shaker, cell lysate were then collected and centrifuged for 10 minutes at 12000xg to pellet cellular debris. The protein-containing supernatant were then collected and quantitated. Next, 25 μg protein extract was loaded onto an 8-16% gradient SDS-PAGE (Novex). Following electrophoresis, proteins were transferred to PVDF membranes, and then blocked with 5% nonfat dry milk in TTBS (0.05% Tween 20 and 10OmM Tris-Cl) for 1 hour. Blots were then probed with rabbit anti-Pax2 primary antibody (Zymed, San Francisco, CA) at a 1 :2000 dilution. After washing, the membranes were incubated with anti-rabbit antibody conjugated to horseradish peroxidase (HRP) (dilution 1:5000; Sigma), and signal detection was visualized using chemilluminescence reagents (Pierce) on an Alpha Linotech Fluorchem 8900. As a control, blots were stripped and reprobed with mouse anti-/5-actin primary antibody (1:5000; Sigma-Aldrich) and HRP- conjugated anti-mouse secondary antibody (1:5000; Sigma-Aldrich) and signal detection was again visualized. Phase Contrast Microscopy

The effect of PAX2 knock-down on cell growth was analyzed by phase contrast microscopy. Here, 1-2 xlO⁴ cells were seeded onto 6 well culture plates (BD Falcon, USA). The following day cells were treated with media only, negative control non-specific siRNA or PAX2 siRNA and allowed to incubate for six days. The cells were then viewed under an inverted Zeiss IM 35 microscope (Carl Zeiss, Germany) at 32x magnification. Phase contrast pictures of a field of cells were obtained using the SPOT Insight Mosaic 4.2 camera (Diagnostic Instruments, USA).

MTT Cytotoxicity Assay

DU145, PC3 and LNCaP cells (IxIO⁵) were transfected with 0.5μg of the PAX2 siRNA pool or control siRNA pool using Codebreaker transfection reagent according to the manufacturer's protocol (Promega). Next, cell suspensions were diluted and seeded onto a 96-well plate at 1-5 xlO³ cells per well and allowed to grow for 2-, 4- or 6 days. After culture, cell viability was determined by measuring the conversion of 3-[4,5- dimethylthiazol-2yl]-2,5 diphenyl tetrazolium bromide, MTT (Promega), to a colored formazan product. Absorbance was read at 540 nm on a scanning multiwell spectrophotometer.

Pan-Caspase Detection

Detection of caspase activity in the prostate cancer cell lines was performed using APO LOGIXTM Carboxyfluorescin Caspase detection kit (Cell Technology, Mountain View, CA). Active caspases were detected through the use of a FAM-VAD-FMK inhibitor that irreversibly binds to active caspases. Briefly, cells (1-2 XlO^) onto 35 mm glass bottom microwell dishes (Matek, Ashland, MA) and treated with media only or PAX2 siRNA as previously described. Next, 10 μl of a 3OX working dilution of carboxyfluorescein labeled peptide fiuoromethyl ketone (FAM-VAD-FMK) was added to 300μl of media and added to each 35 mm dish. Cells were then incubated for 1 hour at 37⁰C under 5% CO2. Then, the medium was aspirated and the cells were washed twice with 2 ml of a IX Working dilution Wash Buffer. Cells were viewed under differential interference contrast (DIC) or under laser excitation at 488nm. The fluorescent signal was analyzed using a confocal microscope (Zeiss LSM 5 Pascal) and a 63X DIC oil lens with a Vario 2 RGB Laser Scanning Module.

Quantitative Real-time RT-PCR

Quantitative real-time RT-PCR was performed in order to verify gene expression after PAX2 siRNA treatment in PC3, DU145 and LNCaP cell lines. Total RNA was isolated using the SV Total RNA Isolation System (Promega). Briefly, approximately 1 x 10⁶ cells were harvested by trypsinizing, and rinsed in PBS. Cells were then lysed and total RNA was isolated by centrifugation through spin columns. Total RNA (0.5 μg per reaction) was reverse transcribed into cDNA utilizing Oligo (dT) 15 primer (Promega) and AMV Reverse Transcriptase II enzyme (500 units per reaction; Promega) for first strand synthesis and TfI DNA Polymerase for for second strand synthesis (500 units per reaction; Promega) as per the manufacturers' protocol, with identical control samples treated without RT enzyme. Typically, 50 pg of each cDNA was used per ensuing PCR reactionTwo-step QRT- PCR was performed on cDNA generated using the MultiScribe Reverse Transcripatase from the TaqMan Reverse Transcription System and the SYBR Green PCR Master Mix (PE Biosystems). The primer pairs for BAX, BID and BAD were generated from the published sequences (Table3). Reactions were performed in MicroAmp Optical 96-well Reaction Plate (PE Biosystems). Forty cycles of PCR were performed under standard conditions using an annealing temperature of 6O⁰C. Quantification was determined by the cycle number where exponential amplification began (threshold value) and averaged from the values obtained from the triplicate repeats. There was an inverse relationship between message level and threshold value. In addition, GAPDH was used as a housekeeping gene to normalize the initial content of total cDNA. Gene expression was calculated as the relative expression ratio between the pro-apoptotic genes and GAPDH. All reactions were carried out in triplicate.

Results siRNA Inhibition ofPAXl Protein

In order to confirm that the siRNA effective targeted the PAX2 mRNA, Western Analysis was performed to monitor PAX2 protein expression levels over a six day treatment period. Cells were given a single round of transfection with the pool of PAX2 siRNA. The results confirmed specific targeting of PAX2 mRNA by showing knock-down of PAX2 protein by day four in DUl 45 (Figure 6a) and by day six in PC3 (Figure 6b).

Knock-down ofPAX2 inhibit Prostate Cancer Cell Growth

Cells were analyzed following a six day treatment period with media only, negative control non-specific siRNA or PAX2 siRNA (Figure 7). DU145 (a), PC3 (d) and LNCaP (g) cells all reached at least 90% confluency in the culture dishes containing media only. Treatment of DUl 45 (b), PC3 (e) and LNCaP (h) with negative control non-specific siRNA had no effect on cell growth, and cells again reached confluency after six days. However, treatment with PAX2 siRNA resulted in a significant decrease in cell number. DUl 45 cells were approximately 15% confluent (c) and PC3 cells were only 10% confluent (f). LNCaP cell were 5% confluent following siRNA treatment.

Cytotoxicity Assays

Cell viability was measured after two-, four-, and six-day exposure times, and is expressed as a ratio of the 570-630 nm absorbance of treated cells divided by that of the untreated control cells (Figure 8). Relative cell viability following 2 days of treatment was 77% in LNCaP, 82% in DU145 and 78 % in PC3. After four days, relative cell viability was 46% in LNCaP, 53% in DU145 and 63% in PC3. After six days of treatment, relative cell viability decreased to 31% in LNCaP, 37% in PC3, and was 53% in DU145. As negative controls, cell viability was measured in after a six day treatment period with negative control non-specific siRNA or transfection reagent alone. For both conditions, there was no statistically significant change in cell viability compared to normal growth media (data not shown).

Pan-Caspase Detection

Caspase activity was detected by confocal laser microscopic analysis. DUl 45, PC3 and LNCaP cells were treated with PAX2 siRNA and activity was monitored based on the binding of FAM-labeled peptide to caspases in cells actively undergoing apoptosis which will fluoresce green. Analysis of cells with media only under DIC shows the presence of viable DUl 45 (A), PC3 (E) and LNCaP (I) cells at 0 hours (Figure 9). Excitation by the confocal laser at 488 nm produced no detectable green staining which indicates no caspase activity in untreated DU145 (B), PC3 (F) or LNCaP (J). Following four days of treatment with PAX2 siRNA, DU145 (C), PC3 (G) and LNCaP (K) cells were again visible under DIC. Under fluorescence, the treated DUl 45 (D), PC3 (H) and LNCaP (L) cells presented green staining indicating caspase activity.

Effect ofPax2 Inhibition on Pro-apoptotic Factors

DUl 45, PC3 and LNCaP cells were treated with siRNA against PAX2 for six days and expression of pro-apoptotic genes dependent and independent of p53 transcription regulation were measured to monitor cell death pathways. For BAX, there was a 1.81 -fold increase in LNCaP, a 2.73-fold increase in DU145, and a 1.87-fold increase in PC3 (Figure 10a). Expression levels of BID increased by 1.38-fold in LNCaP and 1.77-fold in DU145 (Figure 10b). However, BID expression levels decreased by 1.44-fold in PC3 following treatment (Figure 10c). Analysis of BAD revealed a 2.0-fold increase in expression in LNCaP, a 1.38-fold increase in DU145, and a 1.58-fold increase in PC3.

Conclusion

Despite significant advances in cancer therapy there is still little progress in the treatment of advanced disease. Successful drug treatment of prostate cancer requires the use of therapeutics with specific effects on target cells while maintaining minimal clinical effects on the host. The goal of cancer therapy is to trigger tumor-selective cell death. Therefore, understanding the mechanisms in such death is critical in determining the efficacy of a specific treatment.

The dependency of prostate cancer cell survival on PAX2 expression is shown here. In order to distinguish between death observed in the p53-expressing cell line LNCaP, the p53-mutated line DU145, and the p53-null line PC3 downstream events that follow p53 activation as a result of PAX2 knock-down were examined. Caspase activity was detected in all three lines indicative of the initiation of programmed cell death. With this, changes in the expression of pro-apoptotic genes were examined. Here, BAX expression was upregulated in all three cell lines independent of p53 status. The expression of pro- apoptotic factor BAD was increased in all three lines following PAX2 inhibition. Following treatment with PAX2 siRNA, BID expression was increased in LNCaP and DUl 45, but actually decreased in PC3. This indicates that cell death observed in prostate cancer is influenced by but is not dependent on p53 expression. The initiation of apoptosis in prostate cancer cells through different cell death pathways irrespective of p53 status indicates that PAX2 inhibits other tumor suppressors

Example III

Inhibition of PAX2 Oncogene Results in DEFBl-Mediated Death of Prostate Cancer Cells

Abstract

The identification of tumor-specific molecules that serve as targets for the development of new cancer drugs is considered to be a major goal in cancer research. Example I demonstrated that there is a high frequency of DEFBl expression loss in prostate cancer, and that induction of DEFBl expression results in rapid apoptosis in androgen receptor negative-stage prostate cancer. These data show that DEFBl plays a role in prostate tumor suppression. In addition, given that it is a naturally occurring component of the immune system of normal prostate epithelium, DEFBl is expected to be a viable therapeutic agent with little to no side effects. Example II demonstrated that inhibition of PAX2 expression results in prostate cancer cell death independent of p53. These data indicate that there is an addition pro-apoptotic factor or tumor suppressor that is inhibited by PAX2. hi addition, the data show that the oncogenic factor PAX2, which is over-expressed in prostate cancer, is a transcriptional repressor of DEFBl. The purpose of this study is to determine if DEFBl loss of expression is due to aberrant expression of the PAX2 oncogene, and whether inhibiting PAX2 results in DEFBl -mediated cell death.

The data show that loss of DEFBl expression occurs at the transcriptional level. Furthermore, computational analysis of the DEFBl promoter revealed the presence of a GJJCCDNA binding site for the PAX2 transcriptional repressor next to the DEFBl TATA box (Figure 1). The results presented here show that PAX2 and DEFBl exhibit several attributes of suitable cancer targets, including a role in the suppression of cell death. Therefore, DEFBl plays a role in tumor immunity and its expression is modulated through therapeutic down-regulation of the PAX2 oncogene. Materials and Methods

RNA Isolation and Quantitative RT-PCR

In order to verify changes in DEFBl expression levels RNA was collected after 4 days of PAX2 siRNA treatment. Briefly, total RNA was isolated using the SV Total RNA Isolation System (Promega, Madison, WT) from approximately 1 x 10⁶ cells harvested by trypsinizing. Here, cells were lysed and total RNA was isolated by centrifugation through spin columns. Total RNA (0.5 μg per reaction) from both sources was reverse transcribed into cDNA utilizing random primers (Promega). AMV Reverse Transcriptase II enzyme (500 units per reaction; Promega) was used for first strand synthesis and TfI DNA Polymerase for second strand synthesis (500 units per reaction; Promega) as per the manufacturer's protocol, hi each case, 50 pg of cDNA was used per ensuing PCR reaction. Two-step QRT-PCR was performed on cDNA generated using the MultiScribe Reverse Transcripatase from the TaqMan Reverse Transcription System and the SYBR Green PCR Master Mix (Applied Biosystems).

The primer pair for DEFBl was generated from the published DEFBl sequence (Accession No. U50930). Forty cycles, of PCR were performed under standard conditions using an annealing temperature of 56⁰C. In addition, GAPDH was amplified as a housekeeping gene to normalize the im^'tial content of total cDNA. DEFBl expression was calculated as the relative expression ratio between DEFBl and GAPDH and was compared in cells lines before and after siRNA knock-down of PAX2 expression. All reactions were run three times in triplicate.

Generation of the DEFBl Reporter Construct

The pGL3 luciferase reporter plasmid was used to monitor DEFBl reporter activity. Here, a region 160 bases upstream of the DEFBl transcription initiation site and included the DEFBl TATA box. The region also included the GTTCC sequence which is necessary for PAX2 binding. The PCR primers were designed to contain Kpnl and Nhel restriction sites. The DEFBl promoter PCR products were restriction digested Kpn I and Nhel and ligated into a similary restriction digested pGL3 plasmid (Figure 2). The constructs were transfected into E. coli and individual clones were selected and expanded. Plasmids were isolated and sequence integrity of the DEFBl/pGL3 construct was verified by automated sequencing. Lucifer ase Reporter Assay

Here, lμg of the DEFBl reporter construct or the control pGL3 plasmid was transfected into IxIO⁶ DU145 cells. Next, 0.5xl0³ cells were seeded onto each well of a 96- well plate and allowed to grow overnight. Then fresh medium was added containing PAX2 siRNA or media only and the cells were incubated for 48 hours. Luciferase was detected by the BrightGlo kit accourding to the manufacturer's protocol (Promega) and the plates were read on a Veritas automated 96-well lummometer. Promoter activity was expressed as relative luminescence.

Analysis of Membrane Permeability

Acridine orange (AO)/ethidium bromide (EtBr) dual staining was performed to identify changes in cell membrane integrity, as well as apoptotic cells by staining the condensed chromatin. AO stains viable cells as well as early apoptotic cells, whereas EtBr stains late stage apoptotic cells that have lost membrane permeability. Briefly, cells were seeded into 2 chamber culture slides (BD Falcon, USA). Cells transfected with empty pIND plasmid/pvgRXR or pIND DEFBl/pvgRXR were induced for 24 or 48 h with media containing 10 μM Ponasterone A. Control cells were provided fresh media at 24 and 48h. In order to determine the effect of PAX2 inhibition on membrane integrity, separate culture slides containing DU145, PC3 and LNCaP were treated with PAX2 siRNA and incubated for 4 days. Following this, cells were washed once with PBS and stained with 2 ml of a mixture (1:1) of AO (Sigma, USA) and EtBr (Promega, USA) (5ug/ml) solution for 5 min. Following staining, the cells were again washed with PBS. Fluorescence was viewed by a Zeiss LSM 5 Pascal Vario 2 Laser Scanning Confocal Microscope (Carl Zeiss Jena, Germany). The excitation color wheel contain BS505-530 (green) and LP560 (red) filter blocks which allowed for the separation of emitted green light from AO into the green channel and red light from EtBr into the red channel. The laser power output and gain control settings within each individual experiment were identical between control and DEFBl induced cells. The excitation was provided by a Kr/Ar mixed gas laser at wavelengths of 543nm for AO and 488 ran for EtBr. Slides were analyzed under 4OX magnification and digital images were stored as uncompressed TIFF files and exported into Photoshop CS software (Adobe Systems, San Jose, CA) for image processing and hard copy presentation. ChIP Analysis ofPAX2

Chromatin immunoprecipitation (ChIP) allows the identification of binding sites for DNA-binding proteins based upon in vivo occupancy of a promoter by a transcription factor and enrichment of transcription factor bound chromatin by immunoprecipitation (66). A modification of the protocol described by the Farnham laboratory ((67, 68) was used; also on line at http://mcardle.oncology. wisc.edu/farnham/). The DU145 and PC3 cell lines over- expresses the PAX2 protein, but does not express DEFBl. Cells were incubated with PBS containing 1.0% formaldehyde for 10 minutes to crosslink proteins to DNA. Samples were then sonicated to yield DNA with an average length of 600 bp. Sonicated chromatin precleared with Protein A Dynabeads was incubated with PAX2 -specific antibody or "no antibody" control [isotype-matched control antibodies]. Washed immunoprecipitates were then collected. After reversal of the crosslinks, DNA was analyzed by PCR using promoter- specific primers to determine whether DEFBl is represented in the PAX2- immunoprecipitated samples. Primers were designed to amplify the 160 bp region immediately upstream of the DEFBl mRNA start site which contained the DEFBl TATA box and the functional GTTCC PAX2 recognition site. For these studies, positive controls included PCR of an aliquot of the input chromatin (prior to immunoprecipitation, but crosslinks reversed). All steps were performed in the presence of protease inhibitors.

Results siRNA Inhibition ofPAX2 Increases DEFBl Expression

QRT-PCR analysis of DEFBl expression before siRNA treatment revealed relative expression levels of 0.00097 in DU145, 0.00001 in PC3, and .00004 LNCaP (Figure 13). Following siRNA knock-down of PAX2, relative expression was .03294 (338-fold increase) in DU145, .00020 (22.2-fold increase) in PC3 and 0.00019 (4.92-fold increase) in LNCaP. As a negative control, the human prostate epithelial cell line (hPrEC) which is PAX2 null, revealed expression levels at 0.00687 before treatment and 0.00661 following siRNA treatment confirming no statistical change in DEFBl expression.

DEFBl Causes Cell Membrane Permeability

Membrane integrity was monitored by confocal analysis (Figure 14). Here, intact cells stain green due to AO which is membrane permeable. In addition, cells with compromised plasma membranes would stain red by EtBr which is membrane impermeable. Here, uninduced DUl 45 (A) and PC3 (D) cells stained positively with AO and emitted green color, but did not stain with EtBr. However, DEFBl induction in both DU145 (B) and PC3 (E) resulted in the accumulation of EtBr in the cytoplasm at 24 hours indicated by the red staining. By 48 hours, DUl 45 (C) and PC3 (F) possessed condensed nuclei and appeared yellow, which was due to the presence of both green and red staining resulting from the accumulation of AO and EtBr, respectively.

Inhibition ofPAX2 Results in Membrane Permeability

Cells were treated with PAX2 siRNA for 4 days and membrane integrity was monitored again by confocal analysis (Figure 15). Here, both DUl 45 (B) and PC3 (E) possessed condensed nuclei and appeared yellow. However, LNCaP cells' cytoplasm and nuclei remained green following siRNA treament. Also red staining at the cell periphery indicates the maintenance of cell membrane integrity. These findings indicate that the inhibition of PAX2 results in specifically DEFBl -mediated cell death in DUl 145 and PC3, but not LNCaP cells. Death observed in LNCaP (refer to Chapter II) is due to the transactivation of the existing wild-type p53 in LNCap following PAX2 inhibition.

siRNA Inhibition ofPAX2 Increases DEFBl Promoter Activity

Analysis of DEFBl promoter activity in DU145 cells containing the DEFBl/pGL3 construct revealed a 2.65 fold increase in relative light units following 48 hours of treatment compared to untreated cells (Figure 16). hi PC3 cells, there was a 3.78-fold increase in relative light units compared to untreated cells.

PAX2 Binds to the DEFBl Promoter

ChIP analysis was performed on DU145 and PC3 cells to determine if the PAX2 transcriptional repressor is bound to the DEFBl promoter (Figure 17). Lane 1 contains a 100 bp molecular weight marker. Lane 2 is a positive control representing 160 bp region of the DEFBl promoter amplified from DUl 45 before cross-linking and immunoprecipitation. Lane 3 is a negative control representing PCR performed without DNA. Lane 4 and 5 are negative controls representing PCR from immunoprecipitations performed with IgG from cross-linked DU145 and PC3, respectively. PCR amplification of 25pg of DNA (lane 6 and 8) and 50pg of DNA (lane 7 and 9) immunoprecitipated with anti-PAX2 antibody after crosslinking show 160 bp promoter fragment in DU145 and PC3, respectively. Conclusion

The present novel data are the first to disclose the role of DEFBl in prostate cancer tumor immunity. The data also show that the oncogenic factor PAX2 suppresses DEFBl expression. One of the hallmarks of defensin cytotoxicity is the disruption of membrane integrity. The present results show that ectopic expression of DEFBl in prostate cancer cells results in a loss of membrane potential due to compromised cell membranes. The same phenomenon is observed after inhibiting PAX2 protein expression. ChIP analysis was also performed and confirmed that PAX2 is bound to the DEFBl promoter resulting in the repression of DEFBl expression. Therefore, suppression of PAX2 expression or function, results in the re-establishment of DEFBl expression and subsequently DEFBl -mediated cell death. Also, the present data establish the utility of DEFBl as a directed therapy for prostate cancer treatment through innate immunity.

Example IV

Expression of DEFBl Results in Tumor Shrinkage

The anti-tumoral ability of DEFBl is evaluated by injecting tumor cells that overexpress DEFBl into nude mice. DEFBl is cloned into pBI-EGFP vector, which has a bidirectional tetracycline responsible promoter. Tet-Off Cell lines are generated by transfecting pTet-Off into DU145, PC3 and LNCaP cells and selecting with G418. The pBI- EGFP-DEFBl plasmid is co-transfected with pTK-Hyg into the Tet-off cell lines and selected with hygromycin. Only single-cell suspensions with a viability of &gt;90% are used. Each animal receives approximately 500,000 cells administered subcutaneously into the right flank of female nude mice. There are two groups, a control group injected with vector only clones and a group injected with the DEFBl over-expressing clones. 35 mice are in each group as determined by a statistician. Animals are weighed twice weekly, tumor growth monitored by calipers and tumor volumes determined using the following formula: volume = 0.5 x (width)2 x length. All animals are sacrificed by CO₂ overdose when tumor size reaches 2 mm or 6 months following implantation; tumors are excised, weighed and stored in neutral buffered formalin for pathological examination. Differences in tumor growth between the groups are descriptively characterized through summary statistics and graphical displays. Statistical significance is evaluated with either the t-test or non- parametric equivalent.

Example V

Expression of PAX2 siRNA Results in Up-Regulation of DEFBl Expression and

Tumor Shrinkage In Vivo

Hairpin PAX2 siRNA template oligonucleotides utilized in the in vitro studies are utilized to examine the effect of the up-regulation of DEFBl expression in vivo. The sense and antisense strand (see Table 4) are annealed and cloned into pSilencer 2.1 U6 hygro siRNA expression vector (Ambion) under the control of the human U6 RNA pol III promoter. The cloned plasmid is sequenced, verified and transfected into PC3, Dul45, and LNCap cell lines. Scrambled shRNA is cloned and used as a negative control in this study. Hygromycin resistant colonies are selected, cells are introduced into the mice subcutaneously and tumor growth is monitored as described above.

