Multiplex in situ immunohistochemical analysis

p00001In situ multiplex immunohistochemical analysis

p000025 Immunofluorescence is a method of detecting the distribution of an antigen in a biological sample through the specific binding of an antibody that, in turn, is coupled to a fluorescent agent The antibody specifically binds to the target molecule so that the fluorescent label qualitatively and / or quantitatively indicates the presence of the target.

p00003Different methods have been developed for the union of the fluorescent brand. The direct labeling method uses a primary antibody (an antibody that recognizes the target) which is then coupled to the fluorescent agent. This method requires a lot of work and a certain amount of antibody could be inactivated in the process (if the brand itself binds to the antibody antigen recognition region).

p00004fifteen The indirect method uses a secondary antibody - an antibody that recognizes the primary antibody - coupled to a fluorescent agent to bind to the label. Several different variations of this method have been described. Often the primary antibody is first applied to the sample, followed by a washing step and the application of a species-specific secondary antibody bearing a fluorescent label. This often results in background problems due to nonspecific binding of the secondary antibody to the tissue. Another strategy has used previously formed primary-secondary antibody complexes (Tuson et al. 1990). This method allows indirect labeling of primary antibodies derived from the same species, but the use of divalent secondary antibodies can lead to cross-linked complexes.

p00005A similar strategy that avoids this problem is the use of monovalent Fb-specific Fab fragments for the

p0000625 generation of previously formed complexes and has been marketed by Molecular Probes (Zenon; Eugene, OR). Others have modified this method using Fab fragments that recognize both the Fc and f (ab ') 2 regions of the primary antibody (Brown et al. 2004). This strategy is described in US application 10 / 118,204 filed on April 5, 2002 and in document WO 03/030817.

p00007All of the above methods have in common that the primary antibody is labeled before contacting it with a biological sample. The primary antibody is directly labeled with a fluorophore (through chemical means, by binding to the secondary antibody or a Fab fragment labeled with a fluorescent agent) or the primary antibodies are detected with a bivalent secondary antibody. which is marked with a fluorophore (usually by chemical means). This can cause problems, especially in a tissue sample.

p0000835 included in paraffin and fixed that is generally less accessible to large molecules than other biological samples (for example, permeabilized and fixed cultured cells). For example, an antibody in a complex previously formed with a secondary antibody has twice the molecular weight of the primary antibody. An antibody in a complex previously formed with Fab fragments has approximately twice the molecular weight of the primary antibody if three Fab fragments are bound by antibody.

p00009The larger size of these complexes can prevent sufficient tissue penetration and, therefore, restrict or inhibit detection of the target molecule, cause excessive background tinting and, therefore, , complicate the detection of the target molecule. This is especially relevant for the detection of a nuclear biomarker, where antibody-Fab complexes are unable to penetrate the complexed protein of the nucleus and instead

p00010Four. Five found accumulated in the cytoplasm. Therefore, there is a need for improved methods to analyze intracellular antigens.

p00011GM Wessel and DR McClay, Journal of Histochemistry and Cytochemistry vol 34, no. 6 pages 703-706 (1986) discloses an immunohistochemical method in which the sample is contacted with non-labeled antibodies specific for a given target antigen and subsequently contacted with labeling reagent. The method is used to detect two (and not more) targets, specifically in sea urchin tissue.

p00012The document M Semar et al. (1969) Quantitative Comparison Immunohistochemistry. Clinical Chemistry 15 (6) pgs. 505-508 reveals the autofluorescence of tissue proteins. The document SA Pilen et al. (1997) Journal of

p0001355 Pathology 183, pgs. 116-123 provides a comparison of different methods of antigen recovery techniques in immunohistochemistry.

p00014There is increasing evidence that the proliferation of tumor cells is important in the prognosis for various tumors that usually occur, including lymphoma (Braylan RC, Diamond LW, Powell ML, Harty-Golder B. Percentage of cells in the S phase of the cell cycle in human lymphoma determined by flow cytometry: Correlation with labeling index and patient survival.Cytometry 1980; 1: 171-174; and Bauer KD, Merkel DE, Winter JN, et al. Prognostic implications of ploidy and proliferative activity in diffuse large cell lymphomas. Cancer Res 1986; 46: 3173-3178), breast cancer (Clark GM, Dressler LG :, Owens MA, Pounds G., Oldaker T., McGuire WL Predictions of relapse or survival in patients with mode-negative breast cancer by DNA flow cytometry 65 N. Engl J Med 1989; 320: 627-633; Silvestrini R., Daidone MG, Gasparini G. Cell kinetics as a prognostic marker in node-negative breast cancer. Cancer 1985; 56: 982-1987; and Sigurdsson H, Baldetorp B, Borg A., et al. Indicators of

p00015prognosis in node negative breast cancer. N Engl J Med 1990; 322: 1045-1053) and colon cancer (Bauer KD, Lincoln ST, Vera-Roman JM, et al. Prognostic implications of proliferative activity and DNA aneuploidy in colonic adenocarcinomas Lab Invest 1987; 57: 329-335). In some studies, the proliferation of tumor cells is important in the independent prognosis, even though the analysis of the total DNA content ("ploid") does not

p000165 have it (Visscher DW, Zarbo RJ, Greenawald KA, Crissman JD Prognostic significance of morphological parameters and flow cytometric DNA analysis in carcinoma of the breast. Pathol Ann 1990; 25 (Part-I): 171-210).

p00017Flow cytometry (FCM) has been widely used to determine cell cycle activity, primarily by quantifying the S phase part of the DNA content analysis ("ploid"). This method suffers from a series of serious technical limitations, however. First, it may be difficult to obtain suspensions of individual cells from solid tumors, and varying amounts of tumor cells may be lost during preparation. Secondly, tumor cells are diluted variably by normal and benign inflammatory cells, which can lead to underestimation of the S phase fraction, particularly for tumors with diploid DNA. Third, the complexity of the analysis of the DNA content ("ploid"), which is

p00018fifteen consisting of a series of overlapping curves, you can exclude the precise use of curve fitting algorithms to measure the phase S part of the histogram. Multicenter studies have shown poor reproducibility for S-phase fraction of flow cytometry, making the practical clinical practice of the medicine somewhat doubtful. Another problem associated with the measurement of cell kinetics by flow cytometry is that, normally, only the S-phase fraction is determined, while a significant proportion of the population of tumor cells can reside in the G1 phase of the cell cycle, composed of cells willing to enter the cycle but still do not synthesize DNA. Possibly, two tumors may have identical phase S fractions but differ significantly in the total fraction of cells in a non-resting state and, therefore, may show growth and response to chemotherapeutic agents. different cycle dependent tools.

p0001925 For all these reasons, in situ methods of tumor cell cycle analysis can provide more biologically meaningful information than can be obtained using disaggregated tumor cells (Weinberg DS Relative applicability of image analysis and flow cytometry in clinical medicine In: Bauer KD, Duque RE, eds. Flow cytometry: Principles and applications Baltimore: Williams and Wllkins; 1992: 359-372; and Weinberg DS Proliferation indices in solid tumors. Adv Pathol Lab Med 1992; 5: 163--191). In addition to ensuring that acquired measurements are made specifically in tumor cells, in situ methods can allow for a wider sampling of the tumor and determination of the heterogeneity of the cells. Tumor

Summary of the invention

p0002035 The present invention is based in part on the surprising discovery that combining a single antigen recovery technique and in situ fluorescent hybridization autofluorescence elimination techniques (FISH) allows highly sensitive immunohistochemical detection of multiple target antigens in tissue samples. Accordingly, the invention provides a method for detecting at least three target molecules in biological samples that are sections of tissue included in paraffin.

p00021The invention provides methods of detecting three or more targets in a biological sample. Three, four, five, six, seven, eight, nine, ten, fifteen or more targets are detected in a biological sample.

p00022Therefore, according to the invention an immunohistochemical method is provided to detect

p00023Four. Five Simultaneously the presence or absence of at least three targets in a biological sample comprising the steps of:

<dl><dt>(to)</dt><dd> perform antigen recovery in the biological sample, wherein said antigen recovery comprises the steps of: </dd></dl>

i. dewax and rehydrate the biological sample; and

ii. bring to boiling in antigen recovery buffer;

<dl><dt>(b)</dt><dd> perform autofluorescence reduction in the biological sample before stage (a), stage (c) or stage </dd></dl>

p0002455 (d), wherein said autofluorescence reduction comprises incubating said biological sample in a solution comprising 1% hydrochloric acid and 70% ethanol;

<dl><dt>(c)</dt><dd> contacting the biological sample with (1) a first antibody specific for a first target, (2) a first labeling reagent wherein said first labeling reagent comprises an antibody binding moiety for said first antibody and a first detection moiety, (3) a second antibody specific for a second target, (4) a second labeling reagent comprising an antibody binding moiety for said second antibody and a second rest of detection, (5) a third antibody specific for a third target, and (6) a third labeling reagent comprising an antibody binding moiety for said third antibody and a third detection moiety; and</dd></dl>

<dl><dt>(d)</dt><dd> detecting each of said first, second and third labeling reagents, respectively, in said </dd></dl>

p0002565 biological sample whereby the presence of said first, second and third labeling reagents, respectively, indicates the presence of said first, second or third targets, respectively, in said biological sample and the absence of said first, second or third labeling reagents indicates the absence of said first, second or third targets, respectively, in said biological sample,

p00026wherein said biological sample is human tissue included in paraffin.

p000275 Targets are detected by contacting a biological sample with a detection reagent and a labeling reagent under conditions in which the target, the detection reagent and the labeling reagent are capable of forming a complex. The detection reagent attached to the labeling reagent is then detected by the appropriate detection system (eg, fluorescence microscope). The presence of the labeling reagent indicates the presence of the target in the biological sample. Similarly, the absence of the labeling reagent indicates the absence of the target in the biological sample. Additionally, the concentration of the target in the biological sample is determined by comparing the amount of labeling reagent detected with a control sample. The determination of the target concentrations allows to determine relations of two or more targets in a sample. The relationship is related to a predetermined interval to indicate a disease status. The control sample is for example a peptide microarray. In some aspects, the detection of the target is indicative of the

p00028fifteen heterogeneity of tumor cells. Optionally, the biological sample is washed before and / or after the addition of the detection reagent. The biological sample is contacted with the detection reagent and the labeling reagent sequentially. Alternatively, the biological sample is contacted with the detection reagent and the labeling reagent concurrently. Optionally, a first detection reagent is allowed to form a complex with a first labeling reagent before coming into contact with the biological sample.

p00029The biological sample is a section of human tissue included in paraffin or a section of cryogenically conserved tissue. The biological sample is immobilized on a surface, in some aspects the biological sample is substantially free of nucleic acids before detection of the labeling reagent.

p0003025 The detection reagent is, for example, an antibody or fragment thereof specific for the target of interest. The antibody is, for example, a monoclonal antibody. The target is a cell surface antigen, an intracellular antigen or a nuclear antigen. For example, the target is an oncoprotein. Exemplary targets include an androgen receptor, a cytokeratin 18 protein or a PTEN protein.

p00031The labeling reagent contains a binding moiety to the detection reagent and a detection moiety, that is, a label. An antibody binding moiety is, for example, a monovalent antibody fragment such as a Fab or Fab 'fragment. The rest of the antibody binding is derived from a polyclonal or monoclonal antibody. The antibody binding fragment is an anti-Fc antibody fragment, an anti-chain antibody fragment

p0003235 light kappa, a lambda light chain anti-fragment antibody or a single chain antibody fragment. Alternatively, the rest of the antibody binding is a non-antibody protein such as protein G, a protein A, an L protein and a lectin. The rest of the detection is, for example, a fluorescent moiety, a radioactive moiety or an enzyme.

p00033Although not in accordance with the present invention according to the claims, a platform for multiplexed quantitative antigenic evaluation combining immunofluorescence (IF) detection (for example, using any of the m) could be provided. All methods described in this document) with computer-assisted image analysis. Computer-generated measurements that reflect the presence, intensity and distribution of fluorescent labels in tissue images are subject to supervised mathematical approaches to generate

p00034Four. Five models, for example, for the diagnosis and prognosis of the disease.

p00035Unless otherwise defined, all the technical and scientific terms used herein have the same meaning as that usually understood by an expert in the field to which the invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below.

p00036In addition, the materials, methods and examples are illustrative only.

p0003755 Other features and advantages of the invention will be apparent from the following detailed description, and from the claims.

Brief description of the drawings

p00038Figure 1 is a schematic representation of the methods of the invention. Figure 2 are photographs showing the detection of the androgen receptor in prostate tissue with IgG rabbit polyclonal using conventional methods (left panel) and the methods of the invention (panel right). Figure 3 is a schematic representation of Multiplex biomarker detection.

p0003965 Figure 4 are photographs showing the simultaneous detection of Ki-67 and the androgen receptor (AR) with rabbit polyclonal anti-AR IgG and mouse monoclonal anti-AR IgM.

p00040Figure 5 is a schematic representation of Multiplex detection of biomarkers in tissue sections included in paraffin. Figure 6 is a schematic representation of the use of a peptide matrix to quantify expression. of a biomarker.

p000415 Figure 7 is a graph showing the standard curve of the pTyr peptide matrix. Figure 8 is a graph showing the standard curve of the AR peptide matrix. Figure 9 is a schematic representation of amplification with the methods of the invention. Figure 10 is a series of photographs comparing non-amplified versus amplified biomarker detection using the methods of the invention. Figure 11 are photographs showing a single region of interest in patient ID 4752-1. Figure 12 are photographs showing a single region of interest in patient ID 4754-2. Figure 13 are photographs showing M-plex duplex with CD4 and CD8. Note the adjacent stromal location epithelial cells positive for CK18. Figure 14 are photographs showing M-plex triplex with CD25, 69 and 86. Note the stromal location

p00042fifteen Adjacent epithelial cells positive for CK18 Figure 15 are photographs showing M-plex duplex in spleen illustrating the distribution and cellular location of CD8 and 86. Note the abundance of CD8 lymphocytes present in the spleen along with the expected mature activated B cells, as demonstrated by staining with CD86. (AF = Autofluorescence). Figure 16 is a scheme illustrating the spectral detection of CD8 and CD86 in splenic tissue. Figure 17 are photographs showing M-plex triplex in spleen illustrating the distribution and cellular location of CD4, 25 and 69. Note the abundance of CD4 lymphocytes in the spleen as expected with amounts CD25 and CD69 variables. Figure 18 are photographs showing a quintplex. Figure 19 are photographs showing a 7-plex in prostate tissue.

p0004325 Figure 20 are photographs showing a quintplex in cell lines. Figure 21 are photographs showing a quintplex in cell lines.

