Polynucleotides and polypeptide sequences involved in the process of bone remodeling
Abstract
Pharmaceutical composition for use in modulating the differentiation of osteoclasts in vivo, in the prevention of osteopathies or in the treatment of osteopathies comprising an isolated polypeptide comprising a sequence selected from the group consisting of: a) SEQ ID No. 48, b) a polypeptide encoded by SEQ ID No. 1, c) a fragment of any of a) or b) that is capable of favoring or inhibiting osteoclast differentiation, and d) an analogue of any of a) or b) that is capable of favoring or inhibiting the differentiation of osteoclasts, wherein said analogue has at least 90% sequence similarity to the a) or b) polypeptide, and a pharmaceutically acceptable carrier.

Term
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Projected expiry 13 February 2027, counted from filing; an application has no term until it is granted.
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16 claims: 8 independent, 8 dependent
- 1ES 2 397 441 T3 REIVINDICACIONES 1. Composición farmacéutica para uso en la modulación de la diferenciación de los osteoclastos in vivo, en la prevención de osteopatías o en el tratamiento de osteopatías que comprende un polipéptido aislado que comprende una secuencia seleccionada del grupo que consiste en:a) SEQ ID n.° 48, b) un polipéptido codificado por SEQ ID n.° 1, c) un fragmento de cualquiera de a) o b) que es capaz de favorecer o inhibir la diferenciación de los osteoclastos, y d) un análogo de cualquiera de a) o b) que es capaz de favorecer o inhibir la diferenciación de los osteoclastos, en donde dicho análogo tiene al menos una similitud de secuencia del 90% con el polipéptido de a) o b), y un vehículo farmacéuticamente aceptable.
- 2Composición farmacéutica para uso en la modulación de la diferenciación de los osteoclastos in vivo, en la prevención de osteopatías o en el tratamiento de osteopatías, en donde la composición farmacéutica comprende un polinucleótido aislado seleccionado del grupo que consiste en:a) un polinucleótido que comprende la SEQ ID n.° 1, b) un polinucleótido que comprende el marco abierto de lectura de los nucleótidos 150 a 1136 de SEQ ID n.° 1, c) un polinucleótido que comprende una secuencia idéntica a a) al menos al 80% a lo largo de toda la longitud del polinucleótido, d) un polinucleótido que comprende una secuencia idéntica a b) al menos al 90% a lo largo de toda la longitud del polinucleótido, e) un polinucleótido que comprende una secuencia complementaria a a) al menos al 80% a lo largo de toda la longitud del polinucleótido, y f) un polinucleótido que comprende una secuencia complementaria a b) al menos al 90% a lo largo de toda la longitud del polinucleótido, y un vehículo farmacéuticamente aceptable.
- 3Polinucleótido aislado seleccionado del grupo que consiste en:a) un polinucleótido que comprende la SEQ ID n.° 1, b) un polinucleótido que comprende el marco abierto de lectura de los nucleótidos 150 a 1136 de SEQ ID n.° 1, c) un polinucleótido que comprende una secuencia idéntica a a) al menos al 80% a lo largo de toda la longitud del polinucleótido, d) un polinucleótido que comprende una secuencia idéntica a b) al menos al 90% a lo largo de toda la longitud del polinucleótido, e) un polinucleótido que comprende una secuencia complementaria a a) al menos al 80% a lo largo de toda la longitud del polinucleótido, y f) un polinucleótido que comprende una secuencia complementaria a b) al menos al 90% a lo largo de toda la longitud del polinucleótido, para el uso en la modulación de la diferenciación de los osteoclastos in vivo, en la prevención de osteopatías o en el tratamiento de una osteopatía.
- 4Polinucleótido aislado para uso en la modulación de la diferenciación de los osteoclastos in vivo, en la prevención de osteopatías o en el tratamiento de una osteopatía de acuerdo con la reivindicación 3, en donde la osteopatía se selecciona del grupo que consiste en la osteoporosis, osteopenia, osteomalacia, hiperparatiroidismo, hipertiroidismo, hipogonadismo, tirotoxicosis, mastocitosis sistémica, hipofosfatasia adulta, hipercorticalismo, osteogénesis imperfecta, enfermedad de Paget, enfermedad/síndrome de Cushing, síndrome de Turner, enfermedad de Gaucher, síndrome de Ehlers-Danlos, síndrome de Marfan, síndrome de Menkes, síndrome de Fanconi, mieloma múltiple, hipercalciemia, hipocalciemia, artritis, periodontitis, raquitismo, fibrogénesis imperfecta ósea, trastornos osteoescleróticos y daño ocasionado por procesos inflamatorios mediados por macrófagos. 104 ES 2 397 441 T3
- 5Polipéptido aislado que comprende una secuencia seleccionada del grupo que consiste en:a) SEQ ID n.° 48, b) un polipéptido codificado por SEQ ID n.° 1, c) un fragmento de cualquiera de a) o b) que es capaz de favorecer o inhibir la diferenciación de los osteoclastos, y d) un análogo de cualquiera de a) o b) que es capaz de favorecer o inhibir la diferenciación de los osteoclastos, en donde dicho análogo tiene una similitud de secuencia de al menos el 90% con el polipéptido de a) o b), para el uso en la modulación de la diferenciación de los osteoclastos in vivo, en la prevención de osteopatías o en el tratamiento de una osteopatía.
- 6Polipéptido aislado para uso en la modulación de la diferenciación de los osteoclastos in vivo, en la prevención de osteopatías o en el tratamiento de una osteopatía de acuerdo con la reivindicación 5, en donde la osteopatía se selecciona del grupo que consiste en osteoporosis, osteopenia, osteomalacia, hiperparatiroidismo, hipertiroidismo, hipogonadismo, tirotoxicosis, mastocitosis sistémica, hipofosfatasia adulta, hipercorticalismo, osteogénesis imperfecta, enfermedad de Paget, enfermedad/síndrome de Cushing, síndrome de Turner, enfermedad de Gaucher, síndrome de Ehlers-Danlos, síndrome de Marfan, síndrome de Menkes, síndrome de Fanconi, mieloma múltiple, hipercalciemia, hipocalciemia, artritis, periodontitis, raquitismo, fibrogénesis imperfecta ósea, trastornos osteoescleróticos y daño ocasionado por procesos inflamatorios mediados por macrófagos.
- 7Compuesto capaz de interferir con la actividad o expresión de un polipéptido seleccionado entre la SEQ ID n.° 48 o un polipéptido codificado por la SEQ ID n.° 1 para uso en la modulación de la diferenciación de los osteoclastos in vivo, en la prevención de osteopatías o en el tratamiento de una osteopatía, en donde dicho compuesto se selecciona del grupo que consiste en anticuerpos o fragmentos de fijación a antígeno del mismo que se fijan específicamente a un polipéptido seleccionado entre SEQ ID n.° 48 o a un fragmento del mismo, y los siRNA o shRNA que inhiben específicamente la actividad o la expresión de un polipéptido codificado por la SEQ ID n.° 1.
- 8Compuesto para uso en la modulación de la diferenciación de los osteoclastos in vivo, en la prevención de osteopatías o en el tratamiento de una osteopatía de acuerdo con la reivindicación 7, en donde dicho anticuerpo es un anticuerpo monoclonal, anticuerpo policlonal, anticuerpo quimérico o un anticuerpo humanizado o un fragmento de fijación a antígeno del mismo.
- 9Compuesto para uso en la modulación de la diferenciación de los osteoclastos in vivo, en la prevención de osteopatías o en el tratamiento de una osteopatía de acuerdo con la reivindicación 7, en donde dicho fragmento de fijación a antígeno es un fragmento Fab, un fragmento F(ab')2 o un fragmento Fv.
- 10Compuesto para uso en la modulación de la diferenciación de los osteoclastos in vivo, en la prevención de osteopatías o en el tratamiento de una osteopatía de acuerdo con una cualquiera de las reivindicaciones 7 a 9, en donde la osteopatía se selecciona del grupo que consiste en osteoporosis, osteopenia, osteomalacia, hiperparatiroidismo, hipertiroidismo, hipogonadismo, tirotoxicosis, mastocitosis sistémica, hipofosfatasia adulta, hipercorticalismo, osteogénesis imperfecta, enfermedad de Paget, enfermedad/síndrome de Cushing, síndrome de Turner, enfermedad de Gaucher, síndrome de Ehlers-Danlos, síndrome de Marfan, síndrome de Menkes, síndrome de Fanconi, mieloma múltiple, hipercalciemia, hipocalciemia, artritis, periodontitis, raquitismo, fibrogénesis imperfecta ósea, trastornos osteoescleróticos y daño ocasionado por procesos inflamatorios mediados por macrófagos.
- 11Utilización de un polinucleótido aislado, polipéptido aislado o compuesto como el definido en cualquiera de las reivindicaciones 3, 5, 7, 8 o 9 en la fabricación de un medicamento para la modulación de la diferenciación de los osteoclastos in vivo, para la prevención de osteopatías o para el tratamiento de una osteopatía.
- 12Utilización de acuerdo con la reivindicación 11, en donde la osteopatía se selecciona del grupo que consiste en osteoporosis, osteopenia, osteomalacia, hiperparatiroidismo, hipertiroidismo, hipogonadismo, tirotoxicosis, mastocitosis sistémica, hipofosfatasia adulta, hipercorticalismo, osteogénesis imperfecta, enfermedad de Paget, enfermedad/síndrome de Cushing, síndrome de Turner, enfermedad de Gaucher, síndrome de Ehlers-Danlos, síndrome de Marfan, síndrome de Menkes, síndrome de Fanconi, mieloma múltiple, hipercalciemia, hipocalciemia, artritis, periodontitis, raquitismo, fibrogénesis imperfecta ósea, trastornos osteoescleróticos y daño ocasionado por procesos inflamatorios mediados por macrófagos.
- 13Utilización de al menos un polinucleótido seleccionado del grupo que consiste en:a) un polinucleótido que comprende la SEQ ID n.° 1;b) un polinucleótido que comprende el marco abierto de lectura de los nucleótidos 150 a 1136 de la SEQ ID n.° 1;c) un polinucleótido que comprende una secuencia idéntica a a) al menos al 80% a lo largo de toda la longitud del polinucleótido;105 ES 2 397 441 T3 d) un polinucleótido que comprende una secuencia idéntica a b) al menos al 90% a lo largo de toda la longitud del polinucleótido, e) un polinucleótido que comprende una secuencia complementaria a a) al menos al 80% a lo largo de toda la longitud del polinucleótido, y f) un polinucleótido que comprende una secuencia complementaria a b) al menos al 90% a lo largo de toda la longitud del polinucleótido, en el diagnóstico in vitro de una osteopatía.
- 14Utilización de acuerdo con la reivindicación 13, en donde la osteopatía se selecciona del grupo que consiste en osteoporosis, osteopenia, osteomalacia, hiperparatiroidismo, hipertiroidismo, hipogonadismo, tirotoxicosis, mastocitosis sistémica, hipofosfatasia adulta, hipercorticalismo, osteogénesis imperfecta, enfermedad de Paget, enfermedad/síndrome de Cushing, síndrome de Turner, enfermedad de Gaucher, síndrome de Ehlers-Danlos, síndrome de Marfan, síndrome de Menkes, síndrome de Fanconi, mieloma múltiple, hipercalciemia, hipocalciemia, artritis, periodontitis, raquitismo, fibrogénesis imperfecta ósea, trastornos osteoescleróticos y daño ocasionado por procesos inflamatorios mediados por macrófagos.
- 15Procedimiento para identificar un compuesto inhibidor capaz de afectar la expresión o la función de un polipéptido de SEQ ID n.° 48, o un polipéptido codificado por la SEQ ID n.° 1, en donde el procedimiento comprende poner en contacto dicho polipéptido o una célula que expresa dicho polipéptido con un compuesto candidato y medir la expresión o la función de dicho polipéptido, por medio de lo cual una reducción de la capacidad del polipéptido para favorecer la diferenciación de los osteoclastos identifica positivamente un compuesto inhibidor adecuado.
- 16Procedimiento de acuerdo con la reivindicación 15, que además comprende una etapa de inducción de la diferenciación de los osteoclastos cuando se pone en contacto dicho polipéptido o célula con un compuesto candidato. 106
Independent claims16
811 paragraphs in 91 sections, as filed
ES 2 397 441 T3
DESCRIPTION
Polynucleotide and polypeptide sequences involved in the bone remodeling process.
Field of the invention
The invention relates, in part, to unique and newly identified genetic polynucleotides that are involved in the process of bone remodeling; variants and derivatives of the polynucleotides and the corresponding polypeptides; uses of polynucleotides, polypeptides, variants, and derivatives; methods and compositions for the amelioration of symptoms caused by bone remodeling disorders, including but not limited to, osteoporosis, osteopenia, osteomalacia, hyperparathyroidism, hypothyroidism, hyperthyroidism, hypogonadism, thyrotoxicosis, systemic mastocytosis, adult hypophosphatasia, hypercorticalism, osteogenesis imperfection , Paget's disease, Cushing's disease / syndrome, Turner's syndrome, Gaucher's disease, Ehlers-Danlos syndrome, Marfan syndrome, Menkes syndrome, Fanconi syndrome, multiple myeloma, hypercalcemia, hypocalcemia, arthritis, periodontitis, rickets (including hypophosphatemic rickets linked to the X chromosome, and vitamin D-dependent types I and II), fibrogenesis imperfecta bone marrow, osteosclerotic disorders such as pycnodysostosis, and damage caused by macrophage-mediated inflammatory processes.
In particular, this invention relates to polynucleotide expression profiling in active osteoclasts, the isolation and identification of polynucleotides, polypeptides, variants and derivatives involved in osteoclast activity, validation of the identified polynucleotides to see if they are possibly therapeutic targets , and use of polynucleotides, polypeptides, variants and derivatives for the amelioration of disease states and research purposes, as well as for the diagnosis of pathological states or for the predisposition to suffer them.
Background of the invention
Bone is a dynamic connective tissue comprised of populations of cells that perform different functions necessary to maintain the structural, mechanical, and biochemical integrity of bone and mineral homeostasis in the human body. The main cell types involved include osteoblasts responsible for bone formation and maintenance of bone mass, and osteoclasts responsible for osteoclasia (bone resorption). Osteoblasts and osteoclasts are involved in a dynamic process called bone remodeling. The development and proliferation of these cells from their progenitors are governed by networks of growth factors and cytokines produced in the bone microenvironment, as well as by systemic hormones. Bone remodeling occurs throughout the individual's life and is necessary for the maintenance of healthy bone tissue and mineral homeostasis. The process remains largely in balance and is governed by a complex interplay of systemic hormones, peptides, and downstream proteins in signaling pathways, local transcription factors, cytokines, growth factors, and matrix remodeling genes.
Any interference or imbalance that arises in the bone remodeling process can lead to osteopathy, so that the most common bone disorders are characterized by a net decrease in bone mass. An important cause of this reduction in bone mass is an increase in the number of osteoclasts and / or their activity. The most common of these diseases, and perhaps the best known, is osteoporosis, which occurs particularly in women after the onset of menopause. In fact, osteoporosis is the most significant underlying cause of bone fractures in middle-aged and elderly women. While there has been much emphasis on estrogen deficiency as a factor in postmenopausal osteoporosis, there is much evidence that remodeling is a locally controlled process that takes place in discrete stretches throughout the skeleton, as described by first time Frost about forty years ago (Frost HM 1964).
Since bone remodeling takes place in discrete stretches, locally produced hormones and enzymes may be more important for the initiation of osteoclasia and the normal remodeling process than systemic hormones. Such local control is mediated by osteoblasts and osteoclasts in the microenvironment in which they operate. For example, osteoclasts adhere to the bone matrix and form independent compartments between themselves and the bone surface, delimited by a sealing zone formed by an actin ring that surrounds the rough or brush border. Many small vesicles carry the enzymes into the bone matrix and take up the partially digested bone matrix. The microenvironment within the seal zone is rich in lysosomal enzymes and highly acidic compared to the normal physiological pH of the body. The brush border membrane also expresses RANK, the RANKL receptor, and the macrophage colony stimulating factor (M-CSF) receptor, both of which are responsible for osteoclast differentiation, as is the calcitonin receptor. it is capable of rapidly inactivating the osteoclast (Baron, R. 2003).
In a complex structure of inhibition and stimulation that is not yet fully understood, growth hormone, insulin-like growth factor 1, sex corticosteroids, thyroid hormone, calcitrophic hormones, such as PTH and prostaglandin E2, various cytokines , such as interleukin-1 β, interleukin 6 and tumor necrosis factor α, and 1,25-dihydroxyvitamin D (calcitriol) act in coordination in the bone remodeling process (Jilka et al., 1992; Poli et al., 1994; Srivastava et al. 1998; de Vemejoul 1996).
Thus, it is reasonable that the unique locales created by these specialized cells are due to the expression of either unique genetic sequences that are not expressed in other tissues, and / or splice variants.
ES 2 397 441 T3 from polynucleotides and polypeptides expressed in other tissues. The isolation and identification of polynucleotides, polypeptides and their specific variants and derivatives of osteoclast activity will allow a clearer understanding of the remodeling process and will offer tissue-specific therapeutic targets for the treatment of pathological states related to bone remodeling.
Many diseases associated with bone remodeling are poorly understood, are generally untreatable, or can only be treated to a limited extent. For example, osteoarthritis is difficult to treat because there is no cure and treatment is focused on relieving pain and preventing deformation of the affected joint. Non-steroidal anti-inflammatory drugs (NSAIDs) are widely used to relieve pain.
Another example is osteoporosis, in which the only drugs currently approved by the FDA for use in the United States are drugs that inhibit osteoclasia that prevent bone loss. Estrogen replacement therapy is an example of an osteoclasia inhibitor drug. Others include alendronic acid (Fosamax, a bisphosphonate-like osteoclasia inhibitor), risedronic acid (Actonel, a bisphosphonate-like osteoclasia inhibitor), raloxifene (Evista, a selective estrogen receptor modulator [SERM, by name in English]), calcitonin (Calxynar, a hormone), and parathyrin / teriparatide (Forteo, a synthetic version of the human hormone, parathyrin, which helps regulate calcium metabolism).
Bisphosphonates such as alendronic acid and risedronic acid are permanently attached to the surface of bone and interfere with osteoclast activity. This allows the osteoblasts to function faster than the rate of resorption. The most common side effects are nausea, abdominal pain, and peristaltic movement disorder. However, alendronic acid has also been reported to cause irritation and inflammation of the esophagus and, in some cases, esophageal ulcers. Risedronic acid is chemically different from alendronic and is also less likely to cause esophageal irritation. However, some foods, calcium, iron supplements, vitamins and minerals, or antacids containing calcium, magnesium, or aluminum can reduce the absorption of risedronic acid, resulting in a loss of efficacy.
The most common side effect of raloxifene and other SERMs (such as tamoxifen) is hot flashes. However, raloxifene and other hormone replacement therapies have been shown to increase the risk of blood clots, including deep vein thrombosis and pulmonary embolism, cardiovascular disease, and cancer.
Calcitonin is not as effective as estrogens and other drugs that inhibit osteoclasia in increasing bone density or strengthening bone. Common side effects of injected or nasal spray calcitonin are nausea and skin irritation. Patients may experience nasal irritation, runny nose, or epistaxis. Injectable calcitonin can cause redness of the skin at the injection site, rash, and skin irritation.
One situation that demonstrates the connection between various disorders or disease states that affect bone remodeling is the use of etidronic acid (Didronel) first authorized by the FDA to treat Paget's disease. Paget's disease is an osteopathy characterized by disorderly and accelerated remodeling of the bone, leading to bone weakness and pain. Didronel has been used for off-label indications and has been shown in some studies to increase bone density in women with osteoporosis after menopause. It has also been found to be effective for the prevention of osteopenia in patients who require long-term steroidal drugs (such as prednisone or cortisone). However, continuous or high-dose use of Didronel can lead to another osteopathy called osteomalacia. Like osteoporosis, osteomalacia can lead to weakening of the bones with an increased risk of fractures. Due to the problem of osteomalacia and there are not yet enough studies on the reduction in the rate of bone fractures, the US FDA has not authorized Didronel for the treatment of osteoporosis.
Treatment of osteoporosis has largely focused on osteoclasia inhibitor drugs that reduce the rate of osteopenia, but new treatments show promise by increasing bone mineral density rather than simply maintaining it or slowing its loss. The first osteoporosis strategies consist largely of candidate drugs from new therapeutic classes, in particular, cathepsin K inhibitors, osteoprotegerin, and calcilytics, as well as new bisphosphonates. Some of them are examples where genomics programs exploiting new drugs are being developed based on a deeper understanding of bone biology and have the potential to change hopes for the treatment of bone disorders in the long term.
Accordingly, there is a need to better understand the bone remodeling process and to provide new compositions that are useful for the diagnosis, prognosis, treatment, prevention and evaluation of treatments for bone remodeling and associated disorders. A method to analyze polynucleotide expression patterns has been developed and applied to identify polynucleotides, polypeptides, variants, and derivatives specifically involved in bone remodeling.
The present invention seeks to satisfy these and other needs.
ES 2 397 441 T3
Compendium of the invention
The present invention relates to a pharmaceutical composition that is used in the modulation of the differentiation of osteoclasts in vivo, in the prevention of osteopathies or in the treatment of osteopathies, which comprises an isolated polypeptide comprising a sequence selected from the group consisting in:
a) SEQ ID No. 48,
b) a polypeptide encoded by SEQ ID No. 1,
c) a fragment of any one of a) or b) that is capable of promoting or inhibiting osteoclast differentiation, and
d) an analog of any one of a) or b) that is capable of promoting or inhibiting osteoclast differentiation, wherein said analog has a sequence similarity of at least 90% with the polypeptide of a) or b), and a pharmaceutically acceptable carrier.
The present invention also relates to a pharmaceutical composition that is used in the modulation of the differentiation of osteoclasts in vivo, in the prevention of osteopathies or in the treatment of osteopathies, wherein the pharmaceutical composition comprises an isolated polynucleotide selected from the group that consists in:
a) a polynucleotide comprising SEQ ID No. 1,
b) a polynucleotide comprising the open reading frame of nucleotides 150 to 1136 of SEQ ID No. 1,
c) a polynucleotide comprising a sequence identical to aa) at least 80% along the entire length of the polynucleotide,
d) a polynucleotide comprising a sequence identical to b) at least 80% along the entire length of the polynucleotide,
e) a polynucleotide comprising a sequence complementary to aa) at least 80% along the entire length of the polynucleotide, and
f) a polynucleotide comprising a sequence complementary to b) at least 90% along the entire length of the polynucleotide, and a pharmaceutically acceptable carrier.
The present invention also relates to an isolated polynucleotide selected from the group consisting of:
a) a polynucleotide comprising SEQ ID No. 1,
b) a polynucleotide comprising the open reading frame of nucleotides 150 to 1136 of SEQ ID No. 1,
c) a polynucleotide comprising a sequence identical to aa) at least 80% along the entire length of the polynucleotide,
d) a polynucleotide comprising a sequence identical to b) at least 90% along the entire length of the polynucleotide,
e) a polynucleotide comprising a sequence complementary to aa) at least 80% along the entire length of the polynucleotide, and
f) a polynucleotide comprising a sequence complementary to b) at least 90% along the entire length of the polynucleotide, for use in modulating osteoclast differentiation in vivo, in the prevention of osteopathies or in the treatment of osteopathies.
The present invention also relates to an isolated polypeptide comprising a sequence selected from the group consisting of:
a) SEQ ID No. 48,
b) a polypeptide encoded by SEQ ID No. 1,
c) a fragment of any one of a) or b) that is capable of promoting or inhibiting osteoclast differentiation, and
ES 2 397 441 T3
d) an analog of any one of a) or b) that is capable of promoting or inhibiting osteoclast differentiation, wherein said analog has a sequence similarity of at least 90% with the polypeptide of a) or b) , for use in modulating osteoclast differentiation in vivo, in the prevention of osteopathies or in the treatment of osteopathies.
The present invention also relates to a compound capable of interfering with the activity or expression of a polypeptide selected from SEQ ID No. 48 or a polypeptide encoded by SEQ ID No. 1 for use in modulating differentiation of osteoclasts in vivo, in the prevention of osteopathies or in the treatment of osteopathies, wherein said compound is selected from the group consisting of antibodies or antigen-binding fragments thereof that specifically bind to a polypeptide selected from SEQ ID No. 48 or a fragment thereof, and siRNA or shRNA that specifically inhibit the activity or expression of a polypeptide encoded by SEQ iD No. 1. In some embodiments, the antibody is a monoclonal antibody, polyclonal antibody, chimeric antibody, or a humanized antibody or antigen-binding fragment thereof. In some embodiments, the antigen-binding fragment is a Fab fragment, an F (ab ') 2 fragment, or an F „fragment.