Example VI

Small Molecule Inhibitors of PAX2 Binding Results in Up-Regulation of DEFBl Expression and Tumor Shrinkage In Vivo

The DNA recognition sequence for PAX2 binding resides in the DEFBl promoter between nucleotides -75 and -71 [+1 refers to the transcriptional start site]. Short oligonucleotides complementary to the PAX2 DNA-binding domain are provided. Examples of such oligonucleotides include the 20-mer and 40-mer oligonucleotides containing the GTTCC recognition sequence provided below. These lengths were randomly selected, and other lengths are expected to be effective as blockers of binding. As a negative control, oligonicleotides with a scrambled sequence (CTCTG) were designed to verify specificity. The oligonucleotides are transfected into the prostate cancer cells and the HPrEC cells with lipofectamine reagent or Codebreaker transfection reagent (Promega, Inc). In order to confirm DNA-protein interactions, double stranded oligonucleotides will be labeled with [32P] dCTP and electrophoretic mobility shift assays are performed. In addition, DEFBl expression is monitored by QRT-PCR and Western analysis following treatment with oligonucleotides. Finally, cell death is detected by MTT assay and flow cytometry as previously described.

Recognition Sequence #1: CTCCCTTCAGTTCCGTCGAC (SEQ ID NO:9) Recognition Sequence #2: CTCCCTTCACCTTGGTCGAC (SEQ ID NO: 10) Scramble Sequence #1 : CTCCCTTCACTCTGGTCGAC (SEQ ID NO: 11) Recognition Sequence #3:

ACTGTGGCACCTCCCTTCAGTTCCGTCGACGAGGTTGTGC (SEQ ID NO: 12) Recognition Sequence #4:

ACTGTGGCACCTCCCTTCACCTTGGTCGACGAGGTTGTGC (SEQ ID NO: 13) Scramble Sequence #2: ACTGTGGCACCTCCCTTCACTCTGGTCGACGAGGTTGTGC (SEQ ID NO: 14)

Further examples of oligonucleotides of the invention include: Recognition Sequence #1: 5'-AGAAGTTCACCCTTGACTGT-S' (SEQ ID NO:X) Recognition Sequence #2: 5'-AGAAGTTCACGTTCCACTGT-S' (SEQ ID NO:X) Scramble Sequence #1: 5'-AGAAGTTCACGCTCTACTGT-S' (SEQ ID NO:X) Recognition Sequence #3:

5'-TTAGCGATTAGAAGTTCACCCTTGACTGTGGCACCTCCC-S' (SEQ ID NO:X) Recognition Sequence #4:

5'-GTTAGCGATTAGAAGTTCACGTTCCACTGTGGCACCTCCC-S' (SEQ ID NO:X) Scramble Sequence #2: 5'-GTTAGCGATTAGAAGTTCACGCTCTACTGTGGCACCTCCC-S' (SEQ ID NO:X)

This set of alternative inhibitory oligonucleotides represents the recognition sequence (along with the CCTTG core sequence) for the PAX2 binding domain and homeobox. These include actual sequences from the DEFBl promoter.

The PAX2 gene is required for the growth and survival of various cancer cells including prostate. In addition, the inhibition of PAX2 expression results in cell death mediated by the innate immunity component DEFB 1. Suppression of DEFB 1 expression and activity is accomplished by binding of the PAX2 protein to a GTTCC recognition site in the DEFBl promoter. Therefore, this pathway provides a viable therapeutic target for the treatment of prostate cancer. In this method, the sequences bind to the PAX2 DNA binding site and block PAX2 binding to the DEFBl promoter thus allowing DEFBl expression and activity. The oligonucleotide sequences and experiment described above are examples of and demonstrate a model for the design of additional PAX2 inhibitor drugs.

Given that the GTTCC sequence exists in interleukin-3, interleukin-4, the insulin receptor and others, PAX2 regulates their expression and activity as well. Therefore the PAX2 inhibitors disclosed herein have utility in a number of other diseases including those directed related to inflammation including prostatitis and benign prostatic hypertrophy

(BPH).

Example VII Loss of DEFBl Expression Results in Increased Tumorigenesis

Generation of Loss of Function Mice

The Cre/loxP system has been useful in elucidating the molecular mechanisms underlying prostate carcinogenesis. Here a DEFBl Cre conditional KO is used for inducible disruption within the prostate. The DEFBl Cre conditional KO involves the generation of a targeting vector containing loxP sites flanking DEFBl coding exons, targeted ES cells with this vector and the generation of germline chimeric mice from these targeted ES cells. Heterozygotes are mated to prostate-specific Cre transgenics and heterozygous intercross is used to generate prostate-specific DEFBl KO mice. Four genotoxic chemical compounds have been found to induce prostate carcinomas in rodents: N-methyl-N-nitrosourea (MNU), N-nitrosobis 2-oxopropyl. amine (BOP), 3,2X-dimethyl-4-amino-biphenyl (MAB) and 2- amino-l-methyl-6-phenylimidazow 4,5-bxpyridine (PhIP). DEFBl -transgenic mice are treated with these carcinogenic compounds via intra-gastric administration or i.v. injection for prostate adenoma and adenocarcinoma induction studies. Prostate samples are studied for differences in tumor growth and changes gene expression though histological, immunohistological, mRNA and protein analyses.

Generation of GOF mice

For PAX2 inducible GOF mice, PAX2 GOF (bi-transgenic) and wild-type (mono- transgenic) littermates are administered doxycycline (Dox) from 5 weeks of age to induce prostate-specific PAX2 expression. Briefly, PROBASIN-rtTA mono-transgenic mice (prostate cell-specific expression of tet-dependent rtTA inducer) are crossed to our PAX2 transgenic responder lines. For induction, bi-transgenic mice are fed Dox via the drinking water (500 mg/L freshly prepared twice a week). Initial experiments verify low background levels, good inducibility and cell-type specific expression of PAX2 and the EGFP reporter using transgenic founder line in bi-transgenic mice. Regarding experimental group sizes, 5- 7 age- and sex-matched individuals in each group (wild-type and GOF) allow for statistical significance. For all animals in this study, prostate tissues are collected initially at weekly intervals for analysis and comparison, to determine carcinogenic time parameters.

PCR Genotyping, RT-PCR and qPCR

PROBASIN-rtTA transgenic mice are genotyped using the following PCR primers and conditions: PROBASIN5 (forward) 5'-ACTGCCCATTGCCCAAACAC-S'; RTTA3 (reverse) 5'-AAAATCTTGCCAGCTTTCCCC-S'; 95°C denaturation for 5 min, followed by 30cycles of 95°C for 30 sec, 57°C for 30 sec, 72⁰C for 30 sec, followed by a 5 min extension at 72°C, yielding a 600 bp product. PAX2 inducible transgenic mice are genotyped using the following PCR primers and conditions: PAX2For 5'- GTCGGTTACGGAGCGGACCGGAG-3'; Rev5'IRES 5'-

TAACATATAGACAAACGCACACCG-3'; 95°C denaturation for 5 min, followed by 34cycles of 95°C for 30 sec, 63°C for 30 sec, 72°C for 30 sec, followed by a 5 min extension at 72°C, yielding a 460 bp product. Immortomouse hemizygotes are be genotyped using the following PCR primers and conditions: Irnmoll, 5'-GCGCTTGTGTC GCCATTGTATTC-3'; Immol2, 5'-GTCACACCACAGAAGTAAGGTTCC-S'; 94⁰C 30 sec, 58⁰C 1 min, 72⁰C lmin 30 sec, 30 cycles to yield a ~lkb transgene band. For genotyping PAX2 knockout mice, the following PCR primers and conditions are used: PAX2 For 5'-GTCGGTTACGGAGCGGACCGGAG-S'; PAX2Rev 5'- CACAGAGCATTGGCGATCTCGATGC-3'; 94⁰C 1 min, 65⁰C 1 min, 72⁰C 30 sec, 36 cycles to yield a 280 bp band.

DEFBl Peptide Animal Studies

Six-week-old male athymic (nude) mice purchased from Charles River Laboratories are injected sub-cutaneously over the scapula with 10⁶ viable PC3 cells. One week after injection, the animals are randomly allocated to one of three groups -group I: control; group II: intraperitoneal injections of DEFBl, 100 μg/day, 5 days a week, for weeks 2-14; group III: intraperitoneal injections of DEFBl, 100 mg/day, 5 days a week, for weeks 8-14. Animals are maintained in sterile housing, four animals to a cage, and observed on a daily basis. At 10-day intervals, the tumors are measured by using calipers, and the volumes of the tumors are calculated by using V = (L ^x W2)/2.

Appendix A

LOCUS HUMPAX201 7331 bp DNA linear PRI 28-JAN-2002

DEFINITION Homo sapiens paired-box protein (PAX2) gene, promoter and exon 1. ACCESSION L09748 AF433639 VERSION L09748.2 GL18141563 KEYWORDS . SEGMENT 1 of 3 SOURCE Homo sapiens (human) ORGANISM Homo sapiens

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo.

REFERENCE 1 (bases 7096 to 7291)

AUTHORS Stapleton,P., Weith,A., Urbanek,P., Kozmik,Z. and Busslinger,M. TITLE Chromosomal localization of seven PAX genes and cloning of a novel family member, PAX-9 JOURNAL Nat. Genet. 3 (4), 292-298 (1993) PUBMED 7981748 REFERENCE 2 (bases 1 to 7331)

AUTHORS Pfeffer,P.L., Payer,B., Reim_^G., di Magliano,M.P. and Busslinger,M. TITLE The activation and maintenance of Pax2 expression at the mid-hindbrain boundary is controlled by separate enhancers JOURNAL Development 129 (2), 307-318 (2002) PUBMED 11807024 REFERENCE 3 (bases 7096 to 7291)

AUTHORS Stapleton,P., Weith,A, Urbanek,P., Kozmik,Z. and Busslinger,M. TITLE Direct Submission JOURNAL Submitted (12-JUN-1993) Research Institute of Molecular Pathology,

Dr. Bohr-Gasse 7, Vienna, Austria REFERENCE 4 (bases 1 to 7331) AUTHORS Pfeffer,P.L. and Busslinger,M. TITLE Direct Submission JOURNAL Submitted (14-JAN-2002) Research Institute of Molecular Pathology,

Dr. Bohr-Gasse 7, Vienna, Austria REMARK Sequence update by submitter

COMMENT On Jan 14, 2002 this sequence version replaced gi:292378. FEATURES Location/Qualifiers source 1..7331

/organism="Homo sapiens" /mol_type=" genomic DNA" /db_xref="taxon:9606" /chromosome=" 10" /map="10q22.1-q24.3" gene order(2034..733 l,L09746.1 : 1..206,L09747.1 : 1..&gt;238)

/gene-"PAX2" enhancer 2034..2518

/gene="PAX2" /note="distal (late) enhancer" enhancer 2850..2974

/gene="PAX2"

/note="intermediate (early) enhancer" enhancer 3516..3898

/gene="PAX2"

/note="proximal (late) enhancer" mRNA join(6532..7271,L09746.1:21..186,L09747.1:21..&gt;218)

/gene="PAX2"

/product="paired-box protein" exon 6532..7271

/gene="PAX2"

/number=l CDS join(7229..7271,L09746.1:21..186,L09747.1:21..&gt;218)

/gene="PAX2"

/codon_start=l

/product="paired-box protein"

/protein_id="AAC41711.1"

/db_xref="GI:553607¹¹

/translation="MDMHCKADPFSAMHRHGGVNQLGGVFVNGRPLPDWRQRIVELA

HQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKWDKIAEY

KRQNPTMFAWEIRDRLLAEGICDNDTVPSVSSIN"

ORIGIN

1 ttcccccttt ccangagggc ctaatccgtt gcgcgcgcgc acgcggacac acacacacac 61 acacacacac acacacacac acacacggcc cccatagcca ccgcaactct cagcagcagn 121 ncctagctcc tctgacccga ggccccaaga cggcgggcac aggaacccct gggacgtcct 181 ggctccaggc tggacgtagg cggaggtggc aggagtggac aaacccaggc gggtcccacg 241 acgccccttt cctcgggtct ctccttgttt cagccagccg ctctcgcccc tggtcccctc 301 ttccctgcgt tagggtcctt tgtctccagc cacctcgcag cctgtccccg cctcggcggc 361 cctgcccttt gggcctccca gatctctctg gcgggtcccc ctgccttacc agctcccggc 421 tgtggcgcgc tcttcgcctg ctcctcacat ncacacagct gctgggagag gaggaaggaa 481 aggcggncgc gccgcggatg gatccgagac ggtagatttg gtgccggctc gcaaactctg 541 ggaaacttaa ngccggttct tccgcccctc tncaactatg nccagcgcgg cccggtcgcg 601 cgcgctcacc ccgcggggac cctttccttt tcctgtattt cggctgcggc tgtttcgctt 661 cctctggtct cccagccttt ggagtggctt ccctggccct gcactccgtt ccctttcggc 721 cgcccccggc tgtcgcctgc ccccaccctc cgcaggtccc acggtcgcgg cggcgatgac 781 tgtggaggta acgccgggga cgtcctgggt cagcctgcac cgtctccctc gaccacagcc 841 cgatgaggcc gcgggctccg ggccggctgc taagagagtt aatcattact tcgccagcga 901 cactcagcct ccccttccga ctctctcgcc cggcctaggg gaggagggga ggggacagct 961 ggccaggtgg ggacttcggc ttcgcacaaa ccagcctctt caggcctccc agagacaggt 1021 ggtggcttct cagttccctc ggcaactctc taaggtcctc tttcttcccc tcctgtctct 1081 ccctccttcg agcctcctcc cagccaggcc tctccccacc gtctcctgtc cgctctggct 1141 ttgactgatt aactgcaggt cctgggagaa ccaactttct ttgtttggaa ccggaccgga 1201 cgggatttcc ttccctaggt ctccgccaat gggccagctc ctcccgacgg ttttggcgga 1261 ctggctgaag aggaccgcgc ctgaggccac aattaacccg gctgttggtg gtggtggttg 1321 gggggtgggc agtgaggaat ttaaccgatc ctctagcagc tgcgctggtg cagttgggag 1381 gggggtgcag gaagtgggaa tggaggagtg gcaggaggta tagacagagg gaagaacgat 1441 aaacctggac aggtgtggca tagccaatag aaggggaaac aaaataaaac aggaaggcgg 1501 cgcggggagg aatccccagt aacctttata ggattgaagt tgggtggaaa acgccacctc 1561 ctgccctacc ttagcactca gatccctcct ttacctcttt gtgaaagggt aagagttcag 1621 aaagctggcc atttactcca taatctacta gagaaatgtc tgggtttgca aaatgcctat 1681 tgattagctc catggagtag acaagacagg cgtaattatc cccattttac aggtgagaaa 1741 actgagtctc aaagaagcaa agggactgtg tatgtagtgg ctgtcacttt ttcctgtagg 1801 ctgtggggtg agtggcccct ttagctgtgc agaggtccat gggtatctag ggaggcggta 1861 caggctgtgt ccaggtctga gccagaagta ccagggcctc acggggctcc tagccctttt 1921 agcttgttct ctgttggaca ggaccttcac tcttactctc tagacctgct ggctgggttt 1981 ctcccagctt cgctattttt tcagttccct agtagagtgg cccatgggcg gtagccacct 2041 ggctggcccg tgccactaag aggcagcttt ggtggccaag tggcttgcat tgttgttgct 2101 cctcaaaggg cctgtgaagg gctgggcagg tcgcaaagac ctcttgtgag gggaaagcta 2161 gattaaaggg ggtaaggatc ctggaggata aaggccaagc acgtgcgcct ggactccaca 2221 ggaccaacag accgagcggg cggggccngc tgggagtcag gccccccggg cttcacgcag 2281 ggagcccaaa tattgggaac aaaagcagga aaagaagagt gagagcagga gggagggagg 2341 gagcgaggaa gcagaaatta gggggtctta gatgaaaaaa aaaagaaagt agctttaggg 2401 ggaatgtgct gtggagtgtg aaattgcagc ccatggtgct ccatattgta ccagaagctc 2461 ttccaaaaaa aaaaaaaaaa accatcctcc aacgtgacca gagggccagg cagggggaag 2521 ggcggggaga gaatggggag gaggaggggg aaaggccggg caggagccgg tcaggccttt 2581 ctgcggaagg ggctggggtg taagtttcgg ctccctggga tctgacagcc gagggtatgc 2641 gccctggggt gcgccgggac ccagagggcg agtgagcctc ggttggtcgg ctctggagtt 2701 cggttgtcag aagaactttt atttttcttt ttggtggtga cttctaaaag tgggaataat 2761 ccagaaatga agctcagctg cggagctgca gctctgttct ccctctctcc cctgcctttc 2821 tgcttctctt cccttcggac tacttttctc cccttggttc taaatagctt tttcccctct 2881 gaactttaat gcatttaatt tggtccgcgc tgtggggagc atttcctggg gagatgcatt 2941 taatttcgga atttctaatc ccctccctca gaccccggtc ctagctcccc tagccgctcc 3001 ccgggaagtg gaaggaggaa ggcaggtccc ggccacgggg gaggggcgcg gctgggatgc 3061 tcccgcggcc ccctccgtct caccaaggct cagccgcctt cccaagctac tggaggccgg 3121 gcgcctgggc cccgggtcag ggccctgcan gaagaagaga ggcaaccccc gctttctgcc 3181 ttttcttcgc ctgggcaaga aaacgctggg ccagggaact ggaaaccgga aaacaggaga 3241 aagggtttnt ggaaggcanc gggagcgggt ggcagncggg gcancgggca ntggactagg 3301 tctacaccgg cacttcactt ttgcacaaca tgcccagaaa cgcatttgag agccctggag 3361 tcgcgcttgg cttggcttgg ggcgccggtg cgtgggtaca ctcgaggtcg gggtgcctat 3421 ccgccacccc gacacctaca cccagtgcag agcaggcgcg gcccagccag acaaccaggc 3481 cggcagtagc tcggcctgga gggcggaggc aaggttgggg gccgccaggc gcctgggcaa 3541 gcctggcagg gaagggagcc gagaaggcaa aggagccgag atccacaagg aagattnntt 3601 gggcagatca gatgcacaga ggcggctaat gaagcaaatc ccgagatggg tttcagagca 3661 actccccaaa agtttatttt gcctttaaat ttccgcaggg aggcgggctc cttgtttgaa 3721 gtgtaaatgc ccctaggttg gggggtggaa gggccgcttt gaaaacacca gagagaaaag 3781 gttcatttag aggcggacgg gaaaagcaac caaccctgac aggtcggagc ccgggtagtg 3841 tttggggttg ggtngttttc tttctttctc tttcttttcc cctttcctct tctttcttcc 3901 cttttgtgnn ttttnnttgt tttttttntn ttntttttnt ttaantggct ttcttgcttc 3961 cccccacccc tctactagac tctatagaag aaagagaaca gaaaaggggg agtcagagga 4021 gcggccagtg actggatgaa ggccagccct tcatcctgga gccccaggag aaggcagagc 4081 tttggagaaa aggggttcct aatctccagg gagcattact ctttgactct ctagacccag 4141 gaatgggctg gacgctaatg gggaagcggc caggaacccg gcctggcgga agagtgagtg 4201 tccagctagt gcagtgctgg gaagacgatc ccaggagcag gggggactct caggggctac 4261 ctgggaatgg gactatcaga agggtcttta ctcctcanaa ggtgcatgtg aaggacaggt 4321 gtgtgaggac aacttccagc acacttggcg cattaagtcc ccttctctac aaaatggaaa 4381 atccttctcg cccaacatgt gaaaatgctt gttgtgggca cccacatttc atggtacttg 4441 taacatagga catgtctagc tggttctaga aaaatctgtg tctgtgtgga aggggggggg 4501 tttactcaca gctttcttcc ttcaatagtt cacacacccc gagacaaatt cctggatgac 4561 caacttggag agacctgggg caaaggttac tttagttctg agctcctcta aataaggacc 4621 ctttctcaac gttcctttca ccccagttct gggttaatta cttccagtta gtgcgtgttc 4681 gtggggttgt gaggccaaag caaacccggg agcgccatct gcaggcctca agaggaagag 4741 actgacctta gaggctaggc cctgcgtctt caacctctag cccaagggaa ccaacctgcc 4801 tagccaccca agggaagtgg gataggggct gggaggggca ggcggtgagg agtgttttcc 4861 tcccagactt taccccgcag gtggattaag cttattgggc tctggaggat acaggaggga 4921 gggcaaatgc caggatccca gcggacccag gccccacagg agtgagaggc tcagaacctc 4981 gtcccgctga gcctggcctg agctcctcct gaggaataag ggcatcccaa aaacccgggt 5041 acaagacgcc cagtagtagt agttaggctg agtcaggcag gtgcatctct ccccatggta 5101 tctgccgccc aggctccggc cagagggagg ggagcgcgag tccgcggcgc ttccgcgggg 5161 cgcccggaac tgcagacggg ggctggagga atctcggatt cgggctgcaa gagcgctgcg 5221 caagcttcgc cgagccgccc tttcgcagac ccagggaagc ggggggaggg agcgaaggag 5281 ggagagagag ttaaaacatc agcttgaaag tgcccaagat gattttatta agaccgaggg 5341 gaaaattatt ttcatgaaag attctccccg gaatatttct tgtacttaac ccagttagga 5401 agacaaaggg cttctttctg cctggtgcgg tgcgagcgga ccccagcgag caagggagct 5461 agtgccaaag agaactgcgg aggctccggc aggagtgggg acgtccccgt ggttgcgcct 5521 cctgcgctcg ccccggatcc accgagctag cagcgggcgg cgctcagccg cgtccgcagc 5581 ctcctcttct ccccagccgg ggagagccag cctcgtctcc cacatcctct gccgccagcg 5641 acctgcagct ccgcactgtt tccctcccct gtaccccctt cccagtcacc cgagggttca 5701 gaaaccaagt cccccggctc tcccgccatc cgctgggtcc caccgaggca ggtgggtact 5761 cgccggaggt cttcagctcg attctgaacc aagcgttctg gactgcccag acccggtggg 5821 caaggggact ggggaggccc tgcgcacagt cgcgtggaac gggaggggac aagacaaact 5881 gctggacact tttccgtgga atgagaagtg gggggtgcgt gggtgggaag gtacctccgg 5941 agggaaaggc caaagggaag gaccagaaag agaggaagga agagccggga aggaacggaa 6001 gggaactcag agccgagggt ggtggggttg gggctaggga tgcgcactgg gcccggggcc 6061 gcgcggccca ggcgggcact ggccagtgga tggcagggct gggcgagtta gaactgagag 6121 cccggcttca cagcgcagcg cgctccgagg ccctctgtcg ttacctgaat attcattaga 6181 ctgaccgctc tttatcctta tctaacgttt atcttatcgg cgagtttcgt ttctcagtgt 6241 agttttaatc ccgggctccc attccccctc ccccggtccg ctcccctccc tccctcttcc 6301 ttcgccggct gctccctccc tccctccctc ccatttctcc ctcccctgcc ctccccttgc 6361 cggcaccgga gtgacaggct cggggccctc ctcgccgaag ctcggggctc cagcgctggc 6421 gaatcacaga gtggtggaat ctattgcctt tgtctgacaa gtcatccatc tcccggcgcg 6481 gggaggggga ggaggtctgg agggggcttt gcagctttta gagagacaca caccgggagc 6541 cgaggctcca gtctccggcc gagtcttcta gcagccgcaa cccacctggg gccagcccag 6601 agctgccagc gccgctcggc tccctccctc cctcccggcc cttcggccgc ggcggcgtgc 6661 gcctgccttt tccgggggcg ggggcctggc ccgcgcgctc ccctcccgca ggcgccacct 6721 cggacatccc cgggattgct acttctctgc caacttcgcc aactcgccag cacttggaga 6781 ggcccggctc ccctcccggc gccctctgac cgcccccgcc ccgcgcgctc tccgaccacc 6841 gcctctcgga tgaacaggtt ccaggggagc tgagcgagtc gcctcccccg cccagcttca 6901 gccctggctg cagctgcagc gcgagccatg cgcccccagt gcaccccggc ccggcccacc 6961 gccccggggc cattctgctg accgcccagc cccgagcccc gacagtggca agttgcggct 7021 actgcggttg caagctccgg ccaacccgga ggagccccag cggggagcgc agtgttgcgc 7081 cccccgcccc cgcgcgcgcc gcagcagccg ggcgttcact catcctccct cccccaccgt 7141 ccctcccttt tctcctcaag tcctgaagtt gagtttgaga ggcgacacgg cggcggcggc 7201 cgcgctgctc ccgctcctct gcctccccat ggatatgcac tgcaaagcag accccttctc 7261 cgcgatgcac cgtgagtacc cgcgcccggc tcctgtcccg gctcgggctc tccgtcccaa 7321 ccctgtccag t

Appendix B

LOCUS NM_003987 4276 bp mRNA linear PRI 24-SEP-2005

DEFINITION Homo sapiens paired box gene 2 (PAX2), transcript variant a, mRNA. ACCESSION NM_003987 VERSION NM_003987.2 GL34878698 KEYWORDS .