Detailed Description

p00044The invention provides an improved method for the detection of three or more targets in a biological sample. More specifically, the present invention is based on a method of simultaneous in situ analysis of multiple intracellular targets. The methods of the invention allow a high spatial resolution for precise cellular location of antigen and high spectral resolution to allow simultaneous detection of multiple immunohistochemical stains. . The methods are particularly suitable for the detection of nuclear antigens. The

p0004535 Methods are useful in a number of fields such as, for example, in cancer diagnosis and prognosis.

p00046The present invention is advantageous with respect to the methods described above as it provides the benefits of indirect marking with the ease and flexibility of direct marking for the determination of a desired target in a biological sample. Specific labeling reagents for a target binding antibody are complexed after addition with a biological sample. Labeling reagents according to the present invention typically comprise a monovalent antibody fragment (Fab) that binds to the Fc and / or F (ab ') 2 part of the primary antibody and is covalently or non-covalently bound to a fluorescent brand. Therefore, unlike the methods described above, the independently applied labeling reagent does not comprise a bivalent antibody that recognizes the primary antibody, but an antibody fragment

p00047Four. Five monovalent much smaller, (Fab) or F (ab ') 2 that has a greater potential to penetrate tissue included in paraffin and fixed with formalin. Therefore, the present invention provides numerous advantages over conventional immunostaining methods.

p00048Definitions

p00049"Affinity" is defined as the strength of the interaction of two molecule binding, such as an antigen and its antibody, which is defined for antibodies and other molecules with more than one site. of binding as the binding force of the ligand at a specific binding site. Although the non-covalent binding of a ligand to an antibody is usually not as strong as a covalent binding, "High affinity" is for a ligand that binds to a

p0005055 antibody having an affinity constant (Ka) of more than 104 M-1, usually 105-1011 M-1; as determined by inhibition ELISA or an equivalent affinity determined by comparable techniques such as, for example, Scatchard charts or using Kd / dissociation constant, which is the reciprocal of the Ka , etc. "Antibody" is defined as an immunoglobulin (Ig) superfamily protein that binds non-covalently to certain substances (for example antigens and immunogens) to form an antigen-antibody complex, including, although not limited to, antibodies produced by hybridoma cell lines, by immunization to elicit a polyclonal antibody response, by chemical synthesis and by recombinant host cells that have been transformed with an expression vector encoding the antibody. In humans, immunoglobulin antibodies are classified as IgA, IgD, IgE, IgG and

p0005165 IgM and it is said that members of each class have the same isotype. Isotypes of human IgA and IgG are further subdivided into subtypes IgG1, and IgA2, and IgG1, IgG2, IgG3, and IgG4. Mice usually

p00053they have the same isotypes as humans, but the IgG isotype is subdivided into subtypes IgG1, IgG2a, IgG2b and IgG3. Therefore, it will be understood that the term "antibody" as used herein includes within its scope (a) any of the various classes or subclasses of immunoglobulin, for example, IgG, IgM, IgE derived of any of the conventionally used animals and (b) polyclonal and monoclonal antibodies, such as murine, chemical or humanized antibodies. Antibody molecules have amino acid sequence regions that can act as an antigenic determinant, for example the Fc region, the kappa light chain, the lambda light chain, the hinge region, etc. An antibody that is generated against a selected region is called anti- (region), for example anti-Fc, anti-kappa light chain, lambda light chain, etc. An antibody is normally generated against an antigen by immunizing an organism with a macromolecule to initiate lymphocyte activation to express the immunoglobulin protein. The term "antibody", as used herein, also encompasses any polypeptide, antibody fragment, or protein that has a binding domain that is, or is homologous to, an antibody binding domain, including, without limitation, single chain Fv molecules (scFv), in which a VH domain and a VL domain are linked by a peptide linker that allows the two domains associate to form an antigen binding site (Bird et al., Science 242, 423 (1988) and Huston et al., Proc. Natl. Acad. Sci. United States 85,)). These can be derived from natural sources, or they can be produced partially or totally synthetically. "Antibody fragments" is defined as antibody fragments that retain the main elective binding characteristics of the entire antibody. Particular fragments are known in the art, for example, Fab, Fab 'and F (ab') 2, which are obtained by digestion with various proteases and lacking the Fc fragment of an intact antibody or so-called fragments of "Half-molecule" obtained by reductive cleavage of the disulfide bridges that connect the heavy chain components in the intact antibody. Such fragments also include isolated fragments constituted by the variable light chain region, "Fv" fragments constituted by the variable regions of the heavy and light chains and recombinant single chain polypeptide molecules in which variable regions Light and heavy are connected by a peptide linker. Other examples of binding fragments include (i) the Fd fragment, consisting of the VH and CH1 domains; (ii) the dAb fragment (Ward, et al., Nature 341, 544 (1989)), which is constituted by a VH domain; (iii) isolated CDR regions; and (iv) single chain Fv molecules (scFv) described above, in addition, using recombinant technology, arbitrary fragments can be made that retain antigen recognition characteristics. "Antigen" is defined as a molecule that induces, or is capable of inducing, the formation of an antibody or to which an antibody selectively binds, including but not limited to, a biological material. Antigen also refers to "immunogen." An antibody selectively binds to an antigen when there is a relative lack of cross-reactivity with or interference with other substances present. "Biological sample" or "biological material" is defined as a sample recovered from humans in particular. The sample may be from a healthy tissue, diseased tissue or tissue suspected of being diseased tissue. The sample may be a biopsy taken, for example, during a surgical procedure. The sample can be collected by aspiration through a fine needle, scraping or washing a cavity to collect cells or tissue from it. The sample can be from a tumor for example, solid and hematopoietic tumors as well as from adjacent healthy tissue. The sample is a section of tissue included in paraffin. Typically, the sample comprises tissue, cell cells, cell extracts, homogenates of cells, purified or reconstituted proteins, recombinant proteins, body fluids and other biological fluids, viruses or viral particles. , prions, subcellular components or synthesized proteins. Possible sources of cellular material used to prepare the sample of the invention include, without limitation, plants, animals, fungi, protists, bacteria, cellular archeobacteria derived from said organisms. "Complex" is defined as two other molecules that are held together by non-covalent bonding, which are normally non-covalent combinations of biomolecules such as a protein complexed with another protein. In contrast, a protein is covalently labeled with a substance when there is a covalent chemical bond between the substance and the protein. "Detectable distinct" is defined as the signal that is distinguishable or separable by a physical property by instrumental observation. For example, although without limitation, a fluorophore is easily distinguishable, by spectral characteristics or by fluorescence intensity, life cycle, polarization or photobleaching rate of another fluorophore in the sample, as well. As of additional materials that are optionally present. "Directly detectable" is defined to mean that the presence of a material or the signal generated from the material is immediately detectable by observation, instrumentation or film without requiring chemical modifications. "Immunoconjugates" are defined to mean that proteins of the invention are labeled, where instead of a detectable label is bound to the protein, a therapeutic ophthalmic agent is bound. The term immunoconjugate is used interchangeably with protein labeled with a drug. "Monovalent antibody fragment" is defined as an antibody fragment that has only one antigen binding site. Examples of monovalent antibody fragments include, but are not limited to, Fab fragments (without hinge region), Fab 'fragments (monovalent fragments containing a heavy chain hinge region) and variable chain fragment proteins simple (ScFv). "Multiplex Identification" refers to the simultaneous identification of one or more targets in a single mixture. For example, a two-plex amplification refers to the simultaneous identification, in a single reaction mixture, of two different targets. "Selectively binds" is defined as the situation in which a member of a specific intra- or interspecies junction pair will not show any significant binding to different molecules of its binding partner. n specific intra- or inter-species (for example, an affinity of approximately 100 times less), that is

p000545 minimal cross reactivity.

p00055Detection method

p00056In various aspects, the invention provides: detection methods of at least three targets in a biological sample. Targets are detected by contacting a biological sample with a target detection reagent, for example, an antibody or fragment thereof and a labeling reagent. Targets are detected by the presence or absence of the detection reagent-label reagent complex. Preferably, the biological sample is contacted with the target detection reagent and the labeling reagent sequentially. For example, the biological sample is incubated with the detection reagent under conditions that allow

p00057fifteen that a complex is formed between the detection reagent and the target. After complex formation, the biological sample is optionally washed one more time to remove unbound detection reagent. The biological sample is also contacted with a labeling reagent that specifically binds to the detection reagent that is bound to the target. The biological sample is optionally washed one or more times to remove unbound labeling reagent. The presence or absence of the target in the biological sample is then determined by detecting the labeling reagent. Alternatively, the biological sample is contacted with the target detection reagent and the labeling reagent concurrently.

p00058The invention enables the detection of multiple targets in a sample. Multiple targets include the discrete epitope for which the target binding antibody has affinity, as well as molecules or structures to which the

p0005925 epitope Therefore, the identification of multiple targets includes cell phenotyping based on the concentration of the same cell surface marker in different cells. In this way, the identification of multiple targets is not limited to the discrete epitope to which the target binding antibody binds, although this is clearly a way in which minimal targets can be identified. multiple, that is, based on the affinity of the binding antibody to the target.

p00060Multiple targets are identified by contacting the biological sample with additional detection reagents followed by an additional labeling reagent specific for the additional detection reagents using the method described above. For example, subsets of labeling reagents with different brands are prepared, for example, fluorophores that are distinguished by their emission spectra, for example, one that emits in the

p0006135 green spectra and one that emits in the red spectra. The subsets of the labeling reagent are then added to the biological sample containing target detection reagent complexes in a controlled relationship, for example, two parts of a labeling reagent (for example , green emission) and a part of the other labeling reagent (eg, red emission) by antibody binding the target, in this way immunolabelled complexes can be used to detect a target. If immunolabelled mother complexes were added to the sample, the original target could be distinguished from the target detected later.

p00062In alternative methods, three or more targets are identified in a biological sample by previously mixing a first detection reagent with a first labeling reagent to form a first complex. Optionally, after complex formation, the mixture is purified to remove the detection reagent and the reagent from

p00063Four. Five marked not complexed. The biological sample is incubated with the first complex and a second detection reagent. Optionally, 3, 4, 5, 6, 7, 8, 9, 10 or more targets are detected in a sample. Depending on the number of targets to be detected, 3, 4, 5, 6, 7, 8, 9, 10 or more detection reagents can be used. Subsequently, the biological sample is incubated with a second labeling reagent that specifically binds to the second detection reagent that is bound to the second target. Optionally, before incubating with the second labeling reagent, the biological sample is washed one more time to remove the first complex and the second unbound detection reagent. The presence or absence of the target in the biological sample is then determined by detecting the labeling reagent. Optionally, before detecting the labeling reagent, the biological sample is washed one more time to remove unbound labeling reagents.

p0006455 The sample is defined to include any material that may contain a target for which an antibody has affinity. Normally, the sample is of biological origin and comprises tissue, a cell or a population of cells, cell extracts, cell homogenates, purified or reconstituted proteins, recombinant proteins, body fluids and others. biological fluids, virus or viral particles, prions, subcellular components or synthesized proteins. The sample is a section of human tissue included in paraffin. Examples of sources of such samples include muscle, eye; skin, glands, lymph nodes, heart, brain, lung, liver, kidney, spleen, solid tumors, macrophages or mesothelium. The sample is prepared in a manner that makes the target, which is determined by the end user, in the sample accessible to immunolabelled complexes. Normally, the samples used in the invention are composed of tissue cells. Preferably, the tissue or cells to be tested will be obtained by surgical procedures, for example, biopsy. The tissue or cells are fixed,

p0006565 to allow histological sectioning. In situ detection is used to determine the presence of a particular target and to determine the distribution of the target in the examined tissue. General on-site detection techniques are well known to those skilled in the art. See, for example, the Ponder document, "Cell Marking Techniques and Their Application" in Mammalian Development: A Practical Approach, Monk (ed.), 115 (1987). Treatments that permeabilize the plasma membrane, such as electroporation, shock treatments or high extracellular ATP, can be used to introduce reagents into the cells.

p000665 The methods of the invention provide significant advantages over existing technology, since they do not depend on nucleic acid hybridizations. Therefore, the methods of the invention can be performed in the presence of nucleases, for example, non-specific nucleases, ANDase and RNase.

p00067The target is any compound of biological or synthetic origin that is present as a molecule or as a group of molecules. Normally, the target is a biological material or antigenic determinant. The chemical identity of the target antigen may be known or unknown. Biological materials include, but are not limited to, antibodies, amino acids, proteins, peptides, polypeptides, enzymes, enzyme substrates, hormones, lymphokines, metabolites, antigens, haptens, lectins. , avidin, streptavidin, toxins, poisons, contaminants

p00068fifteen environmental, carbohydrates, oligosaccharides, polysaccharides, glycoproteins, glycolipids, nucleitides, oligonucleotides, nucleic acids and derivatized nucleic acids (including deoxyribonucleic and ribonucleic acids and peptidonucleic acids), DNA and RNA fragments and derivatized fragments (including single and multiple chain fragments), natural and synthetic drugs, receptors, virus particles, bacterial particles, virus components, Biological cells, cellular components (including membranes and cellular organelles), natural and synthetic lipid vesicles, and polymeric membranes. Normally, the target material is present as a component or contaminant of a sample taken from a biological or environmental system.

p00069The target is a transmembrane marker. Alternatively, the target is an intracellular or nuclear antigen. Intracellular antigens include, for example, alpha-fetoprotein (AFP), human chorionic gonadotropin (HCG),

p0007025 colon specific p-antigen (CSAp), prostatic acid phosphatase, pancreatic oncofetal antigen, placental alkaline phosphatase, parathormone, calcitonin, tissue polypeptide antigen, galactosyl transferase-II ( GT-II), viral gp-52 associated antigen, ovarian cystadenocarcinoma associated antigen (OCAA), ovarian tumor specific antigen (OCA), neck cancer antigens of the uterus (CA-58, CCA, TA-4), basic fetoprotein (BFP), terminal deoxynucleotidyl transferase (TdT), cytoplasmic melanoma associated antigens, human astrocytoma associated antigen (HAAA), common glioma antigen (CGA), glioembryonic antigen (GEA), glial fibrillar acid protein (GFA) ), common meningioma antigen (CMA), pMTOR, pAKT, PSMA, prostate specific antigen (PSA), x-methylacil-CoA racemase (AMACR), vascular endothelial growth factor ( VEGF), and tumor angiogenesis factor (TAF). Nuclear antigens include, for example, PTEN, Ki67, Cyclin D1, EZH2, p53, IGFBP2, p-STAT-3. Other targets include those listed in Tables 1 and 2 below.

p0007135 The detection reagent is a compound that is capable of specifically binding to the target of interest. The detection reagent is selected based on the desired target. The detection reagent is, for example, a polypeptide such as a target specific antibody or a fragment thereof. As used herein, the term "antibody" refers to immunoglobulin molecules and immunologically active parts of immunoglobulin (Ig) molecules, that is, molecules containing a site. of binding to the antigen that specifically binds to (immunoreacts with) an antigen. Such antibodies include, polyclonal, monoclonal, chimeric, single chain, Fab, Fab 'and F (ab') 2 fragments, and a Fab expression library. By "specifically binds to" or "immunoreacts with" is meant that the antibody reacts with one or more antigenic determinants of the desired antigen and does not react (ie, does not bind) with other polypeptides. or does it with a very affinity

p00072Four. Five low (Kd> 10-6) with other polypeptides.

p00073Monoclonal antibodies are particularly advantageous for practicing the methods of the present invention. Generally, monoclonal antibodies are more sensitive and specific than polyclonal antibodies. In addition, unlike polyclonal antibodies, which depend on the longevity of the animal that produces the antibody, the supply of monoclonal antibodies is undefined. Polyclonal antibodies, however, are useful when it is necessary to use antibodies with multiple isotypes, since generally the majority of monoclonal antibodies are of the IgG1 subclass.