The invention also relates to the use of an isolated polynucleotide, isolated polypeptide or compound as defined above in the manufacture of a medicament for the modulation of osteoclast differentiation in vivo, for the prevention of osteopathies or for the treatment of osteopathies. .
The invention also relates to the use of at least one polynucleotide selected from the group consisting of:
a) a polynucleotide comprising SEQ ID No. 1;
b) a polynucleotide comprising the open reading frame of nucleotides 150 to 1136 of SEQ ID No. 1;
c) a polynucleotide comprising a sequence identical to aa) at least 80% along the entire length of the polynucleotide;
d) a polynucleotide comprising a sequence identical to b) at least 90% along the entire length of the polynucleotide,
e) a polynucleotide comprising a sequence complementary to aa) at least 80% along the entire length of the polynucleotide, and
f) a polynucleotide comprising a complementary sequence to b) at least 90% along the entire length of the polynucleotide, in the in vitro diagnosis of osteopathy.
The present invention also relates to a method for identifying an inhibitory compound capable of altering the expression or activity of a polypeptide of SEQ ID No. 48, or a polypeptide encoded by SEQ ID No. 1, wherein the method comprises contacting said polypeptide or a cell expressing said polypeptide with a candidate compound and measuring the expression or activity of said polypeptide, whereby a suitable inhibitory compound is positively identified by a reduction in the ability of the polypeptide to promote osteoclast differentiation. Such a method may further comprise a step of inducing osteoclast differentiation when said polypeptide or cell is contacted with a candidate compound.
In some embodiments of the present invention, osteopathy is selected from the group consisting of osteoporosis, osteopenia, osteomalacia, hyperparathyroidism, hyperthyroidism, hypogonadism, thyrotoxicosis, systemic mastocytosis, adult hypophosphatasia, hypercorticalism, osteogenesis imperfecta, Paget's disease / syndrome, Cushing, Turner syndrome, Gaucher disease, Ehlers-Danlos syndrome, Marfan syndrome, Menkes syndrome, Fanconi syndrome, multiple myeloma, hypercalcemia, hypocalcemia, arthritis, periodontitis, rickets, fibrogenesis imperfecta bone, osteosclerotic disorders and damage caused by inflammatory processes mediated by macrophages.
Disclosed herein are polynucleotides comprising sequences involved in the bone remodeling process, the open reading frame of such sequences, substantially identical sequences (eg, variants [eg, allelic variant], orthologs non-human), substantially complementary sequences and fragments of any one of the same mentioned above.
The present invention refers to a polypeptide that comprises sequences that intervene in the bone remodeling process, among them, biologically active analogs and biologically active fragments thereof. The present invention also relates to compositions that are useful for the diagnosis, prognosis, treatment, prevention, and / or evaluation of treatments for bone remodeling and associated disorders.
Also described herein is a method for analyzing polynucleotide expression patterns, and is applied in the identification of polynucleotides, polypeptides, variants and derivatives that are specifically involved in bone remodeling.
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The present description refers to the expression profiles of osteoclast polynucleotides, the isolation and identification of polynucleotides, their corresponding polypeptides, variants and derivatives that intervene in the activity of osteoclasts, the validation of these elements identified by their potential as therapeutic targets and the use of said polynucleotides, polypeptides, variants and derivatives for the improvement of disease states.
Disclosed herein are related polynucleotides and / or polypeptides that have been isolated and identified. More specifically, disclosed herein (isolated or substantially purified) polynucleotides comprising or consisting of any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86, their coding sequence (open reading frame), substantially identical sequence (eg, variants, orthologs [eg. g., SEQ ID No. 35]), substantially complementary sequences and related polypeptides comprising any one of SEQ ID No. 48-80 and polypeptides encoded by SEQ ID No. 85 or SEQ ID No. 86 which have been shown to be induced in a very specific way in osteoclasts. Also described herein are polypeptide analogs, variants (eg, SEQ ID No. 81), and fragments thereof.
NSEQ refers generally to polynucleotide sequences described herein and includes, for example, SEQ ID No. 1 to 33, SEQ ID No. 85, or sEq ID No. 86, while PSEQ refers specifically to general to polypeptide sequences described herein and includes, for example, SEQ ID No. 48 to 82 and polypeptides encoded by SEQ ID No. 85 or SEQ ID No. 86. Of course, it will be understood that NSEQ also encompasses polynucleotide sequences that are designed or derived from SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86, e.g., their coding sequence, complementary sequences Non-limiting examples of such sequences are described herein (eg, SEQ ID Nos. 42-45).
As used herein, the term "NSEQ" refers generally to polynucleotide sequences that comprise or consist of any one of SEQ ID Nos. 1 to 33, 85, or 86 (eg, an isolated form) or comprise or consist of a fragment of any one of SEQ ID Nos. 1 to 33, 85 or 86. The term "NSEQ" refers more specifically to a polynucleotide sequence comprising or consisting of a transcribed portion of any one of SEQ ID Nos. 1 to 33, 85 or 86, which may be, for example, portion-free or untranslated or untranslatable portions (ie, a coding portion of any one of SEQ ID Nos. 1 to 33, 85 or 86). The term "NSEQ" further refers to a sequence substantially identical to any one of the foregoing and more specifically substantially identical to the polynucleotide sequence comprising or consisting of a transcribed portion of any one of SEQ ID Nos. 1 to 33 , 85 or 86, which may be, for example, free of untranslated or untranslatable portion (s). The term "NSEQ" further refers to a region of the polynucleotide sequence of any one of SEQ ID Nos. 1 to 33, 85 or 86 that encodes or is capable of encoding a polypeptide. The term "NSEQ" also refers to a polynucleotide sequence capable of encoding any one of the polypeptides described herein or a polypeptide fragment of any one of the foregoing. Finally, the terminology "NSEQ" also comprises a sequence substantially complementary to any one of the above.
The term "inhibitory NSEQ" generally refers to a sequence substantially complementary to any one of SEQ ID Nos. 1 to 33, 85 or 86, substantially complementary to a fragment of any one of SEQ ID Nos. 1 to 33, 85 or 86, substantially complementary to a sequence substantially identical to SEQ ID Nos. 1 to 33, 85 or 86 and, more specifically, substantially complementary to a transcribed portion of any one of SEQ ID Nos. 1 to 33, 85, or 86 (eg, that may be without the untranslated or untranslatable portion) and that may have an attenuating or even inhibiting action on the transcription of an mRNA or the expression of a polypeptide encoded by the corresponding SEQ ID No. 1 to 33, 85 or 86 The ideal "inhibitory NSEQ" may have, for example and without limitation, about 10 to about 30 nucleotides, about 10 to about 25 nucleotides, or about 15 to about 20 nucleotides. As used herein, the term "nucleotide" means deoxyribonucleotide or ribonucleotide. The use of nucleotide analogs is also contemplated in the present invention.
Polynucleotides can have a sequence identity of at least about 80% to about 100% (eg, 80%, 90%, 95%, etc.) to a polynucleotide sequence selected from the group consisting of polynucleotides comprising (a) any one of SEQ ID No. 1 to 33 or SEQ ID No. 85 or SEQ ID No. 86; (b) an open reading frame of (a); (c) a full complement of (a) or (b); (d) a fragment of any one of (a) to (c).
As used herein, the term "untranslatable region" can include, for example, a promoter region (or portion thereof), silencing region, enhancer region, etc., of a polynucleotide sequence.
As used herein, "untranslatable region" can include, for example, an initiator portion of a polynucleotide sequence (upstream of an initiation codon, eg, AUG), intronic regions, stop codon and / or region downstream of a stop codon (including the polyA tail, etc.).
The isolated polynucleotide sequence complements described herein may be those that, for example, hybridize under high stringency conditions to any one of the nucleotide sequences in (a) or (b).
ES 2 397 441 T3
High stringency conditions may comprise, for example, a hybridization reaction at 65 ° C in 5X SSC, 5X Denhardt's solution, 1% sDs, and 100 µg / ml denatured salmon sperm DNA.
In accordance with the present invention, the polynucleotide sequence can be used, for example, in the treatment of diseases or disorders involving bone remodeling.
The fragments of the polynucleotides can be used, for example, as probes to determine the presence of the isolated polynucleotide (or its complement or fragments thereof) in a sample, cell, tissue, etc., for experimental purposes or for the purpose of diagnosis of diseases or disorders involving bone remodeling.
Also described herein is a combination comprising a multitude of polynucleotides (substantially purified and / or isolated). Polynucleotides can be co-expressed with one or more genes known to be involved in bone remodeling. Furthermore, the numerous polynucleotides can be selected, for example, from the group consisting of a polynucleotide comprising (a) any one of SEQ ID Nos. 1 to 33, SEQ ID No. 85 or sEq ID No. 86; (b) an open reading frame of (a); (c) a polynucleotide sequence comprising or consisting of a transcribed portion of any one of SEQ ID Nos. 1 to 33, 85 or 86 which may be, for example, free of untranslated or untranslatable portion (s); (d) a sequence complementary to any one of (a) to (c); (e) a sequence that hybridizes under conditions of high stringency to any one of the nucleotide sequences of (a) to (d); and (f) fragments of any one of (a) to (e).
Also described herein is a polynucleotide that encodes any one of the polypeptides described herein. The polynucleotide (RNA, DNA, etc.) can encode a polypeptide that can be selected from the group consisting of any one of SEQ ID No. 48 to 80, polypeptide encoded by SEQ ID No. 85 or 86, analogs or fragments thereof (eg, biologically active fragments, immunologically active fragments, etc.).
Also described herein is an isolated nucleic acid molecule comprising the polynucleotides described herein, operably linked to a nucleotide sequence encoding a heterologous polypeptide by which a fusion polypeptide is encoded.
Also described herein is a polypeptide encoded by a polynucleotide of SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86 or more specifically of the open reading frame of any one of the SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86, or a portion thereof. Also described herein is the product of a gene that is co-expressed with one or more genes known to be involved in bone remodeling.
Also described herein is a naturally occurring isolated allelic variant, as well as synthetic variants (eg, made by recombinant DNA technology or by chemical synthesis, etc.), such as a biologically active variant that it may comprise one or more amino acid substitutions (as compared to a naturally occurring polypeptide), such as a conservative or non-conservative amino acid substitution.
Also disclosed is a vector (mammalian, bacterial, viral, etc.) comprising the polynucleotides described herein or fragments thereof, such as an expression vector. The vector may further comprise a nucleic acid sequence that can aid in the regulation of polynucleotide expression and / or a nucleotide sequence that encodes a tag (eg, affinity tag; HA, GST, His, etc).
Described herein is an expression vector that may comprise, for example, the following operably linked elements:
a) a transcription promoter;
b) a polynucleotide segment (which may comprise an open reading frame of any one of SEQ ID Nos. 1 to 33, 85 or 86); Y
c) a transcription terminator.
Also described herein is an expression vector comprising a polynucleotide described herein, a host cell transformed with the expression vector, and a method for producing a polypeptide of the present invention.
Also described herein is a vector comprising a polynucleotide or polynucleotide fragment. Vectors that may comprise a sequence substantially complementary to the polynucleotides described herein (eg, siRNA, shRNA) are, therefore, encompassed herein. The vector may comprise sequences that allow transcription of the polynucleotide or polynucleotide fragment.
ES 2 397 441 T3
Disclosed herein is a cell that may be genetically modified to contain and / or express the polynucleotide (including complements and fragments) and / or polypeptides of the present invention. The cell can be, for example, a mammalian cell, an insect cell, a bacterial cell, etc.
Accordingly, a host cell is disclosed herein which may comprise a vector as described herein. The cell can be, for example, a mammalian cell, an insect cell, a bacterium, etc. The cell may be capable of expressing or does express a polypeptide encoded by the polynucleotide described herein.
Methods for producing the polypeptides encompassed herein include, for example, culturing the cell under conditions that allow transcription of a gene or expression of the polypeptide. The polypeptide can be recovered, for example, from cell lysate or cell supernatant.
The present specification describes the use of at least one polynucleotide comprising any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86, its coding sequence, substantially identical sequences, sequences substantially complementary or fragments thereof, in an ordered matrix. The matrix can be used in a procedure to diagnose a bone remodeling disease or disorder by hybridizing the matrix with a patient sample under conditions that allow complex formation, detect complex formation, and compare the amount of complexes formed. in the patient sample with that of the standards for normal and diseased tissues, wherein the formation of complexes in the patient sample indicates the presence of a bone remodeling disease or disorder. Of course, the use of a polynucleotide described herein in a diagnostic method is not solely dependent on the achievement of a specific assay. The sequence or sequences can be used in conventionally used diagnostic methods known in the art.
Also described is a method for ameliorating the symptoms of bone remodeling disease or disorder, or for inhibiting or delaying bone disease or disorder, wherein the procedure may comprise: contacting a compound capable of specifically inhibiting the activity or expression of a polynucleotide sequence described herein or a polypeptide described herein, with osteoclasts, such that symptoms of the disease or disorder can be ameliorated remodeling, or the disease or disorder can be prevented, delayed, or lessened.
Also described is a method for ameliorating the symptoms of bone remodeling disease or disorder, or for inhibiting or delaying bone disease or disorder, wherein the procedure may comprise: contacting a compound capable of specifically promoting the activity or expression of a polynucleotide sequence described herein or a polypeptide described herein, with osteoclasts, such that symptoms of the disease or disorder can be ameliorated remodeling, or the disease or disorder can be prevented, delayed, or lessened.
Also described is a method for treating a condition in a mammal, characterized by the lack, or need, of bone growth or replacement and / or an undesirable level of osteoclasia, wherein said method may comprise administration, to a mammalian subject in need of such treatment, of an effective amount of a suitable compound described herein.
Also described is a method of using a polynucleotide sequence described herein, a polypeptide described herein in a matrix, and for using the matrix in a method of diagnosing a bone remodeling disease or disorder by hybridizing the matrix with a patient sample under conditions that allow the formation of complexes, detection of the complexes formed, and comparing the amount of complexes formed in the patient sample with that of standards for normal and diseased tissues, wherein complexation in the patient sample may indicate the presence of a bone remodeling disease or disorder.
The polynucleotide sequence described herein can be used for somatic cell gene therapy or for stem cell gene therapy.
Also described herein is a pharmaceutical composition comprising a polynucleotide described herein or a polypeptide encoded by the selected polynucleotide or portion thereof, and a suitable pharmaceutical carrier.
Also described herein are products, compositions, procedures and methods comprising a polynucleotide described herein, a polypeptide encoded by the polynucleotides, a portion thereof, their variants or derivatives, for research and for biological purposes, clinical and therapeutic.
The NSEQ and PSEQ can be used in the diagnosis, prognosis, treatment, prevention, and selection and evaluation of treatments for diseases and disorders that involve bone remodeling, including but not limited to, osteoporosis, osteopenia, osteomalacia, hyperparathyroidism, hyperthyroidism, hypogonadism, thyrotoxicosis, systemic mastocytosis, adult hypophosphatasia, hypercorticalism, osteogenesis imperfecta, Paget's disease,
ES 2 397 441 T3 Cushing's disease / syndrome, Turner syndrome, Gaucher disease, Ehlers-Danlos syndrome, Marfan syndrome, Menkes syndrome, Fanconi syndrome, multiple myeloma, hypercalcemia, hypocalcemia, arthritis, periodontitis, rickets ( including X-linked hypophosphatemic rickets, and vitamin D-dependent types I and II), bone fibrogenesis imperfecta, osteosclerotic disorders such as pycnodysostosis, and damage caused by macrophage-mediated inflammatory processes.
Using NSEQ as a screening tool
The polynucleotides obtained herein can be used to detect and isolate expression products, eg, mRNA, complementary DNAs (cDNAs), and proteins derived from or homologous to NSEQ. In one example, the expression of mRNAs homologous to the NSEQs of the present invention can be detected, for example, by hybridization analysis, reverse transcription, and in vitro nucleic acid amplification methods. Such procedures allow the detection of mRNAs in many types of tissues or at different stages of development. The nucleic acids in question that are expressed in a tissue-specific way or in a developmental stage-specific way are useful as tissue-specific markers or to define the developmental stage of a sample of cells or tissues that can define a state. specific pathological. One skilled in the art can easily adapt the NSEQs for these purposes.
Those skilled in the art will also recognize that NSEQs, and their expression products such as cDNA nucleic acids and genomic DNA, can be used to prepare short oligonucleotide sequences. For example, oligonucleotides having ten to twelve nucleotides or more can be made to specifically hybridize to the NSEQs and cDNAs present, and allow the detection, identification, and isolation of unique nucleic acid sequences by hybridization. Sequences of, for example, at least 15 to 20 nucleotides, can be used and selected in regions that lack homology to other known sequences. Sequences of 20 or more nucleotides that lack such homology show increased specificity for the target sequence. Useful hybridization conditions for probes and primers are readily determinable by those of skill in the art. The stringent hybridization conditions encompassed by this specification are those that can allow the hybridization of nucleic acids that have a homology of greater than 90%, but that can prevent the hybridization of nucleic acids whose homology is below 70%. The specificity of a probe can be determined by finding out whether it is designed from a unique region, a regulatory region, or a conserved motif. Both the specificity of the probe and the stringency of diagnostic hybridization or amplification reactions (maximum, high, intermediate, or low) can be determined based on whether the probe accurately identifies complementary sequences, allelic variants, or related sequences. . Probes designed to detect related sequences can have at least 50% sequence identity with any one of the selected polynucleotides.
It should be understood herein that NSEQs (substantially identical sequences and fragments thereof) can hybridize to a substantially complementary sequence found in a test sample. Additionally, a sequence substantially complementary to the NSEQ can bind to the NSEQ found in a test sample.
In addition, a probe can be labeled by any method known in the art, for example, by incorporating nucleotides attached to a "reporter molecule." An "reporter molecule", as used herein, can be a molecule that provides an analytically identifiable signal that allows detection of a hybridized probe. Detection can be qualitative or quantitative. The most commonly used reporter molecules include fluorophores, enzymes, biotin, chemiluminescent molecules, bioluminescent molecules, digoxigenin, avidin, streptavidin, or radioisotopes. The most commonly used enzymes include horseradish peroxidase, alkaline phosphatase, glucose oxidase, and β-galactosidase, among others. The enzymes can be conjugated to avidin or streptavidin for use with a biotinylated probe. Similarly, the probes can be conjugated with avidin or streptavidin for use with a biotinylated enzyme. Incorporation of a reporter molecule into a DNA probe can be by any method known to those skilled in the art, for example nick translation, primer extension, random priming with oligonucleotides, by labeling at the 3 'or 5 end 'or by other means. Furthermore, hybridization probes include the cloning of nucleic acid sequences into vectors for the production of mRNA probes. Such vectors are known in the art, are commercially available, and can be used to synthesize RNA probes in vitro. The labeled polynucleotide sequences can be used in Southern or Northern analysis, dot blotting, or other membrane-based technologies; in PCR technologies; and in microarrays using subject samples to detect any alteration in expression. Oligonucleotides useful as probes for screening samples by hybridization assays or as primers for amplification can be packaged as kits. Such kits can contain the probes or primers in a predetermined or predetermined amount, as well as other reagents and conveniently packaged material that are necessary for the particular hybridization or amplification protocol. In another embodiment, the invention comprises a substantially purified polypeptide encoded by NSEQ polynucleotides, polypeptide analogs, or polypeptide fragments thereof. Polypeptides, either in a pre-mature, mature or fused form, can be isolated from lysed cells, or from culture medium, and purified as necessary for use as designed. Those skilled in the art can easily purify these proteins, polypeptides, and peptides by any available method. For example, purification can be
ES 2 397 441 T3 be carried out by salt fractionation, size exclusion chromatography, ion exchange chromatography, reverse phase chromatography, affinity chromatography and the like.
Use of the NSEQ for the development of an expression system
To express a biologically active polypeptide, the NSEQ or derivatives thereof can be introduced into an expression vector, namely a vector containing the elements for transcriptional and translational control of the inserted coding sequence in a particular host. These elements can include regulatory sequences, such as enhancers, constitutive and inducible promoters, and 5 'and 3' untranslated regions. Procedures that are well known to those of skill in the art can be used to construct such expression vectors. These procedures include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination.
Numerous expression vector / host cell systems known to those of skill in the art can be used to express NSEQ. These include, but are not limited to, microorganisms such as bacteria transformed with DNA expression vectors on recombinant bacteriophages, plasmids, or cosmids; yeast transformed with yeast expression vectors; insect cell systems infected with baculovirus vectors; plant cell systems transformed with viral or bacterial expression vectors; or animal cell systems. For long-term production of recombinant proteins in mammalian systems, stable expression can be effected in cell lines. For example, NSEQ can be transformed into cell lines by expression vectors that may contain viral origins of replication and / or endogenous expression elements and a selection or visibility marker gene in the same or a different vector. The description will not be limited by the vector or the host cell employed.
In general, host cells containing NSEQ and expressing a polypeptide encoded by NSEQ, or a portion thereof, can be identified by many procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations, PCR amplification, and protein bioassay or immunoassay techniques that include membrane, solution, or chip-based technologies to detect and / or quantify nucleic acid or amino acid sequences. Immune methods for detecting and measuring the expression of polypeptides with specific monoclonal or polyclonal antibodies are well known in the art. Examples of such techniques include enzyme immunoassays (ELISA), radioimmunoassays (RIA), and fluorescence activated cell sorting (FACS). Those skilled in the art can readily adapt these methodologies to the present invention.
In the present specification a bioassay is described to evaluate compounds that are potential antagonists of the polypeptide described in the present specification, the bioassay may comprise:
a) culturing test cells in a culture medium containing increasing concentrations of at least one compound whose ability to inhibit the action of a polypeptide described herein is intended to be determined, wherein the test cells may contain a described polynucleotide sequence herein (for example, in a form that enhances transcriptional activity by transactivation relative to wild-type polynucleotide, and comprising a response element operably linked to a reporter gene); and then
b) monitoring the level of expression of the reporter gene product in cells as a reflection of the concentration of the possible antagonist compound in the culture medium, thereby indicating the ability of the possible antagonist compound to inhibit the activation of the polypeptide encoded by the polynucleotide sequence described herein.
Also described herein is a bioassay to evaluate compounds that are potential agonists for a polypeptide encoded by the polynucleotide sequence described herein, the bioassay may comprise:
a) the cultivation of the test cells in a culture medium containing increasing concentrations of at least one compound whose ability to promote the action of the polypeptide encoded by the polynucleotide sequence described herein is intended to determine, where the test cells can contain a polynucleotide sequence described herein (e.g., in a form that enhances transcriptional activity by transactivation relative to wild-type polynucleotide, and comprising a response element operably linked to a reporter gene); and then
b) monitoring the level of expression of the reporter gene product in cells as a reflection of the concentration of the possible agonist compound in the culture medium, thereby indicating the ability of the possible agonist compound to favor the activation of an encoded polypeptide by the polynucleotide sequence described herein.
Host cells transformed with NSEQ can be cultured under conditions that allow expression and recovery of the polypeptide from cell culture. The polypeptide produced by a transgenic cell can
ES 2 397 441 T3 be secreted by the cell or be retained within it according to the sequence and / or vector used. As those skilled in the art will know, expression vectors containing NSEQ can be designed to contain signal sequences that direct secretion of the polypeptide through a membrane of a prokaryotic or eukaryotic cell. Due to the inherent degeneracy of the genetic code, other DNA sequences encoding substantially the same or a functionally equivalent amino acid sequence can be produced and used to express the polypeptide encoded by the NSEQ. The nucleotide sequences described herein can be genetically modified using procedures generally known in the art to alter nucleotide sequences for numerous purposes, including, but not limited to, cloning, processing, and / or modification. or expression of the gene product. DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides can be used to construct nucleotide sequences. For example, site-specific mutagenesis by oligonucleotides can be used to introduce mutations that create new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, and so on.
In addition, a host cell strain can be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed polypeptide in the desired manner. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation. Post-translational processing, which cleaves a "prepro" form of the polypeptide, can also be used to specify the destination, folding, and / or activity of proteins. Different host cells are available on the market and in the American Type Culture Collection (ATCC) (e.g. g., CHO, HeLa, MDCK, HEK293 and W138) that have specific cellular machinery and characteristic mechanisms for post-translational activities and can be chosen to ensure correct modification and processing of the expressed polypeptide.
Those skilled in the art will readily appreciate that natural, modified, or recombinant nucleic acid sequences can be linked to a heterologous sequence that results in translation of a fusion polypeptide containing heterologous polypeptide residues in any of the aforementioned host systems. . Such heterologous polypeptide moieties can facilitate purification of fusion polypeptides with commercially available affinity matrices. Such residues include, but not limited to, glutathione S-transferase (GST), maltose-binding protein, thioredoxin, calmodulin-binding peptide, 6-His (His), FLAG, cmyc, hemagglutinin (HA), and antibody epitopes. monoclonal.