SOURCE Homo sapiens (human) ORGANISM Homo sapiens

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 4276) AUTHORS Yoshimura,K., Yoshida,S., Yamaji,Y., Komori,A., Yoshida,A.,

Hatae,K., Kubota,T. and Ishibashi,T. TITLE De novo insG619 mutation in PAX2 gene in a Japanese patient with papillorenal syndrome

JOURNAL Am. J. Ophthalmol. 139 (4), 733-735 (2005) PUBMED 15808183

REMARK GeneRIF: Molecular genetic analysis of the PAX2 gene in combination with renal ultrasonography can help in making an earlier diagnosis of the disease.

REFERENCE 2 (bases 1 to 4276) AUTHORS Mazal,P.R., Stichenwirth,M., Koller,A., Blach,S., Haitel,A. and

Susani,M. TITLE Expression of aquaporins and PAX-2 compared to CD 10 and cytokeratin

7 in renal neoplasms: a tissue microarray study JOURNAL Mod. Pathol. 18 (4), 535-540 (2005) PUBMED 15502805 REMARK GeneRIF: PAX-2 is a reliable marker for clear cell renal cell carcinomas of lower grades but not for higher grades. REFERENCE 3 (bases 1 to 4276)

AUTHORS Higashide,T., Wada,T., Sakurai,M._? Yokoyama,H. and Sugiyama,K. TITLE Macular abnormalities and optic disk anomaly associated with a new

PAX2 missense mutation

JOURNAL Am. J. Ophthalmol. 139 (1), 203-205 (2005) PUBMED 15652857

REMARK GeneRIF: A new PAX2 missense mutation, R71T, may cause macular abnormalities in addition to anomalies of the optic disk and the kidney.

REFERENCE 4 (bases 1 to 4276) AUTHORS Buttiglieri,S., Deregibus,M.C, Bravo,S., Cassoni,P., Chiarle,R.,

Bussolati,B- and Camussi,G.

TITLE Role of Pax2 in apoptosis resistance and proinvasive phenotype of Kaposi's sarcoma cells JOURNAL J. Biol. Chem. 279 (6), 4136-4143 (2004)

PUBMED 14627715

REMARK GeneRIF: expression of Pax2 by Kaposi's sarcoma cells correlated with an enhanced resistance against apoptotic signals and with the preinvasive phenotype REFERENCE 5 (bases 1 to 4276) AUTHORS Brophy,P.D., Lang,K.M. and Dressler,G.R. TITLE The secreted frizzled related protein 2 (SFRP2) gene is a target of the Pax2 transcription factor

JOURNAL J. Biol. Chem. 278 (52), 52401-52405 (2003) PUBMED 14561758 REMARK GeneRIF: Pax2 protein regulates expression of secreted frizzled related protein 2

REFERENCE 6 (bases 1 to 4276)

AUTHORS Schimmenti,L.A., Manligas,G.S. and Sieving,P.A. TITLE Optic nerve dysplasia and renal insufficiency in a family with a novel PAX2 mutation, Argl 15X: further ophthalmologic delineation of the renal-coloboma syndrome

JOURNAL Ophthalmic Genet. 24 (4), 191-202 (2003) PUBMED 14566649 REMARK GeneRTF: PAX2 mutation is associated with Optic nerve dysplasia and renal insufficiency of the renal-coloboma syndrome REFERENCE 7 (bases 1 to 4276)

AUTHORS Muratovska,A., Zhou,C, He₅S., Goodyer,P. and Eccles,M.R. TITLE Paired-Box genes are frequently expressed in cancer and often required for cancer cell survival JOURNAL Oncogene 22 (39), 7989-7997 (2003) PUBMED 12970747 REMARK GeneRIF: The PAX2 gene was frequently expressed in a panel of 406 common primary tumor tissues and endogenous PAX gene expression is often required for the growth and survival of cancer cells REFERENCE 8 (bases 1 to 4276) AUTHORS Gough,S.M., McDonald,M., Chen,X.N., Korenberg,J.R., Neri,A-,

Kahn,T., Eccles,M.R. and Morris,C.M. TITLE Refined physical map of the human PAX2/HOX11/NFKB2 cancer gene region at 10q24 and relocalization of the HPV6AI1 viral integration site to l4ql3.3-q21.1

JOURNAL BMC Genomics 4 (1), 9 (2003) PUBMED 12697057 REFERENCE 9 (bases 1 to 4276) AUTHORS Hoffmeister,A., Ropolo,A., Vasseur,S., Mallo,G.V., Bodeker,H.,

Ritz-Laser,B., Dressler,G.R., Vaccaro,M.L, DagomJ.C, Moreno,S. and IovannaJ.L. TITLE The HMG-I/Y-related protein ρ8 binds to p300 and Pax2 trans-activation domain-interacting protein to regulate the trans-activation activity of the Pax2A and Pax2B transcription factors on the glucagon gene promoter JOURNAL J. Biol. Chem. 277 (25), 22314-22319 (2002) PUBMED 11940591 REMARK GeneRIF: The HMG-I/Y-related protein p8 binds to p300 and Pax2 trans-activation domain-interacting protein to regulate the trans-activation activity of the Pax2A and Pax2B transcription factors on the glucagon gene promoter. REFERENCE 10 (bases 1 to 4276) AUTHORS Cai,Y., LechnerJVLS., Nihalani,D., Prindle,MJ., Holzman,L.B. and

Dressler,G.R. TITLE Phosphorylation of Pax2 by the c-Jun N-terminal kinase and enhanced

Pax2-dependent transcription activation JOURNAL J. Biol. Chem. 277 (2), 1217-1222 (2002) PUBMED 11700324 REFERENCE 11 (bases 1 to 4276)

AUTHORS Becker,K., Beales,P.L., Calver,D.M.₃ Matthijs,G. and Mohammed,S.N. TITLE Okihiro syndrome and acro-renal-ocular syndrome: clinical overlap, expansion of the phenotype, and absence of PAX2 mutations in two new families

JOURNAL J. Med. Genet. 39 (1), 68-71 (2002) PUBMED 11826030 REMARK GeneRIF: The absence of PAX2 mutations has been identified in two families with histories of clinical overlap of Okihiro and acro-renal-ocular syndromes. REFERENCE 12 (bases 1 to 4276) AUTHORS Eccles,M.R., He₅S., Legge,M., Kumar,R., Fox,J., Zhou,C, French,M. and Tsai,R.W. TITLE PAX genes in development, and disease: the role of PAX2 in urogenital tract development

JOURNAL Lit. J. Dev. Biol. 46 (4), 535-544 (2002) PUBMED 12141441 REMARK Review article

GeneRIF: PAX2 has a role in urogenital tract development and disease [review]

REFERENCE 13 (bases 1 to 4276) AUTHORS Chung,G.W., Edwards,A.O., Schimmenti,L.A., Manligas,G.S.,

Zhang, Y.H. and Ritter,R. UI.

TITLE Renal-coloboma syndrome: report of a novel PAX2 gene mutation JOURNAL Am. J. Ophthalmol. 132 (6), 910-914 (2001) PUBMED 11730657 REMARK GeneRIF: The causal relationship between PAX2 gene mutations and renal-coloboma syndrome is further supported REFERENCE 14 (bases 1 to 4276) AUTHORS Nishimoto,K., Iijima,K., Shirakawa,T., Kitagawa,K., Satomura,K.,

Nakamura,H. and Yoshikawa,N.

TITLE PAX2 gene mutation in a family with isolated renal hypoplasia JOURNAL J. Am. Soc. Nephrol. 12 (8), 1769-1772 (2001) PUBMED 11461952 REFERENCE 15 (bases 1 to 4276)

AUTHORS Ritz-Laser,B., Estreicher,A., Gauthier,B. and PhilippeJ. TITLE The paired homeodomain transcription factor Pax-2 is expressed in the endocrine pancreas and transactivates the glucagon gene promoter

JOURNAL J. Biol. Chem. 275 (42), 32708-32715 (2000) PUBMED 10938089 REFERENCE 16 (bases 1 to 4276) AUTHORS Lechner,M.S., Levitan,! and Dressler,G.R. TITLE PTIP, a novel BRCT domain-containing protein interacts with Pax2 and is associated with active chromatin JOURNAL Nucleic Acids Res. 28 (14), 2741-2751 (2000) PUBMED 10908331 REFERENCE 17 (bases 1 to 4276) AUTHORS Tavassoli,K.₅ Ruger,W. and HorstJ. TITLE Alternative splicing in PAX2 generates a new reading frame and an extended conserved coding region at the carboxy terminus JOURNAL Hum. Genet. 101 (3), 371-375 (1997) PUBMED 9439670 REFERENCE 18 (bases 1 to 4276) AUTHORS DaM₅E., Koseki,H. and Balling,R. TITLE Pax genes and organogenesis JOURNAL Bioessays 19 (9), 755-765 (1997) PUBMED 9297966 REMARK Review article REFERENCE 19 (bases 1 to 4276) AUTHORS Schimmenti^A., Cunliffe,H.E., McNoe,L.A., WardJ.A., French,M.C,

Shim,H.H., Zhang,Y.H., Proesmans,W., Leys,A., Byerly,K.A.,

Braddock,S.R., Masuno,M., Imaizumi,K., Devriendt,K. and Eccles,M.R. TITLE Further delineation of renal-coloboma syndrome in patients with extreme variability of phenotype and identical PAX2 mutations JOURNAL Am. J. Hum. Genet. 60 (4), 869-878 (1997) PUBMED 9106533 REFERENCE 20 (bases 1 to 4276) AUTHORS Narahara,K., Baker,E., Ito,S., Yokoyama,Y., Yu₅S., Hewitt,D.,

Sutherland,G.R., Eccles,M.R. and Richards,R.I. TITLE Localisation of a 1 Oq breakpoint within the P AX2 gene in a patient with a de novo t(10;13) translocation and optic nerve coloboma-renal disease

JOURNAL J. Med. Genet. 34 (3), 213-216 (1997) PUBMED 9132492 REFERENCE 21 (bases 1 to 4276)

AUTHORS Dehbi,M., Ghahremani,M., Lechner,M., Dressler,G. and Pelletier,J. TITLE The paired-box transcription factor, PAX2, positively modulates expression of the Wilms' tumor suppressor gene (WTl) JOURNAL Oncogene 13 (3), 447-453 (1996) PUBMED 8760285 REFERENCE 22 (bases 1 to 4276) AUTHORS Sanyanusin,P., NorrishJ.H., Ward,T.A., Nebel,A., McNoe,L.A. and

Eccles,M.R.

TITLE Genomic structure of the human PAX2 gene JOURNAL Genomics 35 (1), 258-261 (1996) PUBMED 8661132 REFERENCE 23 (bases 1 to 4276) AUTHORS Sanyanusin,P., Schimmenti,L.A., McNoe,L.A., Ward,T.A.,

Pierρont,M.E., Sullivan,MJ., Dobyns,W.B. and Eccles,M.R. TITLE Mutation of the PAX2 gene in a family with optic nerve colobomas, renal anomalies and vesicoureteral reflux JOURNAL Nat. Genet. 9 (4), 358-364 (1995) PUBMED 7795640 REFERENCE 24 (bases 1 to 4276)

AUTHORS Ward,T.A., Nebel,A., Reeve,A.E. and Eccles,M.R. TITLE Alternative messenger RNA forms and open reading frames within an additional conserved region of the human PAX-2 gene JOURNAL Cell Growth Differ. 5 (9), 1015-1021 (1994) PUBMED 7819127 REFERENCE 25 (bases 1 to 4276) AUTHORS NoIl₅M. TITLE Evolution and role of Pax genes JOURNAL Curr. Opin. Genet. Dev. 3 (4), 595-605 (1993) PUBMED 8241771 REMARK Review article REFERENCE 26 (bases 1 to 4276)

AUTHORS Stapleton,P., Weith,A., Urbanek,P., Kozmik,Z. and Busslinger,M. TITLE Chromosomal localization of seven PAX genes and cloning of a novel family member, PAX-9

JOURNAL Nat. Genet. 3 (4), 292-298 (1993) PUBMED 7981748 REFERENCE 27 (bases 1 to 4276) AUTHORS PiIz₅AJ., Povey,S., Gruss,P. and Abbott,C.M. TITLE Mapping of the human homologs of the murine paired-box-containing genes

JOURNAL Mamm. Genome 4 (2), 78-82 (1993) PUBMED 8431641 REFERENCE 28 (bases 1 to 4276) AUTHORS Eccles,M.R., WaIHs₃LJ., Fidler,A.E., Spurr,N.K., GoodfellowJΛJ. and Reeve,A.E.

TITLE Expression of the PAX2 gene in human fetal kidney and Wilms' tumor JOURNAL Cell Growth Differ. 3 (5), 279-289 (1992) PUBMED 1378753 COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from U45255.1 and BM671839.1.

On Sep 22, 2003 this sequence version replaced gi:4557822.

Summary: PAX2 encodes paired box gene 2, one of many human homologies of the Drosophila melanogaster gene prd. The central feature of this transcription factor gene family is the conserved DNA-binding paired box domain. PAX2 is believed to be a target of transcriptional supression by the tumor supressor gene WTl. Mutations within PAX2 have been shown to result in optic nerve colobomas and renal hypoplasia. Alternative splicing of this gene results in multiple transcript variants. Transcript Variant: This variant (a) uses an alternate in-frame splice site in the 3' coding region, compared to variant e, resulting in a shorter protein (isoform a) that has a shorter, distinct C-terminus compared to isoform e. COMPLETENESS: complete on the 3' end. FEATURES Location/Qualifiers source 1..4276

/organism="Homo sapiens"

/mol_type="mRNA"

/db_xref="taxon:9606"

/chromosome^" 10"

/map="10q24" gene 1..4276

/gene="PAX2"

/db_xref="GeneID:5076"

/db_xref=ΗGNC:8616"

/db_xref="MIM:167409" CDS 687..1937

/gene="PAX2"

/note="PAX2 gene is. a member of the paired-box containing genes which encode transcription factors involved in embryonic and fetal development; the gene product is nuclear protein which binds DNA isoform a is encoded by transcript variant a; paired box homeotic gene 2; go_component: nucleus [goid 0005634] [evidence IEA]; go_function: ATP binding [goid 0005524] [evidence IEA]; go_function: DNA binding [goid 0003677] [evidence IEA]; go_function: DNA binding [goid 0003677] [evidence TAS]

[pmid 9106533]; go_function: nucleoside diphosphate kinase activity [goid

0004550] [evidence IEA]; gojprocess: development [goid 0007275] [evidence IEA]; gojprocess: transcription [goid 0006350] [evidence IEA]; go_process: CTP biosynthesis [goid 0006241] [evidence

IEA]; go_process: GTP biosynthesis [goid 0006183] [evidence

IEA]; go_process: UTP biosynthesis [goid 0006228] [evidence

IEA]; go_process: axonogenesis [goid 0007409] [evidence TAS]

[pmid 9106533]; gojprocess: cell differentiation [goid 0030154] [evidence

IEA]; gojprocess: visual perception [goid 0007601] [evidence

TAS] [pmid 9106533]; gojprocess: regulation of transcription, DNA-dependent

[goid 0006355] [evidence IEA]; go_process: transcription from RNA polymerase II promoter

[goid 0006366] [evidence TAS] [pmid 8760285]"

/codon_start=l

/product="paired box protein 2 isoform a"

/protein_id="NP_003978.2"

/db_xref=^llGI:34878699"

/db_xref^"GeneID:5076"

/db_xref="HGNC:8616"

/db_xref^"MIM: 167409"

/translation="MDMHCKJUDPFSAMHPGHGGVNQLGGVFVNGRPLPDVVRQRIVELAH

QGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVDKIAEYK

RQNPTMFAWEIRDRLLAEGICDNDTVPSVSSINRIIRTKVQQPFHPTPDGAGTGVTA

PGHTΓVPSTASPPVSSASNDPVGSYSINGILGIPRSNGEKRKRDEVEVYTDPAHIRGG

GGLHLVWTLRDVSEGSVPNGDSQSGVDSLRKHLRADTFTQQQLEALDRVFERPSY

PDVFQASEHΠCSEQGNEYSLPALTPGLDEVKSSLSASTNPELGSNVSGTQTYPWTG

RDMASTTLPGYPPHVPPTGQGSYPTSTLAGMVPGSEFSGNPYSHPQYTAYNEAWRF

SNPALL

SSPYYYSAAPRSAPAAAAAAYDRH" STS 1926..2132

/gene="PAX2"

/standard jname="RH80285 "

/db_xref^"UniSTS:88437" STS 3124..3276

/gene="PAX2"

/standard_name="D 10S2478"

/db_xref="UniSTS:74159" polyA_signal 4230..4235

/gene="PAX2" polyA_signal 4234..4239

/gene="PAX2" polyA_signal 4241..4246

/gene="PAX2" polyA_site 4259

/gene="PAX2" ORIGIN

1 aggctccagt ctccggccga gtcttctcgc agccgcaacc cacctggggc cagcccagag 61 ctgccagcgc cgctcggctc cctccctccc tcccggccct tcggccgcgg cggcgtgcgc 121 ctgccttttc cgggggcggg ggcctggccc gcgcgctccc ctcccgcagg cgccacctcg 181 gacatccccg ggattgctac ttctctgcca acttcgccaa ctcgccagca cttggagagg 241 cccggctccc ctcccggcgc cctctgaccg cccccgcccc gcgcgctctc cgaccaccgc 301 ctctcggatg accaggttcc aggggagctg agcgagtcgc ctcccccgcc cagcttcagc 361 cctggctgca gctgcagcgc gagccatgcg cccccagtgc accccggccc ggcccaccgc 421 cccggggcca ttctgctgac cgcccagccc cgagccccga cagtggcaag ttgcggctac 481 tgcagttgca agctccggcc aacccggagg agccccagcg gggagcgcag tgttgcgccc 541 cccgcccccg cgcgccccgc agcagccggg cgttcactca tcctccctcc cccaccgtcc 601 ctcccttttc tcctcaagtc ctgaagttga gtttgagagg cgacacggcg gcggcggccg 661 cgctgctccc gctcctctgc ctccccatgg atatgcactg caaagcagac cccttctccg 721 cgatgcaccc agggcacggg ggtgtgaacc agctcggggg ggtgtttgtg aacggccggc 781 ccctacccga cgtggtgagg cagcgcatcg tggagctggc ccaccagggt gtgcggccct 841 gtgacatctc ccggcagctg cgggtcagcc acggctgtgt cagcaaaatc ctgggcaggt 901 actacgagac cggcagcatc aagccgggtg tgatcggtgg ctccaagccc aaagtggcga 961 cgcccaaagt ggtggacaag attgctgaat acaaacgaca gaacccgact atgttcgcct 1021 gggagattcg agaccggctc ctggccgagg gcatctgtga caatgacaca gtgcccagcg 1081 tctcttccat caacagaatc atccggacca aagttcagca gcctttccac ccaacgccgg 1141 atggggctgg gacaggagtg accgcccctg gccacaccat tgttcccagc acggcctccc 1201 ctcctgtttc cagcgcctcc aatgacccag tgggatccta ctccatcaat gggatcctgg 1261 ggattcctcg ctccaatggt gagaagagga aacgtgatga agttgaggta tacactgatc 1321 ctgcccacat tagaggaggt ggaggtttgc atctggtctg gactttaaga gatgtgtctg 1381 agggctcagt ccccaatgga gattcccaga gtggtgtgga cagtttgcgg aagcacttgc 1441 gagctgacac cttcacccag cagcagctgg aagctttgga tcgggtcttt gagcgtcctt 1501 cctaccctga cgtcttccag gcatcagagc acatcaaatc agaacagggg aacgagtact 1561 ccctcccagc cctgacccct gggcttgatg aagtcaagtc gagtctatct gcatccacca 1621 accctgagct gggcagcaac gtgtcaggca cacagacata cccagttgtg actggtcgtg 1681 acatggcgag caccactctg cctggttacc cccctcacgt gccccccact ggccagggaa 1741 gctaccccac ctccaccctg gcaggaatgg tgcctgggag cgagttctcc ggcaacccgt 1801 acagccaccc ccagtacacg gcctacaacg aggcttggag attcagcaac cccgccttac 1861 taagttcccc ttattattat agtgccgccc cccggtccgc ccctgccgct gctgccgctg 1921 cctatgaccg ccactagtta ccgcggggac cacatcaagc ttcaggccga cagcttcggc 1981 ctccacatcg tccccgtctg accccacccc ggagggaggg aggaccgacg cgacgcgatg 2041 cctcccggcc accgccccag cctcacccca tcccacgacc cccgcaaccc ttcacatcac 2101 ccccctcgaa ggtcggacag gacgggtgga gccgtgggcg ggaccctcag gcccgggccc 2161 gccgccccca gccccgcctg ccgcccctcc ccgcctgcct ggactgcgcg gcgccgtgag 2221 ggggattcgg cccagctcgt cccggcctcc accaagccag ccccgaagcc cgccagccac 2281 cctgccggac tcgggcgcga cctgctggcg cgcgccggat gtttctgtga cacacaatca 2341 gcgcggaccg cagcgcggcc cagccccggg cacccgcctc ggacgctcgg gcgccaggag 2401 gcttcgctgg aggggctggg ccaaggagat taagaagaaa acgactttct gcaggaggaa 2461 gagcccgctg ccgaatccct gggaaaaatt cttttccccc agtgccagcc ggactgccct 2521 cgccttccgg gtgtgccctg tcccagaaga tggaatgggg gtgtgggggt ccggctctag 2581 gaacgggctt tgggggcgtc aggtctttcc aaggttggga cccaaggatc ggggggccca 2641 gcagcccgca ccgatcgagc cggactctcg gctcttcact gctcctcctg gcctgcctag 2701 ttccccaggg cccggcacct cctgctgcga gacccggctc tcagccctgc cttgccccta 2761 cctcagcgtc tcttccacct gctggcctcc cagtttcccc tcctgccagt ccttcgcctg 2821 tcccttgacg ccctgcatcc tcctccctga ctcgcagccc catcggacgc tctcccggga 2881 ccgccgcagg accagtttcc atagactgcg gactggggtc ttcctccagc agttacttga 2941 tgccccctcc cccgacacag actctcaatc tgccggtggt aagaaccggt tctgagctgg 3001 cgtctgagct gctgcggggt ggaagtgggg ggctgcccac tccactcctc ccatcccctc 3061 ccagcctcct cctccggcag gaactgaaca gaaccacaaa aagtctacat ttatttaata 3121 tgatggtctt tgcaaaaagg aacaaaacaa cacaaaagcc caccaggctg ctgctttgtg 3181 gaaagacggt gtgtgtcgtg tgaaggcgaa acccggtgta cataacccct ccccctccgc 3241 cccgccccgc ccggccccgt agagtccctg tcgcccgccg gccctgcctg tagatacgcc 3301 ccgctgtctg tgctgtgaga gtcgccgctc gctggggggg aaggggggga cacagctaca 3361 cgcccattaa agcacagcac gtcctggggg aggggggcat tttttatgtt acaaaaaaaa 3421 attacgaaag aaaagaaatc tctatgcaaa atgacgaaca tggtcctgtg gactcctctg 3481 gcctgttttg ttggctcttt ctctgtaatt ccgtgttttc gctttttcct ccctgcccct 3541 ctctccctct gcccctctct cctctccgct tctctccccc tctgtctctg tctctctccg 3601 tctctgtcgc tcttgtctgt ctgtctctgc tctttcctcg gcctctctcc ccagacctgg 3661 cccggccgcc ctgtctccgc aggctagatc cgaggtggca gctccagccc ccgggctcgc 3721 cccctcgcgg gcgtgccccg cgcgccccgg gcggccgaag gccgggccgc cccgtcccgc 3781 cccgtagttg ctctttcggt agtggcgatg cgccctgcat gtctcctcac ccgtggatcg 3841 tgacgactcg aaataacaga aacaaagtca ataaagtgaa aataaataaa aatccttgaa 3901 caaatccgaa aaggcttgga gtcctcgccc agatctctct cccctgcgag ccctttttat 3961 ttgagaagga aaaagagaaa agagaatcgt ttaagggaac ccggcgccca gccaggctcc 4021 agtggcccga acggggcggc gagggcggcg agggcgccga ggtccggccc atcccagtcc 4081 tgtggggctg gccgggcaga gaccccggac ccaggcccag gcctaacctg ctaaatgtcc 4141 ccggacggtt ctggtctcct cggccacttt cagtgcgtcg gttcgttttg attctttttc 4201 ttttgtgcac ataagaaata aataataata ataaataaag aataaaattt tgtatgtcaa 4261 aaaaaaaaaa aaaaaa

Appendix C

LOCUS NM_000278 4207 bp mRNA linear PRI 24-SEP-2005

DEFINITION Homo sapiens paired box gene 2 (PAX2), transcript variant b, mRNA. ACCESSION NM_000278 VERSION NM_000278.2 GL34878700 KEYWORDS .