p00074As used herein, the term "epitope" includes any protein determinant capable of

p0007555 specific binding to an immunoglobulin, an scFv, or a T-cell receptor. The term "epitope" includes any protein determinant capable of specific binding to an immunoglobulin or receptor. of T cells. Epitopic determinants usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains and usually have specific three-dimensional structural characteristics, as well as characteristics. specific load rates.

p00076As used herein, the terms "immunological binding" and "immunological binding properties" refer to non-covalent interactions of the type that occur between an immunoglobulin molecule and an antigen for which the immunoglobulin is specific. The strength, or affinity of immunological binding interactions can be expressed in terms of the dissociation constant (Kd) of the interaction, in the

p0007765 that a smaller Kd represents a greater affinity. The immunological binding properties of selected polypeptides are quantified using methods well known in the art. One such method involves measuring the velocities of formation and dissociation of the antigen / antigen binding site complex, at which these speeds depend on the concentrations of the complex's partners, the affinity of the interaction, and geometric parameters that equally influence the speed in both directions. Therefore, both the "association constant" (Kon) and the "dissociation constant" (Koff) can be determined by calculating the

p000785 concentrations and actual rates of association and dissociation. (See Nature 361: 186-87 (1993)). The Koff / Kon relay allows the cancellation of all parameters not related to affinity, and is equal to the dissociation constant Kd. (See, in general, Davies et al. (1990) Annual Rev Biochem 59: 439-473).

p00079The labeling reagent contains an antibody binding moiety and a detection moiety. The rest of the antibody binding and the rest of the detection are covalently linked. Alternatively, the rest of the antibody binding and the rest of the detection are non-covalently linked.

p00080The remaining antibody binding selectively binds with high affinity to a selected region of the detection reagent, for example, the antibody binding target. The binding region for the rest of the antibody binding

p00081fifteen it may be a selected peptide linker (which includes the J region), light chain or heavy chain of the target binding antibody; preferably the labeling protein binds to the Fc region of the target binding antibody.

p00082The rest of the antibody binding is an antibody or fragment thereof, such as, but not limited to, anti-Fc, an isotype anti-Fc, anti-J chain, anti-light chain kappa, anti-light chain lambda , or a single chain fragment variable protein. Preferably, the rest of the antibody binding is monovalent. Alternatively, the remaining antibody binding is a non-antibody peptide or protein, such as, for example, but not limited to, soluble Fc receptor, protein G, protein A, protein na L, lectins or a fragment thereof. Optionally, the non-antibody optic protein is coupled with albumin such as bovine and human serum albumin and

p0008325 ovalbumin.

p00084Typically, the antibody binding moiety is a Fab fragment specific for the Fc part of the target binding antibody or for an isotype of the Fc part of the binding antibody of the target. Monovalent Fab fragments are produced from monoclonal antibodies or murine polyclonal antibodies generated in various animals, for example, but not limited to, rabbit or goat. These fragments can be generated from any isotype such as IgM, IgG1, IgG2a, IgG2b or murine IgG3.

p00085The rest of the detection, that is, the brand, is any substance used to facilitate the identification and / or quantification of a target. Detection residues are observed or measured directly or observed or measured indirectly. Detection residues include, but are not limited to, radiolabels that can be measured with radiation counting devices; pigments, dyes or other chromogens that can be observed visually or measured with a spectrophotometer; spin marks that can be measured with a spin mark analyzer; and fluorescent moieties, where the output signal is generated by the excitation of a suitable molecular adduct and that can be visualized by excitation with light that is absorbed by the dye or can be measured with fluorometers or imaging systems Conventional, for example. The rest of the detection can be a luminescent substance such as a phosphorus or fluorgene; a bioluminescent substance; a chemiluminescent substance, where the output signal is generated by chemical modification of the signal compound; a substance that contains a metal; or an enzyme, where a secondary generation of enzyme-dependent signal is produced, such as the formation of a colored product from a colorless substrate. The rest of the detection 45 can also take the form of a chemical or biochemical, or an inert particle, including but not limited to colloidal gold, microspheres, quantum dots or inorganic crystals such as nanocrystals ophthalms (see, for example, the document Beverloo, et al., Anal. Biochem. 203, 326-34 (1992)). The term "remainder of detection" also refers to a "tag" or hapten that can be selectively bound to a labeled molecule so that the labeled molecule, when added later, is used to generate a detectable signal. For example, biotin, iminobiotin or destiobiotin can be used as a label and then use a rhodium radish peroxidase (HRP) avidin or streptavidin conjugate to bind the label, and then use a chromogenic substrate ( for example, tetramethylbenzidine) or a fluorogenic substrate such as Amplex Red or Amplex Gold. (Molecular Probes, Inc.) to detect the presence of HRP. Similarly, the tag can be a hapten or antigen (eg, digoxigenin), and an enzyme-labeled antibody can be used, so

p0008655 fluorescent or radioactively to join the tag. Those skilled in the art are aware of numerous brands and include, but are not limited to, particles, fluorescent dyes, haptens, enzymes and their chromogenic, fluorogenic and chemiluminescent substrates, and other brands described in the Molecular Probes document. Richard P. Handbook Of Fluorescent Probes And Research Chemicals Haugland, 6th Ed., (1996), and subsequent updates of 7th edition and 8th edition edited on CD ROM in November 1999 and May 2001, respectively and in other published sources.

p00087A fluorophore is any chemical moiety that shows a maximum absorption beyond 280 nm, and when covalently bound to a labeling reagent retains its spectral properties. The fluorophores include, without limitation; a pyrene (including any of the corresponding derivative compounds disclosed in US Patent No. 5,132,432), an anthracene, a naphthalene, an acridine, a stilbene, an indole or bencindol, an oxazole or benzoxazole, a thiazole or benzothiazole, a 4-amino-7-nitrobenz-2-oxa-1,3-diazole (NBD), a cyanine (including any corresponding compounds in U.S. serial documents 09 / 968,401 and 09 / 969,853), a carbocyanin (including any corresponding compounds in U.S. Serial Nos. 09 / 557,275; 09 / 969,853 and 09 / 968,401; U.S. Patents No. 4,981,977; 5,268,486; 5,569,587; 5,569,766; 5,486,616; 5,627,027; 5,808,044; 5,877,310; 6,002,003; 6,004,536; 5 6,008,373; 6,043,025; 6,127,134; 6,130,094; 6,133,445; and publications WO 02 / 26891, WO 97/40104, WO 99/51702, WO 01/21624; EP 1 065 250 A1), a carbostyril, a porphyrin, a salicylate, an anthranilate, a blue, a perylene, a pyridine, a quinoline, a borapoliazaindacene (including any corresponding compounds disclosed in U.S. Patent Nos. 4,774,339 ; 5,187,288; 5,248,782; 5,274,113; and 5,433,896), a xanthene (including any corresponding compounds disclosed in U.S. Pat. Nos. 6,162,931; 6,130,101; 6,229,055; 6,339,392 ; 5,451,343 and US documents with serial No. 09 / 922,333), an oxazine (including any corresponding compounds disclosed in US Patent No. 4,714,763) or a benzoxazine, a carbazine (including any corresponding compounds disclosed in the U.S. Patent No. 4,810,636), a phenalenone, a coumarin (including corresponding compounds disclosed in U.S. Patent Nos. 5,696,157; ​​5,459,276;

p00088fifteen 5,501,980 and 5,830,912), a benzofuran (including corresponding compounds disclosed in United States Patents No. 4,603,209 and 4,849,362) and benzofenalenone (including any corresponding compounds disclosed in United States Patent No. 4,812. 409) and its derivatives. As used herein, oxazines include resorrufins (including any corresponding compounds disclosed in Patent No. 5,242,805), aminooxazinones, diaminooxazines and their benzo substituted analogs.

p00089When the fluorophore is a xanthene, the fluorophore is optionally a fluorescence, a rhodol (including any corresponding compounds disclosed in US Patent Nos. 5,227,487 and 5,442,045), or a rhodamine (including any corresponding compounds in U.S. Patent Nos. 5,798,276; 5,846,737; U.S. documents with serial No. 09 / 129,015). As used herein, fluorescence includes benzo- or dibenzofluorescens, seminaphofluorescens or naphofluorescens. Similarly, as used herein, rhodol includes seminaftorodafluoro (including any corresponding compounds disclosed in United States Patent No. 4,945,171). Alternatively, the fluorophore is a xanthene that is linked by a bond that is a single covalent bond at position 9 of the xanthene. Preferred xanthenes include 3H-xanthen-6-ol-3-one derivatives attached at position 9, 6-amino-3H-xanthen-3-one derivatives linked at position 9, or derivatives of 6 -amino-3H-xanthen-3imine attached at position 9. Preferred fluorformers of the invention include xanthene (rhodol, rhodamine, fluorescein and derivatives thereof) coumarin, cyanine, pyrene, oxazine and Boropoliazaindacene. Most preferred are sulfonated xanthenes, fluorinated xanthenes, sulfonated coumarins, fluorinated coumarins and sulfonated cyanines. The choice of fluorophore bound to the labeling reagent will determine the absorption properties and

p0009035 fluorescence emission of the labeling reagent and the immunostained complex. The physical properties of a fluorophore mark include spectral characteristics (absorption, emission and displacement of Stokes), fluorescence intensity, life cycle, polarization and photobleaching speed all of which can be used to distinguish one fluorophore of another.

p00091Normally the fluorophore contains one or more aromatic or heteroaromotic rings, which are optionally substituted one or more times by various substituents, including without limitation, halogen ring system, nitro, cyano , alkyl, perfluoroalkyl, alkoxy, alkenyl, alkynyl, cycloalkyl, arylalkyl, acyl, aryl or heteroaryl, benzo or other substituents normally present in fluorformers known in the art.

p00092Four. Five In one aspect of the invention, the fluorophore has a maximum absorption beyond 480 nm. In a particularly useful embodiment, the fluorophore absorbs at or near 488 nm at 514 nm (particularly suitable for excitation by the exit of the excitation source by argon ion lasers) or about 546 nm (particularly suitable for excitation by a mercury arc lamp).

p00093Preferably, the rest of the detection is a fluorescent dye. The fluorescent dye includes, for example, Fluorescena, Rhodamina, Texas Red, Cy2, Cy3, Cy5, Cy0, Cy0.5, Cyl, Cy1.5, Cy3.5, Cy7, VECTOR Red, ELF ™ (by Enzyme- Labeled Fluorescence), FluorX, Calce na, Calce na-AM, CRYPTOFLUOR ™ 'S, Orange (42 kDa), Tangerine (35 kDa), Gold (31 kDa), Red (42 kDa), Crimson (40 kDa) , BHMP, BHDMAP, Br-Oregon, Lucifer Yellow, Alexa family of dyes, N- (6- (7-nitrobenz-2-oxa-1, 3-diazol-4-yl) amino) capro) (NBD) , BODIPY ™, Dipyrrometene Difluoride

p0009455 of boron, Oregon Green, MITOTRACKER ™ Red, DiOC7 (3), DiIC18, phycoerythrin, phycobiliprotene BPE (240 kDa) RPE (240 kDa) CPC (264 kDa) APC (104 kDa), Spectrum Blue, Spectrum Aqua, Spectrum Green, Spectrum Gold, Spectrum Orange, Spectrum Red, NADH, NADPH, FAD, Infrared Dyes (IR), GDP-Cyclic Ribose (cGDPR), Calcofluor White, Tyrosine and Tryptophan.

p00095Many of the fluorophores can also function as chromophores and, therefore, the fluorophores described are also preferred chromophores.

p00096In addition to fluorophores, enzymes are also useful as detectable moieties. Enzymes are desirable detectable moieties because amplification of the detectable signal can be obtained resulting in increased sensitivity of the assay. The enzyme itself does not produce a detectable response but works to break down a substrate when an appropriate substrate comes into contact with it, so that the substrate

p00097Converted produces a fluorescent, colorimetric or luminescent signal. Enzymes amplify the detectable signal because an enzyme in a labeling reagent can result in multiple substrates that become a detectable signal. This is advantageous when there is a low amount of target present in the sample or there is no fluorophore that will give a comparable signal stronger than the enzyme. However, the

p000985 Fluorophores are the most preferred since they do not require additional test steps and, therefore, reduce the overall time required to complete an assay. The enzyme substrate is selected to give the preferred measurable product, for example calorimetric, fluorescent or chemiluminescence. Such substrates are widely used in the art, many of which are described in the MOLECULAR PROBES HANDBOOK document, above.

p00099A combination of calorimetric or fluorogen substrate and preferred enzyme uses oxidoreductases such as horseradish peroxidase and a substrate such as 3,3'-diaminobenzidine (DAB) and 3-amino-9-ethylcarbazole (AEC ), which produce a distinctive color (brown and red, respectively). Other calorimetric oxidoreductase substrates that produce detectable products include, but are not limited to: 2,2-azino-bis (3-ethylbenzothiaz-olin-615 sulfonic acid) (ABTS), o-phenylenediamine (OPD), 3,3 ', 5,5'-tetramethylbenzidine (TMB), o-dianisidine, 5-aminosalicylic acid, 4-chloro-1-naphthol. Fluorogenic substrates include, but are not limited to, homovanilic acid or 4-hydroxy-3-methoxyphenylacetic acid, reduced phenoxazines and reduced benzothiazines, including Amplexe Red reagent and its variants (U.S. Patent No. 4,384. 042) and reduced dihydroxanthenes, including dihydrofluorescens (US Pat. No. 6,162,931) and dihydrorrodamines including dihydroxydamine 123. Peroxidase substrates that are tyramides (U.S. Patent Nos. 5,196,306; 5,583,001 and 5,731,158) represent a unique class of peroxidase substrates, since they can be intrinsically detectable before the action of the enzyme but are "fixed in place" by the action of a peroxidase in the process described as signal amplification by tyramide (TSA). These substrates are widely used to mark targets in samples that are cells, tissues or matrices for subsequent detection by microscopy, flow cytometry, optical scanning and

p0010025 fluorometry

p00101An additional combination of calorimetric substrate (and in some cases fluorogen) and enzyme uses a phosphatase enzyme such as an acidic phosphatase, an alkaline phosphatase or a recombinant version of said phosphatase in combination with a calorimetric substrate such as 5-bromo-6-chloro-3-indolyl phosphate (BCIP), 6-chloro-3-indolyl phosphate, 5-bromo-6-chloro-3-indolyl phosphate, p-nitrophenyl phosphate or o-nitrophenyl phosphate or with a fluorogenic substrate such as 4-methylumbelliferyl phosphate, 6,8-difluoro-7-hydroxy-4-methylcoumarinyl phosphate (DiFMUP, U.S. Patent No. 5,830,912) Fluorescence bisphosphate, 3-O-methylfluoresce phosphate, resorruphine phosphate, 9H- phosphate (1,3-dichloro-9,9-dimethylacridin-2-one-7-yl) ( DDAO phosphate), or ELF 97, ELF 39 or related phosphates (US Pat. Nos. 5,316,906 and 5,443,986).