Also described herein is an isolated polynucleotide that may comprise a nucleotide sequence encoding a fusion protein, wherein the fusion protein may comprise a fusion partner fused to a peptide fragment of a protein encoded by the polynucleotide sequence described in herein, or a naturally occurring allelic variant polypeptide encoded by it.
Those skilled in the art will readily recognize that nucleic acid and polypeptide sequences can be synthesized, in whole or in part, by chemical or enzymatic procedures well known in the art. For example, peptide synthesis can be performed with different solid phase techniques and machines such as the ABI 431A peptide synthesizer (PE Biosystems), which can be used to automate synthesis. If desired, the amino acid sequence can be altered during synthesis and / or combined with sequences from other proteins to produce a variant protein.
Use of the NSEQ as a diagnostic screening tool
One of skill in the art will readily recognize that NSEQ can be used for diagnostic purposes in determining the absence, presence, or altered expression (ie, increase or decrease compared to normal) of the gene. Polynucleotides may be at least 10 nucleotides in length or at least 12 nucleotides in length or at least 15 nucleotides in length to any desired length, and may comprise complementary DNA and RNA molecules, branched nucleic acids, and / or acids. peptidonucleic (PNA). In an alternative, the polynucleotides can be used to detect and quantify gene expression in samples whose expression of NSEQ correlates with disease. In another alternative, NSEQ can be used to detect disease-associated genetic polymorphisms. These polymorphisms can be detected in the transcribed cDNA.
Disclosed herein is the use of at least one polynucleotide comprising NSEQ (e.g. g., an open reading frame of the NSEQ, a substantially complementary sequence, a substantially identical sequence, and fragments thereof) in a matrix and the use of such a matrix in a diagnostic procedure for a bone remodeling disease or disorder by hybridization of the matrix with a patient sample under conditions that allow complex formation, detect complex formation and compare the amount of complexes formed in the patient sample with that of standards for normal and diseased tissues, where complex formation in the patient sample indicates the presence of a bone remodeling disease or disorder .
Also disclosed herein is one or more compartmentalized kits for the detection of disease states of osteoclasia. A first kit can have a receptacle that contains at least one insulated probe. Such
ES 2 397 441 T3 probe can be a nucleic acid fragment that is present / absent in the genomic DNA of normal cells, but that is absent / present in the genomic DNA of affected cells. Such a probe can be specific for a DNA site that is normally active / inactive, but which can be inactive / active in certain cell types. Similarly, such a probe can be site-specific in DNA that can be abnormally expressed in certain cell types. Finally, such a probe can identify a specific mutation in DNA. By DNA site specific it is meant that the probe may be capable of hybridizing to the DNA sequence that is mutated, or that it may be capable of hybridizing to DNA sequences adjacent to the mutated DNA sequences. The probes provided in the present kits may have a covalently attached reporter molecule. Those skilled in the art will be able to prepare the probes and reporter molecules with ease as described above.
Using the NSEQ as a treatment
One of skill in the art will readily appreciate that the expression systems and assays discussed above can also be used to evaluate the efficacy of a given therapeutic treatment regimen, in animal studies, in clinical trials, or to monitor the treatment of a patient. Once the presence of disease is established and a treatment protocol is initiated, hybridization or amplification assays can be repeated regularly to determine if the level of expression in the patient begins to approach the level observed in a healthy subject. The results obtained from successive trials can be used to show the effectiveness of the treatment over a period of time ranging from several days to many years.
In yet another aspect of the invention, an NSEQ, a portion thereof, or its complement can be used therapeutically in order to express mRNA and polypeptide, or conversely, to block mRNA transcription or translation. Expression vectors can be constructed with elements from retrovirus, adenovirus, herpes virus or vaccinia virus, or bacterial plasmids, and the like. These vectors can be used to deliver the nucleotide sequences to a particular target organ, tissue, or cell population. Procedures well known to those of skill in the art can be used to construct vectors to express the nucleic acid sequences or their complements.
Alternatively, NSEQ, a portion thereof, or its complement can be used for somatic cell or stem cell gene therapy. Vectors can be introduced in vivo, in vitro, and ex vivo. For ex vivo treatment, vectors are introduced into stem cells taken from the subject, and the resulting transgenic cells are clonally propagated for autologous transplantation back to the same subject. Delivery of the NSEQ by transfection, injections of liposomes, or aminopolycationic polymers can be accomplished by procedures that are well known in the art. Additionally, endogenous expression of NSEQ can be inactivated by homologous recombination procedures that insert an inactive gene sequence into the coding region or other target region of NSEQ.
Depending on the specific goal to be achieved, vectors containing NSEQ can be introduced into a cell or tissue to express an absent polypeptide or to replace a non-functional polypeptide. Of course, when it is desired to express the PSEQ in a cell or tissue, an NSEQ capable of encoding such a PSEQ can be used for that purpose or the PSEQ can be administered directly to said cell or tissue.
On the other hand, when it is desired to attenuate or inhibit the expression of PSEQ, one can use an NSEQ (eg, an inhibitory NSEQ) that is substantially complementary to at least a portion of an NSEQ capable of encoding such a PSEQ.
Expression of an inhibitory NSEQ can be accomplished by cloning the inhibitory NSEQ into a vector and introducing the vector into a cell to decrease the expression of a polypeptide encoded by the target NSEQ.
Vectors containing NSEQ (eg, including inhibitory NSEQ) can be transformed in a cell or tissue to express a missing polypeptide or to replace a nonfunctional polypeptide. Similarly, a vector constructed to express NSEQ complement can be transformed into a cell to decrease overexpression of a polypeptide encoded by the NSEQ polynucleotides, or a portion thereof. Antisense or complementary sequences can consist of an oligonucleotide from the transcription start site; nucleotides between positions about 10 and +10 from ATG are preferred. Similarly, inhibition can be achieved with the triple helix base pairing methodology. Triple helix pairing is useful because it inhibits the ability of the double helix to open wide enough for polymerases, transcription factors, or regulatory molecules to bind. Recent therapeutic advances using triple DNA have been written in the literature (see, eg, Gee et al., 1994).
Ribozymes, RNA molecules with enzymatic activity, can also be used to catalyze mRNA cleavage and decrease the amount of certain mRNAs, such as those that comprise the polynucleotide sequences of the invention. Ribozymes can cleave mRNA at specific cleavage sites. Alternatively, ribozymes can cleave mRNAs at positions dictated by the flanking regions that
ES 2 397 441 T3 form complementary base pairs with the target mRNA. The construction and production of ribozymes is well known in the art.
RNA molecules can be modified to increase intracellular stability and half-life. Possible modifications include, but not exclusively, the addition of flanking sequences at the 5 'and / or 3' ends of the molecule, or the use of phosphorothioate or 2'O-methyl instead of phosphodiester bonds within the molecule. skeleton of the molecule. Alternatively, non-traditional bases such as inosine, cheosine, and wibutosin can be added, as well as acetyl-, methyl-, thio-, and similarly modified forms of adenine, cytidine, guanine, thymine, and uridine that endogenous endonucleases do not recognize with. ease.
In addition to the active ingredients, a pharmaceutical composition may contain pharmaceutically acceptable carriers comprising excipients and auxiliaries that facilitate processing of the active compounds into pharmaceutically usable preparations.
For any compound, the therapeutically effective dose can be estimated initially both by cell culture assays and by animal models such as mice, rats, rabbits, dogs, or pigs. An animal model can also be used to determine the concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans. These techniques are well known to one of ordinary skill in the art and a therapeutically effective dose refers to the amount of active ingredient that ameliorates the symptoms or the condition. Therapeutic efficacy and toxicity can be determined by standard pharmaceutical procedures in cell culture or with experimental animals, such as by calculating and statistically comparing the ED50 (the therapeutically effective dose in 50% of the population) and the LD50. (the lethal dose for 50% of the population). Any of the therapeutic compositions described above can be applied to any subject in need of such treatment, including but not limited to, mammals such as dogs, cats, cows, horses, rabbits, monkeys, and most preferably humans.
The pharmaceutical compositions used in this invention can be administered by many routes, including but not limited to, oral, intravenous, intramuscular, intraarterial, intramedullary, intrathecal, intraventricular, transdermal, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, or rectal.
The term "Treatment" for the purposes of this description refers to both therapeutic treatment and prophylactic or preventive measures, where the aim is to prevent or delay (alleviate) the pathological disorder or condition of interest. Those in need of treatment include those already suffering from the disorder as well as those prone to suffering from the disorder or those to be prevented from the disorder.
Use of the NSEQ in general research
Disclosed herein are products, compositions, procedures, and methods that utilize NSEQ, its open reading frame, or a polypeptide encoded by NSEQ polynucleotides or its open reading frame, or a portion thereof, its variants. , analogs, derivatives and fragments for research, biological, clinical and therapeutic purposes. For example, to identify splice variants, mutations, and polymorphisms.
NSEQ can be extended with a partial nucleotide sequence and by various PCR-based procedures known in the art to detect upstream sequences such as promoters and other regulatory elements. Additionally, an XL-PCR kit (PE Bioystems, Foster City, Calif.), Nested primers, and commercially available cDNA libraries (Life Technologies, Rokville Md.) Or genomic libraries (Clontech, Palo Alto, Calif. .) to extend the sequence.
Polynucleotides can also be used as targets on a microarray. The microarray can be used to monitor the expression patterns of a large number of genes simultaneously and to identify splice variants, mutations, and polymorphisms. Information from expression pattern analyzes can be used to determine gene function, to understand the genetic basis of a disease, to diagnose a disease, and to develop and monitor the activities of therapeutic drugs used to treat disease. . Microarrays can also be used to detect genetic diversity, single nucleotide polymorphisms that can characterize a particular population, at the genomic level.
In yet another example, the polynucleotides can be used to generate hybridization probes useful for mapping the naturally occurring genomic sequence. Fluorescent in situ hybridization (FISH) can be correlated with other physical chromosome mapping techniques and genetic mapping data.
Also described herein is a method for representatively identifying an endogenously differentially expressed sequence involved in osteoclast differentiation. The sequence can, for example, be differentially expressed in a differentiated osteoclast cell compared to an undifferentiated osteoclast precursor cell.
The procedure described herein may comprise:
ES 2 397 441 T3
a) separately providing the total messenger RNA of the differentiated human osteoclast cell (mature or intermediate), wherein the total messenger RNA may comprise, for example, at least one endogenously differently expressed sequence,
b) generating single stranded cDNA from each differentiated human osteoclast cell messenger RNA and (eg, randomly) tagging the 3 'end of the single stranded cDNA with a promoter sequence for RNA polymerase and a first sequence tag;
c) generating single stranded cDNA from each undifferentiated human osteoclast precursor cell messenger RNA and (eg, randomly) tagging the 3 'end of the single stranded cDNA with a promoter sequence for RNA polymerase and a second sequence tag;
d) separately generating partial or fully 5 'tagged double-stranded DNA from each of b) and c), wherein the 5' tagged double-stranded DNA may therefore comprise in a 5 'to 3' direction a promoter double stranded for RNA polymerase, a first or second sequence tag, and an endogenously expressed sequence,
e) separately linearly amplifying a first and second tagged sense RNA of each of d) with an RNA polymerase enzyme (which can be selected based on the promoter used for tagging),
f) generating a first or second tagged and single-stranded DNA that is complementary to one of e),
g) hybridize the first or second complementary, single-stranded labeled DNA of f) with the other linearly amplified sense RNA of e),
h) recovering the unhybridized RNA with the aid of the first or second sequence tag (for example, by PCR or hybridization); Y
i) identifying (determining) the nucleotide sequence of the unhybridized RNA.
Steps b) and / or c) may comprise the generation of a single copy of a single-stranded cDNA.
The method may further comprise the step of comparatively determining the presence of the endogenously identified and differentially expressed sequence in a differentiated osteoclast cell from an undifferentiated osteoclast precursor cell.
Accordingly, a sequence can be selected that is substantially absent (eg, totally absent or present in a very low amount) from one of the differentiated osteoclast cell or an undifferentiated osteoclast precursor cell, and present in the other. differentiated osteoclast cell or an undifferentiated osteoclast precursor cell.
Thus, the selected sequence can be a positive regulator of osteoclast differentiation and, therefore, it can represent an attractive target that can be used advantageously to promote osteoclasia or alternatively such target can be inhibited to decrease or prevent osteoclasia. .
Alternatively, the sequence selected with the above procedure may be a negative regulator of osteoclast differentiation and may, therefore, represent an attractive target that can be advantageously induced (e.g., at the level of transcription, translation, activity, etc.) or provide a cell to decrease or prevent osteoclasia. Similarly, such a negative regulator can, after its inhibition, serve as a target to promote osteoclasia.
The sequence may further be selected based on reduced or substantially absent expression in other normal tissue, thus representing a candidate sequence specifically involved in osteoclast differentiation and bone remodeling.
The method may also further comprise a step for determining the complete sequence of the nucleotide sequence and may also comprise determining the coding sequence for the nucleotide sequence.
Also described herein is the endogenously isolated and differentially expressed sequence (polynucleotide and polypeptide) that is identified by the method described herein.
Also described herein is a polynucleotide that can comprise the identified polynucleotide sequence, a polynucleotide that can comprise the open reading frame of the identified polynucleotide sequence, a polynucleotide that can comprise a nucleotide sequence substantially identical to the identified polynucleotide by the described procedure In the present memory, a polynucleotide that can comprise a nucleotide sequence substantially complementary to the polynucleotide identified by the method described herein, fragments and splice variants thereof, as long as the sequence does not consist of or comprise SEQ ID No. 34.
ES 2 397 441 T3
The endogenously isolated and differentially expressed sequence described herein can be a complete or partial RNA molecule.
The isolated DNA molecule capable of being transcribed into the RNA molecule described herein is also encompassed by this document, as well as vectors (including expression vectors) that comprise such a DNA or RNA molecule.
Also described herein are libraries comprising at least one endogenously isolated and differentially expressed sequence that is identified herein [p. (eg, partial or complete DNA or RNA, substantially identical sequences or substantially complementary sequences (eg, probes) and fragments thereof (eg, oligonucleotides)].
The endogenously isolated and differentially expressed sequence described herein may be selected, for example, from the group consisting of a polynucleotide which may consist of or comprise:
a) any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86,
b) the open reading frame of any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86,
c) a polynucleotide that may comprise a nucleotide sequence substantially identical to a) or b), and;
d) a polynucleotide that may comprise a nucleotide sequence substantially complementary to any one of a) to c),
e) fragments of any one of a) to d).
Also described herein is a polypeptide that can be encoded by the endogenously isolated and differentially expressed sequence described herein.
Also described herein is a polynucleotide capable of encoding a polypeptide described herein. Due to the degeneracy of the genetic code, it should be understood herein that many polynucleotide sequences can encode the same polypeptide sequence and are therefore encompassed herein.
Exemplary polypeptides may comprise a sequence selected from the group consisting of any one of SEQ ID No. 48 to 80, a polypeptide encoded by SEQ ID No. 85 or SEQ ID No. 86.
Also described herein is an isolated non-human ortholog polynucleotide sequence (involved in bone remodeling), non-human ortholog open reading frame, substantially identical sequences, substantially complementary sequences, fragments, and splice variants thereof.
Also described herein is an isolated polypeptide encoded by the non-human ortholog polynucleotide, as well as biologically active analogs and biologically active fragments thereof.
Exemplary embodiments of non-human (eg, mouse) ortholog polynucleotides encompassed by this document include, for example, SEQ ID No. 35.
Exemplary embodiments of isolated polypeptide encoded by some non-human orthologs identified herein include, for example, a polypeptide such as SEQ ID No. 82.
Also described herein is an isolated polynucleotide that can be differentially expressed in the differentiated osteoclast cell as compared to the undifferentiated human osteoclast precursor cell.
The isolated polynucleotide may comprise a member selected from the group consisting of:
a) a polynucleotide that can comprise any one of SEQ ID No. 1 to SEQ ID No. 33, SEQ ID No. 85 or SEQ ID No. 86.
b) a polynucleotide that can comprise the open reading frame of any one of SEQ ID No. 1 to SEQ ID No. 33, SEQ ID No. 85 or SEQ ID No. 86;
c) a polynucleotide that may comprise a transcribed or transcribable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, SeQ ID No. 85 or SEQ ID No. 86, which may be , for example, free of untranslated or untranslatable portion (s);
d) a polynucleotide that may comprise a translated or translatable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, SEQ ID No. 85, or SEQ ID No. 86 (eg, portion encoding),
e) a polynucleotide that may comprise a substantially identical sequence (eg, an identity of about 50 to 100%, or about 60 to 100%, or about 70 to 100% or
ES 2 397 441 T3 approximately 80 to 100% or approximately 85, 90, 95 to 100% throughout the entire sequence or portion of the sequences) aa), b), c) or d),
f) a polynucleotide that may comprise a substantially complementary sequence (eg, complementary of about 50 to 100%, or about 60 to 100% or about 70 to 100% or about 80 to 100% or about the 85, 90, 95 at 100% throughout the entire sequence or portion of the sequences) aa), b), c) or d); Y
g) a fragment of any one of a) to f).
h) which includes polynucleotides consisting of the above.
Exemplary polynucleotide fragments listed above comprise polynucleotides of at least 10 nucleic acids that can be substantially complementary to the nucleotide sequence of any one of SEQ ID Nos. 1 to 33, SEQ ID Nos. 85, or SEQ ID # 86, eg, fragments selected from the group consisting of any one of SEQ ID # 42 to 45.
Also described herein is an isolated polynucleotide involved in osteoclast differentiation, wherein the isolated polynucleotide can be selected, for example, from the group consisting of:
a) a polynucleotide comprising any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86,
b) a polynucleotide comprising the open reading frame of any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86,
c) a polynucleotide that may comprise a transcribed or transcribable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, SeQ ID No. 85 or SEQ ID No. 86, which may be , for example, free of untranslated or untranslatable portion (s);
d) a polynucleotide that may comprise a translated or translatable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, SEQ ID No. 85, or SEQ ID No. 86 (eg, portion encoding),
e) a polynucleotide substantially identical to aa), b), c) or d); Y
f) a sequence of at least 10 nucleic acids that can be substantially complementary to the nucleic acid sequence of any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86 or more in particular of a), b),
c) or d).
According to the present invention, the isolated polynucleotide may be capable of promoting differentiation of osteoclasts (eg, in a mammal or a mammalian cell thereof), that is, it may be a positive regulator of differentiation. of the osteoclasts.
Further in accordance with the present invention, the isolated polynucleotide may be capable of inhibiting, preventing, or decreasing osteoclast differentiation (eg, in a mammal or a mammalian cell thereof), that is, it may be a negative regulator of osteoclast differentiation.
In yet another aspect, the present invention relates to an isolated polynucleotide that may be capable of inhibiting osteoclast differentiation (eg, in a mammal or a mammalian cell thereof). The polynucleotide can be selected, for example, from the group consisting of polynucleotides that can comprise a sequence of at least 10 nucleic acids that is complementary to the nucleotide sequence of any one of the NSEQs described herein.
Suitable polynucleotides include, for example, a polynucleotide having or comprising those selected from the group consisting of SEQ ID Nos. 42 to 45.
Suitable polynucleotides may be those that may be capable of inhibiting osteoclast differentiation that has been induced by an inducer of osteoclast differentiation, such as those discussed herein.
According to the present invention, the polynucleotide can be, for example, an RNA molecule, a DNA molecule, including those that are partial or full, single or double stranded, hybrids, etc.
Also described herein is a vector (eg, an expression vector) comprising the polynucleotide of the present invention.
Also described herein is a library of polynucleotide sequences that can be differentially expressed in a differentiated osteoclast cell compared to an undifferentiated osteoclast precursor cell. The library may comprise, for example, at least one member selected from the group consisting of:
ES 2 397 441 T3
a) a polynucleotide that can comprise any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86,
b) a polynucleotide that can comprise the open reading frame of any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86,
c) a polynucleotide that may comprise a transcribed or transcribable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, SeQ ID No. 85 or SEQ ID No. 86, which may be , for example, free of untranslated or untranslatable portion (s);
d) a polynucleotide that may comprise a translated or translatable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, SEQ ID No. 85, or SEQ ID No. 86 (eg, portion encoding),
e) a polynucleotide that may comprise a substantially identical sequence (eg, an identity of about 50 to 100%, or about 60 to 100% or about 70 to 100% or about 80 to 100% or about 85, 90, 95 to 100% throughout the entire sequence or portion of the sequences) aa), b), c) or d);
f) a polynucleotide that may comprise a substantially complementary sequence (eg, complementary of about 50 to 100%, or about 60 to 100% or about 70 to 100% or about 80 to 100% or about the 85, 90, 95 at 100% throughout the entire sequence or portion of the sequences) aa), b), c) or d); Y
g) a fragment of any one of a) to d).
Also described herein is an expression library that may comprise a library of polynucleotides described herein. Each polynucleotide can be contained within an expression vector.
Arrays and kits comprising a library of polynucleotide sequences (comprising at least one polynucleotide such as complementary sequences) described herein are also encompassed herein.
Also disclosed herein is a pharmaceutical composition for inhibiting osteoclast differentiation (osteoclasia and osteoclasia-related diseases or disorders), wherein the pharmaceutical composition may comprise, for example:
a) an isolated polynucleotide as defined herein (eg, capable of inhibiting osteoclast differentiation); Y
b) a pharmaceutically acceptable carrier.
Also described herein is a method of inhibiting osteoclast differentiation (eg, to inhibit osteoclasia or to improve osteoclasia) in a mammal (individual) in need thereof (or in a mammalian cell), wherein the method may comprise the administration of an isolated polynucleotide (eg, capable of inhibiting osteoclast differentiation) or of a suitable pharmaceutical composition comprising such a suitable polynucleotide.
In accordance with the present invention, the mammal in need thereof may suffer, for example and without limitation, a condition selected from the group consisting of osteoporosis, osteopenia, osteomalacia, hyperparathyroidism, hyperthyroidism, hypogonadism, thyrotoxicosis, systemic mastocytosis, adult hypophosphatasia, hypercorticalism , Osteogenesis imperfecta, Paget's disease, Cushing's disease / syndrome, Turner's syndrome, Gaucher's disease, Ehlers-Danlos syndrome, Marfan syndrome, Menkes syndrome, Fanconi syndrome, multiple myeloma, hypercalcemia, hypocalcemia, arthritis, periodontitis, rickets (including vitamin D-dependent rickets types I and II, and X-linked hypophosphatemic), fibrogenesis imperfecta bone, osteosclerotic disorders such as pycnodysostosis and damage caused by inflammatory processes mediated by macrophages, etc.
In another aspect, the present invention relates to the use of an isolated polynucleotide (eg, capable of inhibiting osteoclast differentiation) for the preparation of a medicament for the treatment of an osteoclassical disease.
The present invention, in another aspect thereof, provides a pharmaceutical composition to promote the differentiation of osteoclasts in a mammal in need thereof. The pharmaceutical composition can comprise, for example:
to. an isolated polynucleotide (eg, capable of promoting osteoclast differentiation); Y
ES 2 397 441 T3
b. a pharmaceutically acceptable carrier.
Also described herein is a method of promoting osteoclast differentiation in a mammal in need thereof (or a mammalian cell), wherein the method may comprise, for example, administration of an isolated polynucleotide (e.g. g., capable of promoting osteoclast differentiation) or a suitable pharmaceutical composition as described above.
The present invention further relates to the use of an isolated polynucleotide (eg, capable of promoting osteoclast differentiation) for the preparation of a medicament for the treatment of a disease associated with insufficient osteoclasia (eg, hyperostosis) or excessive bone growth.
Also described herein is the use of at least one polynucleotide that can be selected from the group consisting of:
a) a polynucleotide comprising any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86,
b) a polynucleotide comprising the open reading frame of any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86,
c) a polynucleotide that may comprise a transcribed or transcribable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, SEQ ID No. 85 or SEQ ID No. 86, which may be , for example, free from the untranslated or untranslatable portion (s);
d) a polynucleotide that may comprise a translated or translatable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, SEQ ID No. 85, or SEQ ID No. 86 (eg, portion encoding),
e) a polynucleotide comprising a substantially identical sequence (eg, an identity of about 50 to 100%, or about 60 to 100% or about 70 to 100% or about 80 to 100% or about the 85, 90, 95 at 100% throughout the entire sequence or portion of the sequences) aa), b), c) or d);
f) a polynucleotide comprising a substantially complementary sequence (eg, a complementarity of about 50 to 100%, or about 60 to 100% or about 70 to 100% or about 80 to 100% or about the 85, 90, 95 at 100% throughout the entire sequence or portion of the sequences) aa), b), c) or d);
g) a fragment of any one of a) to f); Y
h) a library comprising any one of a) to g) in the diagnosis of a condition related to bone remodeling (an osteopathy).