SOURCE Homo sapiens (human) ORGANISM Homo sapiens ,

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 4207) AUTHORS Yoshimura,K., Yoshida,S., Yamaji.Y., Komori,A., Yoshida,A.,

Hatae,K., Kubota,T. and Ishibashi,T. TITLE De nova insG619 mutation in PAX2 gene in a Japanese patient with papillorenal syndrome

JOURNAL Am. J. Ophthalmol. 139 (4), 733-735 (2005) PUBMED 15808183

REMARK GeneRIF: Molecular genetic analysis of the PAX2 gene in combination with renal ultrasonography can help in making an earlier diagnosis of the disease.

REFERENCE 2 (bases 1 to 4207) AUTHORS MazalJPJL, Stichenwirth,M., Koller,A., Blach,S., Haitel,A. and

Susani,M. TITLE Expression of aquaporins and P AX-2 compared to CD 10 and cytokeratin

7 in renal neoplasms: a tissue microarray study JOURNAL Mod. Pathol. 18 (4), 535-540 (2005) PUBMED 15502805 REMARK GeneRIF: PAX-2 is a reliable marker for clear cell renal cell carcinomas of lower grades but not for higher grades. REFERENCE 3 (bases 1 to 4207)

AUTHORS Higashide,T., Wada,T., Sakurai,M., Yokoyama,H. and Sugiyama,K. TITLE Macular abnormalities and optic disk anomaly associated with a new

PAX2 missense mutation

JOURNAL Am. J. Ophthalmol. 139 (1), 203-205 (2005) PUBMED 15652857

REMARK GeneRIF: A new PAX2 missense mutation, R71T, may cause macular abnormalities in addition to anomalies of the optic disk and the kidney.

REFERENCE 4 (bases 1 to 4207) AUTHORS Buttiglieri,S., Deregibus,M.C, Bravo.S., Cassoni,P., Chiarle,R.,

Bussolati,B- and Camussi,G. TITLE Role of Pax2 in apoptosis resistance and preinvasive phenotype of

Kaposi's sarcoma cells

JOURNAL J. Biol. Chem. 279 (6), 4136-4143 (2004) PUBMED 14627715 REMARK GeneRIF: expression of Pax2 by Kaposi's sarcoma cells correlated with an enhanced resistance against apoptotic signals and with the proinvasive phenotype REFERENCE 5 (bases 1 to 4207) AUTHORS Brophy,P.D., Lang,K.M. and Dressler,G.R. TITLE The secreted frizzled related protein 2 (SFRP2) gene is a target of the Pax2 transcription factor

JOURNAL J. Biol. Chem. 278 (52), 52401-52405 (2003) PUBMED 14561758 REMARK GeneRIF: Pax2 protein regulates expression of secreted frizzled related protein 2

REFERENCE 6 (bases 1 to 4207)

AUTHORS Schimmenti,L.A., Manligas,G.S. and Sieving,P.A. TITLE Optic nerve dysplasia and renal insufficiency in a family with a novel PAX2 mutation, Argl 15X: further ophthalmologic delineation of the renal-coloboma syndrome

JOURNAL Ophthalmic Genet. 24 (4), 191-202 (2003) PUBMED 14566649 REMARK GeneRIF: PAX2 mutation is associated with Optic nerve dysplasia and renal insufficiency of the renal-coloboma syndrome REFERENCE 7 (bases 1 to 4207)

AUTHORS Muratovska,A., Zhou,C, He₅S., Goodyer,P. and Eccles,M.R. TITLE Paired-Box genes are frequently expressed in cancer and often required for cancer cell survival JOURNAL Oncogene 22 (39), 7989-7997 (2003) PUBMED 12970747 REMARK GeneRIF: The PAX2 gene was frequently expressed in a panel of 406 common primary tumor tissues and endogenous PAX gene expression is often required for the growth and survival of cancer cells REFERENCE 8 (bases 1 to 4207) AUTHORS Gough,S.M., McDonakLM., Chen,X.N., Korenberg,J.R., Neri,A.,

Kahn,T., Eccles,M.R. and Morris,C.M. TITLE Refined physical map of the human PAX2/HOX11/NFKB2 cancer gene region at 10q24 and relocalization of the HPV6AI1 viral integration site to l4ql3.3-q21.1

JOURNAL BMC Genomics 4 (1), 9 (2003) PUBMED 12697057 REFERENCE 9 (bases 1 to 4207) AUTHORS Hoffmeister,A., Ropolo,A., Vasseur,S., MaIIo₅G. V., Bodeker,H.,

Ritz-Laser,B.₅ Dressler,G.R., Vaccaro,M.L, DagornJ.C, Moreno,S. and IovannaJ.L. TITLE The HMG-I/Y-related protein p8 binds to p300 and Pax2 trans-activation domain-interacting protein to regulate the trans-activation activity of the Pax2A and Pax2B transcription factors on the glucagon gene promoter JOURNAL J. Biol. Chem. 277 (25), 22314-22319 (2002) PUBMED 11940591 REMARK GeneRIF: The HMG-I/Y-related protein ρ8 binds to ρ300 and Pax2 trans-activation domain-interacting protein to regulate the trans-activation activity of the Pax2A and Pax2B transcription factors on the glucagon gene promoter. REFERENCE 10 (bases 1 to 4207) AUTHORS Cai,Y., Lechner,M.S., Nihalani,D., Prindle,M.J., Holzman,L.B. and

Dressler,G.R. TITLE Phosphorylation of Pax2 by the c-Jun N-terminal kinase and enhanced

Pax2-dependent transcription activation JOURNAL J. Biol. Chem. 277 (2), 1217-1222 (2002) PUBMED 11700324 REFERENCE 11 (bases 1 to 4207)

AUTHORS Becker,K., Beales,P.L., Calver,D.M., Matthijs,G. and Mohammed,S.N. TITLE Okihiro syndrome and acro-renal-ocular syndrome: clinical overlap, expansion of the phenotype, and absence of PAX2 mutations in two new families

JOURNAL J. Med. Genet. 39 (1), 68-71 (2002) PUBMED 11826030 REMARK GeneRJJF: The absence of PAX2 mutations has been identified in two families with histories of clinical overlap of Okihiro and acro-renal-ocular syndromes. REFERENCE 12 (bases 1 to 4207) AUTHORS Eccles,M.R., He₅S., Legge,M., Kumar,R., FoxJ., Zhou,C, French,M. and Tsai,R.W. TITLE PAX genes in development and disease: the role of PAX2 in urogenital tract development

JOURNAL Int. J. Dev. Biol. 46 (4), 535-544 (2002) PUBMED 12141441 REMARK Review article

GeneRIF: PAX2 has a role in urogenital tract development and disease [review]

REFERENCE 13 (bases 1 to 4207) AUTHORS Chung,G.W., Edwards,A.O., Schimmenti,L.A., Manligas,G.S.,

Zhang, Y.H. and Ritter,R. UI.

TITLE Renal-coloboma syndrome: report of a novel PAX2 gene mutation JOURNAL Am. J. Ophthalmol. 132 (6), 910-914 (2001) PUBMED 11730657 REMARK GeneRIF: The causal relationship between PAX2 gene mutations and renal-coloboma syndrome is further supported REFERENCE 14 (bases 1 to 4207) AUTHORS Nishimoto,K., Iijima,K., Shirakawa,T., Kitagawa,K., Satomura,K.,

Nakamura,H. and Yoshikawa,N.

TITLE PAX2 gene mutation in a family with isolated renal hypoplasia JOURNAL J. Am. Soc. Nephrol. 12 (8), 1769-1772 (2001) PUBMED 11461952 REFERENCE 15 (bases 1 to 4207)

AUTHORS Ritz-Laser,B., Estreicher,A., Gauthier,B. and PhilippeJ. TITLE The paired homeodomain transcription factor Pax-2 is expressed in the endocrine pancreas and transactivates the glucagon gene promoter

JOURNAL J. Biol. Chem. 275 (42), 32708-32715 (2000) PUBMED 10938089 REFERENCE 16 (bases 1 to 4207) AUTHORS Lechner,M.S., LevitanJ. and Dressler,G.R. TITLE PTlP, a novel BRCT domain-containing protein interacts with Pax2 and is associated with active chromatin JOURNAL Nucleic Acids Res. 28 (14), 2741-2751 (2000) PUBMED 10908331 REFERENCE 17 (bases 1 to 4207) AUTHORS Tavassoli,K., Ruger,W. and Horst,J. TITLE Alternative splicing in PAX2 generates a new reading frame and an extended conserved coding region at the carboxy terminus JOURNAL Hum. Genet. 101 (3), 371-375 (1997) PUBMED 9439670 REFERENCE 18 (bases 1 to 4207) AUTHORS Dahl,E., Koseki,H. and Balling,R. TITLE Pax genes and organogenesis JOURNAL Bioessays 19 (9), 755-765 (1997) PUBMED 9297966 REMARK Review article REFERENCE 19 (bases 1 to 4207) AUTHORS Schimmenti,L.A., Cunliffe,H.E., McNoe,L.A., Ward,T.A., French,M.C,

Shim,H.H., Zhang, Y.H., Proesmans,W., Leys,A., Byerly,K.A.,

Braddock,S.R., Masuno,M., Imaizumi,K., Devriendt,K. and Eccles,M.R. TITLE Further delineation of renal-coloboma syndrome in patients with extreme variability of phenotype and identical PAX2 mutations JOURNAL Am. J. Hum. Genet. 60 (4), 869-878 (1997) PUBMED 9106533 REFERENCE 20 (bases 1 to 4207) AUTHORS Narahara,K., Baker,E., Ito,S., Yokoyama,Y., Yu₅S., Hewitt,D.,

Sutherland, G.R., Eccles,M.R. and Richards,R.I. TITLE Localisation of a 1 Oq breakpoint within the P AX2 gene in a patient with a de novo t(10;13) translocation and optic nerve coloboma-renal disease

JOURNAL J. Med. Genet. 34 (3), 213-216 (1997) PUBMED 9132492 REFERENCE 21 (bases 1 to 4207)

AUTHORS Dehbi,M., Ghahremani,M., Lechner,M., Dressler,G. and PelletierJ. TITLE The paired-box transcription factor, PAX2, positively modulates expression of the Wilms' tumor suppressor gene (WTl) JOURNAL Oncogene 13 (3), 447-453 (1996) PUBMED 8760285 REFERENCE 22 (bases 1 to 4207) AUTHORS Sanyanusin,P., NorrishJ.H., Ward,T.A., Nebel,A., McNoe,L.A. and

Eccles,M.R.

TITLE Genomic structure of the human PAX2 gene JOURNAL Genomics 35 (1), 258-261 (1996) PUBMED 8661132 REFERENCE 23 (bases 1 to 4207) AUTHORS Sanyanusin,P., Schimmenti,L.A., McNoe,L.A., Ward,T.A.,

Pierpont,M.E., Sullivan,M.J., Dobyns,W.B. and Eccles,M.R. TITLE Mutation of the PAX2 gene in a family with optic nerve colobomas, renal anomalies and vesicoureteral reflux

JOURNAL Nat. Genet. 9 (4), 358-364 (1995)

PUBMED 7795640 REFERENCE 24 (bases 1 to 4207)

AUTHORS Ward,T.A., NebeLA-, Reeve,A.E. and Eccles,M.R.

TITLE Alternative messenger RNA forms and open reading frames within an additional conserved region of the human PAX-2 gene

JOURNAL Cell Growth Differ. 5 (9), 1015-1021 (1994)

PUBMED 7819127 REFERENCE 25 (bases 1 to 4207)

AUTHORS NoIl₅M.

TITLE Evolution and role of Pax genes

JOURNAL Curr. Opin. Genet. Dev. 3 (4), 595-605 (1993)

PUBMED 8241771

REMARK Review article REFERENCE 26 (bases 1 to 4207)

AUTHORS Stapleton,P., Weith,A., Urbanek,P., Kozmik,Z. and Busslinger,M.

TITLE Chromosomal localization of seven PAX genes and cloning of a novel family member, PAX-9

JOURNAL Nat. Genet. 3 (4), 292-298 (1993)

PUBMED 7981748 REFERENCE 27 (bases 1 to 4207)

AUTHORS PiIz₅AJ., Povey,S., Gruss,P. and Abbott,C.M.

TITLE Mapping of the human homologs of the murine paired-box-containing genes

JOURNAL Mamm. Genome 4 (2), 78-82 (1993)

PUBMED 8431641 REFERENCE 28 (bases 1 to 4207)

AUTHORS Eccles,M.R., WaIHs₅LJ., Fidler,A.E., Spurr,N.K.₅ Goodfellow,P J. and Reeve,A.E.

TITLE Expression of the PAX2 gene in human fetal kidney and Wilms' tumor

JOURNAL Cell Growth Differ. 3 (5), 279-289 (1992)

PUBMED 1378753

COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from U45255.1 and BM671839.1. On Sep 22, 2003 this sequence version replaced gi:4557820.

Summary: PAX2 encodes paired box gene 2, one of many human homologues of the Drosophila melanogaster gene prd. The central feature of this transcription factor gene family is the conserved DNA-binding paired box domain. PAX2 is believed to be a target of transcriptional supression by the tumor supressor gene WTl . Mutations within PAX2 have been shown to result in optic nerve colobomas and renal hypoplasia. Alternative splicing of this gene results in multiple transcript variants.

Transcript Variant: This variant (b) lacks an alternate in-frame exon and uses an alternate splice site in the 3' coding region, compared to variant e. This results in a protein (isoform b) with a shorter, distinct C-terminus compared to isoform e. COMPLETENESS: complete on the 3' end. FEATURES Location/Qualifiers source L.4207

/organism="Homo sapiens"

/mol_type="mRNA"

/db_xref="taxon:9606"

/chromosome=" 10"

/map="10q24" gene 1..4207

/gene="PAX2"

/db_xref="GeneID:5076"

/db_xref=ΗGNC:8616"

/db_xref="MIM: 167409" CDS 687..1868

/gene="PAX2"

/note="PAX2 gene is a member of the paired-box containing genes which encode transcription factors involved in embryonic and fetal development; the gene product is nuclear protein which binds DNA isoform b is encoded by transcript variant b; paired box homeotic gene 2; go_component: nucleus [goid 0005634] [evidence IEA]; go_function: ATP binding [goid 0005524] [evidence IEA]; go_function: DNA binding [goid 0003677] [evidence IEA]; go_function: DNA binding [goid 0003677] [evidence TAS]

[pmid 9106533]; go_function: nucleoside diphosphate kinase activity [goid

0004550] [evidence IEA]; gojprocess: development [goid 0007275] [evidence IEA]; gojprocess: transcription [goid 0006350] [evidence IEA]; go_process: CTP biosynthesis [goid 0006241] [evidence

IEA]; go_process: GTP biosynthesis [goid 0006183] [evidence

IEA]; go_process: UTP biosynthesis [goid 0006228] [evidence

IEA]; gojprocess: axonogenesis [goid 0007409] [evidence TAS]

[pmid 9106533]; gojprocess: cell differentiation [goid 0030154] [evidence

IEA]; gojprocess: visual perception [goid 0007601] [evidence

TAS] [pmid 9106533]; gojprocess: regulation of transcription, DNA-dependent

[goid 0006355] [evidence IEA]; gojprocess: transcription from RNA polymerase II promoter

[goid 0006366] [evidence TAS] [pmid 8760285]"

/codon start=l /product="paired box protein 2 isoform b" /protein_id="NP_000269.2" /db_xref="GI:34878701 " /db_xref^"GeneID:5076" /db_xref="HGNC:8616" /db_xref^"MIM: 167409"

/translation="MDMHCKADPFSAMHPGHGGVNQLGGVFVNGRPLPDVVRQRIVELAH

QGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKWDKIAEYK

RQNPTMFAWEIRDRLLAEGICDNDTVPSVSSINRIIRTKVQQPFHPTPDGAGTGVTA

PGHTΓVTSTASPPVSSASNDPVGSYSINGILGIPRSNGEKRKRDEDVSEGSVPNGDSQ

SGVDSLRKHLRADTFTQQQLEALDRVFERPSYPDVFQASEHIKSEQGNEYSLPALTP

GLDEVKSSLSASTNPELGSNVSGTQTYPWTGRDMASTTLPGYPPHVPPTGQGSYP

TSTLAGMVPGSEFSGNPYSHPQYTAYNEAWRFSNPALLSSPYYYSAAPRSAPAAAA

AAYDR

H" STS 1857..2063

/gene="PAX2"

/standard_name="RH80285 "

/db_xref^"UniSTS:88437" STS 3055..3207

/gene="PAX2"

/standard_name="D10S2478"

/db_xref="UniSTS :74159" polyA_signal 4161..4166

/gene="PAX2" polyA_signal 4165..4170

/gene="PAX2" polyA__signal 4172..4177

/gene="PAX2" polyA_site 4190

/gene="PAX2" ORIGIN

1 aggctccagt ctccggccga gtcttctcgc agccgcaacc cacctggggc cagcccagag 61 ctgccagcgc cgctcggctc cctccctccc tcccggccct tcggccgcgg cggcgtgcgc 121 ctgccttttc cgggggcggg ggcctggccc gcgcgctccc ctcccgcagg cgccacctcg 181 gacatccccg ggattgctac ttctctgcca acttcgccaa ctcgccagca cttggagagg 241 cccggctccc ctcccggcgc cctctgaccg cccccgcccc gcgcgctctc cgaccaccgc 301 ctctcggatg accaggttcc aggggagctg agcgagtcgc ctcccccgcc cagcttcagc 361 cctggctgca gctgcagcgc gagccatgcg cccccagtgc accccggccc ggcccaccgc 421 cccggggcca ttctgctgac cgcccagccc cgagccccga cagtggcaag ttgcggctac 481 tgcagttgca agctccggcc aacccggagg agccccagcg gggagcgcag tgttgcgccc 541 cccgcccccg cgcgccccgc agcagccggg cgttcactca tcctccctcc cccaccgtcc 601 ctcccttttc tcctcaagtc ctgaagttga gtttgagagg cgacacggcg gcggcggccg 661 cgctgctccc gctcctctgc ctccccatgg atatgcactg caaagcagac cccttctccg 721 cgatgcaccc agggcacggg ggtgtgaacc agctcggggg ggtgtttgtg aacggccggc 781 ccctacccga cgtggtgagg cagcgcatcg tggagctggc ccaccagggt gtgcggccct 841 gtgacatctc ccggcagctg cgggtcagcc acggctgtgt cagcaaaatc ctgggcaggt 901 actacgagac cggcagcatc aagccgggtg tgatcggtgg ctccaagccc aaagtggcga 961 cgcccaaagt ggtggacaag attgctgaat acaaacgaca gaacccgact atgttcgcct 1021 gggagattcg agaccggctc ctggccgagg gcatctgtga caatgacaca gtgcccagcg 1081 tctcttccat caacagaatc atccggacca aagttcagca gcctttccac ccaacgccgg 1141 atggggctgg gacaggagtg accgcccctg gccacaccat tgttcccagc acggcctccc 1201 ctcctgtttc cagcgcctcc aatgacccag tgggatccta ctccatcaat gggatcctgg 1261 ggattcctcg ctccaatggt gagaagagga aacgtgatga agatgtgtct gagggctcag 1321 tccccaatgg agattcccag agtggtgtgg acagtttgcg gaagcacttg cgagctgaca 1381 ccttcaccca gcagcagctg gaagctttgg atcgggtctt tgagcgtcct tcctaccctg 1441 acgtcttcca ggcatcagag cacatcaaat cagaacaggg gaacgagtac tccctcccag 1501 ccctgacccc tgggcttgat gaagtcaagt cgagtctatc tgcatccacc aaccctgagc 1561 tgggcagcaa cgtgtcaggc acacagacat acccagttgt gactggtcgt gacatggcga 1621 gcaccactct gcctggttac ccccctcacg tgccccccac tggccaggga agctacccca 1681 cctGcaccct ggcaggaatg gtgcctggga gcgagttctc cggcaacccg tacagccacc 1741 cccagtacac ggcctacaac gaggcttgga gattcagcaa ccccgcctta ctaagttccc 1801 cttattatta tagtgccgcc ccccggtccg cccctgccgc tgctgccgct gcctatgacc 1861 gccactagtt accgcgggga ccacatcaag cttcaggccg acagcttcgg cctccacatc 1921 gtccccgtct gaccccaccc cggagggagg gaggaccgac gcgacgcgat gcctcccggc 1981 caccgcccca gcctcacccc atcccacgac ccccgcaacc cttcacatca cccccctcga 2041 aggtcggaca ggacgggtgg agccgtgggc gggaccctca ggcccgggcc cgccgccccc 2101 agccccgcct gccgcccctc cccgcctgcc tggactgcgc ggcgccgtga gggggattcg 2161 gcccagctcg tcccggcctc caccaagcca gccccgaagc ccgccagcca ccctgccgga 2221 ctcgggcgcg acctgctggc gcgcgccgga tgtttctgtg acacacaatc agcgcggacc 2281 gcagcgcggc ccagccccgg gcacccgcct cggacgctcg ggcgccagga ggcttcgctg 2341 gaggggctgg gccaaggaga ttaagaagaa aacgactttc tgcaggagga agagcccgct 2401 gccgaatccc tgggaaaaat tcttttcccc cagtgccagc cggactgccc tcgccttccg 2461 ggtgtgccct gtcccagaag atggaatggg ggtgtggggg tccggctcta ggaacgggct 2521 ttgggggcgt caggtctttc caaggttggg acccaaggat cggggggccc agcagcccgc 2581 accgatcgag ccggactctc ggctcttcac tgctcctcct ggcctgccta gttccccagg 2641 gcccggcacc tcctgctgcg agacccggct ctcagccctg ccttgcccct acctcagcgt 2701 ctcttccacc tgctggcctc ccagtttccc ctcctgccag tccttcgcct gtcccttgac 2761 gccctgcatc ctcctccctg actcgcagcc ccatcggacg ctctcccggg accgccgcag 2821 gaccagtttc catagactgc ggactggggt cttcctccag cagttacttg atgccccctc 2881 ccccgacaca gactctcaat ctgccggtgg taagaaccgg ttctgagctg gcgtctgagc 2941 tgctgcgggg tggaagtggg gggctgccca ctccactcct cccatcccct cccagcctcc 3001 tcctccggca ggaactgaac agaaccacaa aaagtctaca tttatttaat atgatggtct 3061 ttgcaaaaag gaacaaaaca acacaaaagc ccaccaggct gctgctttgt ggaaagacgg 3121 tgtgtgtcgt gtgaaggcga aacccggtgt acataacccc tccccctccg ccccgccccg 3181 cccggccccg tagagtccct gtcgcccgcc ggccctgcct gtagatacgc cccgctgtct 3241 gtgctgtgag agtcgccgct cgctgggggg gaaggggggg acacagctac acgcccatta 3301 aagcacagca cgtcctgggg gaggggggca ttttttatgt tacaaaaaaa aattacgaaa 3361 gaaaagaaat ctctatgcaa aatgacgaac atggtcctgt ggactcctct ggcctgtttt 3421 gttggctctt tctctgtaat tccgtgtttt cgctttttcc tccctgcccc tctctccctc 3481 tgcccctctc tcctctccgc ttctctcccc ctctgtctct gtctctctcc gtctctgtcg 3541 ctcttgtctg tctgtctctg ctctttcctc ggcctctctc cccagacctg gcccggccgc 3601 cctgtctccg caggctagat ccgaggtggc agctccagcc cccgggctcg ccccctcgcg 3661 ggcgtgcccc gcgcgccccg ggcggccgaa ggccgggccg ccccgtcccg ccccgtagtt 3721 gctctttcgg tagtggcgat gcgccctgca tgtctcctca cccgtggatc gtgacgactc 3781 gaaataacag aaacaaagtc aataaagtga aaataaataa aaatccttga acaaatccga 3841 aaaggcttgg agtcctcgcc cagatctctc tcccctgcga gcccttttta tttgagaagg 3901 aaaaagagaa aagagaatcg tttaagggaa cccggcgccc agccaggctc cagtggcccg 3961 aacggggcgg cgagggcggc gagggcgccg aggtccggcc catcccagtc ctgtggggct 4021 ggccgggcag agaccccgga cccaggccca ggcctaacct gctaaatgtc cccggacggt 4081 tctggtctcc tcggccactt tcagtgcgtc ggttcgtttt gattcttttt cttttgtgca 4141 cataagaaat aaataataat aataaataaa gaataaaatt ttgtatgtca aaaaaaaaaa 4201 aaaaaaa