p0010235 Glucosidases, in particular beta-galactosidase, beta-glucuronidase and beta-glucosidase, are additional suitable enzymes. Appropriate colorimetric substrates include, but are not limited to, 5-bromo4-chloro-3-indolyl betaD-galactopyranoside (X-gal) and similar indolyl galactosides, glucosides and glucurides, o-nitrophenyl beta-Dgalactopyranide (ONPG) and p-nitrophenyl beta-D-galactopyranide. Preferred fluorogenic substrates include beta-D-galactopyranoside resorruphine, digalactose fluorescence (FDG), diglucurid fluorescence and their structural variants (US Pat. Nos. 5,208,148; 5,242,805 ; 5,362,628; 5,576,424 and 5,773,236), 4-methylumbelliferyl beta-D-galactopyranide, carboxymbelliferyl beta-D-galactopyranide and coumarin beta-Dgalactopyranides fluoride (U.S. Patent No. 5,830,912) .

p00103Four. Five Additional enzymes include, but are not limited to, hydrolases such as cholinesterase and peptidases, oxidases such as glucose oxidase and cytochrome oxidases, and reductases for which suitable substrates are known.

p00104Enzymes and their appropriate substrates that produce chemiluminescence are preferred for some assays. These include, but are not limited to, natural and recombinant forms of luciferases and aequorins. Substrates that produce chemiluminescence for phosphatases, glucosidases and oxidases such as those containing stable dioxetans, luminol, isoluminol and acridinium esters are additionally useful. For example, the enzyme is luciferase or aequorin. The substrates are luciferin, ATP, Ca ++ and coelenterazine.

p00105In addition to enzymes, haptens such as biotin are useful detectable moieties. Biotin is useful because it can

p0010655 operate in an enzymatic system to further amplify the detectable signal, and can function as a label for use in affinity chromatography for isolation purposes. For detection purposes, an enzyme conjugate having biotin affinity, such as avidin-HRP, is used. Subsequently a peroxidase substrate is added to produce a detectable signal.

p00107Haptens also include hormones, naturally occurring and synthetic drugs, contaminants, allergens, affective molecules, growth factors, chemokines, cytokines, lymphokines, amino acids, peptides, intermediates Atmic or nucleitide.

p00108A detectable moiety is a fluorescent protein. Exemplary fluorescent proteins include the green protein

p0010965 fluorescent (GFP) phycobiliproteen and derivatives thereof, luciferase or aequorin. Fluorescent proteins, especially phycobiliprotein, are particularly useful for creating dye marked in tandem and

p00110marking reagents These dyes in tandem comprise a fluorescent protein and a fluorophore for the purpose of obtaining a greater Stokes shift in which the emission spectra are much more displaced from the wavelength of the absorption spectra of the fluorescent protein. This is particularly advantageous for detecting a low amount of a target in a sample in which the emitted fluorescent light 5 is optimized to the maximum, in other words, little or none of the emitted light is reabsorbed by the fluorescent protein . For this to work, the fluorescent protein and fluorophore function as an energy transfer pair in which the fluorescent protein emits at the wavelength at which the fluorophore and fluoride absorb The light then emits a wavelength farther away from the fluorescent proteins from which it could have been obtained with only the fluorescent protein. A particularly useful combination is the phycobiliproteen disclosed in US Pat. Nos. 4,520,110; 4,859,582; 5,055,556 and the sulphforhodamine fluorophores disclosed in Patent No. 5,798,276, or the sulfonated cyanine fluorophores disclosed in U.S. serial documents 09/968401 and 09/969853; the sulphonated xanthene derivatives disclosed in Patent No. 6,130,101 and those combinations disclosed in United States Patent

p001114,542,104. As an alternative, the fluorophore functions as an energy donor and the fluorescent protein is the energy acceptor 15.

p00112The preparation of a labeling reagent using low molecular weight reactive dyes is known to those skilled in the art and is well documented, for example, by Richard P. Haugland, Molecular Probes Handbook Of Fluorescent Probes And Research Chemicals, Cap Titles 1-3 (1996) and by Brinkley, Bioconjugate Chem. 3, 2 (1992). Labeling proteins are usually the result of mixing appropriate reactive dyes and the protein to be conjugated in a suitable solvent in which both are soluble. Most of the preferred dyes of the invention are easily soluble in aqueous solutions, facilitating conjugation reactions with most of the biological materials. For those reactive dyes that are photoactivated, the conjugation requires illumination of the reaction mixture to activate the reactive dye.

p0011325 The display methods of the rest of the detection depend on the brand.

p00114At any time after the addition of the immunostained complex to the sample, the sample is illuminated with a wavelength of light selected to give a detectable optical response, and is observed with a means to detect the optical response. . The equipment that is useful for illuminating the fluorescent compounds of the present invention includes, but is not limited to, ultraviolet hand lamps, mercury arc lamps, xenon lamps, lasers and laser diodes. These sources of illumination are optically integrated in laser scanners, readers or patterns of fluorescent microplates or microfluorometers. The degree and / or location of the signal, in comparison to an expected employer response, indicates whether and to what degree the sample has a characteristic

p0011535 given, that is the desired target.

p00116The optical response is optionally detected by visual inspection, or by using any of the following devices: CCD camera, camcorder, photographic film, laser scanning devices, fluoride meters, photodiodes, quantum counters, epifluorescence microscopes, scanning microscopes, flow cytometers, fluorescence microplate readers or by means to amplify the signal such as photomultiplier tubes. Where the sample is examined using a flow cytometer, the examination of the sample optionally includes classifying parts thereof according to its fluorescence response.

p00117When an indirectly detectable mark is used, then the illumination stage normally includes the

p00118Four. Five adding a reagent that facilitates a detectable signal such as a colorimetric enzyme substrate. Radioisotopes are also considered indirectly detectable in which an additional reagent is not required but instead the radioisotope must be exposed to an X-ray film or some other mechanism for recording and measuring the radioisotope signal. This may also be true for some chemiluminescent signals that are best observed after exposure to the film.

Application

p00119An embodiment of the invention relates to an immunohistochemical method of detecting at least three target epitopes in a biological sample. The epitope can be any epitope in an antigen. The antigen can be

p0012055 any tissue antigen including, for example, a nuclear antigen, a cytoplasmic antigen or a membrane bound antigen. The method comprises the following stages

p00121(a) perform antigen recovery in the biological sample, in which said antigen recovery comprises the steps:

p00122i. dewax and rehydrate the biological sample; and

p00123ii. bring to boiling in antigen recovery buffer;

p0012465 (b) perform autofluorescence removal in the biological sample before stage (a), stage (c) or stage (d), in which said autofluorescence removal comprises incubating said biological sample gica in a solution comprising 1% hydrochloric acid and 70% ethanol;

p00125(c) contacting the biological sample with a first antibody specific for a target, a first labeling reagent in which said first labeling reagent comprises an antibody binding moiety for said first antibody and a first detection residue, a second antibody specific for a

p001265 second target, a second labeling reagent comprising an antibody binding moiety for said second antibody and a second detection moiety, a third antibody specific for a third target, and a third labeling reagent comprising an antibody binding moiety for said third antibody and a third detection moiety; and

p00127(d) detecting each of said first, second and third labeling reagents, respectively, in said biological sample whereby the presence of said first, second and third labeling reagents, respectively, indicates the presence of the target in said biological sample and the absence of said labeling reagent indicates the absence of said target in said biological sample, indicates the presence of said first, second or third targets, respectively, in said biological sample and the absence of said first, second

p00128or third labeling reagents indicates the absence of said first, second or third targets, respectively, in said biological sample.

p00129Contacting (step (c)) may involve, for example, incubating the sample in PBS and adding a first antibody, suspended in PBS, to the sample. Since the first antibody is specific for the first target epitope, it will bind only at the location where the epitope is present. The biological sample is a section of human tissue included in a solidifying agent that is paraffin. After an appropriate incubation period that may include incubation with agitation (eg, shaking or turning), the first, second and third unbound antibodies can be removed from the tissue section by washing the section with PBS or other appropriate buffer (a first wash step). Washing may be done, for example, by incubating (shaking or turning) the tissue section in containers with PBS.

p0013025 After removal of first unbound antibodies, the biological sample bound to the first antibody is contacted with a Fab fragment (labeling protein) of second antibodies directed against its Fc regions of the first antibody. The Fab fragment is marked with a detectable mark. In a preferred embodiment, the Fab fragment is a Zenon ™ reagent (Invitrogen, Carlsbad, Ca). For example, if the first antibody is a mouse IgG, the second antibody can be a goat anti-mouse IgG antibody. The Fab fragment will bind to the first antibody to produce a first antibody bound to Fab.

p00131The mark on the Fab fragment can be detected directly without a washing step. The distribution of the brand will correspond to the distribution of the epitope. If the detectable mark is a fluorescent moiety, the mark can

p0013235 Detected using a fluorescence microscope. The use of a fluorescence microscope for the detection of a section of marked tissue is well known.

p00133Optionally, the tissue section can be washed to remove unbound Fab fragments before the mark is detected. The washing step may comprise the same steps as the first washing step described above.

p00134The target epitope can be any epitope in a cell, including, for example, an epitope in an antigen. The antigen can be an oncoprotein (for example bcl-2, c-erbB-2) or a protein that is indicative of heterogeneity of tumor cells (p53). Useful antigens include, for example, epitopes for the receptor of

p00135Four. Five androgens (AR), Cytokeratin 18 or PTEN.

p00136In a preferred embodiment, the first antibody penetrates the tissue section and is attached to an epitope inside the section. The addition of the Fab fragment allows the formation of a first antibody-Fab complex within the tissue section.

Multiplex Application

p00137The methods of the invention are used to detect a plurality of (at least three) targets (epitopes) in a biological sample using the following steps:

p0013855 Stage A A first antibody specific for a first target is saturated with labeling protein to create a previously formed complex. Stage B Excess labeling protein is removed after the formation of the previously formed complex (for example, by gel filtration). Stage C The previously formed complex is contacted with a biological sample. Stage D A second antibody specific for a second target is contacted with the same biological sample. The second antibody is not labeled and is not complexed with a labeling protein. Stage D can be performed before, then simultaneously with stage C. Stage E Excess antibody and excess complex previously formed can be removed in one stage

p0013965 optional wash. Stage F A second labeling protein that is at least specific for the second antibody is applied to the biological sample.

p00140In the above method, the second labeling protein that is added in step F will only bind to the second antibody, since all potential binding sites in the first antibody will already be saturated. with the fluorescently labeled Fab fragment (see Figure 5).

p00141Since the first antibody is applied as a previously formed complex, it is preferred that the first antibody be specific to a nuclear antigen where it has been found that tissue penetration is less critical for detection. n.

p0014210 This "multiplexed" detection (described in example 1) is further multiplexed to detect at least three targets by two alternative methods. In alternative method 1, step A may involve the production of a "first antibody / first label protein complex" and a "third antibody / third label complex" prepared in different reaction vessels. Both the first complex and the third complex can

p00143fifteen applied in step C. The result would be a biological sample labeled with three different antibody / label protein complexes (i.e., 1 antibody / 1 label protein; 2 antibody / 2 labeling protein; 3 antibody / 3 labeling protein). If the first, second and third labeling proteins comprise different detectable labels, then a total of three different labels can be detected in the biological sample.

p00144twenty In alternative method 2, a second antibody and a third antibody can be added in step D, wherein the second antibody and the third antibody are specific for different targets. In step F, a second and a third marking protein can be added. The second labeling protein is specific for the second antibody while the third labeling protein is specific for the third antibody. For example, him

p0014525 The second antibody and the third antibody may be of different IgG subclasses and the second and third label proteins may be specific for an IgG subclass. Using this method, a total of three different brands can be detected in the biological sample.

p00146Although the alternative method 1 and the alternative method 2 described above describe the use of two complexes

p0014730 previously formed (stage B) or two antibodies (stage D), it is understood that the method of the invention is not limited to two previously formed complexes or two antibodies. Any number of previously formed complexes or antibodies can be used in the method of the invention. In addition, the alternative method 1 and the alternative method 2 can be combined. For example, if alternative method 1 and alternative method 2 as described above were combined, a total of four different targets can be detected in a sample

p0014835 Biological Additionally, if the alternative method 1 and the alternative method 2 are combined, the alternative method 2 can be repeated to detect a total of seven different different targets in a biological sample.

p00149For all methods of the invention, unbound immunostaining complexes that do not bind to the target can be optionally removed from the sample by conventional methods, such as washing. In a

p0015040 Optional step for all methods of the invention, bound immunostaining complexes that bind to the target can be fixed in place with the fixatives (e.g. formaldehyde, glutaraldehyde) and methods of fixation n usual. The fixation can be used to improve the durability of the sample and to prevent the transfer of the complexed labeling protein in a non-covalent way to other targeting antibodies in the sample that have the same binding region. n specific.

p00151Four. Five Another embodiment of the invention relates to a method for determining a difference in the amount of at least three targets in a tissue section of a tissue to be tested with respect to the amount and distribution of said targets in a tissue section of a normal tissue. Such comparison can be used to determine if a sample shows an abnormal distribution of epitopes or antigens. First, the method involves the stage of detecting

p00152fifty a distribution of at least three targets in a first sample using the method of claim 1. Second, a distribution of corresponding targets in a normal sample is detected using the method of the claim n 1. Third, the distribution of epitopes or antigens of the first sample and the normal sample are compared to determine if there is a distribution difference between the two samples.

p0015355 A method for in situ analysis of a biological sample is also disclosed. First, a first antibody that is specific for a first epitope is contacted with a first Fab that is specific for the Fc part of the first antibody to produce a first antibody-Fab complex. Excess Fab, not bound to the first antibody can be removed at an optional stage. The biological sample is then contacted with this first antibody-Fab complex and a second antibody that is specific for a second epitope for

p0015460 generate a biological sample of antibody. In an optional step, the first unbound antibody-Fab complex and the second unbound antibody can be removed by washing. A second Fab, which comprises a second distinguishable detectable mark of the first detectable mark is then contacted with the biological sample. The second Fab is specific for the Fc part of the second antibody and forms an antibody-Fab complex with the second antibody.

p0015565 In an optional step, the excess of second Fab can be removed by washing. In the final stage, the first and second detectable marks are detected to determine the location and distribution of the epitopes. It is understood that each detectable label is individually detectable in the presence of all other detectable labels in the biological sample.

p001565 Although not in accordance with the present invention according to the claims, a platform could be provided for multiplexed quantitative evaluation of antigens, which combines immunofluorescence (IF) detection with image analysis. computer assisted genes. The computer equipment (hardware and / or software) could measure the presence, intensity and / or distribution of brand or fluorescent marks in tissue images resulting from

p0015710 IF detection, where each mark on an image indicating the presence of a target antigen. This computer equipment could include, for example, the Definiens Cellenger Developer Studio (v. 4.0) package available on the market adapted to segment and classify tissue images into objects (eg stroma, light, n Nuclei, cytoplasm, etc.) and / or to detect fluorescent labels (Figures 11A, 12A, 20 and 21). The Definiens Cellenger product can also be designed and adapted to run scripts that measure the

p00158fifteen presence, intensity and / or distribution of fluorescent tags located within specific tissue cell compartments (eg, such as, fluorescent tags within epithelial ocular nuclei). These measurements (alone or in combination with other observations such as clinical, molecular and / or morphometric observations) may be subject to supervised mathematical approaches, including automatic learning methods such as regression. Support vector for censored data (SVRc), to generate

p00159twenty models for (for example) diagnosis and prognosis of a disease. The methods and systems for generating models and for extracting measurements from tissue images are described in US Common Ownership Publication No. 20050262031.