Also described herein are kits for the diagnosis of a condition related to bone remodeling. The kit can comprise a polynucleotide as described herein.
Also described herein is an isolated polypeptide (polypeptide sequence) involved in osteoclast differentiation (in a mammalian or a mammalian cell thereof). The polypeptide may comprise (or consist of) a sequence selected from the group consisting of:
a) any one of SEQ ID Nos. 48 to 80,
b) a polypeptide that can be encoded and / or is encoded by any one of SEQ ID No. 1 to 33, SEQ ID No. or SEQ ID No. 86 (its coding portion),
c) a biologically active fragment of any one of a) or b),
d) a biologically active analog of any one of a) or b).
According to the present invention, the biologically active analog may comprise, for example, at least one amino acid substitution (conservative or non-conservative) compared to the original sequence. In accordance with the present invention, the analog may comprise, for example, at least one amino acid substitution, deletion or insertion in its amino acid sequence.
The substitution can be conservative or non-conservative. The polypeptide analog may be a biologically active analog or an immunogenic analog that may comprise, for example, at least one amino acid substitution (conservative or non-conservative), for example 1 to 5, 1 to 10, 1 to 15, 1 to 20, 1 to 50, etc. (including any number in between) compared to the original sequence. An immunogenic analog can comprise, for example, at least one amino acid substitution compared to the original sequence and can still be bound by a specific antibody against the original sequence.
ES 2 397 441 T3
In accordance with the present invention, a polypeptide fragment can comprise, for example, at least 6 consecutive amino acids, at least 8 consecutive amino acids or more, of an amino acid sequence described herein.
Also described herein is a pharmaceutical composition that may comprise, for example, a polypeptide as described herein and a pharmaceutically acceptable carrier.
Disclosed herein are methods for modulating osteoclast differentiation in a mammal in need thereof (or a mammalian cell), wherein said methods may comprise administration of an isolated polypeptide (eg, capable to promote osteoclast differentiation) or a suitable pharmaceutical composition described herein.
In other aspects, the present invention relates to the use of an isolated polypeptide (eg, capable of promoting osteoclast differentiation) for the preparation of a medicament for the treatment of a disease associated with insufficient osteoclasia.
Procedures for ameliorating osteoclasia in an individual in need are also encompassed by this document, wherein said procedure may comprise, for example, administration of an isolated polypeptide (eg, capable of inhibiting osteoclast differentiation) or of suitable pharmaceutical compositions which may comprise such a polypeptide.
In accordance with the present invention, the mammal may suffer, for example, a condition selected from the group consisting of osteoporosis, osteopenia, osteomalacia, hyperparathyroidism, hyperthyroidism, hypogonadism, thyrotoxicosis, systemic mastocytosis, adult hypophosphatasia, hypercorticalism, osteogenesis imperfecta, disease of Paget, Cushing's disease / syndrome, Turner syndrome, Gaucher disease, EhlersDanlos syndrome, Marfan syndrome, Menkes syndrome, Fanconi syndrome, multiple myeloma, hypercalcemia, hypocalcemia, arthritis, periodontitis, rickets (including vitamin D-dependent rickets types I and II, and hypophosphatemic X-linked), fibrogenesis imperfecta of bone, osteosclerotic disorders such as pycnodysostosis and damage caused by inflammatory processes mediated by macrophages, etc.
In still another aspect, the present invention relates to the use of a polypeptide capable of inhibiting osteoclast differentiation in the preparation of a medicament for the treatment of an osteoclastic disease in an individual in need thereof.
Also described herein is a compound and the use of a compound capable of inhibiting (eg, in an osteoclast precursor cell) the activity or expression of a polypeptide which can be selected, for example, from the group consisting in SEQ ID No. 48 to 80 or a polypeptide encoded by SEQ ID No. 85 or by SEQ ID No. 86, in the preparation of a medicament for the treatment of osteopathy in an individual in need.
Also described herein is a method for diagnosing a condition related to an osteoclassical disorder or disease in an individual in need thereof. The method may comprise, for example, quantifying a polynucleotide described herein, such as, for example, a polynucleotide selected from the group consisting of those comprising or consisting of (a) SEQ ID Nos. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86, (b) a polynucleotide that may comprise the open reading frame of SEQ ID No. 1 to 33, SEQ ID No. 85 or SEQ ID No. 86, (c) a polynucleotide that may comprise a transcribed or transcribable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, SEQ ID No. 85 or SEQ ID No. 86, ( d) a polynucleotide that may comprise a translated or translatable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, SEQ ID No. 85 or SEQ ID No. 86, (e) substantially identical sequences to any one of (a) to (d); (f) sequences substantially complementary to any one of (a) to (e), or a polypeptide sequence that can be selected, for example, from the group consisting of SEQ ID Nos. 48 to 80 or a polypeptide encoded by SEQ ID No. 85 or SEQ ID No. 86, and analogs thereof in a sample from the individual compared to a standard or normal value.
Also described herein is an assay and method for identifying a gene and / or protein involved in bone remodeling. The assay and method may comprise silencing an endogenous gene from an osteoclast cell and supplying the cell with a candidate gene (or protein). A candidate gene (or protein) positively involved in bone remodeling can be identified by its ability to complement the silenced endogenous gene. For example, a candidate gene involved in osteoclast differentiation delivered to a cell in which an endogenous gene has been silenced may allow the cell to differentiate in the presence of an inducer such as, for example, RANKL.
Also described herein is a cell that expresses an exogenous form of any one of the polypeptides (including variants, analogs, etc.) or polynucleotides of the present invention (including substantially identical sequences, substantially complementary sequences, fragments , variants, orthologs, etc.).
The cell can be, for example, an osteocyte. The cell can be an osteoclast (at any level of differentiation).
ES 2 397 441 T3
As used herein, the term "exogenous form" is to be understood herein as a form that is not naturally expressed in the cell in question.
In another aspect, the present invention relates to an antibody (eg, isolated antibody), or antigen-binding fragment thereof, that can specifically bind to a protein or polypeptide described herein. The antibody can be, for example, a monoclonal antibody, a polyclonal antibody, an antibody generated by recombinant dNa technologies. The antibody can originate, for example, from a mouse, rat, or any other mammal.
The antibody can also be a human antibody that can be obtained, for example, from a transgenic non-human mammal capable of expressing human Ig genes. The antibody may also be a humanized antibody that may comprise, for example, one or more complementarity determining regions of non-human origin. It may also comprise a surface moiety of a human antibody and / or framework regions of a human antibody. The antibody can also be a chimeric antibody that can comprise, for example, variable domains of a non-human antibody and constant domains of a human antibody.
Suitable antibodies can also include, for example, an antigen-binding fragment, a Fab fragment, an F (ab ') 2 fragment, and a Fv fragment; or a single chain antibody comprising an antigen-binding fragment (eg, a single chain Fv).
The antibody can be mutated and selected based on an increase in affinity and / or specificity for one of a polypeptide described herein and / or based on a reduction in immunogenicity in a desired host.
The antibody may further comprise a detectable label attached thereto.
Described herein is a process for producing antibodies capable of binding to one of a polypeptide, polypeptide fragments, or polypeptide analogs described herein, the process being able to comprise:
a) immunizing a mammal (eg, mouse, a transgenic mammal capable of producing human Ig, etc.) with a suitable amount of a PSEQ described herein that includes, for example, a polypeptide fragment comprising at least 6 consecutive amino acids of a PSEQ;
b) collecting serum from a mammal; Y
c) isolating the specific antibodies against the polypeptide in the mammalian serum.
The method may further comprise the step of administering a second dose to the animal.
Also described herein is a process for producing a hybridoma that secretes an antibody that binds to a polypeptide described herein, the process may comprise:
a) immunizing a mammal (eg, mouse, a transgenic mammal capable of producing human Ig, etc.) with a suitable amount of a PSEQ thereof;
b) obtaining lymphocytes from the immunized animal obtained from (a);
c) fusing the lymphocytes with an immortalized cell to produce hybrid cells; Y
d) selecting hybrid cells that produce antibodies that specifically bind to a PSEQ thereof.
Also described herein is a method for producing an antibody that binds to one of the polypeptide described herein, the method may comprise:
a) synthesize a collection of antibodies (antigen-binding fragment) on phage or ribosomes;
b) repeatedly screening the library against a sample by contacting the phage or ribosomes with a composition comprising a polypeptide or polypeptide fragment described herein;
c) isolating the phage that binds to the polypeptide or polypeptide fragment; Y
d) obtaining an antibody from the phage or ribosomes.
The antibody described herein may thus be obtained, for example, from a library (eg, bacteriophage library) which may be prepared, for example, by
a) extraction of cells that are responsible for the production of antibodies in a host mammal;
b) isolation of RNA from cells of (a);
ES 2 397 441 T3
c) reverse transcription of the mRNA to produce cDNA;
d) amplification of the cDNA with a primer (antibody specific); Y
e) inserting the cDNA from (d) into a phage display vector or ribosome display cassette such that the antibodies are expressed on the phage or ribosomes.
The host animal can be immunized with the polypeptide and / or a polypeptide fragment and / or analog described herein to induce an immune response before removing the cells that are responsible for the production of the antibodies.
Described herein is a kit for specifically testing a polypeptide described herein, wherein the kit may comprise, for example, an antibody or antibody fragment capable of specifically binding to the polypeptide described herein.
The present invention further contemplates antibodies that can bind to PSEQ. Suitable antibodies can bind to unique antigenic regions or epitopes on the polypeptides, or a portion thereof. Epitopes and antigenic regions useful for generating antibodies can be found within proteins, polypeptides, or peptides by methods available to one of ordinary skill in the art. For example, unique and short peptide sequences can be identified in proteins and polypeptides that have little or no homology to known amino acid sequences. Preferably, the region of a protein selected to act as a peptide epitope or antigen is not completely hydrophobic; hydrophilic regions are preferable because these regions probably constitute surface epitopes rather than internal regions of proteins and polypeptides. These surface epitopes are more easily detected in samples that have been tested for the presence of proteins and polypeptides. Such antibodies can include, but are not limited to, polyclonal, monoclonal, chimeric, and single chain antibodies, Fab fragments, and fragments produced by a Fab expression library. The production of antibodies is well known to the person skilled in the art.
Peptides can be manufactured by any method known to those skilled in the art, for example, with the use of in vitro translation or chemical synthesis procedures. Short peptides that provide an antigenic epitope, but are too small by themselves to induce an immune response, can be conjugated to a suitable vehicle. Suitable vehicles and connection methods are well known in the art. Suitable carriers are typically large macromolecules such as proteins, polysaccharides, and amino acid polymers. Examples include serum albumin, keyhole limpet hemocyanin (Megathura crenulata), ovalbumin, polylysine, and the like. One skilled in the art can use available procedures and coupling reagents to connect the desired peptide epitope to such a vehicle. For example, coupling reagents can be used to form disulfide bridges or thioether bonds from the carrier to the peptide of interest. If the peptide lacks a disulfide group, one can be provided by the addition of a cysteine residue. Alternatively, the coupling can be accomplished by activating carboxyl groups.
The minimum size of peptides useful for obtaining antigen-specific antibodies can vary widely. The minimum size must be sufficient to provide an antigenic epitope that is specific for the protein or polypeptide. The maximum size is not critical unless it is desired to obtain antibodies against a particular epitope. For example, a large polypeptide can comprise several epitopes, one epitope that is particularly useful and a second epitope that is immunodominant. Typically, antigenic peptides selected from the present proteins and polypeptides will range from 5 to about 100 amino acids in length. However, more typically, such an antigenic peptide will be a maximum of about 50 amino acids in length and preferably a maximum of about 30 amino acids. It is usually desirable to select a sequence of about 6, 8, 10, 12, or 15 amino acids, up to about 20 or 25 amino acids.
Amino acid sequences that comprise useful epitopes can be identified in a number of ways. For example, the preparation of a series of short peptides that together span the entire protein sequence can be used to screen the entire protein sequence. One of skill in the art can screen a few large polypeptides for the presence of an epitope showing a desired reactivity and also progressively screen for overlapping and smaller fragments to identify a preferable epitope with the desired specificity and reactivity.
Antigenic polypeptides and peptides are useful for producing monoclonal and polyclonal antibodies. Antibodies against a polypeptide encoded by NSEQ polynucleotides, polypeptide analogs, or portions thereof can be raised by procedures that are well known in the art. Such antibodies can include, but are not limited to, polyclonal, monoclonal, chimeric, and single chain antibodies, Fab fragments, and fragments produced by a Fab expression library. Neutralizing antibodies, such as those that inhibit dimer formation, are especially preferred for therapeutic use. Monoclonal antibodies can be prepared by any technique that ensures the production of antibody molecules by continuous culture of cell lines. These include, but are not limited to, techniques of
ES 2 397 441 T3 hybridomas, human B-cell hybridoma and EBV-hybridoma. In addition, techniques developed for the production of chimeric antibodies can be used. Alternatively, the techniques described for the production of single chain antibodies can be employed. Fabs can also be generated that may contain specific binding sites for a polypeptide encoded by the NSEQ polynucleotides, or a portion thereof. Various immunoassays can be used to identify antibodies that have the desired specificity. Many protocols for immunoradiometric or competitive binding assays using either monoclonal or polyclonal antibodies with established specificities are well known in the art.
To obtain polyclonal antibodies, a given animal can be immunized with a protein or with a polypeptide. Serum from the animal can be collected and treated according to known procedures. The polyclonal antibodies against the protein or against the polypeptide of interest can then be purified by affinity chromatography. Techniques for producing polyclonal antisera are well known in the art.
Monoclonal antibodies (mAbs) can be generated by one of the many methods available to those skilled in the art, for example, by fusing the antibody-producing cells with immortalized cells, whereby a hybridoma is constructed. The general methodology for the fusion of antibody producing B cells to an immortal cell line is well within the scope of one of ordinary skill in the art. Another example is the generation of mAb from mRNA extracted from bone marrow and splenocytes of immunized animals by combinatorial antibody library technology.
One drawback of mAbs derived from animals or derived cell lines is that, although they can be administered to a patient for diagnostic or therapeutic purposes, they are often recognized as foreign antigens by the immune system and are inappropriate for continued use. Antibodies that are not recognized as foreign antigens by the human immune system have greater potential for diagnosis and treatment. Procedures for generating human and humanized antibodies are now well known in the art.
Chimeric antibodies can be constructed in which regions of a non-human mAb are replaced by their human counterparts. A preferable chimeric antibody is one that has amino acid sequences comprising one or more complementarity determining regions (CDRs) from a non-human mAb that binds to a polypeptide encoded by the NSEQ polynucleotides, or a portion thereof, grafted onto human framework regions (FW). Procedures for making such antibodies are well known in the art. The amino acid residues corresponding to CDRs and FWs are known to the person skilled in the art.
A multitude of procedures have been developed to preserve or improve the affinity for the antigen presented by the antibodies comprising the grafted CDRs. One way is to include in the chimeric antibody the foreign framework residues that influence the conformation of the CDR regions. A second way is to graft the foreign CDRs into the human variable domains with the closest homology to the foreign variable region. Thus, grafting one or more human CDRs onto a human antibody may also involve the substitution of amino acid residues that are adjacent to a particular CDR sequence or that are not contiguous to the CDR sequence, but are packaged against the CDR in the overall structure of the variable domain of the antibody and affecting the conformation of the CDR. Thus, humanized antibodies include human antibodies that comprise one or more non-human CDRs, as well as such antibodies in which other substitutions or replacements have been made to preserve or enhance binding characteristics.
Chimeric antibodies also include antibodies that have been humanized by replacing surface exposed residues that make the mAb appear human. Since the internal packaging of amino acid residues in the vicinity of the antigen-binding site remains unchanged, affinity is preserved. The substitution of the residues exposed on the surface of an encoded polypeptide by the polynucleotides of the antibody against NSEQ (or a portion thereof) according to the invention for the purpose of humanization does not mean the substitution of the residues of the CDR or from adjacent residues that influence affinity for a polypeptide encoded by the nucleotides of NSEQ, or a portion thereof.
Chimeric antibodies can also include antibodies in which some or all of the non-human constant domains have been replaced by the human equivalent. This strategy has the advantage that the antigen binding site remains intact. However, significant amounts of non-human sequences may be present, where the variable domains are derived entirely from non-human antibodies.
The antibodies described herein include human (eg, humanized) antibodies that are antibodies consisting essentially of human sequences. Human antibodies can be obtained from phage display libraries, where combinations of the human variable domains of the light and heavy chains are displayed on the surface of filamentous phages. Combinations of variable domains are typically displayed on filamentous phage as Fabs or scFv. The library can be screened for combinations of variable domains that have the desired antigen-binding characteristics that appear on phages. Preferable variable domain combinations are characterized by high affinity for a polypeptide encoded by the NSEQ polynucleotides, or a portion thereof. The
ES 2 397 441 T3 combinations of preferable variable domains can also be characterized by high specificity for a polypeptide encoded by the NSEQ polynucleotides, or a portion thereof, and by poor cross-reactivity with other related antigens. When screening with very large repertoires of antibody fragments, (2 to 10 x 10<sup>10</sup>) a good diversity of high affinity mAbs can be isolated, and many are expected to have subnanomolar order affinity for a polypeptide encoded by the NSEq polynucleotides, or a portion thereof.
Alternatively, human antibodies can be obtained from transgenic animals into which unreordered human Ig gene segments have been introduced and into which endogenous mouse Ig genes have been inactivated. Preferred transgenic animals contain very large contiguous Ig gene fragments that are greater than 1 Mb in size, but mAbs specific against the human polypeptide of moderate affinity can be generated from transgenic animals containing smaller gene loci. Transgenic animals capable of expressing only human Ig genes can also be used to generate polyclonal antiserum comprising antibodies of only animal origin.
The antibodies described herein may include those for which binding characteristics have been improved by direct mutation or by affinity maturation methods. Affinity and specificity can be modified or improved by mutation of CDRs and by screening for antigen-binding sites that have the desired characteristics. CDRs can be mutated in many ways. One way is to randomize each residue or residue combinations such that in a population of otherwise identical antigen-binding sites, all twenty amino acids can be found at particular positions. Alternatively, mutations along a range of CDR residues can be induced by error-prone PCR methods. Phage display vectors containing the heavy and light chain variable region gene can be propagated in mutant strains of E. coli. These mutagenesis methods are illustrative of the many procedures known to those of skill in the art.
The antibodies described herein can include whole anti-polypeptide antibodies, as well as antibody fragments and derivatives that comprise a binding site for a polypeptide encoded by the NSEQ polynucleotides, or a portion thereof. Derivatives are macromolecules that comprise a binding site linked to a functional domain. Functional domains can include, but are not limited to, signaling domains, toxins, enzymes, and cytokines.
Antibodies obtained by the means described herein may be useful for detecting derived proteins, variants, and polypeptides in specific tissues or body fluids. In addition, the detection of aberrantly expressed protein or protein fragments is evidence of a disease state. For example, the expression of the present polypeptides encoded by the NSEQ polynucleotides, or a portion thereof, may indicate that the protein is being expressed at an inappropriate rate or at an inappropriate developmental stage. Accordingly, the present antibodies may be useful for detecting diseases associated with the expression of the protein of the NSEQs described herein.
A number of protocols for measuring polypeptides, including ELISA, RIA, and FACS, are well known in the art and provide a basis for diagnosing abnormal or altered expression levels. Standard values for polypeptide expression are established by combining samples taken from healthy subjects, preferably humans, with antibodies against the polypeptide under complexing conditions. The amount of complex formed can be quantified by various procedures, such as photometric means. The amount of polypeptide expressed in disease samples can be compared to standard values. The deviation between the standard values and the problem could set the parameters for diagnosing or monitoring a disease.
The design of immunoassays is subject to a great deal of variation and many of these are known in the art. Immunoassays can use a monoclonal or polyclonal antibody reagent that is directed against an epitope on the antigen to be tested. Alternatively, a combination of monoclonal and polyclonal antibodies that are directed against more than one epitope can be used. The protocols can be based, for example, on competition, where competitive drug screening assays can be used in which neutralizing antibodies capable of binding to the polypeptide encoded by the NSEQ polynucleotides, or a portion thereof, specifically compete. with a problem compound by binding to the polypeptide. Alternatively, direct reactions between the antibody and the antigen or sandwich assays can be used, and the protocols can, for example, use solid supports or immunoprecipitation. In addition, to facilitate detection, the antibodies can be labeled with a reporter molecule. Assays that amplify the signal of a bound reagent are also known. Examples include immunoassays using avidin and biotin or using enzyme-labeled antibodies or antigen conjugates, such as ELISA assays.
Kits suitable for immunodiagnosis and containing the appropriate marker reagents include antibodies directed against the epitopes or antigenic regions of the protein in polypeptides, appropriately packaged with the remaining reagents and materials necessary for the performance of the assay, as well as a suitable kit. instructions for the test.
ES 2 397 441 T3
Also disclosed herein is a kit for specifically testing a polypeptide described herein, wherein the kit may comprise, for example, an antibody or antibody fragment capable of specifically binding to the polypeptide described herein.
The kit can be a diagnostic kit, which can comprise:
a) one or more antibodies described herein; Y
b) a detection reagent that may comprise an indicator group.
Antibodies can be immobilized on a solid support. The detection reagent can comprise, for example, an anti-immunoglobulin, protein G, protein A or lectin, etc. The reporter group can be selected, without limitation, from the group consisting of radioisotopes, fluorescent groups, luminescent groups, enzymes, biotin, and coloring particles.
Also described herein is a method for identifying an inhibitory (inhibiting, antagonistic) compound that may be capable of disrupting the function (activity) or expression of a polypeptide described herein, such as, for example, those that they can be selected from the group consisting of SEQ ID No. 48 to 80 or a polypeptide encoded by SEQ ID No. 85 or SEQ ID No. 86, and analogs thereof. The method may comprise contacting the polypeptide or a cell expressing the polypeptide with a candidate compound and measuring the function (activity) or expression of the polypeptide. A reduction in the function or activity of the polypeptide (compared to the absence of the candidate compound) can positively identify a suitable inhibitory compound.
Lack of function or activity may be related to a reduction in the ability of the polypeptide to promote osteoclast differentiation, such as differentiation of osteoclasts induced by an inducer described herein or known in the art.
The cell may unnaturally (endogenously) express (the polypeptide may not be substantially expressed in a cell) the polypeptide or analog or, alternatively, the expression of a naturally expressed polypeptide analog may be repressed.
For example, a suitable procedure for screening an inhibitor of SEQ ID No. 1 may comprise repressing the expression of the mouse ortholog of SEQ ID No. 25 in a mouse osteoclast cell and evaluating cell differentiation of osteoclast comprising SEQ IND # 1 in the presence or absence of a candidate inhibitor and, for example, an inducer of osteoclast differentiation (eg, RANKL).
Also described herein is a method of identifying an inhibitory (inhibiting, antagonistic) compound capable of disrupting the function (activity) or expression of a polypeptide such as, for example, SEQ ID No. 1 or SEQ ID No. 2. The method may comprise, for example, contacting the polypeptide (isolated) or a cell expressing the polypeptide with a candidate compound and measuring the function (activity) or expression of the polypeptide. A reduction in the function or activity of the polypeptide (compared to the absence of the candidate compound) can therefore identify a suitable inhibitory compound.
According to the present invention, the disturbed function or activity may be associated, for example, with a reduction in the ability of the polypeptide to inhibit or promote osteoclast differentiation.
The cell used to carry out the screening analysis may unnaturally (endogenously) express the polypeptide or analogs or, alternatively, the expression of a naturally expressed polypeptide analog may be repressed.
Also described herein is a method for identifying a positive or negative regulator of osteoclast differentiation. The method may comprise, for example, performing a paralyzing effect as described herein. The method may more particularly comprise a) providing an osteoclast cell with a compound (eg siRNA) capable of specifically inhibiting a target sequence (eg. g., a polynucleotide or polypeptide as described herein), b) inducing differentiation (eg, with an inducer such as, for example, RANKL) and c) determining the level of differentiation of the osteoclast cell (eg, measure the number of differentiated cells, their rate of differentiation, specific marker of differentiation, etc.).
After inhibition of a positive regulator, the level of differentiation of osteoclasts will appear low. After inhibition of a negative regulator, the level of differentiation of osteoclasts will appear elevated.