Appendix D

LOCUS NM_003988 4290 bp mRNA linear PRI 24-SEP-2005

DEFINITION Homo sapiens paired box gene 2 (PAX2), transcript variant c, mRNA. ACCESSION NM_003988 VERSION NM_003988.2 GL34878708 KEYWORDS .

SOURCE Homo sapiens (human) ORGANISM Homo sapiens

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 4290) AUTHORS Yoshimura,K., Yoshida,S., Yamaji,Y., Komori,A., Yoshida,A.,

Hatae,K., Kubota,T. and Ishibashi,T. TITLE De novo insG619 mutation in PAX2 gene in a Japanese patient with papillorenal syndrome

JOURNAL Am. J. Ophthalmol. 139 (4), 733-735 (2005) PUBMED 15808183

REMARK GeneRJJF: Molecular genetic analysis of the PAX2 gene in combination with renal ultrasonography can help in making an earlier diagnosis of the disease.

REFERENCE 2 (bases 1 to 4290) AUTHORS Mazal,P.R., Stichenwirth,M., Koller,A., Blach,S., Haitel,A. and

Susani,M. TITLE Expression of aquaporins and PAX-2 compared to CDlO and cytokeratin

7 in renal neoplasms: a tissue microarray study JOURNAL Mod. Pathol. 18 (4), 535-540 (2005) ¹PUBMED 15502805 REMARK GeneRIF: PAX-2 is a reliable marker for clear cell renal cell carcinomas of lower grades but not for higher grades. REFERENCE 3 (bases 1 to 4290)

AUTHORS Higashide,T., Wada,T., Sakurai,M., Yokoyama,H. and Sugiyama,K. TITLE Macular abnormalities and optic disk anomaly associated with a new

PAX2 missense mutation

JOURNAL Am. J. Ophthalmol. 139 (1), 203-205 (2005) PUBMED 15652857

REMARK GeneRIF: A new PAX2 missense mutation, R71T, may cause macular abnormalities in addition to anomalies of the optic disk and the kidney.

REFERENCE 4 (bases 1 to 4290) AUTHORS Buttiglieri,S., Deregibus,M.C, Bravo,S., Cassoni,P., Chiarle,R.,

Bussolati,B- and Camussi,G. TITLE Role of Pax2 in apoptosis resistance and preinvasive phenotype of

Kaposi's sarcoma cells

JOURNAL J. Biol. Chem. 279 (6), 4136-4143 (2004) PUBMED 14627715 REMARK GeneRIF: expression of Pax2 by Kaposi's sarcoma cells correlated with an enhanced resistance against apoptotic signals and with the preinvasive phenotype REFERENCE 5 (bases 1 to 4290) AUTHORS Brophy,P.D., Lang,K.M. and Dressler,G.R. TITLE The secreted frizzled related protein 2 (SFRP2) gene is a target of the Pax2 transcription factor

JOURNAL J. Biol. Chem. 278 (52), 52401-52405 (2003) PUBMED 14561758 REMARK GeneRIF: Pax2 protein regulates expression of secreted frizzled related protein 2

REFERENCE 6 (bases 1 to 4290)

AUTHORS Schimmenti,L.A., Manligas,G.S. and Sieving,P.A. TITLE Optic nerve dysplasia and renal insufficiency in a family with a novel PAX2 mutation, Argl 15X: further ophthalmologic delineation of the renal-coloboma syndrome

JOURNAL Ophthalmic Genet. 24 (4), 191-202 (2003) PUBMED 14566649 REMARK GeneRIF: PAX2 mutation is associated with Optic nerve dysplasia and renal insufficiency of the renal-coloboma syndrome REFERENCE 7 (bases 1 to 4290)

AUTHORS Muratovska,A., Zhou,C, He₅S., Goodyer,P. and Eccles,M.R. TITLE Paired-Box genes are frequently expressed in cancer and often required for cancer cell survival JOURNAL Oncogene 22 (39), 7989-7997 (2003) PUBMED 12970747 REMARK GeneRIF: The PAX2 gene was frequently expressed in a panel of 406 common primary tumor tissues and endogenous PAX gene expression is often required for the growth and survival of cancer cells REFERENCE 8 (bases 1 to 4290) AUTHORS Gough,S.M., McDonald,M., Chen,X.N., Korenberg,J.R.₅ Neri,A,

Kahn,T., Eccles,M.R. and Morris,C.M. TITLE Refined physical map of the human PAX2/HOX11/NFKB2 cancer gene region at 10q24 and relocalization of the HPV6AI1 viral integration site to 14ql3.3-q21.1

JOURNAL BMC Genomics 4 (1), 9 (2003) PUBMED 12697057 REFERENCE 9 (bases 1 to 4290) AUTHORS Hoffrneister,A., Ropolo,A., Vasseur,S., Mallo,G.V., Bodeker,H.,

Ritz-Laser,B., Dressler,G.R., Vaccaro,M.L, DagornJ.C, Moreno,S. and IovannaJ.L. TITLE The HMG-I/Y-related protein p8 binds to p300 and Pax2 trans-activation domain-interacting protein to regulate the trans-activation activity of the Pax2A and Pax2B transcription factors on the glucagon gene promoter JOURNAL J. Biol. Chem. 277 (25), 22314-22319 (2002) PUBMED 11940591 REMARK GeneRIF: The HMG-I/Y-related protein ρ8 binds to ρ300 and Pax2 trans-activation domain-interacting protein to regulate the trans-activation activity of the Pax2A and Pax2B transcription factors on the glucagon gene promoter. REFERENCE 10 (bases 1 to 4290) AUTHORS Cai,Y., Lechner,M.S., Nihalani,D., Prindle,MJ., Holzman,L.B. and

Dressler,G.R. TITLE Phosphorylation of Pax2 by the c-Jun N-terminal kinase and enhanced

Pax2-dependent transcription activation JOURNAL J. Biol. Chem. 277 (2), 1217-1222 (2002) PUBMED 11700324 REFERENCE 11 (bases 1 to 4290)

AUTHORS Becker,K., Beales,P.L., Calver,D.M., Matthijs,G. and Mohamnied,S.N. TITLE Okihiro syndrome and acro-renal-ocular syndrome: clinical overlap, expansion of the phenotype, and absence of PAX2 mutations in two new families

JOURNAL J. Med. Genet. 39 (1), 68-71 (2002) PUBMED 11826030 REMARK GeneRJJP: The absence of PAX2 mutations has been identified in two families with histories of clinical overlap of Okihiro and acro-renal-ocular syndromes. REFERENCE 12 (bases 1 to 4290) AUTHORS Eccles,M.R., He₃S., Legge,M., Kumar,R., Fox,J., Zhou,C, French,M. and Tsai,R.W. TITLE PAX genes in development and disease: the role of PAX2 in urogenital tract development

JOURNAL hit. J. Dev. Biol. 46 (4), 535-544 (2002) PUBMED 12141441 REMARK Review article

GeneRJJF: PAX2 has a role in urogenital tract development and disease [review]

REFERENCE 13 (bases 1 to 4290) AUTHORS Chung,G.W., Edwards,A.O., Schimmenti,L.A., Manligas,G.S.,

Zhang, Y.H. and Ritter,R. DX

TITLE Renal-coloboma syndrome: report of a novel PAX2 gene mutation JOURNAL Am. J. Ophthalmol. 132 (6), 910-914 (2001) PUBMED 11730657 REMARK GeneRIF: The causal relationship between PAX2 gene mutations and renal-coloboma syndrome is further supported REFERENCE 14 (bases 1 to 4290) AUTHORS Nisbimoto,K., Iijima,K., Shirakawa,T., Kitagawa,K., Satomura,K.,

Nakamura,H- and Yoshikawa,N.

TITLE PAX2 gene mutation in a family with isolated renal hypoplasia JOURNAL J. Am. Soc. Nephrol. 12 (8), 1769-1772 (2001) PUBMED 11461952 REFERENCE 15 (bases 1 to 4290)

AUTHORS Ritz-Laser^B., Estreicher,A._? Gauthier,B. and PhilippeJ. TITLE The paired homeodomain transcription factor Pax-2 is expressed in the endocrine pancreas and transactivates the glucagon gene promoter

JOURNAL J. Biol. Chem. 275 (42), 32708-32715 (2000) PUBMED 10938089 REFERENCE 16 (bases 1 to 4290) AUTHORS Lechner,M.S., Levitan,! and Dressler,G.R. TITLE PTEP, a novel BRCT domain-containing protein interacts with Pax2 and is associated with active chromatin JOURNAL Nucleic Acids Res. 28 (14), 2741-2751 (2000) PUBMED 10908331 REFERENCE 17 (bases 1 to 4290) AUTHORS Tavassoli,K., Ruger,W. and Horst,J. TITLE Alternative splicing in PAX2 generates a new reading frame and an extended conserved coding region at the carboxy terminus JOURNAL Hum. Genet. 101 (3), 371-375 (1997) PUBMED 9439670 REFERENCE 18 (bases 1 to 4290) AUTHORS Dahl,K, Koseki,H. and Balling,R. TITLE Pax genes and organogenesis JOURNAL Bioessays 19 (9), 755-765 (1997) PUBMED 9297966 REMARK Review article REFERENCE 19 (bases 1 to 4290)

AUTHORS Schimmenti,L.A., Cunliffe,H.E., McNoe,L.A., Ward,T.A., French,M.C, Shim,H.H., Zhang, Y.H., Proesmans,W., Leys,A., Byerly,K.A., Braddock,S.R., Masuno,M., Imaizumi,K., Devriendt,K. and Eccles,M.R. TITLE Further delineation of renal-coloboma syndrome in patients with extreme variability of phenotype and identical PAX2 mutations JOURNAL Am. J. Hum. Genet. 60 (4), 869-878 (1997) PUBMED 9106533 REFERENCE 20 (bases 1 to 4290) AUTHORS Narahara,K., Baker,E., Ito,S., Yokoyama,Y., Yu₅S., Hewitt,D.,

Sutherland,G.R., Eccles,M.R. and Richards,R.I.

TITLE Localisation of a 1 Oq breakpoint within the PAX2 gene in a patient with a de novo t(10;13) translocation and optic nerve coloboma-renal disease

JOURNAL J. Med. Genet. 34 (3), 213-216 (1997) PUBMED 9132492 REFERENCE 21 (bases 1 to 4290)

AUTHORS Dehbi,M., Ghahremani,M., Lechner,M., Dressler,G. and PelletierJ. TITLE The paired-box transcription factor, PAX2, positively modulates expression of the Wilms' tumor suppressor gene (WTl) JOURNAL Oncogene 13 (3), 447-453 (1996) PUBMED 8760285 REFERENCE 22 (bases 1 to 4290) AUTHORS Sanyanusin,P., NorrishJ.H., Ward,T.A., Nebel,A., McNoe,L.A. and

Eccles,M.R.

TITLE Genomic structure of the human PAX2 gene JOURNAL Genomics 35 (1), 258-261 (1996) PUBMED 8661132 REFERENCE 23 (bases 1 to 4290)

AUTHORS Sanyanusin,P., Schimmenti,L.A., McNoe,L.A., Ward,T.A., Pierpont,M.E., SullivanJVi.J., Dobyns,W.B. and Eccles,M.R. TITLE Mutation of the PAX2 gene in a family with optic nerve colobomas, renal anomalies and vesicoureteral reflux JOURNAL Nat. Genet. 9 (4), 358-364 (1995) PUBMED 7795640 REFERENCE 24 (bases 1 to 4290)

AUTHORS Ward,T.A., NebelΛ, Reeve,A.E. and Eccles,M.R. TITLE Alternative messenger RNA forms and open reading frames within an additional conserved region of the human PAX-2 gene JOURNAL Cell Growth Differ. 5 (9), 1015-1021 (1994) PUBMED 7819127 REFERENCE 25 (bases 1 to 4290) AUTHORS NoIl₅M. TITLE Evolution and role of Pax genes JOURNAL Curr. Opin. Genet. Dev. 3 (4), 595-605 (1993) PUBMED 8241771 REMARK Review article REFERENCE 26 (bases 1 to 4290)

AUTHORS Staρleton,P., Weith,A., Urbanek,P., Kozmik,Z. and Busslinger,M. TITLE Chromosomal localization of seven PAX genes and cloning of a novel family member, PAX-9 JOURNAL Nat. Genet. 3 (4), 292-298 (1993) PUBMED 7981748 REFERENCE 27 (bases 1 to 4290) AUTHORS PiIz₅A-J-, Povey,S., Gruss,P. and Abbott,C.M. TITLE Mapping of the human homologs of the murine paired-box-containing genes

JOURNAL Mamm. Genome 4 (2), 78-82 (1993) PUBMED 8431641 REFERENCE 28 (bases 1 to 4290) AUTHORS Eccles,M.R., WaIHs₅LJ., Fidler,A-E., Spurr,N.K., Goodfellow,PJ. and Reeve,A.E.

TITLE Expression of the PAX2 gene in human fetal kidney and Wilms' tumor JOURNAL Cell Growth Differ. 3 (5), 279-289 (1992) PUBMED 1378753 COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from U45255.1 and BM671839.1.

On Sep 22, 2003 this sequence version replaced gi:4557824.

Summary: PAX2 encodes paired box gene 2, one of many human homologues of the Drosophila melanogaster gene prd. The central feature of this transcription factor gene family is the conserved DNA-binding paired box domain. PAX2 is believed to be a target of transcriptional supression by the tumor supressor gene WTl. Mutations within PAX2 have been shown to result in optic nerve colobomas and renal hypoplasia. Alternative splicing of this gene results in multiple transcript variants.

Transcript Variant: This variant (c) has multiple differences in the coding region, compared to variant e, one of which results in a translational frameshift. The resulting protein (isoform c) has a distinct C-terminus and is shorter than isoform e. COMPLETENESS: complete on the 3' end. FEATURES Location/Qualifiers source L.4290

/organism='Ηomo sapiens"

/mol_type="mRNA"

/db_xref="taxon:9606"

/chrornosome=" 10"

/map="10q24" gene 1..4290

/gene="PAX2"

/db_xref="GeneID:5076"

/db_xref="HGNC:8616"

/db_xref="MIM: 167409" CDS 687..1877

/gene="PAX2"

/note="PAX2 gene is a member of the paired-box containing genes which encode transcription factors involved in embryonic and fetal development; the gene product is nuclear protein which binds DNA isoform c is encoded by transcript variant c; paired box homeotic gene 2; go_component: nucleus [goid 0005634] [evidence IEA]; go_function: ATP binding [goid 0005524] [evidence IEA]; go_function: DNA binding [goid 0003677] [evidence IEA]; go_function: DNA binding [goid 0003677] [evidence TAS]

[pmid 9106533]; go_function: nucleoside diphosphate kinase activity [goid

0004550] [evidence IEA]; go_process: development [goid 0007275] [evidence IEA]; go_process: transcription [goid 0006350] [evidence IEA]; go_process: CTP biosynthesis [goid 0006241] [evidence

EA]; go_process: GTP biosynthesis [goid 0006183] [evidence

IEA]; gojprocess: UTP biosynthesis [goid 0006228] [evidence

IEA]; go_process: axonogenesis [goid 0007409] [evidence TAS]

[pmid 9106533]; go_process: cell differentiation [goid 0030154] [evidence

IEA]; gojprocess: visual perception [goid 0007601] [evidence

TAS] [pmid 9106533]; go_process: regulation of transcription, DNA-dependent

[goid 0006355] [evidence IEA]; go_process: transcription from RNA polymerase II promoter

[goid 0006366] [evidence TAS] [pmid 8760285]"

/codon start=l /product="paired box protein 2 isoform c"

/protein_id="NP_003979.2"

/db_xref="GI:34878709"

/db_xre£="CCDS :CCDS7499.1 "

<img file="WO2007047512A2_D0003.tif" />

/translation="MDMHCKADPFSAMHPGHGGVNQLGGVFVNGRPLPDWRQRIVELAH

QGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVDKIAEYK

RQNPTMFAWEIRDRLLAEGICDNDTVPSVSSINRΠRTKVQQPFHPTPDGAGTGVTA

PGHTIVPSTASPPVSSASNDPVGSYSINGILGIPRSNGEKRKRDEDVSEGSVPNGDSQ

SGVDSLRKHLRADTFTQQQLEALDRVFERPSYPDVFQASEHIKSEQGNEYSLPALTP

GLDEVKSSLSASTNPELGSNVSGTQTYPWTGRDMASTTLPGYPPHVPPTGQGSYP

TSTLAGMVPEAAVGPSSSLMSKPGRKLAEVPPCVQPTGASSPATRTATPSTRPTTRL

GDSA

TPPY" STS 1940..2146

/gene="PAX2"

/standard_name="RH80285"

/db_xref="UniSTS:88437" STS 3138..3290

/gene="PAX2"

/standard_name="D 10S2478 "