p00160Although not according to the present invention according to the claims, tissue samples

p0016125 processed with the IF detection methods described herein could be placed in a Nikon 9Oi automated fluorescence microscope. Fluorescent images are acquired using a CRI Nuance multispectral camera (Cambridge Research &amp; Instrumentation, Inc.) mounted on the microscope and controlled by the MetaMorph online software. Other equipment suitable for image acquisition could also be used. The following description illustrates the use of acquisition and analysis of IF images to detect the presence of

p0016230 Androgen receptor (AR) in tissue. One focus of the study was to identify factors linked to the growth and progression of prostate cancer.

p00163DAPI (4'-6-Diamidino-2-phenylindole), coupled with antibodies to Cytokeratin18 (CK) (DAPI for nuclei and CK18 for epithelial cells), and the androgen receptor were applied to tissue in microarray slides

p0016435 tissue (TMA). Fluorescent images were acquired representing each of the TMA nuclei using the equipment described above. More particularly, 12-bit DAPI images were captured with the camera set at 480 nm using a 50% saturation setting. CK 18, marked with Alexa 488, was purchased using an FITC bandpass filter (Chroma). 12-bit images were captured in 10 nm increments starting at 520 nm. AR, marked with Alexa 568 was captured using a long wave pass filter (Chroma). Images were captured

p0016540 12 bits in 10 nm increments starting at 570 nm. The image stacks were unmixed using the CRI analysis software. Alexa 488 and 568 pure dyes were used as reference spectra for the desmixing process. Typical regions of autofluorescence and other fluorescent objects (eg erythrocytes) were assigned to the spectral profiles. Once the process of unmixing was completed, quantitative images were stored in grayscale in tiff format for analysis. After unmixing, the images in scale

p00166Four. Five grays are combined to produce a composite image for analysis using the Definiens Cellenger scripts. When the images are combined, unique fragment IDs and donors that associate the images with a patient are used.

p00167Definiens Cellenger scripts segment and classify images to detect and

p00168fifty quantify the AR signal present within nuclei of epithelial cells. Measurements were also taken based on biomarker intensities and nuclear areas defined by segmentation with DAPI, where the measurements reflected the overall intensity and distribution of AR present in specific cell types. The table below includes a list of measurements derived from the images provided in the table below.

p00169Quantitative immunofluorescent characteristics of the androgen receptor

Characteristics Definition

p00170averageip0001 Average intensity of the AR marker in epithelial nuclei averageip0002 Average AR intensity in epithelial and stromal nuclei averageipstroma0003 Average intensity of the AR marker in stromal nuclei maxip0007 Maximum AR intensity in epithelial nuclei maxip0008 Maximum AR intensity in epithelial and stromal nuclei objects maxipstroma0009 Maximum AR intensity in stromal nuclei minip0010 Minimum intensity of AR in epithelial nuclei

Characteristics Definition

p00171minip0011 Minimum intensity of AR in stromal and epithelial nuclei minipstroma0012 Minimum AR in stromal nucleus area of ​​epithelial nuclei with positive RA / area of ​​epithelial nuclei with

p00172ratioareaepithnucversusepith0013

p00173Negative AR correlaobject10005 Linear correlation coefficient between DAPI and AR images

p00174From the list of derived measurements for RA, it was determined by supervised mathematical strategies that the characteristic “ratioareaepithnucversusepith0013” was independently associated with the recurrence of PSA when analyzed univariately. This feature represents the relationship of the core areas

p001755 epithelials expressed positively and negatively with RA. Therefore, these data suggest (for example) that the total amount of RA present in both tumor and non-tumor elements is an important factor in the growth and progression of prostate cancer.

BIBLIOGRAPHIC REFERENCES 10

p00177KD BAUER et al .: "Prognostic implications of ploidy and proliferative activity in diffuse large cell lymphomas", CANCER RES, vol. 46, 1986, pages 3173-3178,

p00178KD BAUER et al .: Prognostic implications of proliferative activity and DNA aneuploidy in colonic 15 denocarcinomas ", LAB INVEST, vol. 57, 1987, pages 329-335,

p00179HB BEVERLOO et al .: "Immunochemical detection of proteins and nucleic acids on filters using small luminescent inorganic crystals as markers". ANAL. BIOCHEM., Vol. 203, 1992, pages 326-334.

p00180twenty RC BRAYLAN et al .: "Percentage of cells in the S phase of the cell cycle in human lymphoma determined by flow cytometry: Correlation with labelling index and patient survival", CYTOMETRY, vol. 1, 1980, pages 171174,

p00181JK Brown et al. (2004) Primary antibody- Fab fragment complexes: a flexible alternative to traditional direct and 25 indirect immunolabeling techniques. J Histochem Cytochem. 52: 1219-30.

p00182P. CHAN ET AL: "Method for multiplex cellular detection of mRNAs using quantum dot fluorescent in situ hybridization.", NUCLEIC ACIDS RESEARCH 2005, vol. 33, no. 18, October 13, 2005 (), pages E161-1-E161-8, XP002418825, Oxford UK ISSN: 1362-4962

p00183GM CLARK et al .: "Predictions of relapse or survival in patients with mode-negative breast cancer by DNA flow cytometry", N. ENGL J MED, vol. 320, 1989, pages 627-633,

p00184RP HAUGLAND: "Molecular Probes Handbook Of fluorescent Probes And Research Chemicals", Eugene, OR 35 USA, Molecular Probes Inc., 1996

p00185SA PILERI ET AL .: "Antigen retrieval techniques in immunohistochemistry: comparison of different methods.", JOURNAL OF PATHOLOGY, vol. 183, October 9, 2011 (), pages 116-123, New York, NY United States

p00186M. SEMAR ET AL: "Quantitative comparative immunohistology", CLINICAL CHEMISTRY, vol. 15, no. January 6, 1969 (), Winston-Salem NC United States

p00187R. SILVESTRINI et al .: "Cell kinetics as a prognostic marker in node-negative breast cancer", CANCER, vol. 56, 45 1985, pages 1982-1987,

p00188H. SIGURDSSON et al .: "Indicators of prognosis in node-negative breast cancer", N ENGL J MED, vol. 322, 1990, pages 1045-1053,

p00189fifty JR Tuson et al. (1990) A novel immunohistochemical technique for demonstration of specific binding of human monoclonal antibodies to human cryostat tissue sections. J Histochem Cytochem 38: 923-6.

p00190D. Visscher et al. Prognostic significance of morphological parameters and flow cytometric DNA analysis in carcinoma of the breast. Pathol Ann 1990, 25 (Part I), 171-210.

p0019155 DS Weinberg Proliferation indices in solid tumors. Adv Pathol Lab Med 1992, 5 (1), 163-191.

p00192DS Weinberg Relative applicability of image analysis and flow cytometry in clinical medicine. in: D. Baer et al. Flow cytometry: principles and applications. Baltimore MD, Williams and Wilkens, 1992, 359-372.

p0019360 GM Wessel &amp; DR McClay: "Two embryonic tissue-specific molecules identified by a double-label immunofluorescence technique for monoclonal antibodies", Journal of Histochem &amp; Cytochem, HISTOCHEMICAL SOCIETY, NEW YORK, NY, United States, vol. 34, no. January 6, 1986 (01-011986), pages 703-706, XP002387587, USA ISSN: 0022-1554

5 PATENT REFERENCES

EP 1065 250

p00196US 4520110 US 4859582 US 5055556 US 5208148 US 5242805 US 5362628 15 US 5576424 US 5773236 US 5830912 US 5316906 US 5443986 US 5132432 US 4981977 US 5268486 US 5569587 US 5569587 25 US 5569766 US 5486616 US 5627027 US 5808044 US 5877310 US 6002003 US 6004536 US 6008373 US 604304 US $ 6134133 5187288 US 5248782 US 5274113 US 5433896 US 6162931 US 6130101 US 6229055 45 US 6339392 US 5451343 US 4714763 US 4810636

p00197US 5696157 US 5459276 US 5501980 US 5830912 US 4603209 55 US 4849362 US 4812409 US 5242805 US 5227487 US 5442045 US 5798276 US 5846737 US 4945171

US 09/968401

65 US 09/968401 US 09/557275

p00200US 09/557275 US 09/969853 US 09/968401 US 09/922333 5 US 09/129015 US 09/968401 US 09/969853

US 2005/262031

10 WO 03/030817 WO 02/26891 WO 02/26891 WO 97/40104

p00203fifteen WO99 / ​​51702 WO 01/21624

p00204Examples

p00205twenty EXAMPLE 1: GENERAL METHODS OF SAMPLE PREPARATION

p00206The following methods are generally used during Multiplex detection methods according to the invention.

p0020725 Antigen Recovery:

<dl><dt>1.</dt><dd> Dewax and rehydrate tissue samples according to the conventional Leica 5020 SOP. </dd></dl>

<dl><dt>2.</dt><dd> Preheat 250 ml of Reveal 1X antigen recovery solution to boiling in a microwave water bath (heat the solution for seven (7) minutes to power level seven (7) ). </dd></dl>

p0020830 3. Place slide in the Reveal 1X solution boiling vessel. Allow boiling for 8.0 minutes as described above.

<dl><dt>4.</dt><dd> Once completed, remove the container from the microwave water bath and let cool for 20 minutes. </dd></dl>

<dl><dt>5.</dt><dd> Rinse the slides in PBS briefly followed by 1 x 5 minutes at room temperature. </dd></dl>

p002096. Place the slides in the Nemesis 7200 and start the self-tilt program. 35

p00210Fabric permeabilization:

p00211Incubate slides in PBT (PBS with 0.2% Triton-X) for 30 minutes. The PBT is prepared as follows: 40

<dl><dt>Reagent </dt><dd>Provider Catalog No. Dilution / [Conc.] Quantity Final volume </dd></dl>

<dl><dt>Difco FA buffer </dt><dd>Fisher 223142 1X 1.0 g </dd></dl>

<dl><dt>Triton-X 100 </dt><dd>Fisher BP151-500 0.2% 2.0 ml </dd></dl>

<dl><dt>Tween 20 at 20% </dt><dd>BioCar e TWN20H 1.0% 50.0 ml </dd></dl>

<dl><dt>ddH2O </dt><dd>--- --- --- 948.0 ml 1000 ml </dd></dl>

p00212Elimination of autofluorescence:

p00213Incubate slides in acid-alcohol (1% HCL in 70% EtOH) for 20 minutes. The acid-alcohol is prepared as follows:

<dl><dt>Reagent </dt><dd>Provider Catalog No. Dilution / [Conc.] Quantity Final volume </dd></dl>

<dl><dt>200 degree EtOH </dt><dd>Sigma E7023-4L grade 140 7.28 ml </dd></dl>

<dl><dt>HCl </dt><dd>Fisher A144S-500 1.0% 0.1 ml </dd></dl>

<dl><dt>Tween 20 at 20% </dt><dd>BioCar e TWN20H 1.0% 0.52 ml </dd></dl>

<dl><dt>ddH2O </dt><dd>--- --- --- 2.5 ml 10.4 ml </dd></dl>

p00214Pre-antibody treatment stages

p00215fifty To help penetrate tissue cell structures, samples were incubated in PBS containing 0.2% Triton-X 100 (PBT) at room temperature for thirty minutes, followed by three rinses of three minutes each in PBS To help reduce autofluorescence in the tissue, the samples were incubated in 1% HCl in 70% ethanol at room temperature for twenty minutes, followed by three rinses of three minutes each in PBS. The blocking of non-specific binding sites was performed by incubating the slides in 1% blocking reagent (10.0 mg / ml BSA in PBS) at room temperature for twenty minutes. No washes were performed between the blocking stage and the subsequent hybridization stage.

p00216Hybridization of target specific antibodies with biological samples

p00217Antibodies specific to a target hybridize, for example, as follows:

p0021810 An anti-cytokeratin 18 (CK18) antibody cocktail (Calbiochem) diluted to 1: 7000 and androgen receptor antibody (AR) (clone AR441, LabVision) diluted at 1: 5 dilution was prepared in reagent 1% lock. Approximately 100 µl of this antibody cocktail was applied to the tissue sample, and the antibodies and tissue samples were allowed to hybridize in a humid chamber at room temperature for one hour. The hybridization was followed by two rinses of six minutes each in PBT, a rinsing of six minutes in PBS and a

p00219fifteen Rinse three minutes in PBS.

p00220Marking of hybridized target specific antibodies

p00221Hybridized target specific antibodies are labeled fluorescently, for example, as follows:

p00222twenty A Zenb Alexa Fluor 488 anti-rabbit IgG Fab fragment cocktail and Zenon Alexa Fluor 568 anti-mouse IgG1 Fab fragment (Invitrogen, Carlsbad, CA) was prepared in 1% two-fold boiling reagent the concentrations recommended by the manufacturer (1:50 dilution for each Fab fragment). Approximately 100 μl of this labeling cocktail was applied to the tissue samples, which were then incubated in a moist chamber at

p0022325 room temperature for 30 minutes. The marking reaction was followed by two rinses of six minutes each in PBT, a rinse of six minutes in PBS and a rinse of three minutes in PBS.

p00224Multiplex Detection

p0022530 Multiple targets in a single sample are detected using, for example, the following protocol. To identify 5 targets in a single prostate section using the following protocol: An anti-racemase cocktail (AMACR; clone 13H4, Zeta Corporation) was prepared at a 1:50 dilution with antibody undiluted against high molecular weight cytokeratin + p63 (HMW CK + p63; BioCare Medical). Approximately 100 μl of this antibody cocktail was applied to the tissue sample, and the antibodies were allowed to bind in a humid chamber at temperature.

p0022635 atmosphere for one hour. The incubation was followed by two rinses of six minutes each in PBT, a rinse of six minutes in PBS and a rinse of three minutes in PBS.

p00227For the labeling stage, a Zenon Alexa Fluor 488 anti-rabbit IgG Fab fragment cocktail, Zenon Alexa Fluor 555 anti-mouse IgG1 fragment, and Zenon Alexa Fluor anti-mouse IgG2a Fab fragment 594 was prepared in

p0022840 1% boiling reagent at twice the concentrations recommended by the manufacturer (1:50 dilution for each Fab fragment). Approximately 100 µl of this labeling cocktail was applied to the tissue samples, and the tissue samples were incubated in a moist chamber at room temperature for 30 minutes. The marking reaction was followed by two rinses of six minutes each in PBT, a rinse of six minutes in PBS and a rinse of three minutes in PBS.

p00229Four. Five Tissue samples were then treated with a second round of antibody binding and labeling. An anti-CK-18 cocktail at a 1: 6000 dilution and anti-AR at a 1: 5 dilution was prepared in 1% boiling reagent. Approximately 100 µl of this antibody cocktail was applied to the tissue sample, and the antibodies were allowed to bind in a moist chamber at room temperature for one hour. Hybridization

p00230fifty two rinses of six minutes each in PBT followed, a rinse of six minutes in PBS and a rinse of three minutes in PBS.