Another method of identifying a positive or negative regulator of osteoclast differentiation is to a) provide a cell with one of the target sequences described herein (polypeptide or polynucleotide capable of expressing a polypeptide) b) induce differentiation (e.g. g., with an inducer such as, for example, RANKL) and c) determining the level of differentiation of osteoclast cells (e. (g., measure the number of differentiated cells, their rate of differentiation, specific marker of differentiation, etc.).
ES 2 397 441 T3
A reported cell with a positive regulator of osteoclast differentiation can increase its level of differentiation. A cell provided with a negative regulator of osteoclast differentiation can decrease its level of differentiation.
Also described herein is a method for identifying a compound capable of interfering with osteoclast differentiation, wherein the method may comprise contacting a cell that includes a non-endogenous polynucleotide sequence comprising any one of SEQ ID n. 1 to 33, 85 or 86 (a coding portion) and quantify (eg, the number of) differentiated osteoclasts. A reduction in osteoclast differentiation in the presence of the compound compared to the absence of the compound may be indicative of an antagonist of osteoclast differentiation, whereas an increase in osteoclast differentiation in the presence of the compound compared to the The absence of the compound may be indicative of an agonist of osteoclast differentiation.
The cell can also comprise an endogenous form of a polynucleotide.
As used herein, the term "endogenous" means a substance that occurs naturally within an organism, tissue, or cell. The term "endogenous polynucleotide" refers to a chromosomal form of a polynucleotide or version of RNA (hnRNA, mRNA) produced by a chromosomal form of the polynucleotide. The term "endogenous polypeptide" refers to the form of the protein encoded by an "endogenous polynucleotide".
As used herein, the terminology "non-endogenous" or "exogenous" is used as opposed to "endogenous" in that the substance is provided from an external source, although it can be introduced into the cell. The term "non-endogenous polynucleotide" refers to a synthetic polynucleotide introduced into the cell and includes, for example and without limitation, a vector comprising a sequence of interest, a synthetic mRNA, an oligonucleotide comprising an NSEQ, and the like. The term "non-endogenous polypeptide" refers to the form of the protein encoded by a "non-endogenous polynucleotide."
Also described herein is a method for identifying a compound capable of interfering with osteoclast differentiation, wherein the method may comprise contacting a cell that includes within it a non-endogenous polypeptide sequence comprising any one of SEQ ID # 48-80, and quantify (eg, the number of) differentiated osteoclasts. A reduction in osteoclast differentiation in the presence of the compound compared to the absence of the compound may be indicative of an antagonist of osteoclast differentiation, whereas an increase in osteoclast differentiation in the presence of the compound compared to the The absence of the compound may be indicative of an agonist of osteoclast differentiation.
As used herein, the term "sequence identity" refers to (consecutive) nucleotides of a nucleotide sequence with reference to an original nucleotide sequence. Identity can be compared over a region or over the entire sequence of a nucleic acid sequence.
Thus, "identity" can be compared, for example, over a region of 3, 4, 5, 10, 19, 20 nucleotides or more (and any number in between). It is to be understood herein that non-identical nucleotide gaps can be found between identical nucleic acids. For example, a polynucleotide can have 100% identity to another polynucleotide on a portion thereof. However, when the entire sequence of both polynucleotides is compared, the two polynucleotides can have 50% of their overall (total) sequence identical to each other.
The polynucleotides described herein or the portion thereof that have a sequence identity of from about 50 to about 100%, or from about 60 to about 100%, or from about 100%, are encompassed herein. 70 to about 100%, or from about 80 to about 100%, or from about 85%, about 90%, about 95% to about 100%, with an original polynucleotide. Those of skill in the art know that a polynucleotide having about 50% to about 100% identity can function (eg, hybridize to a substantially complementary sequence) in a manner similar to a parent polynucleotide and thus therefore, it can be used in place of an original polynucleotide. For example, a polynucleotide (a nucleic acid sequence) can comprise or have about 50-100% identity to a parent polynucleotide over a defined region and can still function with the same efficiency or sufficiency.
Percent identity can be determined, for example, with a GAP, BESTFIT, or FASTA algorithm from version 7.0 of the Wisconsin Genetics Software Package, using the default gap weights.
As used herein, the term "sequence complementarity" refers to nucleotides (consecutive) of a nucleotide sequence that are complementary to a reference (parent) nucleotide sequence. Complementarity can be compared over a region or over the entire sequence of a nucleic acid sequence.
ES 2 397 441 T3
The polynucleotides described herein or a portion thereof having a sequence complementarity of from about 50 to about 100%, or from about 60 to about 100%, or from about 70 to about 100% , or from about 80% to about 100%, or from about 85%, about 90%, from about 95% to about 100% with a parent polynucleotide are, therefore, encompassed by this document. Those skilled in the art know that a polynucleotide that has about 50% to about 100% complementarity to an original sequence can be sufficiently aligned to that sequence to carry out the present invention (eg, inhibit expression of the original polynucleotide).
An "analog" is to be understood herein as a molecule that has a similar biological activity and chemical structure as a polypeptide described herein. An "analog" can have a sequence similarity to that of an original sequence or a portion of an original sequence and can also have a modification of its structure as explained herein. For example, an "analog" can have at least 90% sequence similarity to an original sequence or a portion of an original sequence. An "analog" can also have, for example; at least 70% or even 50% sequence similarity (or less, viz. at least 40%) to an original sequence or a portion of an original sequence.
Similarly, an "analog" referred to a polypeptide may have, for example, at least 50% sequence similarity to an original sequence with a combination of one or more modifications to an amino acid backbone or side chain, or an addition of a group or other molecule, etc.
"Polynucleotide" refers generally to any polyribonucleotide or polydeoxyribonucleotide, which may be unmodified RNA or DNA, or modified RNA or DNA. "Polynucleotides" include, without limitation, single and double stranded DNA, DNA that is a mixture of single and double stranded regions, single and double stranded RNA and RNA that is a mixture of single and double stranded regions, hybrid molecules comprising DNA and RNA that can be Single-stranded or, more typically, double-stranded, or a mixture of single-stranded and double-stranded regions. Furthermore, "polynucleotide" refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The term polynucleotide also includes DNA or RNA that contain one or more modified bases and DNA or RNA with modified backbones that give them stability or for other reasons. "Modified" bases include, for example, tritylated bases and unusual bases such as inosine. Numerous modifications can be made to DNA and RNA; thus "polynucleotide" encompasses chemically, enzymatically or metabolically modified forms of polynucleotides as typically found in nature, as well as the chemical forms of DNA and RNA characteristic of viruses and cells. "Polynucleotide" includes, but is not limited to, end-capped and linear molecules. "Polynucleotide" also encompasses relatively short polynucleotides, often referred to as oligonucleotides.
"Polypeptides" refers to any peptide or protein that comprises two or more amino acids linked together by peptide bonds or modified peptide bonds (ie, peptide isoesters). "Polypeptide" refers to both short chains, which are often referred to as peptides, oligopeptides, or oligomers, and to longer chains, which are often referred to as proteins. As described above, polypeptides can contain amino acids other than the 20 proteinogenic amino acids.
As used herein, the term "polypeptide analog" refers to mutants, variants, chimeras, fusions, deletions, additions, and any other type of modification made to a given polypeptide.
As used herein, the term "biologically active" refers to a variant or fragment that retains some or all of the biological activity of the natural polypeptide, namely, that is capable of promoting or inhibiting osteoclast differentiation. . The polypeptides or fragments of the present invention can also include "immunologically active" polypeptides or fragments. "Immunologically active polypeptides or fragments" may be useful for immunization purposes (eg, to generate antibodies).
Thus, biologically active polypeptides in the form of the original polypeptides, fragments (modified or not), analogues (modified or not), derivatives (modified or not), homologues (modified or not) of the polypeptides described herein are encompassed by the present invention.
Accordingly, any polypeptide that has a modification compared to a parent polypeptide that does not significantly destroy a desired biological activity will be encompassed herein. It is well known in the art that a number of modifications can be made to the polypeptides of the present invention without deleteriously affecting their biological activity. These modifications can, on the other hand, maintain or increase the biological activity of the original polypeptide, or they can optimize one or more of the particularities (eg, stability, bioavailability, etc.) of the polypeptides of the present invention that, in some case, it might be desirable. The polypeptides of the present invention may comprise, for example, those containing amino acid sequences modified either by natural processes, such as post-translational processing, or by chemical modification techniques that are well known in the art. Modifications can be
ES 2 397 441 T3 produce at any position in a polypeptide, including the polypeptide backbone, the amino acid side chains, and the amino and carboxyl ends. It will be appreciated that the same type of modification may be present to the same or different magnitude at various sites on the given polypeptide. Similarly, a given polypeptide can contain many types of modifications. It is to be understood herein that a modification of the polypeptides described herein will be encompassed by the present invention as long as the biological activity is similar to that of the original (parent) polypeptide.
As explained above, the modification of the polypeptide can comprise, for example, the insertion (eg, addition), deletion and substitution (ie, replacement) of amino acids, either conservative or non-conservative (eg, D amino acids, deamino acids) in the polypeptide sequence, where such changes do not substantially alter the overall biological activity of the polypeptide.
Examples of substitutions can be those that are conservative (that is, when a residue is replaced by another of the same general type or group) or, when desired, non-conservative (that is, when a residue is replaced by an amino acid of another type ). In addition, a non-naturally occurring amino acid may substitute for a naturally occurring amino acid (i.e., a conservative amino acid substitution that does not occur in nature or a non-conservative amino acid substitution that does not occur in nature. nature).
As is known, naturally occurring amino acids can be subclassified into acidic, basic, neutral and polar, or neutral and apolar. Furthermore, three of the encoded amino acids are aromatic. It may be useful for encoded polypeptides that differ from the particular polypeptide of the present invention to contain codon substitutions for amino acids, which are of the same type or group as the amino acid to be replaced. Thus, in some cases, the basic amino acids Lys, Arg, and His may be interchangeable; the acidic amino acids Asp and Glu can be interchangeable; the neutral polar amino acids Ser, Thr, Cys, Gln and Asn can be interchangeable; the apolar aliphatic amino acids Gly, Ala, Val, Ile, and Leu are interchangeable, but due to their size, Gly and Ala have a closer relationship, and Val, Ile, and Leu have another close relationship to each other, and the aromatic amino acids Phe, Trp and Tyr can be interchangeable.
It should further be noted that if the polypeptides are constructed synthetically, substitutions can also be made with amino acids that are not naturally encoded in DNA (non-naturally occurring amino acid or non-naturally occurring amino acid).
A non-naturally occurring amino acid is to be understood herein to be an amino acid that is not naturally occurring or is not found in a mammal. An amino acid that does not occur naturally comprises a D amino acid, an amino acid that has an acetylaminomethyl group connected to a sulfur atom of a cysteine, a pegylated amino acid, etc. Inclusion of a non-naturally occurring amino acid in a defined polypeptide sequence will therefore generate a derivative of the parent polypeptide. Non-naturally occurring amino acids (residues) also include the ω amino acids of the formula NH2 (CH2) nCOOH, where n is 2-6, neutral apolar amino acids, such as sarcosine, t-butylalanine, t-butylglycine, N -methylisoleucine, norleucine, etc. Phenylglycine can substitute for Trp, Tyr, or Phe; citrulline and methionine sulfoxide are neutral apolar, cysteic acid is acidic, and ornithine is basic. Proline can be substituted for hydroxyproline and retain conformational properties.
It is known in the art that analogs can be generated by surrogate mutagenesis and that they retain the same biological activity as the polypeptides of the present invention. These analogs have at least one amino acid residue in the removed protein molecule and a different residue inserted in its place. For example, a site of interest for surrogate mutagenesis may include, but is not limited to, sites identified as the active site (s), or immune site (s). Other sites of interest may be those, for example, where certain residues obtained from different species are identical. These positions can be important for biological activity. Examples of substitutions identified as "conservative substitutions" are shown in Table A. If such substitutions result in an unwanted change, then other types of substitutions, referred to as "exemplary substitutions" are introduced in Table A, or as further described herein with reference to amino acid classes, and screened for products.
In some cases, it may be interesting to modify the biological activity of a polypeptide by substituting, inserting or deleting amino acids. For example, modification of a polypeptide can lead to increased biological activity of the polypeptide, can modulate its toxicity, can lead to changes in bioavailability or stability, or can modulate its immune activity or immune identity. Substantial modifications of immune function or identity are accomplished by selecting for substitutions whose effect differs significantly in maintaining (a) the polypeptide backbone structure in the area of substitution, for example, as a sheet or helix conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the volume of the literal strand. The naturally occurring residues are divided into groups based on common side chain properties:
(1) hydrophobic: norleucine, methionine (Met), alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile) (2) neutral hydrophiles: cysteine (Cys), serine (Ser), threonine (Thr )
ES 2 397 441 T3 (3) acids: aspartic acid (Asp), glutamic acid (Glu) (4) basic: asparagine (Asn), glutamine (Gln), histidine (His), lysine (Lys), arginine (Arg) (5) residues that influence chain orientation: glycine (Gly), proline (Pro); and aromatics: tryptophan (Trp), tyrosine (Tyr), phenylalanine (Phe).
Non-conservative substitutions will entail the exchange of one member of one of these classes for another.
TABLE A. Exemplary amino acid substitution
<td>Original rest</td><td>Exemplary substitution</td><td>Conservative substitution</td>
<td>Wing (A)</td><td>Val, Leu, Ile</td><td>Val</td>
<td>Arg (R)</td><td>Lys, Gln, Asn</td><td>Lys</td>
<td>Asn (N)</td><td>Gln, His, Lys, Arg</td><td>Gln</td>
<td>Asp (D)</td><td>Glu</td><td>Glu</td>
<td>Cys (C)</td><td>To be</td><td>To be</td>
<td>Gln (Q)</td><td>Asn</td><td>Asn</td>
<td>Glu (E)</td><td>Asp</td><td>Asp</td>
<td>Gly (G)</td><td>Pro</td><td>Pro</td>
<td>His (H)</td><td>Asn, Gln, Lys, Arg</td><td>Arg</td>
<td>Ile (I)</td><td>Leu, Val, Met, Ala, Phe, norleucine</td><td>Leu</td>
<td>Leu (L)</td><td>Norleucine, Ile, Val, Met, Ala, Phe</td><td>Ile</td>
<td>Lys (K)</td><td>Arg, Gln, Asn</td><td>Arg</td>
<td>Met (M)</td><td>Leu, Phe, Ile</td><td>Leu</td>
<td>Phe (F)</td><td>Leu, Val, Ile, Ala</td><td>Leu</td>
<td>Pro (P)</td><td>Gly</td><td>Gly</td>
<td>Be (S)</td><td>Thr</td><td>Thr</td>
<td>Thr (T)</td><td>To be</td><td>To be</td>
<td>Trp (W)</td><td>Tyr</td><td>Tyr</td>
<td>Tyr (Y)</td><td>Trp, Phe, Thr, Ser</td><td>Phe</td>
<td>Val (V)</td><td>Ile, Leu, Met, Phe, Ala, norleucine</td><td>Leu</td>
It is to be understood herein that if a "range" or "group" of substances (eg amino acids), "substituents" or the like are mentioned, or if other types of a given characteristic are mentioned (eg , Temperature, pressure, chemical structure, time, etc.), the present invention relates to each and every one of the specific members, and to any combination of subranges or subgroups thereof, and explicitly incorporates them herein. Thus, any specified interval or group must be understood as a
ES 2 397 441 T3 abbreviated way of referring to each and every one of the members of an interval or group individually, as well as to each and every one of the possible subintervals or subgroups included in these; and in the same way with respect to any subintervals or subgroups in these. Thus, for example, with respect to a percentage (%) identity of approximately 80 to 100%, it should be understood that the% of each and every individual is specifically incorporated herein, as well as the subinterval, such as for example 80%, 81%, 84.78%, 93%, 99%, etc .; and in the same way with respect to other parameters such as concentrations, elements, etc.
Described herein is an isolated polynucleotide for use in the treatment and / or diagnosis of osteopathy and / or for use in modulating osteoclast differentiation, wherein the polynucleotide is differentially expressed in osteoclast cells. differentiated compared to undifferentiated osteoclast precursor cells. The isolated polynucleotide may comprise a member selected from a) a polynucleotide comprising any one of SEQ ID No. 1 to SEQ ID No. 33, 85 or 86; b) a polynucleotide comprising the open reading frame of any one of SEQ ID No. 1 to SEQ ID No. 33, 85 or 86; c) a polynucleotide comprising a transcribable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, 85 or 86; d) a polynucleotide comprising a translatable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, 85 or 86; e) a polynucleotide comprising a sequence substantially identical to any one of a) to d), f) a polynucleotide comprising a sequence substantially complementary to any one of a) to e), and / or g) a fragment of any one of a) af).
Also described herein is an isolated polypeptide sequence for use in the treatment and / or diagnosis of osteopathy and / or for use in modulating osteoclast differentiation, wherein the polypeptide is differentially expressed in the differentiated osteoclast cell compared to undifferentiated osteoclast precursor cell. The isolated polypeptide may comprise a sequence selected from a) any one of SEQ ID No. 48 to 80, b) a polypeptide encoded by any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or 86, c) a biologically active fragment of any one of a) or b), and / or d) a biologically active analog of any one of a) or b).
Also described herein is an isolated and / or purified antibody, wherein said antibody may be capable of specifically binding to a polypeptide comprising a polypeptide sequence encoded by any one of SEQ ID No. 85 or 86 and / or a fragment of at least 6 amino acids of said polypeptide. Also encompassed by the present invention is a hybridoma cell that can produce an antibody capable of specifically binding to a polypeptide encoded by SEQ ID No. 85 or 86 and / or a fragment of at least 6 amino acids of said polypeptide. Also encompassed herein is the use of an isolated polypeptide that may comprise a sequence selected from a) any one of SEQ ID Nos. 48 to 80, b) a polypeptide encoded by any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or 86, c) a biologically active fragment of any one of a) or b), and / or d) a biologically active analog of any one of a) or b) to detect an antibody that specifically binds to the polypeptide.
Also described herein is an immunoassay for the detection of antibodies that specifically bind to at least one isolated polypeptide sequence that is differentially expressed in differentiated osteoclast cells compared to undifferentiated osteoclast precursor cells that may comprise a sequence selected from a) any one of SEQ ID No. 48 to 80, b) a polypeptide encoded by any one of SEQ ID No. 1 to 33, SEQ ID No. 85 or 86, c) a biologically active fragment of any one of a) or b), and / or d) a biologically active analog of any one of a) or b) and / or a biologically active analog that may comprise at least one amino acid substitution in such sequence. The immunoassay may comprise the steps of: a) contacting a sample of a biological fluid sample from a mammal with the polypeptide and / or b) detecting the formation of the immune complex between the polypeptide and the antibodies in said sample.
Also described herein is a method for preventing osteopathy in a mammal in need thereof. The method may comprise administering to said mammal an isolated polynucleotide described herein and / or a pharmaceutical composition that may comprise a polynucleotide described herein.
Also described herein is a method for treating osteopathy in an individual in need thereof. The method may comprise the administration of a compound capable of interfering with the activity and / or expression of a polypeptide described herein, for example, any polypeptide consisting of SEQ ID Nos. 48 to 80 and / or a polypeptide encoded by any one of SeQ ID No. 1 to 33, SEQ ID No. 85 and / or 86.
Also described herein is an isolated and / or purified antibody. An antibody described herein may be capable of specifically binding to a polypeptide encoded by any one of SEQ ID Nos. 85, 86 and / or a fragment of at least 6 amino acids of said polypeptides. Also encompassed herein is a composition that may comprise such an antibody. Also described herein is a method of making an antibody. Such a method may comprise immunizing a non-human animal with an immunogenic fragment of a polypeptide encoded by, for example, SEQ ID No. 85 or 86 and / or a fragment of at least 6 amino acids of said polypeptide. Also described herein is a library of polynucleotide sequences that can be differentially expressed in a
ES 2 397 441 T3 differentiated osteoclast cell compared to an undifferentiated osteoclast precursor cell. The library may comprise any one of SEQ ID No. 85 and / or SEQ ID No. 86 and / or at least one member selected from a) a polynucleotide comprising any one of SEQ ID No. 1 to SEQ ID No. 33, b) a polynucleotide comprising the open reading frame of any one of SEQ ID No. 1 to SEQ ID No. 33, c) a polynucleotide comprising a transcribable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, d) a polynucleotide comprising a translatable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, e) a polynucleotide comprising a sequence substantially identical to any one of a) to d); f) a polynucleotide comprising a sequence substantially complementary to any one of a) to e), and / or g) a fragment of any one of a) to f).
Also described herein is a method for modulating osteoclast differentiation in an individual in need thereof. The method may comprise administering a compound capable of interfering with the activity and / or expression of a polypeptide such as SEQ ID No. 48 to 80 and / or a polypeptide encoded by any one of SEQ ID No. 1 to 33 , SEQ ID No. 85 or 86.
Also described herein is a pharmaceutical composition for modulating osteoclast differentiation. The pharmaceutical composition may comprise an isolated polynucleotide such as a) a polynucleotide comprising any one of SEQ ID No. 1 to SEQ ID No. 33, 85 or 86, b) a polynucleotide comprising the open reading frame of a any of SEQ ID No. 1 to SEQ ID No. 33, 85 or 86, c) a polynucleotide comprising a transcribable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, 85 or 86, d) a polynucleotide comprising a translatable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, 85 or 86, e) a polynucleotide comprising a sequence substantially identical to any one of a) to d), f) a polynucleotide comprising a sequence substantially complementary to any one of a) to e), and / or g) a fragment of any one of a) to f), and a pharmaceutically acceptable carrier.
Also described herein is a siRNA and / or shRNA molecule that can decrease the expression of a polynucleotide such as a) a polynucleotide comprising any one of SEQ ID No. 1 to SEQ ID No. 33, 85 or 86, b) a polynucleotide comprising the open reading frame of any one of SEQ ID No. 1 to SEQ ID No. 33, 85 or 86, c) a polynucleotide comprising a transcribable portion of any one from SEQ ID No. 1 to SEQ ID No. 33, 85 or 86, d) a polynucleotide comprising a translatable portion of any one of SEQ ID No. 1 to SEQ ID No. 33, 85 or 86, e) a polynucleotide comprising a sequence substantially identical to any one of a) to d), f) a polynucleotide comprising a sequence substantially complementary to any one of a) to e), and / or g) a fragment of any one of a) to f).
In particular, it should be understood herein that the processes of the present invention include each and every one of the individual steps described by them, as well as those defined as definitely including certain steps or excluding certain steps or a combination of both; For example, an exclusion definition for a method of the present invention can be read as follows: "as long as said polypeptide does not comprise or does not consist of SEQ ID No. 34 or the open reading frame of SEQ ID No. 34 "or" as long as said polypeptide does not comprise or does not consist of SEQ ID No. 82 "or" as long as said polynucleotide fragment or said polypeptide fragment is less than X units long (p. nucleotides or amino acids) or more than X units (eg nucleotides or amino acids) '.
Other objects, features, advantages, and aspects of the present invention will be apparent to those skilled in the art from the description that follows. However, it should be understood that the description and specific examples that follow, while indicating preferred embodiments of the invention, are offered for illustrative purposes only.
BRIEF DESCRIPTION OF THE DRAWINGS
In the attached drawings:
For each of Figures 1 to 34 and 38 to 39, macroarrays were prepared by amplifying RNA with RAMP from human precursor cells (AF 1) and from intermediate differentiated (AF 2-3) and mature osteoclasts from four human donors (AF 4) and 30 different normal human tissues [adrenal gland (A5), liver (B5), lung (C5), ovary (D5), skeletal muscle (E5), heart (F5), cervix (G5), thyroid ( H5), breast (A6), placenta (B6), adrenal cortex (C6), kidney (D6), vena cava (E6), fallopian tube (F6), pancreas (G6), testicle (H6), jejunum (A7), aorta (B7), esophagus (C7), prostate (D7), stomach ( E7), spleen (F7), ileum (G7), trachea (A8), brain (B8), colon (C8), thymus (D8), small intestine (E8), bladder (F8) and duodenum (G8)]. The STAR double-stranded DNA clone representing the corresponding SEQ ID No. was labeled with<sup>32</sup>P and hybridized to the macroarray. The probe labeling reaction was also enriched with an Arabidopsis double-stranded DNA sequence, which hybridizes to its own sequence (M) deposited on the macroarray to serve as a control for the labeling reaction. Quantification of the hybridization signal at each point was performed with a STORM 820 Phosphorimager and ImageQuant TL software (Amersham Biosciences, Piscataway, NJ). As a basal level, a log2 value was used that represents the average of the signals for the precursors (AF 1) and was subtracted from the log2 value obtained for each of the remaining samples in order to determine their relative abundance in comparison with the precursors, and was represented in a bar graph (right panel).