/db_xre£="UniSTS:74159" polyA_signal 4244..4249

/gene="PAX2" polyA_signal 4248..4253

/gene="PAX2" polyA_signal 4255..4260

/gene="PAX2" polyA_site 4273

/gene="PAX2" ORIGIN

1 aggctccagt ctccggccga gtcttctcgc agccgcaacc cacctggggc cagcccagag 61 ctgccagcgc cgctcggctc cctccctccc tcccggccct tcggccgcgg cggcgtgcgc 121 ctgccttttc cgggggcggg ggcctggccc gcgcgctccc ctcccgcagg cgccacctcg 181 gacatccccg ggattgctac ttctctgcca acttcgccaa ctcgccagca cttggagagg 241 cccggctccc ctcccggcgc cctctgaccg cccccgcccc gcgcgctctc cgaccaccgc 301 ctctcggatg accaggttcc aggggagctg agcgagtcgc ctcccccgcc cagcttcagc 361 cctggctgca gctgcagcgc gagccatgcg cccccagtgc accccggccc ggcccaccgc 421 cccggggcca ttctgctgac cgcccagccc cgagccccga cagtggcaag ttgcggctac 481 tgcagttgca agctccggcc aacccggagg agccccagcg gggagcgcag tgttgcgccc 541 cccgcccccg cgcgccccgc agcagccggg cgttcactca tcctccctcc cccaccgtcc 601 ctcccttttc tcctcaagtc ctgaagttga gtttgagagg cgacacggcg gcggcggccg 661 cgctgctccc gctcctctgc ctccccatgg atatgcactg caaagcagac cccttctccg 721 cgatgcaccc agggcacggg ggtgtgaacc agctcggggg ggtgtttgtg aacggccggc 781 ccctacccga cgtggtgagg cagcgcatcg tggagctggc ccaccagggt gtgcggccct 841 gtgacatctc ccggcagctg cgggtcagcc acggctgtgt cagcaaaatc ctgggcaggt 901 actacgagac cggcagcatc aagccgggtg tgatcggtgg ctccaagccc aaagtggcga 961 cgcccaaagt ggtggacaag attgctgaat acaaacgaca gaacccgact atgttcgcct 1021 gggagattcg agaccggctc ctggccgagg gcatctgtga caatgacaca gtgcccagcg 1081 tctcttccat caacagaatc atccggacca aagttcagca gcctttccac ccaacgccgg 1141 atggggctgg gacaggagtg accgcccctg gccacaccat tgttcccagc acggcctccc 1201 ctcctgtttc cagcgcctcc aatgacccag tgggatccta ctccatcaat gggatcctgg 1261 ggattcctcg ctccaatggt gagaagagga aacgtgatga agatgtgtct gagggctcag 1321 tccccaatgg agattcccag agtggtgtgg acagtttgcg gaagcacttg cgagctgaca 1381 ccttcaccca gcagcagctg gaagctttgg atcgggtctt tgagcgtcct tcctaccctg 1441 acgtcttcca ggcatcagag cacatcaaat cagaacaggg gaacgagtac tccctcccag 1501 ccctgacccc tgggcttgat gaagtcaagt cgagtctatc tgcatccacc aaccctgagc 1561 tgggcagcaa cgtgtcaggc acacagacat acccagttgt gactggtcgt gacatggcga 1621 gcaccactct gcctggttac ccccctcacg tgccccccac tggccaggga agctacccca 1681 cctccaccct ggcaggaatg gtgcctgagg ctgcagttgg tccctcatcc tccctcatga 1741 gcaagccggg gaggaagctt gcagaagtgc ccccttgtgt gcaacccact ggagcgagtt 1801 ctccggcaac ccgtacagcc acccccagta cacggcctac aacgaggctt ggagattcag 1861 caaccccgcc ttactaagtt ccccttatta ttatagtgcc gccccccggt ccgcccctgc 1921 cgctgctgcc gctgcctatg accgccacta gttaccgcgg ggaccacatc aagcttcagg 1981 ccgacagctt cggcctccac atcgtccccg tctgacccca ccccggaggg agggaggacc 2041 gacgcgacgc gatgcctccc ggccaccgcc ccagcctcac cccatcccac gacccccgca 2101 acccttcaca tcacccccct cgaaggtcgg acaggacggg tggagccgtg ggcgggaccc 2161 tcaggcccgg gcccgccgcc cccagccccg cctgccgccc ctccccgcct gcctggactg 2221 cgcggcgccg tgagggggat tcggcccagc tcgtcccggc ctccaccaag ccagccccga 2281 agcccgccag ccaccctgcc ggactcgggc gcgacctgct ggcgcgcgcc ggatgtttct 2341 gtgacacaca atcagcgcgg accgcagcgc ggcccagccc cgggcacccg cctcggacgc 2401 tcgggcgcca ggaggcttcg ctggaggggc tgggccaagg agattaagaa gaaaacgact 2461 ttctgcagga ggaagagccc gctgccgaat ccctgggaaa aattcttttc ccccagtgcc 2521 agccggactg ccctcgcctt ccgggtgtgc cctgtcccag aagatggaat gggggtgtgg 2581 gggtccggct ctaggaacgg gctttggggg cgtcaggtct ttccaaggtt gggacccaag 2641 gatcgggggg cccagcagcc cgcaccgatc gagccggact ctcggctctt cactgctcct 2701 cctggcctgc ctagttcccc agggcccggc acctcctgct gcgagacccg gctctcagcc 2761 ctgccttgcc cctacctcag cgtctcttcc acctgctggc ctcccagttt cccctcctgc 2821 cagtccttcg cctgtccctt gacgccctgc atcctcctcc ctgactcgca gccccatcgg 2881 acgctctccc gggaccgccg caggaccagt ttccatagac tgcggactgg ggtcttcctc 2941 cagcagttac ttgatgcccc ctcccccgac acagactctc aatctgccgg tggtaagaac 3001 cggttctgag ctggcgtctg agctgctgcg gggtggaagt ggggggctgc ccactccact 3061 cctcccatcc cctcccagcc tcctcctccg gcaggaactg aacagaacca caaaaagtct 3121 acatttattt aatatgatgg tctttgcaaa aaggaacaaa acaacacaaa agcccaccag 3181 gctgctgctt tgtggaaaga cggtgtgtgt cgtgtgaagg cgaaacccgg tgtacataac 3241 ccctccccct ccgccccgcc ccgcccggcc ccgtagagtc cctgtcgccc gccggccctg 3301 cctgtagata cgccccgctg tctgtgctgt gagagtcgcc gctcgctggg ggggaagggg 3361 gggacacagc tacacgccca ttaaagcaca gcacgtcctg ggggaggggg gcatttttta 3421 tgttacaaaa aaaaattacg aaagaaaaga aatctctatg caaaatgacg aacatggtcc 3481 tgtggactcc tctggcctgt tttgttggct ctttctctgt aattccgtgt tttcgctttt 3541 tcctccctgc ccctctctcc ctctgcccct ctctcctctc cgcttctctc cccctctgtc 3601 tctgtctctc tccgtctctg tcgctcttgt ctgtctgtct ctgctctttc ctcggcctct 3661 ctccccagac ctggcccggc cgccctgtct ccgcaggcta gatccgaggt ggcagctcca 3721 gcccccgggc tcgccccctc gcgggcgtgc cccgcgcgcc ccgggcggcc gaaggccggg 3781 ccgccccgtc ccgccccgta gttgctcttt cggtagtggc gatgcgccct gcatgtctcc 3841 tcacccgtgg atcgtgacga ctcgaaataa cagaaacaaa gtcaataaag tgaaaataaa 3901 taaaaatcct tgaacaaatc cgaaaaggct tggagtcctc gcccagatct ctctcccctg 3961 cgagcccttt ttatttgaga aggaaaaaga gaaaagagaa tcgtttaagg gaacccggcg 4021 cccagccagg ctccagtggc ccgaacgggg cggcgagggc ggcgagggcg ccgaggtccg 4081 gcccatccca gtcctgtggg gctggccggg cagagacccc ggacccaggc ccaggcctaa 4141 cctgctaaat gtccccggac ggttctggtc tcctcggcca ctttcagtgc gtcggttcgt 4201 tttgattctt tttcttttgt gcacataaga aataaataat aataataaat aaagaataaa 4261 attttgtatg tcaaaaaaaa aaaaaaaaaa

Appendix E

LOCUS NM_003989 4188 bp mRNA linear PRI 24-SEP-2005

DEFINITION Homo sapiens paired box gene 2 (PAX2), transcript variant d, mRNA. ACCESSION NM_003989 VERSION NM_003989.2 GL34878715 KEYWORDS .

SOURCE Homo sapiens (human) ORGANISM Homo sapiens

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 4188) AUTHORS Yoshimura,K., Yoshida,S., Yamaji,Y., Komori,A., Yoshida,A.,

Hatae,K., Kubota,T. and Ishibashi,T. TITLE De novo insG619 mutation in PAX2 gene in a Japanese patient with papillorenal syndrome

JOURNAL Am. J. Ophthalmol. 139 (4), 733-735 (2005) PUBMED 15808183

REMARK GeneRTF: Molecular genetic analysis of the PAX2 gene in combination with renal ultrasonography can help in making an earlier diagnosis of the disease.

REFERENCE 2 (bases 1 to 4188) AUTHORS Mazal,P.R., Stichenwirth,M., Koller,A-, Blach,S., Haitel,A. and

SusaniJM. TITLE Expression of aquaporins and PAX-2 compared to CDlO and cytokeratm

7 in renal neoplasms: a tissue microarray study JOURNAL Mod. Pathol. 18 (4), 535-540 (2005) PUBMED 15502805 REMARK GeneRJJF: PAX-2 is a reliable marker for clear cell renal cell carcinomas of lower grades but not for higher grades. REFERENCE 3 (bases 1 to 4188)

AUTHORS HigashideJ., Wada,T., Sakurai,M., Yokoyama,H. and Sugiyama,K. TITLE Macular abnormalities and optic disk anomaly associated with a new

PAX2 missense mutation

JOURNAL Am. J. Ophthalmol. 139 (1), 203-205 (2005) PUBMED 15652857

REMARK GeneRJF: A new PAX2 missense mutation, R71T, may cause macular abnormalities in addition to anomalies of the optic disk and the kidney.

REFERENCE 4 (bases 1 to 4188) AUTHORS Buttiglieri,S., Deregibus,M.C, Bravo,S., Cassoni,P., Chiarle,R.,

BussolatiJB- and Camussi,G. TITLE Role of Pax2 in apoptosis resistance and preinvasive phenotype of

Kaposi's sarcoma cells

JOURNAL J. Biol. Chem. 279 (6), 4136-4143 (2004) PUBMED 14627715 REMARK GeneRJJF: expression of Pax2 by Kaposi's sarcoma cells correlated with an enhanced resistance against apoptotic signals and with the proinvasive phenotype REFERENCE 5 (bases 1 to 4188) AUTHORS Broρhy,P.D., Lang,K.M. and Dressler,G.R. TITLE The secreted frizzled related protein 2 (SFRP2) gene is a target of the Pax2 transcription factor

JOURNAL J. Biol. Chem. 278 (52), 52401-52405 (2003) PUBMED 14561758 REMARK GeneRIF: Pax2 protein regulates expression of secreted frizzled related protein 2

REFERENCE 6 (bases 1 to 4188)

AUTHORS Schimmenti,L.A., Manligas,G.S. and Sieving,P.A. TITLE Optic nerve dysplasia and renal insufficiency in a family with a novel PAX2 mutation, Argl 15X: further ophthalmologic delineation of the renal-coloboma syndrome

JOURNAL Ophthalmic Genet. 24 (4), 191-202 (2003) PUBMED 14566649 REMARK GeneRIF: PAX2 mutation is associated with Optic nerve dysplasia and renal insufficiency of the renal-coloboma syndrome REFERENCE 7 (bases 1 to 4188)

AUTHORS Muratovska,A., Zhou,C, He,S., Goodyer,P. and Eccles,M.R. TITLE Paired-Box genes are frequently expressed in cancer and often required for cancer cell survival JOURNAL Oncogene 22 (39), 7989-7997 (2003) PUBMED 12970747 REMARK GeneRIF: The PAX2 gene was frequently expressed in a panel of 406 common primary tumor tissues and endogenous PAX gene expression is often required for the growth and survival of cancer cells REFERENCE 8 (bases 1 to 4188) AUTHORS Gough,S.M., McDonald,M., Chen,X.N., KorenbergJ.R., Neri,A-,

Kahn,T., Eccles,M.R. and Morris,C.M. TITLE Refined physical map of the human PAX2/HOX11/NFKB2 cancer gene region at 10q24 and relocalization of the HPV6AI1 viral integration site to 14ql3.3-q21.1

JOURNAL BMC Genomics 4 (1), 9 (2003) PUBMED 12697057 REFERENCE 9 (bases 1 to 4188) AUTHORS Hoffmeister,A., Ropolo,A., Vasseur,S., MaIIo₅G. V., Bodeker,H.,

Ritz-Laser,B-₅ Dressler,G.R., Vaccaro,M.L, Dagorn,J.C, Moreno,S. and Iovanna,J.L. TITLE The HMG-I/Y-related protein p8 binds to ρ300 and Pax2 trans-activation domain-interacting protein to regulate the trans-activation activity of the Pax2A and Pax2B transcription factors on the glucagon gene promoter JOURNAL J. Biol. Chem. 277 (25), 22314-22319 (2002) PUBMED 11940591 REMARK GeneRIF: The HMG-I/Y-related protein p8 binds to ρ300 and Pax2 trans-activation domain-interacting protein to regulate the trans-activation activity of the Pax2A and Pax2B transcription factors on the glucagon gene promoter. REFERENCE 10 (bases 1 to 4188) AUTHORS Cai,Y., Lechner,M.S., Nihalani,D., Prindle,MJ., Holzman,L.B. and

Dressler,G.R. TITLE Phosphorylation of Pax2 by the c-Jun N-terminal kinase and enhanced

Pax2-dependent transcription activation JOURNAL J. Biol. Chem. 277 (2), 1217-1222 (2002) PUBMED 11700324 REFERENCE 11 (bases 1 to 4188)

AUTHORS Becker,K., Beales,P.L., Calver,D.M., Matthijs,G. and Mohammed,S.N. TITLE Okihiro syndrome and acro-renal-ocular syndrome: clinical overlap, expansion of the phenotype, and absence of PAX2 mutations in two new families

JOURNAL J. Med. Genet. 39 (1), 68-71 (2002) PUBMED 11826030 REMARK GeneRTF: The absence of PAX2 mutations has been identified in two families with histories of clinical overlap of Okihiro and acro-renal-ocular syndromes. REFERENCE 12 (bases 1 to 4188) AUTHORS Eccles,M.R., He₃S., Legge,M., Kumar,R., FoxJ., Zhou,C, French,M. and Tsai,R.W. TITLE PAX genes in development and disease: the role of PAX2 in urogenital tract development

JOURNAL Int. J. Dev. Biol. 46 (4), 535-544 (2002) PUBMED 12141441 REMARK Review article

GeneRIF: PAX2 has a role in urogenital tract development and disease [review]

REFERENCE 13 (bases 1 to 4188) AUTHORS Chung,G.W., Edwards,A.O., Schimmenti,L.A., Manligas,G.S.,

Zhang, Y.H. and Ritter,R. III.

TITLE Renal-cploboma syndrome: report of a novel PAX2 gene mutation JOURNAL Am. J. Ophthalmol. 132 (6), 910-914 (2001) PUBMED 11730657 REMARK GeneRIF: The causal relationship between PAX2 gene mutations and renal-coloboma syndrome is further supported REFERENCE 14 (bases 1 to 4188) AUTHORS Nishimoto,K., Iijima,K., Shirakawa,T., Kitagawa,K., Satomura,K.,

Nakamura,H. and Yoshikawa,N.

TITLE PAX2 gene mutation in a family with isolated renal hypoplasia JOURNAL J. Am. Soc. Nephrol. 12 (8), 1769-1772 (2001) PUBMED 11461952 REFERENCE 15 (bases 1 to 4188)

AUTHORS Ritz-Laser,B., Estreicher,A., Gauthier,B. and PhilippeJ. TITLE The paired homeodomain transcription factor Pax-2 is expressed in the endocrine pancreas and transactivates the glucagon gene promoter

JOURNAL J. Biol. Chem. 275 (42), 32708-32715 (2000) PUBMED 10938089 REFERENCE 16 (bases 1 to 4188) AUTHORS Lechner,M.S., Levitan,! and Dressler,G.R. TITLE PTD?, a novel BRCT domain-containing protein interacts with Pax2 and is associated with active chromatin JOURNAL Nucleic Acids Res. 28 (14), 2741-2751 (2000) PUBMED 10908331 REFERENCE 17 (bases 1 to 4188) AUTHORS Tavassoli,K., Ruger,W. and HorstJ. TITLE Alternative splicing in PAX2 generates a new reading frame and an extended conserved coding region at the carboxy terminus JOURNAL Hum. Genet. 101 (3), 371-375 (1997) PUBMED 9439670 REFERENCE 18 (bases 1 to 4188) AUTHORS Dahl,E., Koseki,H. and Balling,R. TITLE Pax genes and organogenesis JOURNAL Bioessays 19 (9), 755-765 (1997) PUBMED 9297966 REMARK Review article REFERENCE 19 (bases 1 to 4188)

AUTHORS Schimmenti,L.A., Cunliffe,H.E., McNoe,L.A., Ward,T.A.₃ French,M.C, Shim,H.H., Zhang,Y.H., Proesmans,W., Leys,A., Byerly,K.A., Braddock,S.R., Masuno,M., Imaizumi,K., Devriendt,K. and Eccles,M.R. TITLE Further delineation of renal-coloboma syndrome in patients with extreme variability of phenotype and identical PAX2 mutations JOURNAL Am. J. Hum. Genet. 60 (4), 869-878 (1997) PUBMED 9106533 REFERENCE 20 (bases 1 to 4188) AUTHORS Narahara,K., Baker,E., Ito,S., Yokoyama,Y., Yu,S., Hewittjλ,

Sutherland,G.R., Eccles,M.R. and Richards,R.I.

TITLE Localisation of a 1 Oq breakpoint within the PAX2 gene in a patient with a de novo t(10;13) translocation and optic nerve coloboma-renal disease

JOURNAL J. Med. Genet. 34 (3), 213-216 (1997) PUBMED 9132492 REFERENCE 21 (bases 1 to 4188)

AUTHORS Dehbi,M., Ghahremani,M., Lechner,M., Dressler,G. and PelletierJ. TITLE The paired-box transcription factor, PAX2, positively modulates expression of the Wilms' tumor suppressor gene (WTl) JOURNAL Oncogene 13 (3), 447-453 (1996) PUBMED 8760285 REFERENCE 22 (bases 1 to 4188) AUTHORS Sanyanusin,P., NorrishJ.H., Ward,T.A., Nebel,A., McNoe,L.A. and

Eccles,M.R.

TITLE Genomic structure of the human PAX2 gene JOURNAL Genomics 35 (1), 258-261 (1996) PUBMED 8661132 REFERENCE 23 (bases 1 to 4188)

AUTHORS Sanyanusin,P., Schimmenti,L.A., McNoe,L.A., Ward,T.A., Pierpont,M.E., Sullivan,M.J., Dobyns,W.B. and Eccles,M.R. TITLE Mutation of the PAX2 gene in a family with optic nerve colobomas, renal anomalies and vesicoureteral reflux

JOURNAL Nat. Genet. 9 (4), 358-364 (1995)

PUBMED 7795640 REFERENCE 24 (bases 1 to 4188)

AUTHORS Ward,T.A., Nebel A, Reeve ,A-E. and Eccles,M.R.

TITLE Alternative messenger RNA forms and open reading frames within an additional conserved region of the human PAX-2 gene

JOURNAL Cell Growth Differ. 5 (9), 1015-1021 (1994)

PUBMED 7819127 REFERENCE 25 (bases 1 to 4188)

AUTHORS NoIl₃M.

TITLE Evolution and role of Pax genes

JOURNAL Curr. Opin. Genet. Dev. 3 (4), 595-605 (1993)

PUBMED 8241771

REMARK Review article REFERENCE 26 (bases 1 to 4188)

AUTHORS Staρleton,P., Weith,A., Urbanek,P.₅ Kozmik,Z. and Busslinger,M.

TITLE Chromosomal localization of seven PAX genes and cloning of a novel family member, PAX-9

JOURNAL Nat. Genet. 3 (4), 292-298 (1993)

PUBMED 7981748 REFERENCE 27 (bases 1 to 4188)

AUTHORS PiIz₅AJ., Povey,S., Gruss,P. and Abbott,C.M.

TITLE Mapping of the human homologs of the murine paired-box-containing genes

JOURNAL Mamm. Genome 4 (2), 78-82 (1993)

PUBMED 8431641 REFERENCE 28 (bases 1 to 4188)

AUTHORS Eccles,M.R., WaIHs₅LJ., Fidler,A.E., Spurr,N.K., Goodfellow,PJ. and Reeve,A.E.

TITLE Expression of the PAX2 gene in human fetal kidney and Wilms' tumor

JOURNAL Cell Growth Differ. 3 (5), 279-289 (1992)

PUBMED 1378753

COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from U45255.1 and BM671839.1. On Sep 22, 2003 this sequence version replaced gi:4557826.

Summary: PAX2 encodes paired box gene 2, one of many human homologues of the Drosophila melanogaster gene prd. The central feature of this transcription factor gene family is the conserved DNA-binding paired box domain. PAX2 is believed to be a target of transcriptional supression by the tumor supressor gene WTl. Mutations within PAX2 have been shown to result in optic nerve colobomas and renal hypoplasia. Alternative splicing of this gene results in multiple transcript variants.

Transcript Variant: This variant (d) lacks an alternate in-frame exon compared to variant e. This results in an isoform (isoform d) that is shorter than isoform e. COMPLETENESS: complete on the 3' end. FEATURES Location/Qualifiers source L.4188

/organism="Homo sapiens"

/mol_type="mRNA"

/db_xref="taxon:9606"

/chromosome=" 10"

/map="10q24" gene 1..4188

/gene="PAX2"

/db_xref="GeneID:5076"

/db_xref=ΗGNC:8616"

/db_xref="HPRD:HPRD_01330"

/db_xref="MIM: 167409" CDS 687..1913

/gene="PAX2"

/note="PAX2 gene is a member of the paired-box containing genes which encode transcription factors involved in embryonic and fetal development; the gene product is nuclear protein which binds DNA isoform d is encoded by transcript variant d; paired box homeotic gene 2; go_comρonent: nucleus [goid 0005634] [evidence IEA]; go_function: ATP binding [goid 0005524] [evidence IEA]; go_function: DNA binding [goid 0003677] [evidence IEA]; go_function: DNA binding [goid 0003677] [evidence TAS]

[pmid 9106533]; go_function: nucleoside diphosphate kinase activity [goid

0004550] [evidence IEA]; go_process: development [goid 0007275] [evidence IEA]; go_process: transcription [goid 0006350] [evidence IEA]; go_process: CTP biosynthesis [goid 0006241] [evidence

IEA]; go_ρrocess: GTP biosynthesis [goid 0006183] [evidence

IEA]; go_process: UTP biosynthesis [goid 0006228] [evidence

IEA]; gojprocess: axonogenesis [goid 0007409] [evidence TAS]

[pmid 9106533]; gojprocess: cell differentiation [goid 0030154] [evidence

IEA]; go_process: visual perception [goid 0007601] [evidence

TAS] [pmid 9106533]; go_process: regulation of transcription, DNA-dependent

[goid 0006355] [evidence IEA]; go_process: transcription fironi RNA polymerase II promoter

[goid 0006366] [evidence TAS] [pmid 8760285]"

/codon start=l /product="paired box protein 2 isoform d"

/protein_id="NP_003980.2"

/db_xre^"GI:34878716"

/db_xre£="GeneID:5076"

/db_xref^"HGNC:8616"

/db_xre£="HPRD:HPRD_01330"

/dbjcref^'MIM: 167409"

/translation="MDMHCKADPFSAMHPGHGGVNQLGGVFVNGRPLPDVVRQRTVELAH

QGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVDKIAEYK

RQNPTMFAWEIRDRLLAEGICDNDTVPSVSSINRIIRTKVQQPFHPTPDGAGTGVTA

PGHTΓVPSTASPPVSSASNDPVGSYSINGILGIPRSNGEKRKRDEDVSEGSVPNGDSQ

SGVDSLRKHLRADTFTQQQLEALDRVFERPSYPDVFQASEHIKSEQGNEYSLPALTP

GLDEVKSSLSASTNPELGSNVSGTQTYPWTGRDMASTTLPGYPPHVPPTGQGSYP

TSTLAGMVPGSEFSGNPYSHPQYTAYNEAWRFSNPALLMPPPGPPLPLLPLPMTATS

YRGDHIKLQADSFGLHIVPV"

STS 1838..2044

/gene="PAX2" /standard_name="RH80285" /db_xre^"UniSTS:88437" STS 3036..3188

/gene="PAX2" /standard_name="D10S2478" /db_xre^"UniSTS:74159" polyA_signal 4142..4147