p00231For the second stage of labeling, a Zenon Alexa Fluor 647 anti-rabbit IgG Fab fragment cocktail and Zenon Alexa Fluor 568 anti-mouse IgG1 fragment was prepared in concentration reagent at 1% n

p0023255 recommended by the manufacturer (dilution 1: 100 for each Fab fragment). Approximately 100 μl of this labeling cocktail was applied to the tissue samples, and the tissue samples were incubated and rinsed as described for the first stage of labeling.

p00233EXAMPLE 2: MULTIPLEX DETECTION OF THE ANDRENDER, CYTOKERATINE AND AMACR RECEPTOR

p0023460 The androgen receptor (AR), Cytokeratin 18 and AMACR have been found to be important biomarkers for the evaluation of prostate cancer tissue. The qualitative and quantitative distribution of these markers in tissue sections included in paraffin, fixed with formalin or tissue microarrays were detected as described below. In this study samples of up to 16 years old were used.

p002351.) Antigen recovery (in Reveal solution, citrate buffer or proteinase K) For the recovery of antigens, tissue sections or TMA were heated in Reveal 1X solution (BioCare Medical) in a recovery chamber “decloaking chamber” according to a conventional protocol already They are then allowed to cool for 15 minutes. Alternative methods of antigen recovery include: 1)

p002365 heat sections of tissue or TMA in 10 mM citrate buffer, pH 6.0, for 15 minutes in a calibrated microwave followed by cooling for 15 minutes or 2) enzymatically digest sections of tissue or TMA in a solution Proteinase K (commercially available from Fisher as a ready-to-use reagent for antigen recovery for 12-15 minutes. After rinsing in distilled water for 15 minutes (this step is skipped to recover antigens with proteinase K), the slides were washed 3 times for 5 minutes in phosphate buffered saline (PBS).

p002372.) Elimination of autofluorescence

p00238Autofluorescence was reduced by incubating the slides in 1% HCl / 70% EtOH for 10 minutes at room temperature. The slides were then rinsed 3 times for 5 minutes in PBS.

p002393.) Fabric permeabilization

p00240The tissue was subsequently permeabilized in PBS containing 0.2% Triton X (PBT) for 30 minutes at room temperature.

p002414.) Blocking with nonspecific IgG

p00242The non-specific binding of antibody or Fab fragment was blocked by incubation with 0.5 μg / ul of BSA in PBT 25 for 20 minutes in a moist chamber. The slides were subsequently clarified in PBT for 5 minutes.

p002435.) Preparation of the previously formed complex for Cytokeratin 18 and Fab

p00244Monoclonal mouse cytokeratin 18 was incubated with mouse-specific Fab fragment labeled with Alexa 488 to prepare a previously formed complex for 10 minutes at room temperature. Then, that unbound Fab was neutralized by adding an excess specific non-specific IgG mouse IgG.

p002456.) Incubation of untreated primary antibodies and the previously formed complex in tissue

p0024635 The previously formed Cytokeratin 18-Fab complex and untreated rabbit polyclonal CD34 and mouse monoclonal pTEN antibody were incubated in the tissue for 1 hour at room temperature in a moist chamber.

p002477.) Removal of unbound antibody

p00248Excess antibody was removed by washing the slides 2 times for 10 minutes in PBT followed by 3 times for 5 minutes in PBS.

p002498.) Incubation with fluorescently labeled Fab

p00250Four. Five A specific Fab fragment of rabbit and rabbit labeled with Alexa 555 and Alexa 594 respectively were added to the slide and incubated for 30 minutes at room temperature in a moist chamber.

p002519.) Elimination of unbound Fab

p00252Unbound Fab fragment was removed by washing the slides 2 times for 10 minutes in PBT followed by 3 times for 5 minutes in PBS.

p0025310.) Fixing

p0025455 The tissue was fixed in 10% formalin for 10 minutes. The slides were rinsed 2 times for 5 minutes in PBS.

p0025511.) Assembly

p00256After adding 100 µl of AntiFade solution containing nuclear counterstain, the slides were covered with coverslips and prepared for image capture.

p0025712.) Image acquisition 65 The samples were placed in a 90i automated fluorescence microscope. The regions of interest are

p00258They identified moving the yx axes of the microscope stage. The exposure time of the image was adjusted to the highest possible brightness level without causing overexposure. The images were acquired with the Nikon 1200DXM CCD camera or a comparable system (alternatively a spectral imaging camera could be used for advanced spectral separation of fluorescent dyes). The images were saved in tiff format and were

p002595 underwent quantitative image analysis.

EXAMPLE 3: MULTIPLEX DETECTION OF EGFR, FOSFO-EGFR AND CYTOKERATINE 18

p00261The epidermal growth factor receptor (EGFR) and downstream signaling members have demonstrated

p0026210 recently being overexpressed in certain types of tumor. As a result, another group of biomarkers in analysis are EGFR, phospho-EGFR and Cytokeratin 18. To measure, the qualitative and quantitative distribution of these biomarkers in tissue sections included in paraffin, fixed with formalin or tissue microarrays were detected as follows:

p00263fifteen Dewaxing and rehydration of tissue samples performed on the Discovery XT automated slide processing machine (Medical Window, Tuscan AZ).

p002641.) Antigen recovery (Proteinase K)

p00265twenty For antigen recovery, tissue sections or TMA were incubated in a proteinase K solution (commercially available as a ready-to-use reagent for antigen recovery) for 12-15 minutes. This was applied to slides in the "pretreatment 1" stage of the machine protocol using a user refillable dispenser (pretreatment 3).

p0026625 2.) Fabric permeabilization

p00267Tissue samples were subsequently permeabilized in PBS containing 0.2% Triton X (PBT) for 28 minutes at room temperature, applied in the "pretreatment 2" stage of the protocol using a user refillable dispenser (enzyme 3 ).

p0026830 3.) Elimination of autofluorescence

p00269Autofluorescence was reduced by incubating the slides in 1% HCl / 70% EtOH for 16 minutes at room temperature, applied in the pretreatment stage 3 of the protocol using a refillable dispenser

p0027035 (pretreatment 4).

p002714.) Blocking with nonspecific IgG

p00272The non-specific binding of antibody or Fab fragments was blocked by incubation with 0.5 μg / ul of BSA in

p0027340 PBT for 20 minutes in a wet chamber. This was applied to the “Option” stage of the protocol using a user-refillable dispenser (option 1).

p002745.) Incubation of untreated primary antibodies

p00275Four. Five Rabbit monoclonal EGFR and rabbit polyclonal phospho-EGFR antibody were diluted together in their respective working dilution and manually applied to slides during the manual titration stage in the Discovery XT apparatus (Ventana Medical, Tuscan AZ) . The operation of the Discovery XT was restarted during an incubation period of one hour.

p00276fifty 6.) Incubation with fluorescently labeled Fab

p00277Fab-specific rabbit and rabbit fragments labeled with Alexa 594 and Alexa 555 respectively were added manually to the slide and incubated for 30 minutes. The operation of the Discovery XT was restarted and allowed to run until it was completed.

p0027855 8.) Removal of unbound antibody

p00279Once the operation was completed, the slides were removed from the Discovery XT, placed on a slide rack 2 times for 6 minutes each in PBT at room temperature. Then the

p0028060 slides were rinsed again 2 times for 3 minutes in PBS.

p002817.) Incubation of the third untreated primary antibody

p00282Mouse monoclonal cytokeratin 18 was diluted to its working dilution and slides were added for 65 hour incubation at room temperature.

p002838.) Incubation with the third Fab fluorescently labeled

p00284The mouse-specific Fab fragment labeled with Alexa 488 was added to the slide and incubated in the dark for 30 minutes at room temperature. 5 9.) Elimination of unbound antibody

p00285Excess antibody was removed by washing the slides 2 times for 6 minutes in PBT followed by 3 times for 3 minutes in PBS.

p002869.) Elimination of unbound Fab

p00287Unbound Fab fragment was removed by washing the slides 2 times for 10 minutes in PBT followed by 3 times for 5 minutes in PBS.

p00288fifteen 10.) Fixing

p00289The tissues were fixed in 10% formalin for 10 minutes. The slides were then clarified 2 times for 5 minutes in PBS.

p0029011.) Assembly

p00291After adding 100 µl of AntiFade solution containing nuclear counterstain, the slides were covered with coverslips and prepared for image capture.

p0029225 12.) Acquisition of images

p00293The samples were placed in a 90i automated fluorescence microscope. The regions of interest were identified by moving the yx axes of the microscope stage. The exposure time of the image was adjusted within the camera to the highest possible brightness level without causing overexposure. The images were acquired with the Nikon 1200DXM CCD camera or a comparable system (alternatively a spectral imaging camera could be used for advanced spectral separation of fluorescent dyes). The images were saved in tiff format and subjected to quantitative analysis of the image.

35 EXAMPLE 4: MULTIPLEX DETECTION OF VEGF, KDR, P-KDR AND CD34

p00295Angiogenesis is a critical process for tumor growth and metastasis. It has been found that vascular endothelial growth factor (VEGF) and its VEGFR-2 receptor (KDR) together with CD34 are important biomarkers for the evaluation of neovascularization and angiogenesis. To measure, the qualitative and quantitative distribution of these biomarkers in tissue sections included in paraffin, fixed with formalin or tissue microarrays were detected as follows;

p002961.) Antigen recovery (in Reveal solution)

p00297Four. Five For the recovery of antigens, tissue sections or TMA were heated in Reveal 1X solution (BioCare Medical) in a "decloaking chamber" recovery chamber according to a conventional protocol and then They are allowed to cool for 15 minutes. Alternative methods of antigen recovery include: 1) heating tissue sections or TMA in 10 mM citrate buffer, pH 6.0, for 15 minutes in a calibrated microwave followed by cooling for 15 minutes . After rinsing in distilled water for 15 minutes, the slides would be washed 3 times for 5 minutes in phosphate buffered saline (PBS).

p002982.) Fabric permeabilization

p00299Tissue samples were subsequently permeabilized in PBS containing 0.2% Triton X (PBT) for 30 minutes at room temperature.

p003003.) Elimination of autofluorescence

p00301Autofluorescence was reduced by incubating the slides in 1% HCl / 70% EtOH for 10 minutes at room temperature. The slides were then rinsed 3 times for 5 minutes in PBS.

p003024.) Blocking with nonspecific IgG

p00303The non-specific binding of antibody or Fab fragment was blocked by incubation with 0.5 μg / ul of BSA in PBT

p0030465 for 20 minutes in a wet chamber. The slides were subsequently clarified in PBT for 5 minutes.

p003055.) Incubation of untreated primary antibodies

p00306Mouse monoclonal VEGF and rabbit polyclonal KDR were diluted together to work dilution and added to slides for one hour incubation in a wet chamber. 5 6.) Elimination of unbound antibody

p00307Excess antibody was removed by washing the slides 2 times for 6 minutes in PBT followed by 2 times for 3 minutes in PBS.

p003087.) Incubation with fluorescently labeled Fab

p00309Fab-specific rabbit and rabbit fragments labeled with Alexa 488 and Alexa 555 respectively were added to the slide and incubated in the dark for 30 minutes.

p00310fifteen 8.) Removal of unbound antibody

p00311Excess antibody was removed by washing the slides 2 times for 10 minutes in PBT followed by 3 times for 5 minutes in PBS.

p003129.) Incubation of the second cluster of untreated primary antibodies

p00313Rabbit monoclonal CD34 and polyclonal KDR phospho-KDR were diluted together to work dilution and added to slides for one hour incubation in a wet chamber.

p0031425 10.) Removal of unbound antibody

p00315Excess antibody was removed by washing the slides 2 times for 6 minutes in PBT followed by 2 times for 3 minutes in PBS

p0031611.) Incubation with fluorescently labeled Fab

p00317Fab-specific rabbit and rabbit fragments labeled with Alexa 568 and Alexa 594 respectively were added to the slide and incubated in the dark for 30 minutes.

p0031835 12.) Removal of unbound antibody

p00319Excess antibody was removed by washing the slides 2 times for 10 minutes in PBT followed by 3 times for 5 minutes in PBS.

p0032010.) Fixing

p00321The tissue was fixed in 10% formalin for 10 minutes. The slides would then be clarified 2 times for 5 minutes in PBS.

p00322Four. Five 11.) Assembly

p00323After adding 100 µl of AntiFade solution containing nuclear counterstain, the slides were covered with coverslips and prepared for image capture.

p0032412.) Acquisition of images

p00325The samples were placed in a 90i automated fluorescence microscope. The regions of interest were identified by moving the yx axes of the microscope stage. The exposure time of the image was adjusted

p0032655 inside the camera at the highest possible brightness level without causing overexposure. The images were acquired with the Nikon 1200DXM CCD camera or a comparable system (alternatively a spectral imaging camera could be used for advanced spectral separation of fluorescent dyes). The images were saved in tiff format and subjected to quantitative analysis of the image.

p00327EXAMPLE 5: MULTIPLEX DETECTION OF THE ANDRENDER, CYTOKERATIN RECEPTOR, α-METILACIL-COA-RACEMASA, P63, CD34 AND NFKB

p00328Androgen receptor (AR, mouse IgG1), Cytokeratin-18 (rabbit IgG), Methylacil-CoA Racemase (AMACR, rabbit IgG), high molecular weight cytokeratin (HMWCK, IgG1) mouse), P63

p0032965 (Mouse IgG2a), CD34 (mouse IgG1) and NFKB (rabbit IgG) are important biomarkers for the evaluation of prostate cancer tissue. The qualitative and quantitative distribution of these markers in tissue sections included in paraffin, fixed with formalin or tissue microarrays, were detected as follows:

p003301.) Antigen recovery (in Reveal solution, citrate buffer or proteinase K)

p003315 For the recovery of antigens, tissue sections or TMA were heated in Reveal 1X solution (BioCare Medical) in a "decloaking chamber" recovery chamber according to a conventional protocol and then They are allowed to cool for 15 minutes. Alternative methods of antigen recovery include: 1) heating tissue sections or TMA in 10 mM citrate buffer, pH 6.0, for 15 minutes in a calibrated microwave followed by cooling for 15 minutes or 2) enzymatically digest sections of tissue or TMA in a proteinase K solution (commercially available as a ready-to-use reagent for antigen recovery) for 12-15 minutes. After rinsing in distilled water for 15 (this step is skipped to recover antigens with proteinase K), the slides were washed 3 times for 5 minutes in phosphate buffered saline (PBS).

p00332fifteen 2.) Elimination of autofluorescence

p00333Autofluorescence was reduced by incubating the slides in 1% HCl / 70% EtOH for 10 minutes at room temperature. The slides were then rinsed 3 times for 5 minutes in PBS.

p003343.) Fabric permeabilization

p00335The tissue was subsequently permeabilized in PBS containing 0.2% Triton X (PBT) for 30 minutes at room temperature.

p0033625 4.) Blocking with nonspecific IgG

p00337The non-specific binding of antibody or Fab fragment was blocked by incubation with 0.5 μg / ul of BSA in PBT for 20 minutes in a moist chamber. The slides were subsequently clarified in PBT for 5 minutes.