ES 2 397 441 T3
Figure 1 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 1 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 2 is a drawing of matrix hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 2 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 3 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 3 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 4 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 4 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 5 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 5 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 6 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 6 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 7 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 7 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 8 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 8 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 9 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 9 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 10 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 10 of the corresponding STAR. The hybridization results obtained confirm its induction in all human osteoclast samples as the expression is generally higher in the more mature osteoclasts (AF
ES 2 397 441 T3
2-4) than in the precursors (AF 1) and there is little or no expression in all or most of the normal tissues (AH 5-6 and AG 7-8);
Figure 11 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 11 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 12 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 12 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 13 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 13 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 14 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 14 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 15 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 15 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 16 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 16 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 17 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 17 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 18 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 18 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 19 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 19 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 20 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for human-specific SEQ ID No. 20
ES 2 397 441 T3 osteoclasts of the corresponding STAR. The hybridization results obtained confirm its induction in all human osteoclast samples as the expression is generally higher in the more mature osteoclasts (AF
2-4) than in the precursors (AF 1) and there is little or no expression in all or most of the normal tissues (AH 5-6 and AG 7-8);
Figure 21 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 21 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 22 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 22 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 23 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 23 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 24 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 24 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 25 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 25 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 26 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 26 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 27 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 27 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 28 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 28 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 29 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 29 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
ES 2 397 441 T3
Figure 30 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 30 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 31 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 31 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 32 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 32 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 33 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 33 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 34 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 34 of the corresponding STAR. The hybridization results obtained confirm its induction in all samples of human osteoclasts, since the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (AF 1) and there is little or no expression in all or most normal tissues (HA 5-6 and GA 7-8);
Figure 35 is a drawing showing the blocking effects of osteoclastogenesis due to attenuation of endogenous expression of SEQ ID No. 1 (AB0326) and SEQ ID No. 2 (AB0369) using shRNA . A significant decrease in the number of plurinucleated osteoclasts was observed from precursor cells infected with the shRNA of AB0326 (Figure 35A; lower panel) the and shRNA of AB0369 (Figure 1B, lower panel) compared to those of the shRNA of lacZ (Figure 35a and B; top panels). These results clearly indicated that the expression of the gene encoding SEQ ID No. 1 (AB0326) and SEQ iD No. 2 (AB0369) are necessary for osteoclast differentiation;
Figure 36 is a drawing showing the osteoclastogenesis blocking effects due to mouse ortholog for AB0326 (SeQ ID No. 35) in RAW model 264.7 using shRNA-0326.2 (SEQ ID No. 45). The RAW-0326.2 cell line produced significantly fewer osteoclasts (Figure 36, lower panel) than the cell line containing the randomized shRNA (Figure 36, upper panel). This result, together with that obtained in human osteoclast precursor cells using the lentiviral shRNA delivery system demonstrate that the AB0326 gene product is clearly needed for osteoclastogenesis in humans and mice;
Figure 37 is a drawing showing the results of a functional complementation assay for SEQ ID No. 1 (AB0326) in RAW-0326.2 cells to screen for inhibitors of osteoclastogenesis. RAW-0326.2 cells transfected with the empty pd2 vector are unable to form osteoclasts in the presence of the RANK ligand (middle panel), indicating that the mouse AB0326 shRNA is still capable of silencing the expression of the AB0326 gene in these cells. cells. Conversely, the human AB0326 cDNA (pd2-hAB0326) rescue transfected cells and thus differentiate more efficiently into osteoclasts in response to the RANK ligand (right panel). Wild-type RAW 264.7 cells containing the empty vector (pd2) do not have altered osteoclast formation in the presence of the RANK ligand (left panel), ruling out any effect due to pd2. Therefore, this complementation assay can be used to screen for inhibitors of human AB0326 polypeptide;
Figure 38 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 85 of the corresponding STAR. Macroarrays were prepared by RNA amplification with RAMP from human precursor cells (AF 1) and intermediate and mature differentiated osteoclasts from four human donors (AF 2-4) and 30 different normal human tissues [adrenal gland, liver,
ES 2 397 441 T3 lung, ovary, skeletal muscle, heart, cervix, thyroid, breast, placenta, adrenal cortex, kidney, vena cava, fallopian tube, pancreas, testicle, jejunum, aorta, esophagus, prostate, stomach, spleen, ileum, trachea, brain, colon, thymus, small intestine, bladder and duodenum (AH 5-6 and AG 7-8)]. The STAR clone representing SEQ ID No. 85 was labeled with<sup>32</sup>P and hybridized to the macroarray. The hybridization results obtained confirm its induction in all human osteoclast samples as the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (A1-F1) and there is little or no expression in all or most of the normal tissues (AH 5-6 and AG 7-8), and;
Figure 39 is a drawing of macroarray hybridization results and signal intensity quantification showing differential expression data for osteoclast-specific human SEQ ID No. 86 of the corresponding STAR. Macroarrays were prepared by RNA amplification with RAMP from human precursor cells (AF 1) and intermediate and mature differentiated osteoclasts from four human donors (AF 2-4) and 30 different normal human tissues [adrenal gland, liver, lung, ovary, skeletal muscle, heart, cervix, thyroid, breast, placenta, adrenal cortex, kidney, vena cava, fallopian tube, pancreas, testicle, jejunum, aorta, esophagus, prostate, stomach, spleen, ileum, trachea, brain, colon, thymus, small intestine, bladder and duodenum (AH 5-6 and GA 7-8)]. The STAR clone representing SEQ ID No. 86 was labeled with<sup>32</sup>P and hybridized to the macroarray. The hybridization results obtained confirm its induction in all human osteoclast samples as the expression is generally higher in the more mature osteoclasts (AF 2-4) than in the precursors (A1-F1) and there is little or no expression in all or most of the normal tissues (HA 5-6 and AG 7-8).
DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS
The applicant employed a carefully planned strategy to identify and isolate genetic sequences involved in osteoclastogenesis and bone remodeling. The process involved the following steps: 1) preparation of highly representative cDNA libraries from mRNA isolated from intermediate and mature differentiated precursors and osteoclasts of human origin; 2) isolation of the sequences induced during osteoclastogenesis; 3) identification and characterization of induced sequences; 4) selection of induced sequences for tissue specificity; and 5) determination of the blocking effects of osteoclastogenesis. The results explained in this description show the advantage of acting selectively on osteoclast genes that are specific to this type of differentiated cells and providing a more efficient screening procedure to study the genetic basis of diseases and disorders. Genes known to be involved in other areas of biology have been shown to play critical roles in osteoclastogenesis and osteoclast function. Genes that are known but not assigned a function up to the present disclosure have also been isolated and play a critical role in osteoclastogenesis and osteoclast function. Finally, new genes that intervene in the process have been identified; however, the applicant reserves its description until further studies have been completed.
The present invention is illustrated in more detail below in a non-limiting manner.
A. - Material and methods
Commercially available reagents quoted in the present invention were used according to the supplier's instructions, unless otherwise stated. Throughout the present description, certain starting materials were prepared as follows:
B. - Preparation of cells differentiated into osteoclasts
The osteoclast precursor cell line RAW 264.7 (RAW) and human precursor cells (peripheral blood mononucleated lymphocytes or CD34 + progenitors) are well known in the art as human and murine models of osteoclastogenesis. These human and murine osteoclasts are therefore excellent sources of material for isolating and characterizing genes specialized in osteoclast function.
Human primary osteoclasts were differentiated from peripheral blood mononucleated lymphocytes mobilized by G-CSF (Cambrex, East Rutherdord, NJ) as described by the supplier in the presence of M-CSF at 35 ng / ml and RANK ligand at 100 ng / ml. Plurinucleated osteoclasts stained with TRAP were visible at 11-14 days. Osteoclasts were also derived from human osteoclast precursor cells (CD34 + progenitors) (Cambrex, East Rutherford, NJ) and cultured as described by the supplier. In the latter case, osteoclasts were obtained after 7 days.
RAW cells were purchased from the American Type Culture Collection and maintained in high glucose DMEM containing 10% fetal bovine serum and antibiotics. Cells were subcultured biweekly for a maximum of 10-12 passages. For osteoclast differentiation experiments, RAW cells were pelleted in 96-well plates at a density of 4 x 10<sup>3</sup> cells / well and multiplied for 24 hours. Differentiation was induced in high glucose DMEM, 10% charcoal treated fetal calf serum (Hyclone, Logan, UT), 0.05% SAB, antibiotics, macrophage colony stimulating factor (M-CSF) a 10 ng / ml and NF-κΒ receptor activator (RANK) ligand at 100 ng / ml. Plates were re-fed on day 3 and osteoclasts
ES 2 397 441 T3 were clearly seen on day 4. Typically, cells were stained for tartrate resistant acid phosphatase (TRAP) on day 4 or 5 unless otherwise noted. For TRAP staining, cells were washed with PBS and fixed in 10% formaldehyde for 1 hour. After two washes with PBS, the cells became slightly permeable in 0.2% Triton X-100 in PBS for 5 min before being washed in PBS. Staining was carried out at 37 ° C for 20-25 minutes in 0.01% AS-MX Naphthol Phosphate, 0.06% Fast Red Violet, 50mM Sodium Tartrate, 100mM Sodium Acetate , pH 5.2. The cells were visualized under a microscope.
C. - Procedure to isolate differentially expressed mRNA
Key to the discovery of differentially expressed sequences that will be unique to osteoclasts is the use of the applicant's patented STAR technology (Substractive Transcription-based Amplification of mRNA; US Patent No. 5,712,127, Malek et al. al., registered on January 27, 1998). In this procedure, mRNA isolated from intermediate and mature osteoclasts is used to prepare "problem RNA" which is hybridized to complementary single-stranded "subtractor DNA" prepared from osteoclast precursor mRNA and only "problem RNA" is recovered. "Without hybridizing, and is used to create cloned cDNA libraries, called" subtractive libraries ". Thus, "subtractive libraries" are enriched for differentially expressed sequences that include new and rare mRNAs that are often not detected in microarray hybridization analysis. These new and rare mRNAs are believed to be representative of important gene targets for the development of better diagnostic and therapeutic strategies.
The clones contained in the "subtractive libraries" are identified by DNA sequence analysis and their possible function is evaluated by acquiring the information available in the public databases (NCBI and GeneCard). The non-redundant clones are then used to prepare DNA microarrays, which are used to quantify their relative differential expression patterns by hybridization to fluorescent cDNA probes. Two classes of cDNA probes can be used, those that are generated from RNA transcripts prepared from the same subtractive libraries (subtractive probes), or from mRNA isolated from different osteoclast samples (standard probes). The use of subtractive probes provides increased sensitivity for detecting low abundance mRNA sequences that are preserved and enriched by STAR. Furthermore, the specificity of the sequences differentially expressed in osteoclasts is measured by hybridization of radiolabeled probes prepared from each selected sequence on macroarrays containing RNA from different osteoclast samples and different normal human tissues. Additionally, Northern blot analysis is performed to confirm the presence of one or more specific mRNA species in the osteoclast samples. After this, representative full-length cDNAs of the mRNA species and / or splice variants are cloned into E. coli DH10B.
A major challenge in gene expression profiling is the small amount of RNA available for molecular analysis. The amount of RNA isolated from many osteoclast samples or human specimens (needle aspiration, laser capture microdissection (LCM) samples, and transfected cell cultures) is often insufficient to prepare: 1) materials conventional subtractor and problem for STAR; 2) standard cDNA probes for DNA microarray analysis; 3) RNA macroarrays to assess expression specificity, 4) Northern blot analysis and 5) complete cDNA clones for subsequent biological validation and characterization, etc. Thus, Applicant has developed a proprietary technology called RAMP (RNA Amplification Procedure) (US Patent Application No. 11/000 958 published under US Patent No. US 2005 / 0153333A1 on July 14, 2005 and entitled "Selective Terminal Tagging of Nucleic Acids"), which linearly amplifies the mRNA contained in total RNA samples and produces microgram quantities of amplified RNA, sufficient for different analytical applications. The RNAs produced by RAMP are full-length mRNA-like sequences as a result of the proprietary procedure for adding a terminal sequence tag to the 3 'ends of single-stranded cDNA molecules, for use in linear amplification of transcription. More than 99.5% of the amplified sequences in RAMP reactions show <2-fold variability, and therefore RAMP provides unbiased RNA samples in sufficient quantity to allow the discovery of unique mRNA sequences involved in osteoclastogenesis.
D. - Preparation of a subtractive library of human osteoclasts
Two human primary stem cells from two different donors (Cambrex, East Rutherford, NJ) and the corresponding intermediate (day 3 and day 7) and mature (day 11 to 14) osteoclasts were prepared as described above. Isolation of cellular RNA followed by purification of mRNA from each was performed by standard procedures (Qiagen, Mississauga, ON). Following the teachings of Malek et al. (US Pat. No. 5,712,127), 2 pg of poly-A + mRNA from each sample were used to prepare highly representative cDNA libraries (> 2 x 10<sup>6</sup> CFU) into specialized plasmid vectors needed to prepare problem and subtractor materials. In each case, the first strand cDNA was synthesized with an oligo-dT11 primer with 3 'closing nucleotides (eg, A, G, or C) and containing a recognition site for NotI. The second strand cDNA was then synthesized according to the manufacturer's procedure for double stranded cDNA synthesis (Invitrogen, Burlington, ON) and the resulting double stranded cDNA was ligated to linkers containing a recognition site for AscI (New England Biolabs, Pickering, ON). Then, the double-stranded cDNAs were digested with the restriction enzymes AscI and NotI (New England Biolabs, Pickering, ON), they were purified from the excess of
ES 2 397 441 T3 linkers using an Invitrogen (Burlington, ON) cDNA fractionation column as specified by the manufacturer and each was ligated into specialized plasmid vectors: p14 (SEQ ID No. 36) and p17 + (SEQ ID No. 37) used to prepare the problem and subtractor materials, respectively. From here, the ligated cDNAs were introduced by transformation into E. coli DH10B to give rise to the desired cDNA libraries (RAW 264.7-precursor-p14, RAW 264.7-precursor-p17 +, RAW 264.7-osteoclasts-p14 and RAW 264.7-osteoclastosp17 +). The plasmid DNA pool from each cDNA library was purified and 2 pg aliquots of each were linearized with the restriction enzyme NotI. In vitro transcription of plasmid libraries in p14 and p17 + digested with NotI was then performed by T7 RNA polymerase and SP6 RNA polymerase, respectively (Ambion, Austin, TX).
Then, to prepare the problem and subtractor libraries with 3 'representation, a 10 pg aliquot of each of the in vitro synthesized RNAs was converted to double-stranded cDNA by first-strand cDNA synthesis as described above. followed by primer-directed synthesis of the second strand DNA [primer OGS 77 for p14 (SEQ ID No. 40) and primer OGS 302 for p17 + (SEQ ID No. 41)] by Taq Advantage-2 polymerase ( BD Biosciences Clontech, Mississauga, ON). The sequences corresponding to OGS 77 and OGS 302 were introduced into the RNA synthesized in vitro by means of the specialized vectors used to prepare the cDNA libraries. 6 1 pg aliquots of each double-stranded cDNA were then digested separately with one of the following restriction enzymes that recognize 4 bases RsaI, Sau3A1, MseI, MspI, MinPII, and Bsh1236I (MBI Fermentas, Burlington, ON), resulting in up to six possible 3 'fragments for each of the RNA species contained in the cDNA library. After digestion, the restriction enzymes were inactivated with phenol and the set of six reactions pooled. The restriction enzyme sites were then blunted with T4 DNA polymerase and ligated to linkers containing an AscI recognition site. Each linker-matched pooled DNA sample was digested with the restriction enzymes AscI and NotI, desalted, and ligated into the specialized plasmid vectors p14 and p17 (plasmid vector p17 is similar to plasmid vector p17 +, except for the part of the sequence corresponds to SEQ ID No. 41) and were introduced by transformation into E. coli DH10B. The plasmid DNA pool for each 3 'representation library in p14 and p17 was purified (Qiagen, Mississauga, ON) and an aliquot of 2 pg of each was digested with the restriction enzyme NotI, and well transcribed in vitro. with T7 RNA polymerase or with SP6 RNA polymerase (Ambion, Austin, TX). The 3 'proxy RNA in p14 was used directly as "test RNA", while the 3' proxy RNA in p17 was used to synthesize the single-stranded cDNA as described above, which was then served as the "subtractor DNA. ». Each reaction with the "subtractor DNA" was treated with RNase A and RNase H to remove RNA, phenol extracted and desalted before use.
The following 3 'proxy libraries were prepared:
Problem 1 (donor 1 - human intermediate osteoclast at day 3) -3 'enp14
Problem 2 (donor 1 - human intermediate osteoclast at day 7) -3 'enp14
Problem 3 (donor 1 - human mature osteoclast at day 11) -3 'on p14
Problem 4 (donor 2 - human intermediate osteoclast at day 3) -3 'enp14
Problem 5 (donor 2 - human intermediate osteoclast at day 7) -3 'enp14
Problem 6 (donor 2 - human mature osteoclast at day 13) -3 'on p14
Subtractor 1 (donor 1- human precursor at day 3) -3 'in p17
Subtractor 2 (donor 2 - human precursor at day 3) -3 'in p17
The samples of the test RNA were subtracted following the teachings of US Patent No. 5,712,127 with the corresponding subtractor DNA in a ratio of 1: 100 for 1 or 2 rounds following the teachings of Malek et al. (US Patent No. 5,712,127). Additionally, the control reactions were prepared that contained the test RNA and no subtractor DNA, and the test RNA plus the subtractor DNA without RNase H. The remaining test RNA in each reaction after subtraction was converted to double-stranded DNA, and a 5% volume was removed and amplified in a standard PCR reaction for 30 cycles for analytical purposes. The remaining 95% that had only the subtractor plus the subtractive samples with RNase H was amplified 4 cycles by PCR, digested with the restriction enzymes AscI and NotI, and one half was ligated with the plasmid vector pCATRMAN (SEQ ID no. 38) and the other half with the plasmid vector p20 (SEQ ID No. 39). The bound materials were introduced by transformation into E. coli DH10B and the various clones contained in the libraries in pCATRMAN were collected for further analysis (DNA sequencing and hybridization), while the clones contained in each library in p20 were pooled for use as subtractive probes. Each 4-cycle cloned and amplified subtractive library contained between 25,000 and 40,000 colonies.
The following cloned subtractive libraries were prepared:
SL90: problem 1 (osteoclast at day 3) minus subtractor 1 (precursor) (1 round) in pCATRMAN;
ES 2 397 441 T3
SL91: problem 2 (osteoclast at day 7) minus subtractor 1 (precursor) (1 round) in pCATRMAN;
SL92: problem 3 (osteoclast at day 11) minus subtractor 1 (precursor) (1 round) in pCATRMAN;
SL108: problem 1 (osteoclast at day 3) minus subtractor 1 (precursor) (2 rounds) in pCATRMAN;
SL109: problem 2 (osteoclast at day 7) minus subtractor 1 (precursor) (2 rounds) in pCATRMAN;
SL110: problem 3 (osteoclast at day 11) minus subtractor 1 (precursor) (2 rounds) in pCATRMAN;
SL93: problem 4 (osteoclast at day 3) minus subtractor 2 (precursor) (1 round) in pCATRMAN;
SL94: problem 5 (osteoclast at day 7) minus subtractor 2 (precursor) (1 round) in pCATRMAN;
SL95: problem 6 (osteoclast at day 13) minus subtractor 2 (precursor) (1 round) in pCATRMAN;
SL87: problem 4 (osteoclast at day 3) minus subtractor 2 (precursor) (2 rounds) in pCATRMAN;
SL88: problem 5 (osteoclast at day 7) minus subtractor 2 (precursor) (2 rounds) in pCATRMAN;
SL89: problem 6 (osteoclast at day 11) minus subtractor 2 (precursor) (2 rounds) in pCATRMAN
A 5 μl aliquot of the 30-cycle PCR amplified subtractive materials described above were visualized on a 1.5% agarose gel containing ethidium bromide and then transferred to a Hybond N + nylon membrane (Amersham Biosciences, Piscataway, NJ) for Southern blot analysis. By using radiolabeled probes specific to the CTSK gene (cathepsin K: NM_000396.2), which is known to be induced in osteoclasts, and GAPDH (glyceraldehyde-3-phosphate dehydrogenase; M32599.1), which is a gene of maintenance that is not differentially expressed, it was evident that there was subtraction of GAPDH, but not of CTSK. Based on these results, it was anticipated that the subtracted libraries were enriched for the induced sequences of differential expression.
E. - Identification of the sequences and annotation of the clones contained in the subtractive libraries:
6912 independent colonies contained in the pCATRMAN subtracted libraries (SL87-95 and SL108-110) described above were randomly picked in 60 µl of sterile water using a Qbot (Genetix Inc., Boston, MA). 42 μl of each were then used in a standard 100 μl PCR reaction containing oligonucleotide primers OGS 1 and OGS 142 and amplified for 40 cycles [94 ° C for 10 minutes, 40x (94 ° C for 40 s, 55 ° C for 30 s and 72 ° C for 2 min) followed by 72 ° C for 7 min] in 96-well microtiter plates using HotStart ™ Taq polymerase (Qiagen, Mississauga, ON). Completed PCR reactions were desalted in 96-well filter plates (Corning) and amplicons were recovered in 100 µl of 10 mM Tris (pH 8.0). A 5 μl aliquot of each PCR reaction was visualized on a 1.5% agarose gel containing ethidium bromide and only reactions containing a single amplified product were selected for DNA sequence analysis using standard DNA sequencing. DNA performed on an ABI 3100 instrument (Applied Biosystems, Foster City, CA). Each DNA sequence obtained was given a sequence identification number and entered into a database for subsequent screening and annotation.
Each sequence was subjected to BLAST analysis with public databases (eg, NCBI). These sequences did not include the standard housekeeping genes (GAPDH, actin, most ribosomal proteins, etc.), which was a good indication that the subtractive library lacked at least the relatively abundant sequences that were not differentially expressed. .
Once the sequencing and annotation of the selected clones was complete, the next step involved the identification of the sequences that were actually induced in the osteoclasts compared to the precursors.
F. - Hybridization analysis to identify induced sequences
The PCR amplicons representing the annotated sequences of the libraries in pCATRMAN described above were used to prepare DNA microarrays. The purified PCR amplicons contained in 70 µl of the PCR reactions prepared in the previous section were lyophilized and each was reconstituted in 20 µl of the depot solution comprising 3X sSc and 0.1% sarcosyl. The DNA microarrays of each amplicon were then prepared in triplicate on CMT-GAP2 supports (Corning, Corning, NY) using the GSM 417 depositor (Affymetrix, Santa Clara, CA).
The DNA microarrays were then hybridized with subtractive or standard cy3 and cy5-labeled cDNA probes, as recommended by the vendor (Amersham Biosciences, Piscataway, NJ). Standard cDNA probes were synthesized from RAMP amplified RNA prepared from the different human osteoclast samples and the corresponding precursors. It is well known to the person skilled in the art that standard cDNA probes only provide poor detection sensitivity and consequently
ES 2 397 441 T3 sparse sequences contained in cDNA probes are usually not detected. Thus, hybridization analysis was also performed with cy3 and cy5-labeled subtractive cDNA probes obtained from subtractive libraries representing the different test and subtractor materials. These subtractive libraries may be enriched for low abundance sequences as a result of following the teachings of Malek et al., And therefore may provide increased sensitivity of detection.
All hybridization reactions were performed by the fluorophore exchange procedure as recommended by the supplier (Amersham Biosciences, Piscataway, NJ) and approximately 500 induced sequences (> 2 times) of possible differential expression were selected for further analysis.
G.- Determination of osteoclast specificity for the differentially expressed sequences that have been identified:
The differentially expressed sequences identified in section F for the different subtractive human osteoclast libraries were checked for osteoclast specific by hybridization to nylon membrane based macroarrays. The macroarrays were prepared with RNA amplified with RAMP from human precursors and osteoclasts (intermediate and mature) from six independent experiments from 4 different donors (3 male and 1 female) and 30 normal human tissues (adrenal gland, liver, lung, ovary, skeletal muscle, heart, neck, thyroid, breast, placenta, adrenal cortex, kidney, vena cava, fallopian tube, pancreas, testicle, jejunum, aorta, esophagus, prostate, stomach, spleen, ileum, trachea, brain, colon, thymus, small intestine, bladder and duodenum) purchased from the market (Ambion, Austin, TX). Due to the small amount of mRNA available for many of these samples, it was first necessary to amplify the mRNA using the RAMP methodology. Each amplified RNA sample was reconstituted at a final concentration of 250 ng / µl in 3X SSC and 0.1% sarcosyl in a 96-well microtiter plate and 1 µl was plated on Hybond N + nylon membranes using the MULTIPRINT apparatus. ™ (VP Scientific, San Diego, CA), air dried and cross-linked with UV light. They were radiolabeled separately with a-<sup>32</sup>P-dCTP 400 different sequences selected between L87-95 and SL108-110 by the supplier's recommended random priming procedure (Amersham, Piscataway, NJ) and were used as probes in the macroarrays. Hybridization and washing steps were performed following standard procedures well known to those of skill in the art.