/gene="PAX2" polyA_signal 4146..4151

/gene="PAX2" polyA_signal 4153..4158

/gene="PAX2" polyA_site 4171

/gene="PAX2" ORIGIN

1 aggctccagt ctccggccga gtcttctcgc agccgcaacc cacctggggc cagcccagag 61 ctgccagcgc cgctcggctc cctccctccc tcccggccct tcggccgcgg cggcgtgcgc 121 ctgccttttc cgggggcggg ggcctggccc gcgcgctccc ctcccgcagg cgccacctcg 181 gacatccccg ggattgctac ttctctgcca acttcgccaa ctcgccagca cttggagagg 241 cccggctccc ctcccggcgc cctctgaccg cccccgcccc gcgcgctctc cgaccaccgc 301 ctctcggatg accaggttcc aggggagctg agcgagtcgc ctcccccgcc cagcttcagc 361 cctggctgca gctgcagcgc gagccatgcg cccccagtgc accccggccc ggcccaccgc 421 cccggggcca ttctgctgac cgcccagccc cgagccccga cagtggcaag ttgcggctac 481 tgcagttgca agctccggcc aacccggagg agccccagcg gggagcgcag tgttgcgccc 541 cccgcccccg cgcgccccgc agcagccggg cgttcactca tcctccctcc cccaccgtcc 601 ctcccttttc tcctcaagtc ctgaagttga gtttgagagg cgacacggcg gcggcggccg 661 cgctgctccc gctcctctgc ctccccatgg atatgcactg caaagcagac cccttctccg 721 cgatgcaccc agggcacggg ggtgtgaacc agctcggggg ggtgtttgtg aacggccggc 781 ccctacccga cgtggtgagg cagcgcatcg tggagctggc ccaccagggt gtgcggccct 841 gtgacatctc ccggcagctg cgggtcagcc acggctgtgt cagcaaaatc ctgggcaggt 901 actacgagac cggcagcatc aagccgggtg tgatcggtgg ctccaagccc aaagtggcga 961 cgcccaaagt ggtggacaag attgctgaat acaaacgaca gaacccgact atgttcgcct 1021 gggagattcg agaccggctc ctggccgagg gcatctgtga caatgacaca gtgcccagcg 1081 tctcttccat caacagaatc atccggacca aagttcagca gcctttccac ccaacgccgg 1141 atggggctgg gacaggagtg accgcccctg gccacaccat tgttcccagc acggcctccc 1201 ctcctgtttc cagcgcctcc aatgacccag tgggatccta ctccatcaat gggatcctgg 1261 ggattcctcg ctccaatggt gagaagagga aacgtgatga agatgtgtct gagggctcag 1321 tccccaatgg agattcccag agtggtgtgg acagtttgcg gaagcacttg cgagctgaca 1381 ccttcaccca gcagcagctg gaagctttgg atcgggtctt tgagcgtcct tcctaccctg 1441 acgtcttcca ggcatcagag cacatcaaat cagaacaggg gaacgagtac tccctcccag 1501 ccctgacccc tgggcttgat gaagtcaagt cgagtctatc tgcatccacc aaccctgagc 1561 tgggcagcaa cgtgtcaggc acacagacat acccagttgt gactggtcgt gacatggcga 1621 gcaccactct gcctggttac ccccctcacg tgccccccac tggccaggga agctacccca 1681 cctccaccct ggcaggaatg gtgcctggga gcgagttctc cggcaacccg tacagccacc 1741 cccagtacac ggcctacaac gaggcttgga gattcagcaa ccccgcctta ctaatgccgc 1801 cccccggtcc gcccctgccg ctgctgccgc tgcctatgac cgccactagt taccgcgggg 1861 accacatcaa gcttcaggcc gacagcttcg gcctccacat cgtccccgtc tgaccccacc 1921 ccggagggag ggaggaccga cgcgacgcga tgcctcccgg ccaccgcccc agcctcaccc 1981 catcccacga cccccgcaac ccttcacatc acccccctcg aaggtcggac aggacgggtg 2041 gagccgtggg cgggaccctc aggcccgggc ccgccgcccc cagccccgcc tgccgcccct 2101 ccccgcctgc ctggactgcg cggcgccgtg agggggattc ggcccagctc gtcccggcct 2161 ccaccaagcc agccccgaag cccgccagcc accctgccgg actcgggcgc gacctgctgg 2221 cgcgcgccgg atgtttctgt gacacacaat cagcgcggac cgcagcgcgg cccagccccg 2281 ggcacccgcc tcggacgctc gggcgccagg aggcttcgct ggaggggctg ggccaaggag 2341 attaagaaga aaacgacttt ctgcaggagg aagagcccgc tgccgaatcc ctgggaaaaa 2401 ttcttttccc ccagtgccag ccggactgcc ctcgccttcc gggtgtgccc tgtcccagaa 2461 gatggaatgg gggtgtgggg gtccggctct aggaacgggc tttgggggcg tcaggtcttt 2521 ccaaggttgg gacccaagga tcggggggcc cagcagcccg caccgatcga gccggactct 2581 cggctcttca ctgctcctcc tggcctgcct agttccccag ggcccggcac ctcctgctgc 2641 gagacccggc tctcagccct gccttgcccc tacctcagcg tctcttccac ctgctggcct 2701 cccagtttcc cctcctgcca gtccttcgcc tgtcccttga cgccctgcat cctcctccct 2761 gactcgcagc cccatcggac gctctcccgg gaccgccgca ggaccagttt ccatagactg 2821 cggactgggg tcttcctcca gcagttactt gatgccccct cccccgacac agactctcaa 2881 tctgccggtg gtaagaaccg gttctgagct ggcgtctgag ctgctgcggg gtggaagtgg 2941 ggggctgccc actccactcc tcccatcccc tcccagcctc ctcctccggc aggaactgaa 3001 cagaaccaca aaaagtctac atttatttaa tatgatggtc tttgcaaaaa ggaacaaaac 3061 aacacaaaag cccaccaggc tgctgctttg tggaaagacg gtgtgtgtcg tgtgaaggcg 3121 aaacccggtg tacataaccc ctccccctcc gccccgcccc gcccggcccc gtagagtccc 3181 tgtcgcccgc cggccctgcc tgtagatacg ccccgctgtc tgtgctgtga gagtcgccgc 3241 tcgctggggg ggaagggggg gacacagcta cacgcccatt aaagcacagc acgtcctggg 3301 ggaggggggc attttttatg ttacaaaaaa aaattacgaa agaaaagaaa tctctatgca 3361 aaatgacgaa catggtcctg tggactcctc tggcctgttt tgttggctct ttctctgtaa 3421 ttccgtgttt tcgctttttc ctccctgccc ctctctccct ctgcccctct ctcctctccg 3481 cttctctccc cctctgtctc tgtctctctc cgtctctgtc gctcttgtct gtctgtctct 3541 gctctttcct cggcctctct ccccagacct ggcccggccg ccctgtctcc gcaggctaga 3601 tccgaggtgg cagctccagc ccccgggctc gccccctcgc gggcgtgccc cgcgcgcccc 3661 gggcggccga aggccgggcc gccccgtccc gccccgtagt tgctctttcg gtagtggcga 3721 tgcgccctgc atgtctcctc acccgtggat cgtgacgact cgaaataaca gaaacaaagt 3781 caataaagtg aaaataaata aaaatccttg aacaaatccg aaaaggcttg gagtcctcgc W

3841 ccagatctct ctcccctgcg agcccttttt atttgagaag gaaaaagaga aaagagaatc 3901 gtttaaggga acccggcgcc cagccaggct ccagtggccc gaacggggcg gcgagggcgg 3961 cgagggcgcc gaggtccggc ccatcccagt cctgtggggc tggccgggca gagaccccgg 4021 acccaggccc aggcctaacc tgctaaatgt ccccggacgg ttctggtctc ctcggccact 4081 ttcagtgcgt cggttcgttt tgattctttt tcttttgtgc acataagaaa taaataataa 4141 taataaataa agaataaaat tttgtatgtc aaaaaaaaaa aaaaaaaa

APPENDIX F

LOCUS NM_003990 4257 bp mRNA linear PRI 24-SEP-2005

DEFINITION Homo sapiens paired box gene 2 (PAX2), transcript variant e, mRNA.

ACCESSION NM_003990 VERSION NM_003990.2 GL34878702 KEYWORDS .

SOURCE Homo sapiens (human) ORGANISM Homo sapiens

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 4257) AUTHORS Yoshimura,K., Yoshida,S., Yamaji,Y., Komori,A., Yoshida,A.,

Hatae,K., KubotaJ. and Ishibashi.T. TITLE De novo insG619 mutation in PAX2 gene in a Japanese patient with papillorenal syndrome

JOURNAL Am. J. Ophthalmol. 139 (4), 733-735 (2005) PUBMED 15808183

REMARK GeneRIF: Molecular genetic analysis of the PAX2 gene in combination with renal ultrasonography can help in making an earlier diagnosis of the disease.

REFERENCE 2 (bases 1 to 4257) AUTHORS Mazal,P.R., Stichenwirth,M., Koller,A., Blach,S., Haitel,A. and

Susani,M. TITLE Expression of aquaporins and PAX-2 compared to CDlO and cytokeratin

7 in renal neoplasms: a tissue microarray study JOURNAL Mod. Pathol. 18 (4), 535-540 (2005) PUBMED 15502805 REMARK GeneRIF: PAX-2 is a reliable marker for clear cell renal cell carcinomas of lower grades but not for higher grades. REFERENCE 3 (bases 1 to 4257)

AUTHORS Higashide,T., Wada,T., Sakurai,M., Yokoyama,H. and Sugiyama,K. TITLE Macular abnormalities and optic disk anomaly associated with a new

PAX2 missense mutation

JOURNAL Am. J. Ophthalmol. 139 (1), 203-205 (2005) PUBMED 15652857

REMARK GeneRIF: A new PAX2 missense mutation, R71T, may cause macular abnormalities in addition to anomalies of the optic disk and the kidney.

REFERENCE 4 (bases 1 to 4257) AUTHORS Buttiglieri,S., Deregibus,M.C, Bravo,S., Cassoni,P., Chiarle,R.,

Bussolati,B. and Camussi,G. TITLE Role of Pax2 in apoptosis resistance and proinvasive phenotype of

Kaposi's sarcoma cells JOURNAL J. Biol. Chem. 279 (6), 4136-4143 (2004) PUBMED 14627715 REMARK GeneRIF: expression of Pax2 by Kaposi's sarcoma cells correlated with an enhanced resistance against apoptotic signals and with the preinvasive phenotype REFERENCE 5 (bases 1 to 4257) AUTHORS Brophy,P.D., Lang,K.M. and Dressler,G.R. TITLE The secreted frizzled related protein 2 (SFRP2) gene is a target of the Pax2 transcription factor

JOURNAL J. Biol. Chem. 278 (52), 52401-52405 (2003) PUBMED 14561758 REMARK GeneRIF: Pax2 protein regulates expression of secreted frizzled related protein 2

REFERENCE 6 (bases 1 to 4257)

AUTHORS Schimmenti,L.A., Manligas,G.S. and Sieving,P.A. TITLE Optic nerve dysplasia and renal insufficiency in a family with a novel PAX2 mutation, Argl 15X: further ophthalmologic delineation of the renal-coloboma syndrome

JOURNAL Ophthalmic Genet. 24 (4), 191-202 (2003) PUBMED 14566649

REMARK GeneRIF: PAX2 mutation is associated with Optic nerve dysplasia and renal insufficiency of the renal-coloboma syndrome REFERENCE 7 (bases 1 to 4257)

AUTHORS Muratovska,A., Zhou,C, He₅S., Goodyer,P. and Eccles,M.R. TITLE Paired-Box genes are frequently expressed in cancer and often required for cancer cell survival JOURNAL Oncogene 22 (39), 7989-7997 (2003) PUBMED 12970747 REMARK GeneRIF: The PAX2 gene was frequently expressed in a panel of 406 common primary tumor tissues and endogenous PAX gene expression is often required for the growth and survival of cancer cells REFERENCE 8 (bases 1 to 4257) AUTHORS Gough,S.M., McDonald,M., Chen,X.N., KorenbergJ.R., Neri,A-,

Kahn,T., Eccles,M.R. and Morris,C.M. TITLE Refined physical map of the human PAX2/HOX11/NFKB2 cancer gene region at 10q24 and relocalization of the HPV6AI1 viral integration site to l4ql3.3-q21.1

JOURNAL BMC Genomics 4 (1), 9 (2003) PUBMED 12697057 REFERENCE 9 (bases 1 to 4257) AUTHORS HoffmeisterA, Ropolo,A., Vasseur,S., Mallo,G.V., Bodeker,H.,

Ritz-Laser,B., Dressler,G.R., Vaccaro,M.L, DagornJ.C, Moreno,S. and Iovanna,J.L. TITLE The HMG-I/Y-related protein ρ8 binds to p300 and Pax2 trans-activation domain-interacting protein to regulate the trans-activation activity of the Pax2A and Pax2B transcription factors on the glucagon gene promoter JOURNAL J. Biol. Chem. 277 (25), 22314-22319 (2002) PUBMED 11940591 REMARK GeneRIF: The HMG-I/Y-related protein p8 binds to p300 and Pax2 trans-activation domain-interacting protein to regulate the trans-activation activity of the Pax2A and Pax2B transcription factors on the glucagon gene promoter. REFERENCE 10 (bases 1 to 4257) AUTHORS Cai,Y., Lechner,M.S., Nihalani,D., Prindle,MJ., Holzman,L.B. and

Dressler,G.R. TITLE Phosphorylation of Pax2 by the c-Jun N-terminal kinase and enhanced

Pax2-dependent transcription activation JOURNAL J. Biol. Chem. 277 (2), 1217-1222 (2002) PUBMED 11700324 REFERENCE 11 (bases 1 to 4257)

AUTHORS Becker,K., Beales,P.L., Calver,D.M., Matthijs,G. and

MohammedjS .N.

TITLE Okihiro syndrome and acro-renal-ocular syndrome: clinical overlap, expansion of the phenotype, and absence of PAX2 mutations in two new families

JOURNAL J. Med. Genet. 39 (1), 68-71 (2002) PUBMED 11826030 REMARK GeneRIF: The absence of PAX2 mutations has been identified in two families with histories of clinical overlap of Okihiro and acro-renal-ocular syndromes. REFERENCE 12 (bases 1 to 4257) AUTHORS Eccles,M.R, He₃S., Legge,M., Kumar,R., FoxJ., Zhou,C, French,M. and Tsai,R.W. TITLE PAX genes in development and disease: the role of PAX2 in urogenital tract development

JOURNAL Int. J. Dev. Biol. 46 (4), 535-544 (2002) PUBMED 12141441 REMARK Review article

GeneRIF: PAX2 has a role in urogenital tract development and disease [review]

REFERENCE 13 (bases 1 to 4257) AUTHORS Chung,G.W., Edwards,A.O., Schimmenti,L.A., Manligas,G.S.,

Zhang,Y.H. and Ritter,R. JH.

TITLE Renal-coloboma syndrome: report of a novel PAX2 gene mutation JOURNAL Am. J. Ophthalmol. 132 (6), 910-914 (2001) PUBMED 11730657 REMARK GeneRIF: The causal relationship between PAX2 gene mutations and renal-coloboma syndrome is further supported REFERENCE 14 (bases 1 to 4257) AUTHORS Nishimoto,K., Iijima,K., Shirakawa,T., Kitagawa,K., Satomura,K.,

Nakamura,H. and Yoshikawa,N.

TITLE PAX2 gene mutation in a family with isolated renal hypoplasia JOURNAL J. Am. Soc. Nephrol. 12 (8), 1769-1772 (2001) PUBMED 11461952 REFERENCE 15 (bases 1 to 4257)

AUTHORS Ritz-Laser,B., Estreicher,A., Gauthier,B. and PhilippeJ. TITLE The paired homeodomain transcription factor Pax-2 is expressed in the endocrine pancreas and transactivates the glucagon gene promoter

JOURNAL J. Biol. Chem. 275 (42), 32708-32715 (2000) PUBMED 10938089 REFERENCE 16 (bases 1 to 4257) AUTHORS Lechner,M.S., LevitanJ. and Dressler,G.R. TITLE PTlP, a novel BRCT domain-containing protein interacts with Pax2 and is associated with active chromatin JOURNAL Nucleic Acids Res. 28 (14), 2741-2751 (2000) PUBMED 10908331 REFERENCE 17 (bases 1 to 4257) AUTHORS Tavassoli,K., Ruger,W. and Horst,J. TITLE Alternative splicing in PAX2 generates a new reading frame and an extended conserved coding region at the carboxy terminus JOURNAL Hum. Genet. 101 (3), 371-375 (1997) PUBMED 9439670 REFERENCE 18 (bases 1 to 4257) AUTHORS Dahl,E., Koseki,H. and Balling,R. TITLE Pax genes and organogenesis JOURNAL Bioessays 19 (9), 755-765 (1997) PUBMED 9297966 REMARK Review article REFERENCE 19 (bases 1 to 4257)

AUTHORS Schimmenti,L.A., Cunliffe,H.E., McNoe,L.A., Ward,T.A.₅

French,M.C,

Shim,H.H., Zhang, Y.H., Proesmans,W., Leys,A., Byerly,K.A.,

Braddock,S.R., Masuno,M., hnaizumi,K., Devriendt,K. and Eccles,M.R. TITLE Further delineation of renal-coloboma syndrome in patients with extreme variability of phenotype and identical PAX2 mutations JOURNAL Am. J. Hum. Genet. 60 (4), 869-878 (1997) PUBMED 9106533 REFERENCE 20 (bases 1 to 4257) AUTHORS Narahara,K., Baker,E., Ito,S., Yokoyama,Y., Yu,S., Hewitt,D.,

Sutherland,G.R., Eccles,M.R. and Richards,R.I. TITLE Localisation of a 1 Oq breakpoint within the PAX2 gene in a patient with a de novo t(10;13) translocation and optic nerve coloboma-renal disease

JOURNAL J. Med. Genet. 34 (3), 213-216 (1997) PUBMED 9132492 REFERENCE 21 (bases 1 to 4257)

AUTHORS Dehbi,M., Ghahremani,M., Lechner,M., Dressier, G. and Pelletier,J. TITLE The paired-box transcription factor, PAX2, positively modulates expression of the Wilms¹ tumor suppressor gene (WTl) JOURNAL Oncogene 13 (3), 447-453 (1996) PUBMED 8760285 REFERENCE 22 (bases 1 to 4257) AUTHORS Sanyanusin,P., NorrishJ.H., Ward,T.A., Nebel,A., McNoe,L.A. and

Eccles,M.R. TITLE Genomic structure of the human PAX2 gene JOURNAL Genomics 35 (1), 258-261 (1996) PUBMED 8661132 REFERENCE 23 (bases 1 to 4257) AUTHORS Sanyanusin,P., Schimmenti,L.A., McNoe,L.A., Ward,T.A.,

Pierρont,M.E., Sullivan,M.J., Dobyns,W.B. and Eccles,M.R. TITLE Mutation of the PAX2 gene in a family with optic nerve colobomas, renal anomalies and vesicoureteral reflux JOURNAL Nat. Genet. 9 (4), 358-364 (1995) PUBMED 7795640 REFERENCE 24 (bases 1 to 4257)

AUTHORS Ward,T.A., Nebel₃A., Reeve,A.E. and EcclesJVLR. TITLE Alternative messenger RNA forms and open reading frames within an additional conserved region of the human PAX-2 gene JOURNAL Cell Growth Differ. 5 (9), 1015-1021 (1994) PUBMED 7819127 REFERENCE 25 (bases 1 to 4257) AUTHORS NoIl₃M. TITLE Evolution and role of Pax genes JOURNAL Curr. Opin. Genet. Dev. 3 (4), 595-605 (1993) PUBMED 8241771 REMARK Review article REFERENCE 26 (bases 1 to 4257)

AUTHORS Stapleton,P., Weith,A., Urbanek,P., Kozmik,Z. and Busslinger,M. TITLE Chromosomal localization of seven PAX genes and cloning of a novel family member, PAX-9 JOURNAL Nat. Genet. 3 (4), 292-298 (1993) PUBMED 7981748 REFERENCE 27 (bases 1 to 4257) AUTHORS PiIz₃AJ., Povey,S.₃ Gruss,P. and Abbott,C.M. TITLE Mapping of the human homologs of the murine paired-box-containing genes

JOURNAL Mamm. Genome 4 (2), 78-82 (1993) PUBMED 8431641 REFERENCE 28 (bases 1 to 4257) AUTHORS Eccles,M.R., WaIHs₅LJ., Fidler₃A.E.₃ Spurr,N.K., Goodfellow,P J. and Reeve,A.E.

TITLE Expression of the PAX2 gene in human fetal kidney and Wilms' tumor JOURNAL Cell Growth Differ. 3 (5), 279-289 (1992) PUBMED 1378753

COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from U45255.1 and BM671839.1.

On Sep 22, 2003 this sequence version replaced gi:4557828.

Summary: PAX2 encodes paired box gene 2, one of many human homologues of the Drosophila melanogaster gene prd. The central feature of this transcription factor gene family is the conserved DNA-binding paired box domain. PAX2 is believed to be a target of transcriptional supression by the rumor supressor gene WTl. Mutations within PAX2 have been shown to result in optic nerve colobomas and renal hypoplasia. Alternative splicing of this gene results in multiple transcript variants.

Transcript Variant: This variant (e) encodes the longest isoform (e).

COMPLETENESS: complete on the 3' end. FEATURES Location/Qualifiers source L.4257

/organism="Homo sapiens" <img file="WO2007047512A2_D0004.tif" />

/db_xref="taxon:9606"

/chromosome=" 10"

/maρ="10q24" gene 1..4257

/gene="PAX2"

/db_xref="GeneID:5076"

/db_xref=ΗGNC:8616"

/db_xref="MM: 167409" CDS 687..1982

/gene="PAX2"

/note="PAX2 gene is a member of the paired-box containing genes which encode transcription factors involved in embryonic and fetal development; the gene product is nuclear protein which binds DNA isoform e is encoded by transcript variant e; paired box homeotic gene 2; go_component: nucleus [goid 0005634] [evidence IEA]; go Junction: ATP binding [goid 0005524] [evidence IEA]; go_function: DNA binding [goid 0003677] [evidence IEA]; gojunction: DNA binding [goid 0003677] [evidence TAS]

[pmid 9106533]; go_function: nucleoside diphosphate kinase activity [goid

0004550] [evidence IEA]; go_process: development [goid 0007275] [evidence IEA]; gojprocess: transcription [goid 0006350] [evidence IEA]; go__process: CTP biosynthesis [goid 0006241] [evidence

IEA]; go_process: GTP biosynthesis [goid 0006183] [evidence

IEA]; go_process: UTP biosynthesis [goid 0006228] [evidence

IEA]; gojprocess: axonogenesis [goid 0007409} [evidence TAS]

[pmid 9106533]; gojprocess: cell differentiation [goid 0030154] [evidence

IEA]; gojprocess: visual perception [goid 0007601] [evidence

TAS] [pmid 9106533]; gojprocess: regulation of transcription, DNA-dependent [goid 0006355] [evidence IEA]; go_process: transcription from RNA polymerase II promoter

[goid 0006366] [evidence TAS] [pmid 8760285]"

/codon_start=l

/product="paired box protein 2 isoform e"

/protein_id="NP_003981.2"

/db_xref^"GI:34878703 "

/db_xref^"GeneID:5076"

/db_xref^"HGNC:8616"

/db_xref="MIM: 167409"

/translation="MDMHCKADPFSAMHPGHGGVNQLGGVFVNGRPLPDVVRQRIVELAH

QGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKWDKIAEYK

RQNPTMFAWEIRDRLLAEGICDNDTVPSVSSINRIIRTKVQQPFHPTPDGAGTGVTA

PGHTΓVPSTASPPVSSASNDPVGSYSINGILGIPRSNGEKRKRDEVEVYTDPAHIRGG

GGLHLVWTLRDVSEGSVPNGDSQSGVDSLRKHLRADTFTQQQLEALDRVFERPSY

PDVFQASEHIKSEQGNEYSLPALTPGLDEVKSSLSASTNPELGSNVSGTQTYPWTG

RDMASTTLPGYPPHVPPTGQGSYPTSTLAGMVPGSEFSGNPYSHPQYTAYNEAWRF

SNPALLMPPPGPPLPLLPLPMTATSYRGDHIKLQADSFGLHΓVPV"

STS 1907..2113

/gene="PAX2"

/standard_name="RH80285"

/db_xre£="UniSTS:88437" STS 3105..3257

/gene="PAX2"

/standard_name="D 10S2478"