p003385.) Preparation of the previously formed complex for high molecular weight cytokeratin cocktail / p63 and AMACR.

p00339High molecular weight monoclonal cytokeratin antibodies of raton / P63 and rabbit polyclonal AMACR se

p0034035 titrated with the same non-specific binding antibody and incubated in tissue for 1 h at room temperature in a moist chamber.

p003416.) Removal of unbound antibody

p00342Excess antibody was removed by washing the slides 2 times for 5 minutes in PBT followed by 2 in PBS, 5 and 3 minutes respectively.

p003437.) Incubation with fluorescently labeled Fab

p00344Four. Five Fab-specific rabbit and rabbit fragments labeled with Alexa 488, Alexa 555 and Alexa 594 respectively were added to the slide and incubated for 30 minutes at room temperature in a moist chamber.

p003458.) Elimination of unbound Fab

p00346Unbound Fab fragment was removed by washing the slides 2 times for 5 minutes in PBT followed by 2 in PBS 5 and 3 minutes respectively.

p003479.) Preparation of the previously formed complex for Cytokeratin 18 and the androgen receptor

p0034855 Rabbit polyclonal monoclonal androgen receptor (AR) antibodies and rabbit cytokeratin 18 were titrated with the same non-specific binding antibody and incubated in tissue for 1 h at room temperature in a chamber meda

p0034910) Elimination of unbound antibody

p00350Excess antibody was removed by washing the slides 2 times for 5 minutes in PBT followed by 2 in PBS, 5 and 3 minutes respectively.

p0035111) Incubation with fluorescently labeled Fab

p0035265 Fab-specific rabbit and rabbit fragments marked with Alexa 680 and Alexa 568 respectively were added

p00353to the slide and incubated for 30 minutes at room temperature in a moist chamber. 12) Elimination of unbound Fab

p003545 Unbound Fab fragment was removed by washing the slides 2 times for 5 minutes in PBT followed by 2 in PBS 5 and 3 minutes respectively. 13) Preparation for overnight application of CD34 antibody Mouse monoclonal CD34 antibody was titrated with the same non-specific binding antibody and incubated during

p00355one night at 4 degrees in a closed wet chamber. 14) Refrigerated slide recovery

p00356fifteen After removing the slides from the refrigerator, the slides were left at room temperature inside the closed chamber for 1 h. 15) Removal of unbound antibody Excess antibody was removed by washing the slides 2 times for 5 minutes in PBT followed by 2 in

p00357PBS, 5 and 3 minutes respectively. 16) Incubated with fluorescently labeled Fab

p0035825 Fab-specific rabbit and rabbit fragment labeled with Alexa 647 was added to the slide and incubated for 30 minutes at room temperature in a moist chamber. 17) Elimination of unbound Fab The unbound Fab fragment was removed by washing the slides 2 times for 5 minutes in PBT followed by 2 in

p00359PBS 5 and 3 minutes respectively. 18) Preparation for an NFKB antibody application

p0036035 Polyclonal rabbit NFKB was titrated with the same non-specific binding antibody and incubated in tissue for 1 h at room temperature in a moist chamber. 19) Removal of unbound antibody Excess antibody was removed by washing the slides 2 times for 5 minutes in PBT followed by 2 in

p00361PBS, 5 and 3 minutes respectively. 20) Incubate with fluorescently labeled Fab

p00362Four. Five Rabies specific Fab fragment labeled with Alexa 660 was added to the slide and incubated for 30 minutes at room temperature in a moist chamber. 21) Removal of unbound Fab The unbound Fab fragment was removed by washing the slides 2 times for 5 minutes in PBT followed by 2 in

p00363PBS 5 and 3 minutes respectively. 22) Fixation

p0036455 The tissue was fixed in 10% formalin for 10 minutes. The slides were rinsed 2 times for 5 minutes in PBS. 20 23) Mounting After adding 100 μl of AntiFade solution containing nuclear contraction, the slides were covered with

p00365coverslips and prepared for image capture. 24) Image acquisition 65 The samples were placed in a 90i automated fluorescence microscope. The regions of interest were identified by moving the yx axes of the microscope stage. The exposure time of the image was adjusted to

p00366highest possible brightness level without causing overexposure. The images were acquired with the Nikon 1200DXM CCD camera or a comparable system (alternatively a spectral imaging camera could be used for advanced spectral separation of fluorescent dyes). The images were saved in tiff format and subjected to quantitative analysis of the image.

p003675 EXAMPLE 6: MULTIPLEX DETECTION OF CYTOKERATIN 18, AMACR RACEMASA, ANDRENGEN RECEIVER, HIGH MOLECULAR WEIGHT KERATIN AND P63 IN PRÉSTATA FABRIC

p00368The conventional MultiPlex assay was used to detect 5 markers including CK18 (Cytokeratin 18), AMACR (Racemasa), AR (Androgen Receptor), HMWK (High Molecular Weight Keratin), p63 (basal cells) and DAPI to identify nuclei in sections of prostate tissue included in paraffin, fixed with formalin.

p00369A section sectioned with H&amp;E (Hematoxylin and Eosin) and five sections in untained paraffin from 6 individual patients were studied. The H&amp;E sections were evaluated by two pathologists for global quality and

p00370fifteen tumor content Using a conventional multiplex protocol described in EXAMPLES 1-4 above, a quintplex test was carried out that included an evaluation of CK18, AMACR, AR, HMWK and p63 on a single slide of each patient. A staining with DAPI was used to identify nuclei. Positive and negative control prostate tissue samples were made in parallel from a tissue microarray. Three images were acquired from selected regions, processed and subsequently analyzed. Data were exported and quantitative measures associated with individual images.

p00371All samples from the six patients contained varying degrees of tumor with associated benign elements and PIN. The overall quality of the sectioned material was acceptable and all samples were tested with the M-Plex quintplex. Triplicate images of each section of prostate tissue were acquired. Images were processed

p0037225 Individual grayscale in tiff format using spectral imaging software and then analyzed with immunofluorescent algorithms to generate quantitative characteristics. About 90 individual features were generated using image analysis scripts. The characteristics represent various phenotypic characteristics of cellular compartments and their association with a specific biomarker. For example, the antigens / biomarker in question are interrogated based on their cellular distribution as well as the global mean and standard deviation with respect to their intensity (quantity) that is derived from pixel levels (px). The individual scripts for the quintplex assay have been previously normalized to justify variations with respect to tissue thickness, variability in fixative penetration, and antigen quality / access. As a means of illustration, two of the six patients will be analyzed in the following sections.

p0037335 The acquired images of the test tissue samples were evaluated based on a review of the segmented images (Figure 11A; note the color key for specific classification) and scale grays for AR (Figure 11B) and AMACR (Figure 11C; NS refers to the non-specific binding of AMACR to the stroma).

p00374For patient ID 4754-2, the average intensity of AR present within epithelial cells that are positive for AMACR was 0.45 versus 0.43 for cells negative for AMACR, illustrating that, even though there are m With AMACR positive glands present, the average AR intensity within the AMACR positive group is low when compared to the AMACR negative cell population. In addition, the average amount of AR intensity in the stroma was 3.09, the relative area of ​​epithelial nuclei that are positive for AR and

p00375Four. Five positive for AMACR was 0.20, the relative area of ​​all epithelial nuclei that are positive for AR was 0.61 and finally the overall intensity of AMACR was 324,849 pixels. Imaging characteristics results define subtle differences between regions of selected interest, cell types and their associated antigens; allowing these differences to be quantified and then included within predictive models or evaluated individually with respect to outcome / response. For the construction of models, specific characteristics are evaluated with respect to a result and their level of precision is evaluated through a confidence interval. The characteristics are initially screened within the context of a training set and then validated in an external cohort for confirmation.

p00376This study confirms the ability to apply the quintplex multiplex assay on tissue sections included in

p0037755 paraffin, fixed with external formalin. The trial was successful in the samples of the 6 r patients, with complete acquisition of images, processing and generation of quantitative characteristics that assess the levels and intensity of the androgen receptor and AMACR in individual tissue samples.

p00378In addition, quintplex was performed in LNCaP and PC3 fixed with formalin and included in paraffin that are known from numerous publications that show both high (LNCaP) and low (PC3) levels of AR expression, respectively. The association of a quantitative value to the AR content within these cell lines is the first step towards understanding RA modulation and the impact on downstream effector molecules as demonstrated by the reduction AMACR within PC3 cells. These in vitro strategies are the first step towards examining the response of RA to a drug (ie androgen deprivation therapy 65 (ADT), histone deacetylase inhibitors, HDAC)) and can be prolonged f Easily to the patient's clinical samples including needle aspirates, biopsy samples to determine the response (on the target), the assessment and the

p00379efficacy of a drug.

EXAMPLE 7: MULTIPLEX DETECTION OF CD4, CD8, CD25, CD69 AND CD86

p003815 The purpose of this study was to develop the necessary immunofluorescent Multiplex (M-Plex) assays for the proposed CD4, CD8, CD25, CD69 and CD86 plus CK18. The CK18 is retained within the two final m-plex assays to identify tissue compartments (epithelial versus stroma) for the development of a quantitative script. This process involves the identification of appropriate commercial sources for all reagents, test development including titration, selection of Alex fluorochrome and analysis using both

p0038210 samples of non-prostate control tissue. The objective was to complete the development of both simplex and M-plex tests for each of the markers and acquire images that can be used later for the development of a quantitative script.

p00383Several commercial sources for the specific antigens / antibodies that were included in the development of the 15 M-plex assays (see Table 1).

p00384Table 1

<dl><dt>Antibody </dt><dd>Provider Catalog No. Clone Isotype Dilution </dd></dl>

<dl><dt>CK-18 (R) </dt><dd>CalBiochem AP1021 synthetic peptide RIGG 1: 1250 </dd></dl>

<dl><dt>CD4</dt><dd> Vector Labs VP-C318 1F6 MIgG1 1:10 </dd></dl>

<dl><dt>CD8</dt><dd> Vector Labs VP-C325 1A5 MIgG1 1:10 </dd></dl>

<dl><dt>CD25 </dt><dd>LabVision MS-203-P1 4C9 MIgG1 1: 200 </dd></dl>

<dl><dt>CD69 </dt><dd>BioLegend 310902 FN50 MIgG1 1:10 </dd></dl>

<dl><dt>CD86 </dt><dd>GeneTex 74653 BU63 MIgG1 1:10 </dd></dl>

p00385Using a series of control tissue samples including tonsils, lymph node and spleen were assessed

p00386twenty each of the individual antibodies and were evaluated by the background pathologist, and specificity / sensitivity of the signal based on the distribution and the cellular location. The antibodies are each tested individually in a simplex IF format and then rapidly advanced to the m-plex assay according to the methods outlined below.

25 Quantitative immunofluorescence

p00387Deparaffinization and rehydration of tissue samples were performed by conventional procedures in a Leica 5020 self-incinement apparatus. Antigen recovery was carried out by boiling the slides in a microwave oven for 7.0. minutes in Reveal 1X solution. The slides were allowed to cool for 20

p0038830 minutes at room temperature and then washed twice for three minutes in PBS.

p00389All tissue samples were stained at room temperature in a Nemesis 7200 automated slide staining apparatus from BioCare Medical. Tissue samples were subjected to the following stages of prehybridization treatment. To help penetrate tissue cell structures, samples were incubated.

p0039035 in PBT (PBS + 0.2% Triton-X 100) for thirty minutes, followed by a three minute rinse in TBS. To help reduce autofluorescence in the tissue, the samples were incubated in 1% HCl in 70% EtOH for twenty minutes, followed by a three minute rinse in TBS. Blocking of non-specific binding sites was performed by incubating the slides in blocking reagent (PBT containing 1.0 mg / ml BSA) for twenty minutes. No washes were performed between the blocking stage and the subsequent hybridization stage.

p0039140 For the final triplex I multiplex, a 1: 200 dilution of CD25 (4C9) in blocking reagent was prepared. For the final duplex multiplex, a 1:10 dilution of CD8 (1A5) was prepared in blocking reagent. Approximately 400.0 μl of the appropriate antibody was applied to the tissue sample, and the antibodies and tissue samples were allowed to hybridize for one hour. Hybridization was followed by a three minute rinse on TBS.

p00392Four. Five The triplex multiplex was marked with Zenon Alexa Fluor of mouse 532, diluted in blocking reagent at twice the concentrations recommended by the manufacturer (dilution 1:50). The duplex multiplex was marked with Zenon Alexa Fluor of mouse 594, diluted as described. Approximately 400.0 μl of the appropriate label were applied to the tissue samples, and the tissue samples were incubated for thirty minutes. The marking reaction will

p00393fifty followed a three minute rinse on TBS.

p00394Tissue samples for both multiplex assays were then treated with a second round of hybridization and labeling. For triplex, a 1:10 dilution of CD69 (FN50) in blocking reagent was prepared. For the duplex, a cocktail of Cytokeratin 18 (CK-18) was prepared at a dilution 1: 1,000 and CD86 (BU63) at a dilution 1:10

p0039555 in blocking reagent. Approximately 400.0 μl of the appropriate antibody cocktail was applied to the tissue sample, and the antibodies and tissue samples were allowed to hybridize for one hour. Hybridization was followed by a three minute rinse on TBS.

p00396For the second marking stage, the triplex was marked with Zenon Alexa Fluor of mouse 555, diluted as it has been

p003975 described The duplex was marked with a cocktail of Zenon Alexa Fluor of mouse 555 and Zenon Alex Fluor of rabbit 647, diluted as described. Approximately 400.0 µl of the appropriate brand or tags were applied to the tissue samples, and the tissue samples were incubated for thirty minutes. The marking reaction was followed by a three minute rinse in TBS.

p00398Tissue samples for the triplex were then treated with a third round of hybridization and labeling. The duplex was advanced to the fixation stage described below. For triplex, a cocktail of Cytokeratin 18 (CK-18) was prepared at a 1: 1,000 dilution and CD4 (1F6) at a 1:10 dilution in blocking reagent. Approximately 400.0 μl of the antibody cocktail was applied to the tissue sample, and the antibodies and tissue samples were allowed to hybridize for one hour. Hybridization was followed by a three-minute rinse in

p00399fifteen TBS

p00400For the third marking, the triplex was marked with a cocktail of Zenon Alexa Fluor of mouse 594 and Zenon Alex Fluor of rabbit 647, diluted as described. Approximately 400.0 μl of the brand cocktail was applied to the tissue samples, and the tissue samples were incubated for thirty minutes. The marking reaction was followed by two three-minute rinses in TBS.

p00401A fixation step was performed by incubating the samples in 10% formalin for 10 minutes, followed by two rinses of three minutes each in TBS. The slides were then removed from the Nemesis 7200 automated slide staining apparatus from BioCare Medical.

p0040225 The Molecular Probe SlowFade Gold fluorescent staining reagent with DAPI (approximately 25.0 μl) was applied to the samples, which were then covered with coverslips. The samples were stored at -20 ° C until the analysis could be performed.