Of the 500 sequences tested, approximately 85% were found to be induced in all osteoclast RNA samples that were used to prepare the macroarrays. However, many of these sequences were also easily detected in most different normal human tissues. Based on these results, sequences that appeared to be associated with experimental variability and those that were detected in many of the other human tissues at a significantly high level were eliminated. Consequently, only the 35 sequences that appeared to be induced and highly specific for osteoclasts were selected for biological validation studies. This set of 35 genes includes 4 (SEQ ID No. 30-33) in which a significant induction was detected in mature osteoclasts compared to most normal tissues, but since the expression of these genes was overall lower in precursor cells, they appeared to increase in normal tissues after quantitation (Figure 30-33, bar graph). However, its expression in normal tissues was still relatively lower than in mature osteoclasts. Thus, these genes may still be important regulators of osteoclastogenesis and osteoclasia and were therefore selected for biological validation. This subset of 35 sequences did not include other genes that had already been identified, such as CTSK, TRAP, MMP9, CST3 and CKB among others, since in the literature it had already been previously described that they were induced in osteoclasts. The macroarray data for CST3 (SEQ ID No. 34) is included to exemplify the hybridization pattern and specificity of a gene that is already known to be a key regulator of the osteoclast resorption process. One gene (ANKH; SEQ ID No. 17) was included in the subset of 35 genes although it was previously described in the databases (NCBI-Gene) that its function was in bone mineralization. However, the bone phenotype observed as a result of mutations in the ANKH gene was not specifically connected to its induction in osteoclasts. Thus, our data suggest that the important function of ANKH may be associated with osteoclast activity during bone remodeling.
Figures 1-33, 38 and 39 show the patterns of the macroarrays and the quantification of the hybridization signals of osteoclasts and normal human tissues against precursor cells for the 35 sequences selected for biological validation. Among the 35 sequences selected there were 24 genes with a functional annotation, 9 genes without any functional annotation, and 2 new sequences (genomic milestones). The identification of the gene products involved in the regulation of osteoclast differentiation and functioning has thus led to the discovery of new targets for the development of new specific treatments for pathological states characterized by abnormal bone remodeling. Representative sequences listed in Table 1 are presented below and the corresponding sequences are illustrated in Table 5.
SEQ ID # 1:
SEQ ID No. 1 (Table 5) corresponds to a previously identified gene that encodes a hypothetical protein,
LOC284266 of unknown function (see Table 1). We have shown that this gene is remarkably induced
ES 2 397 441 T3 in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 1), which had not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 2:
SEQ ID No. 2 (Table 5) corresponds to a previously identified gene encoding a predicted open reading frame, C6orf82, of unknown function (see Table 1). We have shown that this gene is markedly induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 2), which has not been previously described. At least 5 transcription variants of this gene have been identified so far, which encode the 3 protein isoforms that had been identified so far (NCBI). Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 3:
SEQ ID No. 3 (Table 5) corresponds to a previously identified gene that encodes a hypothetical protein, LOC133308, of unknown function (see Table 1), but which may be involved in the pH regulation process. We have shown that this gene is remarkably induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 3), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 4:
SEQ ID No. 4 (Table 5) corresponds to a previously identified gene encoding a hypothetical protein, LOC116211, of unknown function (see Table 1). We have shown that this gene is remarkably induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 4), which had not been previously described. Therefore, it is implicit that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 5:
SEQ ID No. 5 (Table 5) corresponds to a previously identified gene encoding a predicted protein, LOC151194 (similar to liver carcinoma associated antigen HCA557b), of unknown function (see Table 1). We have shown that this gene is markedly induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 5), which had not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 6:
SEQ ID No. 6 (Table 5) corresponds to a previously identified gene encoding a protein, chemokine ligand 5 with CXC motif (CXCL5), which is an inflammatory chemokine belonging to the CXC chemokine family (see Table 1). We have shown that this gene is remarkably induced in mature osteoclasts compared to precursor cells and other normal human tissues (Figure 6), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 7:
SEQ ID No. 7 (Table 5) corresponds to a previously identified gene that encodes a protein, ATPase, the lysosomal accessory protein 2 transporter of H<sup>+</sup> (ATP6AP2), which is associated with adenosine triphosphatases (ATPases). Proton-transporting ATPases play fundamental roles in energy conservation, secondary active transport, acidification of intracellular compartments, and cell pH homeostasis (see Table 1). We have shown that this gene is remarkably induced in mature osteoclasts compared to precursor cells and other normal human tissues (Figure 7), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 8:
SEQ ID No. 8 (Table 5) corresponds to a previously identified gene encoding a protein, the ubiquitin-specific protease 12-type protein 1 (USP12), which is associated with ubiquitin-dependent protein catabolism (see Table 1). We have shown that this gene is markedly induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 8), which had not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
ES 2 397 441 T3
SEQ ID No. 9:
SEQ ID No. 9 (Table 5) corresponds to a previously identified gene encoding a protein, isoform 1 of the ubiquitin-conjugating enzyme E2E (UBC4 / 5 homologous, yeast) (UBE2E1), which is associated to ubiquitin-dependent protein catabolism (see Table 1). So far 2 transcription variants and protein isoforms have been described for this gene. We have shown that this gene is remarkably induced in mature osteoclasts compared to precursor cells and other normal human tissues (Figure 9), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 10:
SEQ ID No. 10 (Table 5) corresponds to a previously identified gene encoding a protein, the emopamil binding protein-like protein (EBPL), which may have cholestenol Δ-isomerase activity (see Table 1). We have shown that this gene is markedly induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 10), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 11
SEQ ID No. 11 (Table 5) corresponds to a previously identified gene that encodes a protein, differentiation and development enhancing factor 1 (DDEF1), which may be involved in cell mobility and adhesion (see Table 1). We have shown that this gene is remarkably induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 11), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 12
SEQ ID No. 12 (Table 5) corresponds to a previously identified gene that encodes a protein, member 7 of the SLAM family (SLAM7), which may have receptor activity and be involved in cell adhesion, but is not yet fully characterized (see Table 1). We have shown that this gene is remarkably induced in mature osteoclasts compared to precursor cells and other normal human tissues (Figure 12), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 13
SEQ ID No. 13 (Table 5) corresponds to a previously identified gene that encodes a protein, the ubiquitin conjugation enzyme E2E 3 (homologous to UBC4 / 5, yeast) (UBE2E3), which is associated with protein catabolism ubiquitin-dependent (see Table 1). So far 2 transcription variants have been documented, encoding the same isoform of the protein. We have shown that this gene is remarkably induced in mature osteoclasts compared to precursor cells and other normal human tissues (Figure 1), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 14
SEQ ID No. 14 (Table 5) corresponds to a previously identified gene encoding a protein, galanin (GAL), which is associated with neuropeptide hormone activity (see Table 1). We have shown that this gene is remarkably induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues except for the colon (Figure 14), which had not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 15
SEQ ID No. 15 (Table 15) corresponds to a previously identified gene encoding a protein, nuclear cytokine-like factor n-pac (N-PAC), which may have oxidoreductase activity (see Table 1). We have shown that this gene is markedly induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 15), which has not been previously described. However, some overexpression of this gene was observed, although below that of mature osteoclasts, in the heart, fallopian tube, spleen and cervix. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 16
SEQ ID No. 16 (Table 5) corresponds to a previously identified gene that encodes a protein, integrin α X (CD11C antigen (p150), α polypeptide) (ITGAX), which is involved in cell adhesion and ion fixation
ES 2 397 441 T3 (see table 1). We have shown that this gene is remarkably induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 16), which has not been previously described. It is observed that this gene has a minimal expression, although much lower than in mature osteoclasts, in the adrenal gland, lung and spleen among normal tissues. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 17:
SEQ ID No. 17 (Table 5) corresponds to a previously identified gene encoding a protein, homologous to progressive ankylosis (mouse) (ANKH), which is involved in the regulation of pyrophosphate levels, and it is suggested that it is a possible mechanism for regulating tissue calcification (see Table 1). We have shown that this gene is remarkably induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 17), which has not been previously described. However, this gene has been reported to be involved in bone mineralization, but without evidence of its induction in osteoclasts (Malkin et al., 2005). Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 18:
SEQ ID No. 18 (Table 5) corresponds to a previously identified gene that encodes a protein, ATPase, V1 subunit A that transports H<sup>+</sup> and 70 kDa lysosomal, which is involved in a rotational mechanism of hydrogen-transporting ATPase activity (see Table 1). We have shown that this gene is markedly induced in mature osteoclasts compared to precursor cells and other normal human tissues (Figure 18), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 19
SEQ ID No. 19 (table 5) corresponds to a previously identified gene encoding an open reading frame encoding the FLJ10874 protein (chromosome 1 open reading frame 75), which has no known function (see table 1). We have shown that this gene is markedly induced in mature osteoclasts compared to precursor cells and other normal human tissues (Figure 19), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 20
SEQ ID No. 20 (Table 5) corresponds to a previously identified gene encoding a protein, Integrin β1-binding protein 1 (ITGB1BP1), which has an important function during integrin-dependent cell adhesion (see Table 1). Two transcriptional variants and protein isoforms have been isolated for this gene. We have shown that this gene is markedly induced in mature osteoclasts compared to precursor cells and other normal human tissues (Figure 20), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 21:
SEQ ID No. 21 (table 5) corresponds to a previously identified gene encoding a protein, thioredoxin type 5 (TXNL5), which has no known function (see table 1). We have shown that this gene is remarkably induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues with the exception of the esophagus (Figure 21), which had not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 22
SEQ ID No. 22 (Table 5) corresponds to a previously identified gene encoding a protein, member E of the C-type lectin family 4 (CLECSF9), which has no known specific function (see Table 1). Members of this family share a common protein fold and have diverse functions, such as cell adhesion, intercellular signaling, glycoprotein turnover, and roles in inflammation and the immune response. We have shown that this gene is remarkably induced in mature osteoclasts compared to precursor cells and other normal human tissues, with the exception of the lung and spleen (Figure 22), which had not been previously described. At this point, we cannot rule out cross hybridization with family members in the lung and spleen. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 23
SEQ ID No. 23 (Table 5) corresponds to a previously identified gene encoding a protein, RAB33A, a member of the RAS (RAB33A) oncogene family, which has GTPase activity (see Table 1). We have
ES 2 397 441 T3 demonstrated that this gene is markedly induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues with the exception of the brain (Figure 23), which had not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 24
SEQ ID No. 24 (Table 5) corresponds to a previously identified gene that encodes a protein, Down syndrome critical region gene 1 (DSCR1), which interacts with calcineurin A and inhibits dependent signaling pathways. of calcineurin, possibly affecting the development of the central nervous system (see Table 1). There are 3 transcription variants and protein isoforms isolated to date. We have shown that this gene is remarkably induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 24), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 25
SEQ ID No. 25 (Table 5) corresponds to a previously identified gene that encodes a protein, the Ykt6 (YKT6) protein of the SNARE group, which is one of the SNARE recognition molecules involved in vesicular transport between secretory compartments. (see table 1). We have shown that this gene is remarkably induced in mature osteoclasts compared to precursor cells and other normal human tissues (Figure 25), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 26
SEQ ID No. 26 (Table 5) corresponds to a previously identified gene encoding a protein, actinin α1 (ACTN1), which is cytoskeletal and is involved in actin binding and adhesion (see Table 1) . We have shown that this gene is remarkably induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 26), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 27
SEQ ID No. 27 (Table 5) corresponds to a previously identified gene encoding a protein, the X homolog of the caseinolytic peptidase ClpX (E. coli) (CLPX), which may be involved in protein turnover (see Table 1). We have shown that this gene is remarkably induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 27), which has not been previously described. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 28
SEQ ID No. 28 (Table 5) corresponds to a previously identified gene encoding a protein, carbonic anhydrase II (CA2), which has carbonate dehydratase activity (see Table 1). Lack of this enzyme is associated with osteopetrosis and renal tubular acidosis (McMahon et al., 2001) and has been shown to be induced in mature osteoclasts under induced acid pH conditions (Biskobing and Fan, 2000). We have shown that this gene is remarkably induced in intermediate and mature osteoclasts compared to precursor cells regardless of the induced acidic pH conditions and other normal human tissues (Figure 28), which had not been previously described. However, high expression of this gene was also observed in the colon and stomach, but still significantly below the level in mature osteoclasts. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 29
SEQ ID No. 29 (Table 5) corresponds to a previously identified gene encoding a protein, sorter nexin 10 (SNX10), whose function has not been determined (see Table 1). We have shown that this gene is markedly induced in mature osteoclasts compared to precursor cells and most normal human tissues (Figure 29), which has not been previously described. However, high expression of this gene was also observed in the liver, brain, lung, adrenal cortex, kidney, and spleen, although significantly below the level in mature osteoclasts. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
ES 2 397 441 T3
SEQ ID No. 30
SEQ ID No. 30 (Table 5) corresponds to a previously identified gene encoding a protein, which contains 3 Tudor domains (TDRD3), whose function has not been determined, but which may be involved in nucleic acid binding ( see table 1). We have shown that this gene is remarkably induced in mature osteoclasts compared to precursor cells and most normal human tissues (Figure 30), which has not been previously described. However, expression of this gene was observed above the baseline level in normal human tissues because the precursor was lower than normal, although it was still significantly below the level in mature osteoclasts. Therefore, the selection for this gene was maintained. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 31
SEQ ID No. 31 (Table 5) corresponds to a previously identified gene that encodes a protein, selenoprotein P, plasma, 1 (SEPP1), which has been involved in oxidative defense in the extracellular space and in the transport of selenium (see table 1). This gene encodes a selenoprotein that contains several selenocysteines. Selenocysteine is encoded by the UGA codon, which is usually stop. Unusual amino acids are denoted by a "U" in the amino acid sequence in SEQ ID No. 78 (Table 5) or by Xaa in the sequence listing. We have shown that this gene is markedly induced in intermediate and mature osteoclasts compared to precursor cells and most normal human tissues (Figure 31), which has not been previously described. However, expression of this gene above baseline was observed in normal human tissues because the level of the precursor was lower than normal, but was still significantly lower than the level in mature osteoclasts. Consequently, the selection for this gene was maintained. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 32
SEQ ID No. 32 (Table 5) corresponds to a previously identified gene encoding a hypothetical protein, KIAA0040, which has no known function (see Table 1). We have shown that this gene is remarkably induced in intermediate and mature osteoclasts compared to precursor cells and most normal human tissues (Figure 32), which has not been previously described. However, expression of this gene above baseline was observed in normal human tissues because the level of the precursor was lower than normal, but was still significantly lower than the level in mature osteoclasts. Consequently, the selection for this gene was maintained. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 33
SEQ ID No. 33 (Table 5) corresponds to a previously identified gene encoding a protein, dipeptidylpeptidase 4 (CD26, adenosine deaminase complex protein 2) (DPP4), which is an intrinsic membrane glycoprotein and a serine exopeptidase that cleaves X-proline dipeptides from the amino terminus of polypeptides (see Table 1). We have shown that this gene is remarkably induced in intermediate and mature osteoclasts compared to precursor cells and most normal human tissues (Figure 33), which has not been previously described. However, the expression of this gene was observed above the baseline level in normal human tissues, except in the placenta, lung, ovary, kidney, prostate and small intestine, because the level of the precursor was lower than normal. , but it was still significantly lower than the level in mature osteoclasts. Consequently, the selection for this gene was maintained. Therefore, it is believed that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
SEQ ID No. 34:
SEQ ID No. 34 (Table 5) corresponds to a previously identified gene encoding a protein, the cystatin C precursor, and members of the cystatin family are known to be inhibitors of cysteine proteases (see Table 1). We have shown that this gene is markedly induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 34), which has not been previously described. However, it is well documented that cystatin C plays a critical role in inhibiting osteoclasia due to osteoclasts (Brage et al., 2005). Therefore, the hybridization profile of this gene is an excellent example of the highly induced and specific sequences related to osteoclasts.
SEQ ID No. 85:
SEQ ID No. 85 (Table 5) encodes an unknown protein found on chromosome 1 (clone RP11344F13), which contains a new gene (see Table 1). We have shown that this gene is markedly induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 38), which has not been previously described. Therefore, it follows that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
ES 2 397 441 T3
SEQ ID No. 86
SEQ ID No. 86 (Table 5) does not code for any known proteins. This is an unknown gene that matches the sequence of an EST that corresponds to BQ182670 in the database and was isolated from a sample of arthritic cartilage (see Table 1). We have shown that this gene is highly induced in intermediate and mature osteoclasts compared to precursor cells and other normal human tissues (Figure 39), which has not been previously described. Therefore, it follows that this gene could be necessary for osteoclastogenesis and / or bone remodeling.
H. - Cloning of the complete cDNAs of the sequences selected from the osteoclast mRNAs:
It was necessary to obtain complete cDNA sequences to perform functional studies of the expressed proteins. More and more splice variants are involved in specific tissue functions and, as such, it is important to work with cDNA clones of the system under study. The applicant also acknowledges that splice variants do not always play a role in this. Therefore, Applicant's strategy has been to isolate the complete and relevant cDNA sequences directly from the osteoclasts to identify the variants and their possible role with respect to specificity.
Coding cDNA clones were isolated with a 5'-RACE strategy (Invitrogen, Burlington, ON) and a standard gene-specific strategy with two PCR primers. The 5'-RACE strategy used cDNA prepared from cap-selected osteoclast RNA and / or rAmP amplified osteoclast RNA. For amplification with gene-specific primers, both cDNA prepared from RNA with RAMP and total RNA were used. All cDNAs were synthesized following standard reverse transcription procedures (Invitrogen, Burlington, ON). The cDNA sequences obtained were cloned into E. coli DH10B and the nucleotide sequence of several clones was determined. The cDNA sequences from each set were then aligned and the open reading frame (s) (ORFs) were identified with standard computer programs (eg, ORF Finder-NCBI). Table 2 shows the consensus sequence of the cDNA clones of the coding region of SEQ ID No. 1 (SEQ ID No. 83) and SEQ ID No. 2 (SEQ ID No. 84) obtained from a sample. of human osteoclasts, which are identical to published sequences corresponding to accession numbers NM_213602 and NM_001014433 (NCBI), respectively.
I. - RNA interference studies
RNA interference is a recently discovered gene regulation mechanism that involves the sequence-specific decrease in the expression of a gene by directing mRNA toward degradation and, although originally described in plants, has been discovered in many kingdoms. animals, from protozoa and invertebrates to higher eukaryotes (reviewed in Agrawal et al., 2003). In the physiological context, the RNA interference mechanism is triggered by the presence of double-stranded RNA molecules that are cleaved by an RNase III-type protein active in cells, called Dicer, which releases siRNAs of 21 to 23 bp. The siRNA, in a homology-driven manner, forms a complex with an amalgam of proteins and RNA called RISC (RNA-Induced Silencing Complex) in the presence of mRNA to cause degradation, resulting in attenuation of the expression of this mRNA (Agrawal et al., 2003).
Current strategies for studying gene function, such as genosuppressed and dominant-negative mice, are often ineffective and generally expensive, and time-consuming. RNA interference is proving to be a procedure of choice for the analysis of large numbers of genes in a rapid and relatively inexpensive manner. Although transfection of synthetic siRNAs is an efficient method, the effects are often transient at best (Hannon G. J, 2002). The introduction of plasmids expressing small forked RNAs by stable transfection has been successful in allowing analysis by RNA interference in long-term studies (Brummelkamp et al., 2002; Elbashir et al., 2001). In addition, more recent advances have allowed the expression of siRNA molecules, in the form of small forked RNA, in primary human cells by methods that use viruses, such as lentiviruses, to introduce them (Lee et al., 2004; Rubinson et al. , 2003).
J. - Determination of the blocking effects of osteoclastogenesis
To develop a screening procedure for human candidate genes, RNA interference was adapted to introduce shRNA into human osteoclast precursor cells, whereby the expression of candidate genes could be attenuated. This strategy would then make it possible to differentiate the osteoclasts in cells that contain a lower expression of these genes to determine whether or not they are necessary in the procedure.
For this purpose, a commercial lentivirus shRNA delivery system (Invitrogen, Burlington, ON) was used to introduce specific shRNAs into human osteoclast precursor cells. The techniques used were those described by the manufacturer, unless otherwise indicated. This example presents the results obtained for two of the candidate genes, SEQ ID No. 1 (AB0326) and SEQ ID No. 2 (AB0369) tested to date. The proteins encoded by both genes have no known function. The shRNA sequences used to specifically target SEQ ID No. 1 and SEQ ID No. 2 were S'-gaggcccaggagtcgaa i 1-3 '(SEQ ID No. 42) and 5'
ES 2 397 441 T3 i cccgtct 11GGGTCAAAA-3 '(SEQ ID No. 43), respectively. Briefly, a template for the expression of shRNA was cloned into the lentivirus expression vector and co-transfected into 293FT cells with expression vectors for the structural proteins of the virus. After two days, the supernatants containing the lentivirus were collected and stored at -80 ° C. Human osteoclast precursors purchased from Cambrex (East Rutherford, NJ) were pelleted in 24-well plates and cultured in complete medium with macrophage colony stimulating factor and allowed to adhere for three days. After washing with PBS, the cells were infected at an MDI (multiplicity of infection) of 20 with lentiviral particles containing a specific shRNA for the bacterial lacZ gene as a control (lacZ shRNA), or with SEQ ID no. 1 (shRNA from AB0326) or SEQ ID No. 2 (shRNA from AB0369). After 24 hours, the infected cells were treated with the same medium containing the RANK ligand at 100 ng / ml for 5 to 8 days to allow differentiation of the osteoclast from the precursor cells. Mature osteoclasts were fixed with formaldehyde and stained for TRAP expression as follows: cells were washed with PBS and fixed in 10% formaldehyde for 1 hour. After two PBS washes, cells were lightly permeabilized in 0.2% Triton X-100 in PBS for 5 minutes before washing in PBS. Staining was carried out at 37 ° C for 20 to 25 min in 0.01% AS-MX Naphthol Phosphate, 0.06% Fast Red Violet, 50mM Sodium Tartrate, 100mM Sodium Acetate , pH 5.2. The stained cells were visualized with the light microscope and photographed (magnification: 40X). A significant decrease in the number of multinucleated osteoclasts was observed from the precursor cells infected with the shRNA of AB0326 (Figure 35A, lower panel) and with the shRNA of AB0369 (Figure 35B, lower panel) compared to those produced with the lacZ shRNA (Figures 35A and B, upper panels). Therefore, in both cases, the corresponding lentiviral shRNA (SEQ ID Nos. 42 and 43, respectively) (Table 4) disturbed osteoclastogenesis. These results clearly indicated that expression of the gene encoding SEQ ID No. 1 (AB0326) and SEQ ID No. 2 (AB0369) is necessary for osteoclast differentiation.
Experiments similar to those described above were carried out with other sequences (SEQ ID No. 3 to SEQ ID No. 33, SEQ ID No. 85 or SEQ ID No. 86).
K.- Biological validation of the mouse ortholog for AB0326 (SEQ ID No. 35) in osteoclastogenesis with the RAW 264.7 model
As a means of developing a drug screening assay for the discovery of therapeutic molecules capable of attenuating the differentiation and activity of human osteoclasts by the identified targets, it was necessary to use another model of osteoclast differentiation. The RAW 264.7 (RAW) osteoclast precursor cell line is well known in the art as a murine model of osteoclastogenesis. However, due to the difficulty for transient transfection of RAW cells, the stable transfection strategy was used, where shRNAs are constitutively expressed in RAW cells. This allowed to carry out long-term studies such as the differentiation of osteoclasts in the presence of certain shRNAs identified as being specific for murine orthologs of human targets.
RAW cells were purchased from the American Type Culture Collection (Manassass, VA) and maintained in high glucose DMEM containing 10% fetal calf serum and antibiotics. Cells were subcultured every two weeks up to a maximum of 10-12 passages. For osteoclast differentiation experiments, RAW cells were inoculated into 96-well plates at a density of 4 x 10<sup>3</sup> cells / well and grown for 24 h. Differentiation was induced in high glucose DMEM, 10% charcoal treated fetal calf serum (obtained from Hyclone, Logan, UT), 0.05% SAB, antibiotics, macrophage colony stimulating factor (M-CSF ) at 10 ng / ml and RANK ligand at 100 ng / ml. Plates were re-fed on day 3 and osteoclasts were clearly visible on day 4. Typically, cells were stained for TRAP on day 4 or 5 unless otherwise indicated.