/db_xre£="UniSTS :74159" polyA_signal 4211..4216

/gene="PAX2" polyA_signal 4215..4220

/gene="PAX2" polyA_signal 4222..4227

/gene="PAX2" polyA_site 4240

/gene="PAX2" ORIGIN

1 aggctccagt ctccggccga gtcttctcgc agccgcaacc cacctggggc cagcccagag 61 ctgccagcgc cgctcggctc cctccctccc tcccggccct tcggccgcgg cggcgtgcgc 121 ctgccttttc cgggggcggg ggcctggccc gcgcgctccc ctcccgcagg cgccacctcg 181 gacatccccg ggattgctac ttctctgcca acttcgccaa ctcgccagca cttggagagg 241 cccggctccc ctcccggcgc cctctgaccg cccccgcccc gcgcgctctc cgaccaccgc 301 ctctcggatg accaggttcc aggggagctg agcgagtcgc ctcccccgcc cagcttcagc 361 cctggctgca gctgcagcgc gagccatgcg cccccagtgc accccggccc ggcccaccgc 421 cccggggcca ttctgctgac cgcccagccc cgagccccga cagtggcaag ttgcggctac 481 tgcagttgca agctccggcc aacccggagg agccccagcg gggagcgcag tgttgcgccc 541 cccgcccccg cgcgccccgc agcagccggg cgttcactca tcctccctcc cccaccgtcc 601 ctcccttttc tcctcaagtc ctgaagttga gtttgagagg cgacacggcg gcggcggccg 661 cgctgctccc gctcctctgc ctccccatgg atatgcactg caaagcagac cccttctccg 721 cgatgcaccc agggcacggg ggtgtgaacc agctcggggg ggtgtttgtg aacggccggc 781 ccctacccga cgtggtgagg cagcgcatcg tggagctggc ccaccagggt gtgcggccct 841 gtgacatctc ccggcagctg cgggtcagcc acggctgtgt cagcaaaatc ctgggcaggt 901 actacgagac cggcagcatc aagccgggtg tgatcggtgg ctccaagccc aaagtggcga 961 cgcccaaagt ggtggacaag attgctgaat acaaacgaca gaacccgact atgttcgcct 1021 gggagattcg agaccggctc ctggccgagg gcatctgtga caatgacaca gtgcccagcg 1081 tctcttccat caacagaatc atccggacca aagttcagca gcctttccac ccaacgccgg 1141 atggggctgg gacaggagtg accgcccctg gccacaccat tgttcccagc acggcctccc 1201 ctcctgtttc cagcgcctcc aatgacccag tgggatccta ctccatcaat gggatcctgg 1261 ggattcctcg ctccaatggt gagaagagga aacgtgatga agttgaggta tacactgatc 1321 ctgcccacat tagaggaggt ggaggtttgc atctggtctg gactttaaga gatgtgtctg 1381 agggctcagt ccccaatgga gattcccaga gtggtgtgga cagtttgcgg aagcacttgc 1441 gagctgacac cttcacccag cagcagctgg aagctttgga tcgggtcttt gagcgtcctt 1501 cctaccctga cgtcttccag gcatcagagc acatcaaatc agaacagggg aacgagtact 1561 ccctcccagc cctgacccct gggcttgatg aagtcaagtc gagtctatct gcatccacca 1621 accctgagct gggcagcaac gtgtcaggca cacagacata cccagttgtg actggtcgtg 1681 acatggcgag caccactctg cctggttacc cccctcacgt gccccccact ggccagggaa 1741 gctaccccac ctccaccctg gcaggaatgg tgcctgggag cgagttctcc ggcaacccgt 1801 acagccaccc ccagtacacg gcctacaacg aggcttggag attcagcaac cccgccttac 1861 taatgccgcc ccccggtccg cccctgccgc tgctgccgct gcctatgacc gccactagtt 1921 accgcgggga ccacatcaag cttcaggccg acagcttcgg cctccacatc gtccccgtct 1981 gaccccaccc cggagggagg gaggaccgac gcgacgcgat gcctcccggc caccgcccca 2041 gcctcacccc atcccacgac ccccgcaacc cttcacatca cccccctcga aggtcggaca 2101 ggacgggtgg agccgtgggc gggaccctca ggcccgggcc cgccgccccc agccccgcct 2161 gccgcccctc cccgcctgcc tggactgcgc ggcgccgtga gggggattcg gcccagctcg 2221 tcccggcctc caccaagcca gccccgaagc ccgccagcca ccctgccgga ctcgggcgcg 2281 acctgctggc gcgcgccgga tgtttctgtg acacacaatc agcgcggacc gcagcgcggc 2341 ccagccccgg gcacccgcct cggacgctcg ggcgccagga ggcttcgctg gaggggctgg 2401 gccaaggaga ttaagaagaa aacgactttc tgcaggagga agagcccgct gccgaatccc 2461 tgggaaaaat tcttttcccc cagtgccagc cggactgccc tcgccttccg ggtgtgccct 2521 gtcccagaag atggaatggg ggtgtggggg tccggctcta ggaacgggct ttgggggcgt 2581 caggtctttc caaggttggg acccaaggat cggggggccc agcagcccgc accgatcgag 2641 ccggactctc ggctcttcac tgctcctcct ggcctgccta gttccccagg gcccggcacc 2701 tcctgctgcg agacccggct ctcagccctg ccttgcccct acctcagcgt ctcttccacc 2761 tgctggcctc ccagtttccc ctcctgccag tccttcgcct gtcccttgac gccctgcatc 2821 ctcctccctg actcgcagcc ccatcggacg ctctcccggg accgccgcag gaccagtttc 2881 catagactgc ggactggggt cttcctccag cagttacttg atgccccctc ccccgacaca 2941 gactctcaat ctgccggtgg taagaaccgg ttctgagctg gcgtctgagc tgctgcgggg 3001 tggaagtggg gggctgccca ctccactcct cccatcccct cccagcctcc tcctccggca 3061 ggaactgaac agaaccacaa aaagtctaca tttatttaat atgatggtct ttgcaaaaag 3121 gaacaaaaca acacaaaagc ccaccaggct gctgctttgt ggaaagacgg tgtgtgtcgt 3181 gtgaaggcga aacccggtgt acataacccc tccccctccg ccccgccccg cccggccccg 3241 tagagtccct gtcgcccgcc ggccctgcct gtagatacgc cccgctgtct gtgctgtgag 3301 agtcgccgct cgctgggggg gaaggggggg acacagctac acgcccatta aagcacagca 3361 cgtcctgggg gaggggggca ttttttatgt tacaaaaaaa aattacgaaa gaaaagaaat 3421 ctctatgcaa aatgacgaac atggtcctgt ggactcctct ggcctgtttt gttggctctt 3481 tctctgtaat tccgtgtttt cgctttttcc tccctgcccc tctctccctc tgcccctctc 3541 tcctctccgc ttctctcccc ctctgtctct gtctctctcc gtctctgtcg ctcttgtctg 3601 tctgtctctg ctctttcctc ggcctctctc cccagacctg gcccggccgc cctgtctccg 3661 caggctagat ccgaggtggc agctccagcc cccgggctcg ccccctcgcg ggcgtgcccc 3721 gcgcgccccg ggcggccgaa ggccgggccg ccccgtcccg ccccgtagtt gctctttcgg 3781 tagtggcgat gcgccctgca tgtctcctca cccgtggatc gtgacgactc gaaataacag 3841 aaacaaagtc aataaagtga aaataaataa aaatccttga acaaatccga aaaggcttgg 3901 agtcctcgcc cagatctctc tcccctgcga gcccttttta tttgagaagg aaaaagagaa 3961 aagagaatcg tttaagggaa cccggcgccc agccaggctc cagtggcccg aacggggcgg 4021 cgagggcggc gagggcgccg aggtccggcc catcccagtc ctgtggggct ggccgggcag 4081 agaccccgga cccaggccca ggcctaacct gctaaatgtc cccggacggt tctggtctcc 4141 tcggccactt tcagtgcgtc ggttcgtttt gattcttttt cttttgtgca cataagaaat 4201 aaataataat aataaataaa gaataaaatt ttgtatgtca aaaaaaaaaa aaaaaaa

Table 3.

Sequences of QRT-PCR Primers.

<img file="WO2007047512A2_D0005.tif" />

Table 4.

PAX2 siRNA Sequences. A pool of four siRNA was utilized to inhibit PAX2 protein expression.

<img file="WO2007047512A2_D0006.tif" />

Table 5.

Quantitative RT-PCR Primers. Nucleotide sequences of primers used to amplify PAX2 and GAPDH.

<img file="WO2007047512A2_D0007.tif" />

Throughout this application, various publications are referenced. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this invention pertains.

References

1. Jemal, A.; Tiwari, R. C; Murray, T.; Ghafoor, A.; Samuels, A.; Ward, E.; Feuer, E. J.; Thun, M. J., Cancer statistics, 2004. CA Cancer J CHn 2004, 54, (I)₅ 8-29.

2. Prasad, M. A.; Trybus, T. M.; Wojno, K. J.; Macoska, J. A., Homozygous and frequent deletion of proximal 8p sequences in human prostate cancers: identification of a potential tumor suppressor gene site. Genes Chromosomes Cancer 1998, 23, (3), 255-62.

3. McNeel, D. G.; Malkovsky, M., Immune-based therapies for prostate cancer. Immunology Letters 2005, 96, (1), 3.

4. Tien, A. H.; Xu, L.; Helgason, C. D., Altered Immunity Accompanies Disease Progression in a Mouse Model of Prostate Dysplasia. Cancer Res 2005, 65, (7), 2947-2955.

5. Banchereau, J.; Palucka, A. K.; Dhodapkar, M.; Burkeholder, S.; Taquet, N.; Rolland, A.; Taquet, S.; Coquery, S.; Wittkowski, K. M.; Bhardwaj, N.; Pineiro, L.; Steinman, R.; Fay, J., Immune and Clinical Responses in Patients with Metastatic Melanoma to CD34+ Progenitor-derived Dendritic Cell Vaccine. Cancer Res 2001, 61, (17), 6451-6458.

6. Fong, L.; Brockstedt, D.; Benike, C; Breen, J. K.; Strang, G.; Ruegg, C. L.; Engleman, E. G., Dendritic Cell-Based Xenoantigen Vaccination for Prostate Cancer Immunotherapy. J Immunol 2001, 167, (12), 7150-7156.

7. Linzmeier, R.; Ho, C. H.; Hoang, B. V.; Ganz, T., A 450-kb contig of defensin genes on human chromosome 8p23. Gene 1999, 233, (1-2), 205-11.

8. Yang, D.; Biragyn, A.; Hoover, D. M.; Lubkowski, J.; Oppenheim, J. J., Multiple Roles of Antimicrobial Defensins, Cathelicidins, and Eosinophil-Derived Neurotoxin in Host Defense. Annual Review of Immunology 2004, 22, (1), 181-215.

9. Donald, C. D.; Sun, C. Q.; Lim, S. D.; Macoska, J.; Cohen, C; Amin, M. B.; Young, A. N.; Ganz, T. A.; Marshall, F. F.; Petros, J. A., Cancer-specific loss of beta-defensin 1 in renal and prostatic carcinomas. Lab Invest 2003, 83, (4), 501-5.

10. Ganz, T., Defensins: antimicrobial peptides of vertebrates. C R Biol 2004, 327, (6),

539-49. 11. ^" Mazzucchelli, R.; Barbisan, F.; Tarquini, L. M.; Galosi, A. B.; Stxamazzotti, D., Molecular mechanisms in prostate cancer. A review. Anal Quant Cytol Histol 2004, 26, (3), 127-33.

12. Ganz, T., Defensins and host defense. Science 1999, 286, (5439), 420-1.

13. Ganz, T.. Immunology. Versatile defensins. Science 2002, 298, (5595), 977-9.

14. Braida, L.; Boniotto, M.; Pontillo, A.; Tovo, P. A.; Amoroso, A.; Crovella, S., A single-nucleotide polymorphism in the human beta-defensin 1 gene is associated with HIV- 1 infection in Italian children. Aids 2004, 18, (11), 1598-600.

15. Gropp, R.; Frye, M.; Wagner, T. O.; Bargon, J., Epithelial defensins impair adenoviral infection: implication for adenovirus-mediated gene therapy. Hum Gene Ther 1999, 10, (6), 957-64.

16. Catalano, M. G.; Pfeffer, U.; Raineri, M.; Ferro, P.; Curto, A.; Capuzzi, P.; Corno, F.; Berta, L.; Fortunati, N., Altered expression of androgen-receptor isoforms in human colon-cancer tissues. Int J Cancer 2000, 86_&gt; (3), 325-30.

17. Takeuchi, S.; Iida, M.; Kobayashi, S.; Jin, K.; Matsuda, T.; Kojima, H., Differential effects of phthalate esters on transcriptional activities via human estrogen receptors alpha and beta, and androgen receptor. Toxicology 2005, 210, (2-3), 223-33.

18. Zucht, H. D.; Grabowsky, J.; Schrader, M.; Liepke, C; Jurgens, M.; Schulz-Knappe, P.; Forssmann, W. G., Human beta-defensin- 1 : A urinary peptide present in variant molecular forms and its putative functional implication. Eur J Med Res 1998, 3, (7), 315-23.

19. Nishimura, M.; Abiko, Y.; Kurashige, Y.; Takeshima, M.; Yamazaki, M.; Kusano, K.; Saitoh, M.; Nakashima, K.; Lioue, T.; Kaku, T., Effect of defensin peptides on eukaryotic cells: primary epithelial cells, fibroblasts and squamous cell carcinoma cell lines. Journal of Dermatological Science 2004, 36, (2), 87.

20. Fromont, G.; Joulin, V.; Chantrel-Groussard, K.; Vallancien, G.; Guillonneau, B.; Validire, P.; Latil, A.; Cussenot, O., Allelic losses in localized prostate cancer: association with prognostic factors. J Urol 2003, 170, (4 Pt 1), 1394-7.

21. Wang, Z.; Lai, F. M., [Analysis of loss of heterozygosity on chromosome 8 in human prostate carcinoma and high grade prostatic intraepithelial neoplasia]. Zhonghua Nan KeXue 2004, 10, (1), 26-8, 31.

22. Hugel, A.; Wernert, N., Loss of heterozygosity (LOH), malignancy grade and clonality in microdissected prostate cancer. Br J Cancer 1999, 79, (3-4), 551-7. 23. Bockmuhl, U.; Ishwad, C. S.; Ferrell, R. E.; Gollin, S. M., Association of 8ρ23 deletions with poor survival in head and neck cancer. Otolaryngol Head Neck Surg 2001, 124, (4), 451-5.

24. Macoska, J. A.; Paris, P.; Collins, C; Andaya, A.; Beheshti, B.; Chaib, H.; Kant, R.; Begley, L.; MacDonald, J. W.; Squire, J. A., Evolution of 8p loss in transformed human prostate epithelial cells. Cancer Genet Cytogenet 2004, 154, (1), 36-43.

25. Chaib, H.; MacDonald, J. W.; Vessella, R. L.; Washburn, J. G.; Quinn, J. E.; Odman, A.; Rubin, M. A.; Macoska, J. A., Haploinsufficiency and reduced expression of genes localized to the 8p chromosomal region in human prostate tumors. Genes Chromosomes Cancer 2003, 37, (3), 306-13.

26. Teixeira, M. R.; Ribeiro, F. R.; Eknaes, M.; Waehre, H.; Stenwig, A. E.; Giercksky, K. E.; Heim, S.; Lothe, R. A., Genomic analysis of prostate carcinoma specimens obtained via ultrasound-guided needle biopsy may be of use in preoperative decision-making. Cancer 2004, 101, (8), 1786-93.

27. Vecchione, A.; Ishii, H.; Baldassarre, G.; Bassi, P.; Trapasso, F.; Alder, H.; Pagano, F.; Gomella, L. G.; Croce, C. M.; Baffa, R., FEZ1/LZTS1 is down-regulated in high-grade bladder cancer, and its restoration suppresses tumorigenicity in transitional cell carcinoma cells. Am J Pathol 2002, 160, (4), 1345-52.

28. Valore, E. V.; Park, C. H.; Quayle, A. J.; Wiles, K. R.; McCray, P. B., Jr.; Ganz, T., Human beta-defensin-1: an antimicrobial peptide of urogenital tissues. J Clin Invest 1998, 101, (8), 1633-42.

29. Gunther, M.; Wagner, E.; Ogris, M., Specific targets in tumor tissue for the delivery of therapeutic genes. CurrMed Chem Anti-Cane Agents 2005, 5, (2), 157-71.

30. Dressier, G. R., Pax-2, kidney development, and oncogenesis. Med Pediatr Oncol 1996, 27, (5), 440-4.

31. Eccles, M. R.; He, S.; Legge, M.; Kumar, R.; Fox, J.; Zhou, C; French, M.; Tsai, R. W., PAX genes in development and disease: the role of PAX2 in urogenital tract development. IntJDevBiol 2002, 46, (4), 535-44.

32. Dressier, G. R.; Woolf, A. S., Pax2 in development and renal disease. IntJDev Biol 1999, 43, (5), 463-8.

33. Khoubehi, B.; Kessling, A. M.; Adshead, J. M.; Smith, G. L.; Smith, R. D.; Ogden, C. W., Expression of the developmental and oncogenic PAX2 gene in human prostate cancer. J Urol 2001, 165, (6 Pt 1), 2115-20. 34. Havik, B.; Ragnhildstveit, E.; Lorens, J. B.; Saelemyr, K.; Fauske, 0.; Knudsen, L. K.; Fjose, A., A novel paired domain DNA recognition motif can mediate Pax2 repression of gene transcription. Biochem Biophys Res Commun 1999, 266, (2), 532-41.

35. Discenza, M. T.; He₃ S.; Lee, T. H.; Chu, L. L.; Bolon, B.; Goodyer, P.; Eccles, M.; Pelletier, J., WTl is a modifier of the Pax2 mutant phenotype: cooperation and interaction between WTl and Pax2. Oncogene 2003, 22, (50), 8145-55.

36. McConnell, M. J.; Cunliffe, H. E.; Chua, L. J.; Ward, T. A.; Eccles, M. R., Differential regulation of the human Wilms tumour suppressor gene (WTl) promoter by two isoforms of PAX2. Oncogene 1997, 14, (22), 2689-700.

37. Yuan, S. S.; Yeh, Y. T.; Lee, E. Y., Pax-2 interacts with RB and reverses its repression on the promoter of Rig- 1, a Robo member. Biochem Biophys Res Commun 2002, 296, (4), 1019-25.

38. Stuart, E. T.; Haffher, R.; Oren, M.; Grass, P., Loss of ρ53 function through PAX- mediated transcriptional repression. Embo J 1995, 14, (22), 5638-45.

39. Michalak, E.; Villunger, A.; Erlacher, M.; Strasser, A., Death squads enlisted by the tumour suppressor p53. Biochem Biophys Res Commun 2005, 331, (3), 786-98.

40. Tokino, T.; Nakamura, Y., The role of p53-target genes in human cancer. Crit Rev Oncol Hematol 2000, 33, (1), 1-6.

41. Muratovska, A.; Zhou, C; He, S.; Goodyer, P.; Eccles, M. R., Paired-Box genes are frequently expressed in cancer and often required for cancer cell survival. Oncogene 2003, 22, (39), 7989-97.

42. Tagge, E. P.; Hanson, P.; Re, G. G.; Othersen, H. B., Jr.; Smith, C. D.; Garvin, A. J., Paired box gene expression in Wilms' tumor. JPediatr Surg 1994, 29, (2), 134-41.

43. Murer, L.; Caridi, G.; Delia Vella, M.; Montini, G.; Carasi, C; Ghiggeri, G.; Zacchello, G., Expression of nuclear transcription factor PAX2 in renal biopsies of juvenile nephrophthisis. Nephron 2002, 91, (4), 588-93.

44. Eccles, M. R.; Wallis, L. J.; Fidler, A. E.; Spurr, N. K.; Goodfellow, P. J.; Reeve, A. E., Expression of the PAX2 gene in human fetal kidney and Wilms¹ tumor. Cell Growth Differ 1992, 3, (5), 279-89.

45. Ogata, T.; Muroya, K.; Sasagawa, L; Kosho, T.; Wakui, K.; Sakazume, S.; Ito, K.; Matsuo, N.; Ohashi, H.; Nagai, T., Genetic evidence for a novel gene(s) involved in urogenital development on 10q26. Kidney M 2000, 58, (6), 2281-90. 40. ϋstrom, L.; Tang, M. J.; Grass, P.; Dressier, G. R., Reduced Pax2 gene dosage increases apoptosis and slows the progression of renal cystic disease. Dev Biol 2000, 219, (2), 250-8.

47. Mazal, P. R.; Stichenwirth, M.; Koller, A.; Blach, S.; Haitel, A.; Susani, M., Expression of aquaporins and PAX-2 compared to CDlO and cytokeratin 7 in renal neoplasms: a tissue microarray study. Mod Pathol 2005, 18, (4), 535-40.

48. Buttiglieri, S.; Deregibus, M. C; Bravo, S.; Cassoni, P.; Chiarle, R.; Bussolati, B.; Camussi, G., Role of Pax2 in apoptosis resistance and proinvasive phenotype of Kaposi's sarcoma cells. J Biol Chem 2004, 279, (6), 4136-43.

49. Gnarra, J. R.; Dressier, G. R., Expression of Pax-2 in human renal cell carcinoma and growth inhibition by antisense oligonucleotides. Cancer Res 1995, 55, (18), 4092-8.

50. Strasser, A., The role of BH3-only proteins in the immune system. Nat Rev Immunol 2005^{^}, 5, (3), 189-200.

51. Lin, S.; Ying, S. Y., Differentially expressed genes in activin-induced apoptotic LNCaP cells. Biochem Biophys Res Commun 1999, 257, (1), 187-92.

52. Perfettini, J. L.; Kroemer, R. T.; Kroemer, G., Fatal liaisons of ρ53 with Bax and Bak. Nat Cell Biol 2004, 6, (5), 386-8.

53. Coultas, L.; Strasser, A., The role of the Bcl-2 protein family in cancer. Semin Cancer Biol 2003, 13, (2), 115-23.

54. Margue, C. M.; Bernasconi, M.; Barr, F. G.; Schafer, B. W., Transcriptional modulation of the anti-apoptotic protein BCL-XL by the paired box transcription factors PAX3 and PAX3/FKHR. Oncogene 2000, 19, (25), 2921-9.

55. Nakamura, Y., Isolation of p53-target genes and their functional analysis. Cancer Sci 2004, 95, (1), 7-11.

56. Perfettini, J. L.; Roumier, T.; Kroemer, G., Mitochondrial fusion and fission in the control of apoptosis. Trends Cell Biol 2005, 15, (4), 179-83.

57. Orlando, V. Mapping chromosomal proteins in vivo by formaldehyde-crosslinked- chromatin immunoprecipitation. Trends Biochem Sci, 25: 99-104., 2000.

58. Boyd, K. E. and Farnham, P. J. Coexamination of site-specific transcription factor binding and promoter activity in living cells. MoI Cell Biol, 19: 8393-8399., 1999.

59. Wells, J. and Farnham, P. J. Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods, 26: 48-56., 2002. 60. Sikorski, R. S. and Hieter, P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics, 122: 19-27., 1989.

61. Nigro, J. M., Sikorski, R., Reed, S. L, and Vogelstein, B. Human ρ53 and CDC2Hs genes combine to inhibit the proliferation of Saccharomyces cerevisiae. MoI Cell Biol, 12: 1357-1365., 1992.

62. Wilson, T. E., Fahrner, T. J., Johnston, M., and Milbrandt, J. Identification of the DNA binding site for NGFI-B by genetic selection in yeast. Science, 252: 1296-1300., 1991.

63. Liu, J., Wilson, T. E., Milbrandt, J., and Johnsen, M. Identifying DNA-binding sites and analyzing DNA-binding domains using a yeast selection system. METHODS: A companion to Methods in Enzymology, 5: 125-137, 1993.

64. Jackers, P., Szalai, G., and Watson, D. K. Ets-dependent regulation of target gene expression during megakaryopoiesis. in preparation, 2003.

It will be apparent to those skilled in the art that various modifications and variations can be made in the present invention without departing from the scope or spirit of the invention. Other embodiments of the invention will be apparent to those skilled in the art from consideration of the specification and practice of the invention disclosed herein. It is intended that the specification and examples be considered as exemplary only, with a true scope and spirit of the invention being indicated by the following claims.