p00403The five antibodies were divided between two M-plex assays due to the common isotype of available reagents. Antibodies were first developed and analyzed in a simplex immunofluorescent assay using samples of lymphoid tissue (i.e. spleen, tonsil, lymph node) where it was anticipated that all markers would be present. The results of the simplex trial were successful in that each of the markers identified subsets of lymphocytes that matched the cell compartment (i.e. cell membrane) and were identified

p0040435 within intermediate follicles and / or germ centers. The original simplex experiments were then grouped in M-plex formats that were applied in similar control tissues as well as in domestic prostate tissue samples where lymphocytic infiltrates were identified by H&amp;E evaluation. . Examples of the data derived from these original M-plex assays are illustrated in Figure 13A and 13B. As demonstrated, two M-plex trials were developed. M-plex I is a duplex containing CD4 and CD8 (+ CK18) while a second M-plex II was a triplex containing CD25, 69 and 86 (+ CK18).

p00405Subsequent to the development of the previous M-plex formats, two additional M-plex combinations were generated to evaluate selected subsets of T cells within given tissue sections (for example activated T cells - CD4 + CD69 + T cells) mixed: CD4 + and CD25 + The new M-plex formats were made up of

p00406Four. Five a duplex containing CD8 and 86 and a triplex containing CD4, 25 and 69. These new M-plex tests were tested on samples of splenic tissue and the tonsil and are illustrated in Figure 14A and 14B. These are the m-plex formats that will be applied in the prostatectomy samples treated by the patient when they arrive in Aureon.

p00407For each M-plex experiment, a spectral profile is identified that identifies the individual Alexa Fluor emission profile for signal quality, differentiation from other profiles, intensity, and evaluation of the Initial quality for quantification for script development (signal / noise). Alexa fluorochromes are selected based on their spectral profiles to preserve the purity of the signal with the minimum amount of overlap. As illustrated in Figure 14B, the spectral profiles for the M-plex duplex identify individual antigens / antibodies, as well as tissue autofluorescence. A similar analysis was also carried out to

p0040855 the m-plex triplex.

p00409Through an evaluation of the localization within lymphoid follicles and individual lymphoid tissue types, the present antibodies within these M-plex formats were able to selectively identify lymphocyte populations. Grayscale images (as outlined in the figures) will be used for the development of algorithms and scripts to successfully quantify these antigens in tissue sections.

p00410The development of both IF simplex and IF M-plex assays for the evaluation of the 5 antibodies / antigens - CD4, CD8, CD25, CD69 and CD86 has been successfully completed. These 5 antibodies have been coupled (in M-plex formats

p0041165 specific) to maximize overlap for script development so that subsets of activated lymphocyte cell populations.

p00412EXAMPLE 8: MICROMATRIZ OF PEPTIDES TO MEASURE THE DYNAMIC INTERVAL AND THE QUANTIFICATION OF THE DETECTION OF THE DIANA.

p004135 Peptides are short amino acid sequences (usually 10 to 30 residues) that are often used as immunogens for the production of antibodies. Since they can be synthesized in vitro, purified peptides can be produced in large quantities. Typically, peptide microarrays are made up of peptides covalently bonded to a glass surface. If an antibody recognizes a specific peptide sequence, a peptide matrix can be used in this way to measure the dynamic range (the interval between the lowest and the highest concentration of the target) that can be detected. with that method. Additionally, since a given peptide concentration in the microarray is linked to a specific fluorescent intensity, the unknown target concentration can be quantitatively evaluated.

p00414A peptide microarray was designed that contained a peptide that is specifically recognized by NeoMarkers

p00415fifteen (Lab Vision Corp.) androgen receptor antibody NM-MS443 (Peptide sequence: STEDTAEYSPFKGGYTK). Additionally, the microarray contained a positive control peptide (Sequence: NFLMDNA (pY) FCEADAKKK) that is specifically detected by an anti-phospho-Tyrosine antibody (Sigma) and a negative control peptide that does not It is related to no known protein (Sequence: SFYGATGESYDPTTKEK). All peptides were located in triplicate in the following concentrations: 100, 500, 250, 125, 62.5, 31.25, 15.63, 7.81, 3.91 and 1.95 micromolar. The microarray was manufactured by JPT Peptide Technologies, Germany. The peptide microarray staining was performed as follows:

p004161.) Attach the camera to the slide of the peptide microarray

p0041725 Each adhesive frame was intercalated between a thin and a thick polyester sheet (while the thin sheet completely covers the adhesive frame, the thick sheet has a removed central part). The thick polyester was removed, leaving the blue frame attached to the thin sheet. Next, the blue adhesive frame on the thin polyester sheet was placed on the glass slide while avoiding contact with the surface presenting the peptide. The blue frame was pressed firmly down without trapping air under the adhesive. The second thin polyester sheet was then removed from the top of the blue adhesive frame. The blue March alone remained attached to the slide.

p004182.) Prepare the test solution with primary

p0041935 A 1.0 µg volume of the mouse monoclonal AR antibody (NeoMarkers, Lab Vision Corp.) was adjusted to 20 µl of 1x PBS buffer in an Eppendorf tube. To experiment with primary antibody labeling with a fluorophore, 5 μl of Zenon 555 Alexa Flour mouse IgG1 was added below. The solution was pipetted up and down to mix and incubate for 10 minutes. As a control, 7 μg / ml of FITC-labeled phospho-Tyrosine antibody (Sigma) was diluted in the tube together with additional AR antibody at its working dilution for a final assay solution volume of 330 μl. The solution was vortexed to ensure mixing, and starting from one end of the adhesive marking, the entire volume was pipetted over the entire surface of the slide.

p004203.) Incubation

p00421Four. Five The peptide microarray was then incubated for 4 hours at 4 ° C in a moist chamber protected from light.

p004224.) Remove the incubation chamber

p00423The test solution was decanted and the incubation chamber is carefully removed by holding the slide with one hand and gently pulling up one edge of the blue adhesive frame. The blue frame rose from the edges of the slide carefully to avoid any adhesive remaining, which would alter the following washes.

p0042455 5.) Removal of unbound antibody

p00425Excess antibody was removed by washing the slide 5 times for 5 minutes with double distilled filtered water. The slide was then washed 5 times for 5 minutes in methanol.

p004266.) Assembly

p00427After the slide was air dried (free of dust particles), 100 µl of AntiFade solution containing nuclear counterstain was added and then covered with a coverslip and prepared for the

p0042865 Image acquisition.

p004297.) Acquisition of images

p00430Peptide matrices were placed in a 90i automated fluorescence microscope. The

p004315 points moving the yx axes of the microscope stage. The exposure time of the image was adjusted within the camera to the highest possible brightness level without causing overexposure. The images were acquired with the Nikon 1200DXM CCD camera or a comparable system (alternatively a spectral imaging camera could be used for advanced spectral separation of fluorescent dyes). The images were saved in tiff format and subjected to quantitative analysis of the image. Finally, the brightness values ​​were represented

p0043210 graphically against peptide concentrations to visualize the dynamic range of detection of the target. Some antigens are expressed only in secondary amounts in the tissue of interest. In order to achieve the detection of these targets, said method can be modified as follows: After adding the primary antibody and removing the unbound antibody by a washing step, it is added also a species specific secondary antibody. For example, if the primary antibody is mouse IgG, an antibody would be added.

p00433fifteen Goat anti-mouse in the second stage. After the species-specific antibody has been removed (in this case the goat anti-mouse IgG), the secondary antibody will be detected with fluorescently labeled Fab. Since more than one goat anti-mouse antibody can bind to each mouse IgG, more fluorescent Fab fragments will bind to the detection complex.

p00434twenty EXAMPLE 9: AMPLIFICATION OF THE SIGNAL

p00435Some antigens are expressed only in secondary amounts in the tissue of interest. In order to achieve the detection of these targets, the simplex and multiplex methods of the invention are modified as follows: after adding the primary antibody and eliminating the unbound antibody by a washing stage,

p0043625 a species-specific secondary antibody is added. For example, if the primary antibody is mouse IgG, a goat anti-mouse antibody would be added in the second stage. After the species-specific antibody is removed (in this case the goat anti-mouse IgG), the secondary antibody will be detected with fluorescently labeled Fab. Since more than one goat anti-mouse antibody can bind to each mouse IgG, more fluorescent Fab fragments will bind to the detection complex.

p0043730 It has been found that the androgen receptor (RA) is an important biomarker for the evaluation of prostate cancer tissue. To increase the intensity of the signal obtained to measure the qualitative and quantitative distribution of these markers in paraffin-embedded tissue sections, fixed with formalin or tissue, the following method was used, were detected as follows way:

p0043835 1) Antigen recovery (in Reveal solution)

p00439For antigen recovery, tissue sections or TMA were boiled in Reveal 1X solution (BioCare Medical) (10 cc) in a high-power microwave oven calibrated for 7½ minutes and then

p0044040 They are allowed to cool for 20 minutes. After cooling, the slides were washed 3 times for 5 minutes in phosphate buffered saline (PBS).

p004412) Fabric permeabilization

p00442Four. Five Tissue samples were subsequently permeabilized in PBS containing 0.2% Triton-X (PBT) for 30 minutes at room temperature.

p004433) Elimination of autofluorescence

p00444fifty Autofluorescence was reduced by incubating the slides in 1% HCl / 70% EtOH for 20 minutes at room temperature. The slides were then rinsed 3 times for 5 minutes in PBS.

p004454) Blocking with nonspecific IgG

p0044655 The non-specific binding of antibody or Fab fragment was blocked by incubation with 0.5 μg / ul of BSA in PBT for 20 minutes in a moist chamber. The slides were not cleared before the addition of the primary antibody to the tissue sample.

p004475) Incubation of untreated primary antibody in tissue

p0044860 Monoclonal androgen receptor antibody of untreated mouse was incubated in the tissue for 1 hour at room temperature in a moist chamber.

p004496) Removal of unbound antibody

p00450Excess antibody was removed by washing the slides 2 times for 10 minutes in PBT followed by 3 times for 5 minutes in PBS. 5 7) Incubation with goat anti-mouse IgG secondary antibody

p00451Goat anti-mouse IgG was diluted in PBT and incubated in the tissue for 20 minutes at room temperature in a moist chamber. 10 8) Elimination of unbound goat anti-mouse IgG

p00452Excess antibody was removed by washing the slides 2 times for 10 minutes in PBT followed by 3 times for 5 minutes in PBS. 15 9) Incubation with fluorescently labeled Fab

p00453Fab-specific mouse fragment marked with Alexa 568 was added to the slide and incubated for 30 minutes at room temperature in a moist chamber. 20 9.) Elimination of unbound Fab

p00454Unbound Fab fragment was removed by washing the slides 2 times for 10 minutes in PBT followed by 3 times for 5 minutes in PBS. 25 10) Fixation

p00455The tissue was fixed in 10% formalin for 10 minutes. The slides were rinsed 2 times for 5 minutes in PBS. 30 11) Assembly

p00456After adding 100 µl of AntiFade solution that contained nuclear counterstain, the slides were covered with coverslips and prepared for image acquisition. 35 12) Acquisition of images

p00457The samples were placed in a 90i automated fluorescence microscope. The regions of interest were identified by moving the yx axes of the microscope stage. The exposure time of the image was adjusted

p0045840 inside the camera at the highest possible brightness level without causing overexposure. The images were acquired with the Nikon 1200DXM CCD camera or a comparable system (alternatively a spectral imaging camera could be used for advanced spectral separation of fluorescent dyes). The images were saved in tiff format and subjected to quantitative analysis of the image.

p00459Four. Five EXAMPLE 10: DETECTION REAGENTS

p00460The following list of antibodies have been successfully immunofluorescently labeled with the secondary labeling technique that uses Zenon ™ Alexa Fluor antibody labeling after the antibody has hybridized to the tissue source. These are antibodies suitable for use in the simplex / multiplex methods

p00461fifty of the invention.

TABLE 2 ANTIBODY COMPA A SOURCE N ° OF ISOTIPO CATALOG

p00462Actin Zymed Laboratories 18-0106 phospho-AKT mouse Abcam Incorporated ab4802 rabbit IgG AMACR Zeta Corporation Z2001 IgG rabbit Androgen receptor NeoMarkers (Lab Vision Corp.) NM-MS443 IgG1 mouse Bax Abcam Incorporated ab7977 Rabbit IgG Bcl-2 DakoCytomation M0887 IgG1 of mouse Caspasa 3 (activated) Chemicon International, Inc. ab3623 Rabbit IgG CD-34 DakoCytomation M7165 IgG1 for mouse CD-45 DakoCytomation M0855 IgG1 for mouse Cytokeratin-14 Vector Laboratories VP-C410 IgG1 for mouse Cytokeratin-18 Vector Laboratories VP-C414 IgG1 for mouse Cyclin D1 BioCare Medicals CP236B rabbit IgG Cyclin E Vector Laboratories VP-C396 IgG2a mouse

<dl><dt>e-caderina </dt><dd>Ventana Medical Systems, Inc. 760-2830 Mouse IgG1 </dd></dl>

<dl><dt>EGFR </dt><dd>DakoCytomation K1492 Mouse IgG </dd></dl>

<dl><dt>pEGFR (YI068) </dt><dd>Abcam Incorporated ab5644 Rabbit IgG </dd></dl>

<dl><dt>EMA </dt><dd>DakoCytomation M0613 Mouse IgG1 </dd></dl>

<dl><dt>phospho-ERK </dt><dd>Cell Signaling Technologies ab4376 Rabbit IgG </dd></dl>

<dl><dt>EZH2 </dt><dd>Zymed Laboratories 18-7395 Rabbit IgG </dd></dl>

<dl><dt>Her-2 / Neu </dt><dd>DakoCytomation A0485 Rabbit IgG </dd></dl>

<dl><dt>KDR </dt><dd>Upstate 07-158 Rabbit IgG </dd></dl>

<dl><dt>fopsfo-KDR </dt><dd>Upstate 07-374 Rabbit IgG </dd></dl>

<dl><dt>Ki-67 </dt><dd>Ventana Medical Systems, Inc. 290-2910 Mouse IgG1 </dd></dl>

<dl><dt>phospho-mTOR </dt><dd>Cell Signaling Technologies ab2971 Rabbit IgG </dd></dl>

<dl><dt>p27 </dt><dd>Vector Laboratories VP-P951 Mouse IgG2a </dd></dl>

<dl><dt>p53 </dt><dd>DakoCytomation M7001 Mouse IgG2b </dd></dl>

<dl><dt>p70 S6 kinase </dt><dd>Cell Signaling Technologies ab9430 Rabbit IgG </dd></dl>

<dl><dt>PI3 kinase </dt><dd>Cell Signaling Technologies ab3821 Rabbit IgG </dd></dl>

<dl><dt>PSA </dt><dd>Ventana Medical Systems, Inc. 760-2506 Rabbit IgG </dd></dl>

<dl><dt>PSMA </dt><dd>Annogen Y-PSMA-1 Mouse IgG2a </dd></dl>

<dl><dt>pTEN </dt><dd>NeoMarkers (Lab Vision Corp.) NM-MS1797 Mouse IgG1 </dd></dl>

<dl><dt>α-tubulin </dt><dd>Zymed Laboratories 18-0092 Mouse IgG1 </dd></dl>

<dl><dt>VEGF </dt><dd>Abcam Incorporated ab1316 Mouse IgG1</dd></dl>