To incorporate shRNA expression cassettes into RAW cell chromosomes, plasmid pSilencer 2.0 (SEQ ID No. 47) was purchased from Ambion (Austin, TX) and sequence-specific oligonucleotides were ligated as recommended by the manufacturer. . Two shRNA expression plasmids were designed and the sequences 5'-3 '(SEQ ID No. 44) and 5'- -3' (SEQ ID No. 45) were used to attenuate the gene expression of the mouse ortholog of AB0326 (SEQ ID No. 35). A plasmid supplied by Ambion containing a shRNA sequence mixed with no homology to any mammalian gene was also included as a negative control in these experiments. RAW cells were inoculated into 6-well plates at a density of 5 x 10<sup>5</sup> cells / well and transfected with 1 pg of each plasmid using Fugene6 (Roche, Laval, QC) as described in the protocol. After selection of stable transfectants in medium containing puromycin at 2 pg / ml, the cell lines were expanded and analyzed for osteoclastogenesis capacity in the presence of the RANK ligand.
The stably transfected cell lines were designated RAW-0326.1, RAW-0326.2, and RAW-ctl. 4000 cells / well were inoculated into 96-well plates in triplicate and treated with RANK ligand at 100 ng / ml. After 4 days, the osteoclasts were stained for TRAP expression and visualized with the light microscope (40X and 100X magnification, as described in the left and right panels, respectively).
Representative results for the RAW-0326.2 line are shown in Figure 36. The RAW-0326.2 cell line produced significantly fewer osteoclasts (Figure 36; lower panel) than the cell line containing the shRNA
ES 2 397 441 T3 randomized (Figure 36, top panel). The RAW-0326.1 cell line also showed the attenuation of the AB0326 mouse ortholog, but not as pronounced (data not shown). Therefore, as was observed for SEQ ID No. 42 and 43, siRNAs for mouse ortholog (SEQ iD No. 44 and 45) (Table 4) disturb the phenotype of osteoclast differentiation. on the mouse model as well. These results, together with those obtained in human osteoclast precursor cells with the shRNA delivery system by lentivirus (section J), demonstrate that the AB0326 gene product is clearly needed for osteoclastogenesis in humans and mice.
L.- A functional complementation assay for SEQ ID No. 1 (AB0326) in RAW 264.6 cells to screen for osteoclastogenesis inhibitors
To establish a screening assay based on SEQ ID No. 1 (AB0326) to find small molecules capable of attenuating osteoclast differentiation, the cDNA encoding human AB0326 was introduced into the RAW-0326.2 cell line. Thus, if human AB0326 performs the same function as mouse ortholog in RAW 264.7 cells, it must restore the ability of RAW-0326.2 cell line to osteoclastogenesis.
To carry out this task, the RAW-0326.2 cell line was transfected with an expression vector for eukaryotes that encodes the full-length human AB0326 cDNA, designated pd2-hAB0326. This expression vector (pd2; SEQ ID No. 47) was modified from a commercial vector, pd2-EGFP-N1 (Clontech, Mountain View, CA), where the EGFP gene was replaced by the coding sequence complete cDNA of human AB0326. The expression of the AB0326 gene was driven from a strong CMV promoter. Stable transfectants were selected for the antibiotic G418. This resulted in a RAW-0326.2 cell line expressing the human AB0326 gene product in which the AB0326 mouse ortholog had been silenced. As a control, RAW-0326.2 cells were transfected with the empty vector pd2, which should not complement the shRNA activity of AB0326. Similarly, the empty vector pd2 was transfected into RAW 264.7 cells to serve as an additional control. After selection of stable pools of cells, 4000 cells / well were inoculated into 96-well plates and treated for 4 days with RANK ligand at 100 ng / ml. After fixation with formaldehyde, cells were stained for TRAP, an osteoclast-specific marker gene. As shown in Figure 37, RAW-0326.2 cells transfected with the empty vector pd2 remain unable to form osteoclasts in the presence of the RANK ligand (middle panel), indicating that the shRNA of mouse AB0326 remains capable of silencing the expression of the AB0326 gene in these cells. Conversely, cells transfected with human AB0326 (pd2-hAB0326) are rescued and thus differentiate into osteoclasts in response to the RANK ligand (right panel). RAW 264.7 cells containing the empty vector (pd2) were not adversely affected by osteoclast formation in the presence of the RANK ligand (left panel). These results confirm that the mouse and human orthologs of AB0326 retain their role in osteoclast differentiation.
This particular type of cell assay can now serve as the basis for screening compounds capable of binding and inhibiting the function of human AB0326. A collection of compounds could be applied to this "rescued" cell line to identify molecules (small molecule drugs, peptides, or antibodies) capable of inhibiting AB0326. Any reduction in osteoclast differentiation measured as a reduction in TRAP expression would be indicative of a decrease in human AB0326 activity. This assay is applicable to any gene required for proper osteoclast differentiation in RAW cells. A complementation assay can be developed for any human gene and used as the basis for drug screening.
Similar experiments to those described above are being carried out for other sequences (SEQ ID No. 3 to SEQ ID No. 33 or SEQ ID No. 85 or SEQ ID No. 86). This type of assay can be used to screen for molecules capable of increasing or decreasing (eg, inhibiting) the activity or expression of NSEQ or PSEQ.
In the NSEQs described herein, their methods, compositions, uses, their assays or the like, the polynucleotide can be alone or in groups (collectively), more particularly it can be (or it can comprise or consist of) either;
a translatable portion of SEQ ID No. 1, of SEQ ID No. 2, of SEQ ID No. 3, of SEQ ID No. 4, of SEQ ID No. 5, of SEQ ID No. 6 , of SEQ ID No. 7, of SEQ ID No. 8, of SEQ ID No. 9, of SEQ ID No. 10, of SEQ ID No. 11, of SEQ ID No. 12, of SEQ ID No. 13, of SEQ ID No. 14, of SEQ ID No. 15, of SEQ ID No. 16, of SEQ ID No. 17, of SEQ ID No. 18, of SEQ ID No. 19, SEQ ID No. 20, SEQ ID No. 21, SEQ ID No. 22, SEQ ID No. 23, SEQ ID No. 24, SEQ ID No. 25, of SEQ ID No. 26, of SEQ ID No. 27, of SEQ ID No. 28, of SEQ ID No. 29, of SEQ ID No. 30, of SEQ ID No. 31, of SEQ ID No. 32, of SEQ ID No. 33, of SEQ ID No. 85 or SEQ ID No. 86;
sequence substantially identical to a translatable portion of SEQ ID No. 1, of SEQ ID No. 2, of SEQ ID No. 3, of SEQ ID No. 4, of SEQ ID No. 5, of SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 9, SEQ ID No. 10, SEQ ID No. 11, SEQ ID No. 12, SEQ ID No. 13, SEQ ID No. 14, SEQ ID No. 15, SEQ ID No. 16, SEQ ID No. 17, SEQ ID No. 18 , of SEQ ID No. 19, of SEQ ID No. 20, of SEQ ID No. 21, of SEQ ID No. 22, of SEQ ID No. 23, of SEQ ID No. 24, of SEQ ID No. 25, of SEQ ID No. 26, of SEQ ID No. 27, of SEQ ID No. 28, of SEQ ID No. 29, of SEQ ID No. 30, of SEQ ID No. 31, of SEQ ID No. 32, SEQ ID No. 33, SEQ ID No. 85 or SEQ ID No. 86;
ES 2 397 441 T3 a sequence substantially complementary to a translatable portion of SEQ ID No. 1, a fragment of a transcribable portion of SEQ ID No. 1, of SeQ ID No. 2, of SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 9, of SEQ ID No. 10, of SEQ ID No. 11, of SEQ ID No. 12, of SEQ ID No. 13, of SEQ ID No. 14, of SEQ ID No. 15, of SEQ ID No. 16, of SEQ ID No. 17, of SEQ ID No. 18, of SEQ ID No. 19, of SEQ ID No. 20, of SEQ ID No. 21, of SEQ ID No. 22, of SEQ ID No. 23, of SEQ ID No. 24, of SEQ ID No. 25, of SEQ ID No. 26, SEQ ID No. 27, SEQ ID No. 28, SEQ ID No. 29, SEQ ID No. 30, SEQ ID No. 31, SEQ ID No. 32, SEQ ID No. 33, SEQ ID No. 85 or SEQ ID No. 86;
a fragment of a sequence substantially identical to a translatable portion of SEQ ID No. 1, of SEQ ID No. 2, of SEQ ID No. 3, of SEQ ID No. 4, of SEQ ID No. 5 , of SEQ ID No. 6, of SEQ ID No. 7, of SEQ ID No. 8, of SEQ ID No. 9, of SEQ ID No. 10, of SEQ ID No. 11, of SEQ ID No. 12, of SEQ ID No. 13, of SEQ ID No. 14, of SEQ ID No. 15, of SEQ ID No. 16, of SEQ ID No. 17, of SEQ ID No. 18, of SEQ ID No. 19, of SEQ ID No. 20, of SEQ ID No. 21, of SEQ ID No. 22, of SEQ ID No. 23, of SEQ ID No. 24, of SEQ ID No. 25, of SEQ ID No. 26, of SEQ ID No. 27, of SEQ ID No. 28, of SEQ ID No. 29, of SEQ ID No. 30, SEQ ID No. 31, SEQ ID No. 32, SEQ ID No. 33, SEQ ID No. 85 or SEQ ID No. 86;
a fragment of a sequence substantially complementary to a translatable portion of SEQ ID No. 1, of SEQ ID No. 2, of SEQ ID No. 3, of SEQ ID No. 4, of SEQ ID No. 5 , of SEQ ID No. 6, of SEQ ID No. 7, of SEQ ID No. 8, of SEQ ID No. 9, of SEQ ID No. 10, of SEQ ID No. 11, of SEQ ID No. 12, of SEQ ID No. 13, of SEQ ID No. 14, of SEQ ID No. 15, of SEQ ID No. 16, of SEQ ID No. 17, of SEQ ID No. 18, of SEQ ID No. 19, of SEQ ID No. 20, of SEQ ID No. 21, of SEQ ID No. 22, of SEQ ID No. 23, of SEQ ID No. 24, of SEQ ID No. 25, of SEQ ID No. 26, of SEQ ID No. 27, of SEQ ID No. 28, of SEQ ID No. 29, of SEQ ID No. 30, SEQ ID No. 31, SEQ ID No. 32, SEQ ID No. 33, SEQ ID No. 85 or SEQ ID No. 86;
or a library comprising any one of the foregoing.
In the PSEQs described herein, their methods, compositions, uses, test kits or others, the polypeptide can be alone or in groups (collectively), more particularly it can be (or it can comprise or consist of) either;
SEQ ID No. 48, SEQ ID No. 49, SEQ ID No. 50, SEQ ID No. 51, SEQ ID No. 52, SEQ ID No. 53, SEQ ID No. 54, SEQ ID No. 55, SEQ ID No. 56, SEQ ID No. 57, SEQ ID No. 58, SEQ ID No. 59, SEQ ID No. 60, SEQ ID No. 61, SEQ ID No. 62, SEQ ID No. 63, SEQ ID No. 64, SEQ ID No. 65, SEQ ID No. 66, SEQ ID No. 67, SEQ ID No. 68, SEQ ID No. 69, SEQ ID No. 70, SEQ ID No. 71, SEQ ID No. 72, SEQ ID No. 73, SEQ ID No. 74, SEQ ID No. 75, SEQ ID No. 76, SEQ ID No. 77, SEQ ID No. 78, SEQ ID No. 79 or SEQ ID No. 80;
a fragment of SEQ ID No. 48, SEQ ID No. 49, SEQ ID No. 50, SEQ ID No. 51, SEQ ID No. 52, SEQ ID No. 53, SEQ ID No. 54, SEQ ID No. 55, SEQ ID No. 56, SEQ ID No. 57, SEQ ID No. 58, SEQ ID No. 59, SEQ ID No. 60, SEQ ID No. 61 , SEQ ID No. 62, SEQ ID No. 63, SEQ ID No. 64, SEQ ID No. 65, SEQ ID No. 66, SEQ ID No. 67, SEQ ID No. 68, SEQ ID No. 69, SEQ ID No. 70, SEQ ID No. 71, SEQ ID No. 72, SEQ ID No. 73, SEQ ID No. 74, SEQ ID No. 75, SEQ ID No. 76, SEQ ID No. 77, SEQ ID No. 78, SEQ ID No. 79 or SEQ ID No. 80;
or a non-human biologically active analog, variant, or ortholog of SEQ ID No. 48, SEQ ID No. 49, SEQ ID No. 50, SEQ ID No. 51, SEQ ID No. 52, SEQ ID No. 53, SEQ ID No. 54, SEQ ID No. 55, SEQ ID No. 56, SEQ ID No. 57, SEQ ID No. 58, SEQ ID No. 59, SEQ ID No. 60, SEQ ID No. 61, SEQ ID No. 62, SEQ ID No. 63, SEQ ID No. 64, SEQ ID No. 65, SEQ ID No. 66, SEQ ID No. 67, SEQ ID No. 68, SEQ ID No. 69, SEQ ID No. 70, SEQ ID No. 71, SEQ ID No. 72, SEQ ID No. 73, SEQ ID No. 74 , SEQ ID No. 75, SEQ ID No. 76, SEQ ID No. 77, SEQ ID No. 78, SEQ ID No. 79 or SEQ ID No. 80.
One of skill in the art will readily recognize that orthologs for all mammals can be identified and verified with techniques well established in the art, and that this disclosure is by no means limited to one mammal. The term "mammal (s)" for the purposes of this description refers to any animal classified as mammal, including humans, domestic and farm animals, and captive, sport or companion animals, such as dogs, cats, cows. , horses, sheep, pigs, goats, rabbits, etc. Preferably the mammal is human.
The sequences from the experiments discussed above are representative of the NSEQs described herein. The description of the roles of NSEQs in osteoclastogenesis and osteoclast function satisfies a need in the art to better understand the bone remodeling process, and provides new compositions that are useful for diagnosis, prognosis, treatment, prevention, and evaluation. of treatments for bone remodeling and associated disorders.
The field of genetic manipulation, molecular biology and drug target development has advanced considerably in the last two decades. It will be readily apparent to those skilled in the art that the newly identified roles for genetic sequences and corresponding protein sequences allow sequences, variants, and derivatives to be used directly or indirectly in real-world applications for research tool development. , tools for diagnosis, therapies and treatments for disorders or pathological states in which genetic sequences intervene.
ES 2 397 441 T3
Table 1: Differentially expressed sequences found in osteoclasts
<td>Nucleotide sequence no.</td><td>NCBI Unique Number / Gene Symbol / Gene ID</td><td>Number of access</td><td>ORF nucleotide positions / polypeptide sequence #</td><td>Function</td>
<td>SEQ ID No. 1</td><td>Hs. 287692</td><td>NM 213602</td><td>150-1136 than</td><td>Hypothetical protein LOC284266;</td>
<td></td><td>/ CD33L3 /</td><td></td><td>encode the</td><td>membrane associated, functional</td>
<td></td><td> 284266</td><td></td><td>SEQ ID No. 48</td><td>unknown</td>
<td>SEQ ID No. 2</td><td>Hs.520070 /</td><td>NM 001014433</td><td>104-700 than</td><td>Open reading frame 82 in the</td>
<td></td><td>C6orf82 /</td><td></td><td>encode the</td><td>chromosome 6; associated with</td>
<td></td><td> 51596</td><td></td><td>SEQ ID No. 49</td><td>membrane, function unknown</td>
<td>SEQ ID No. 3</td><td>Hs. 546482 /</td><td>NM 178833</td><td>633-2246 that</td><td>Hypothetical protein LOC133308</td>
<td></td><td>LOC133308</td><td></td><td>encode the</td><td>possibly involved in</td>
<td></td><td> /133308</td><td></td><td>SEQ ID No. 50</td><td>pH regulation</td>
<td>SEQ ID No. 4</td><td>Hs.135997 /</td><td>NM 138461</td><td>112-741 that</td><td>L6 Family Member 19 of 4</td>
<td></td><td>LOC116211</td><td></td><td>encode the</td><td>transmembrane regions; function</td>
<td></td><td> /116211</td><td></td><td>SEQ ID No. 51</td><td>unknown</td>
<td>SEQ ID No. 5</td><td>Hs. 558655 /</td><td>NM 145 280</td><td>172-82 that</td><td>Hypothetical protein LOC151194</td>
<td></td><td>LOC151194</td><td></td><td>encode the</td><td></td>
<td></td><td> /151194</td><td></td><td>SEQ ID No. 52</td><td></td>
<td>SEQ ID No. 6</td><td>Hs. 89714 /</td><td>NM 002994</td><td>119-463 that</td><td>Ligand 5 precursor of</td>
<td></td><td>CXCL5 /</td><td></td><td>encode the</td><td>chemokines (CXC motif);</td>
<td></td><td> 6374</td><td></td><td>SEQ ID No. 53</td><td>chemokine activity</td>
<td>SEQ ID No. 7</td><td>Hs. 495960 /</td><td>NM 005765</td><td>103-1155 that</td><td>ATPase, H transporter<sup>+</sup>,</td>
<td></td><td>ATP6AP2 /</td><td></td><td>encode the</td><td>lysosomal accessory protein 2;</td>
<td></td><td> 10159</td><td></td><td>SEQ ID No. 54</td><td>receptor activity</td>
<td>SEQ ID No. 8</td><td>Hs.42400 /</td><td>NM 182488</td><td>259-1371 that</td><td>Protein 1 of protease type 12</td>
<td></td><td>USP12 /</td><td></td><td>encode the</td><td>ubiquitin specific; exercise</td>
<td></td><td> 219333</td><td></td><td>SEQ ID No. 55</td><td>cysteine-like endopeptidase</td>
<td>SEQ ID No. 9</td><td>Hs. 164853 /</td><td>NM 003341</td><td>175-756 than</td><td>Isoform 1 of the enzyme E2E 1 of</td>
<td></td><td>UBE2E1 /</td><td></td><td>encode the</td><td>conjugation to ubiquitin; exercise</td>
<td></td><td> 7324</td><td></td><td>SEQ ID No. 56</td><td>ligase</td>
<td>SEQ ID No. 10</td><td>Hs. 433278 /</td><td>NM 032565</td><td>53-673 that</td><td>Fixation-related protein</td>
<td></td><td>EBPL /</td><td></td><td>encode the</td><td>emopamil, Δ7-Δ8; integral</td>
<td></td><td> 84650</td><td></td><td>SEQ ID No. 57</td><td>membranary</td>
<td>SEQ ID No. 11</td><td>Hs. 106015 /</td><td>NM 018482</td><td>29-3418 that</td><td>Factor 1 enhancing the</td>
<td></td><td>DDEF1 /</td><td></td><td>encode the</td><td>differentiation and development;</td>
<td></td><td> 50807</td><td></td><td>SEQ ID No. 58</td><td>membranary</td>
<td>SEQ ID No. 12</td><td>Hs. 517265 /</td><td>NM 021181</td><td>16-1023 that</td><td>SLAM family member 7;</td>
<td></td><td>SLAMF7 /</td><td></td><td>encode the</td><td>receptor activity</td>
<td></td><td> 57823</td><td></td><td>SEQ ID No. 59</td><td></td>
<td>SEQ ID No. 13</td><td>Hs. 470804 /</td><td>NM 006357</td><td>385-1008 than</td><td>E2E 3 conjugation enzyme</td>
<td></td><td>UBE2E3 /</td><td></td><td>encode the</td><td></td>
ES 2 397 441 T3
<td colspan="2"></td><td colspan="2"> 10477</td><td colspan="2"></td><td>SEQ ID No. 60</td><td>ubiquitin; ligase activity</td>
<td>SEQ ID n</td><td> ° 14</td><td>Hs. 278959</td><td> /</td><td>NM</td><td> 015973</td><td>177-548 that</td><td>Galain preproprotein; exercise</td>
<td></td><td></td><td colspan="2">GAL / 51083</td><td></td><td></td><td>encode the</td><td>hormonal neuropeptide</td>
<td></td><td></td><td></td><td></td><td></td><td></td><td>SEQ ID No. 61</td><td></td>
<td>SEQ ID n</td><td> ° 15</td><td colspan="2">NM 032569</td><td>NM</td><td> 032569</td><td>19-1680 that</td><td>Nuclear factor n-pac of cytokine type;</td>
<td></td><td></td><td>/ N-PAC</td><td> /</td><td></td><td></td><td>encode the</td><td>similar to 3-hydroxyisobutyrate</td>
<td></td><td></td><td> 84656</td><td></td><td></td><td></td><td>SEQ ID No. 62</td><td>dehydrogenase</td>
<td>SEQ ID n</td><td> .° 16</td><td>Hs.248472</td><td> /</td><td>NM</td><td> 000887</td><td>68-3559 that</td><td>Integrin α X precursor;</td>
<td></td><td></td><td>ITGAX</td><td> /</td><td></td><td></td><td>encode the</td><td>adhesion to the cell matrix</td>
<td></td><td></td><td> 3687</td><td></td><td></td><td></td><td>SEQ ID No. 63</td><td></td>
<td>SEQ ID n</td><td> .° 17</td><td>Hs.156727</td><td> /</td><td>NM</td><td> 054027</td><td>321-1799 than</td><td>ankylosis homolog</td>
<td></td><td></td><td>ANKH</td><td> /</td><td></td><td></td><td>encode the</td><td>progressive; regulation of</td>
<td></td><td></td><td> 1827</td><td></td><td></td><td></td><td>SEQ ID No. 64</td><td>bone mineralization</td>
<td>SEQ ID n</td><td> .° 18</td><td>Hs. 477155</td><td> /</td><td>NM</td><td> 001690</td><td>67-1920 than</td><td>ATPase, H transporter<sup>+</sup>out of 70</td>
<td></td><td></td><td>ATP6V1A</td><td> /</td><td></td><td></td><td>encode the</td><td>kDa, lysosomal, V1 subunit A,</td>
<td></td><td></td><td> 523</td><td></td><td></td><td></td><td>SEQ ID No. 65</td><td>isoform 1; proton transport; hydrolase activity</td>
<td>SEQ ID n</td><td> .° 19</td><td>Hs. 445386</td><td> /</td><td>NM</td><td> 018252</td><td>139-1191 that</td><td>Hypothetical protein LOC55248</td>
<td></td><td></td><td>FLJ10874</td><td> /</td><td></td><td></td><td>encode the</td><td></td>
<td></td><td></td><td> 55248</td><td></td><td></td><td></td><td>SEQ ID No. 66</td><td></td>
<td>SEQ ID n</td><td> ° 20</td><td>Hs. 467662</td><td> /</td><td>NM</td><td> 004763</td><td>170-772 that</td><td>Domain associated protein 1</td>
<td></td><td></td><td>ITGB1BP1</td><td> /</td><td></td><td></td><td>encode the</td><td>cytoplasmic of the integrins;</td>
<td></td><td></td><td> 9270</td><td></td><td></td><td></td><td>SEQ ID No. 67</td><td>cell adhesion</td>
<td>SEQ ID n</td><td> ° 21</td><td>Hs. 408236</td><td> /</td><td>NM</td><td> 032731</td><td>77-448 that</td><td>Thioredoxin type 5; function</td>
<td></td><td></td><td>TXNL5</td><td> /</td><td></td><td></td><td>encode the</td><td>unknown</td>
<td></td><td></td><td> 84817</td><td></td><td></td><td></td><td>SEQ ID No. 68</td><td></td>
<td>SEQ ID n</td><td> ° 22</td><td>Hs.236516</td><td> /</td><td>NM</td><td> 014358</td><td>152-811 that</td><td>member 9 of the superfamily of</td>
<td></td><td></td><td>CLECSF9</td><td> /</td><td></td><td></td><td>encode the</td><td>type C lectins; integral</td>
<td></td><td></td><td> 26253</td><td></td><td></td><td></td><td>SEQ ID No. 69</td><td>membranary</td>
<td>SEQ ID n</td><td> ° 23</td><td>Hs.56294</td><td> /</td><td>NM</td><td> 004794</td><td>265-978 that</td><td>Rab-33A protein related to</td>
<td></td><td></td><td>RAB33A</td><td> /</td><td></td><td></td><td>encode the</td><td>Ras; signal transduction</td>
<td></td><td></td><td> 9363</td><td></td><td></td><td></td><td>SEQ ID No. 70</td><td>small GTPase mediated</td>
<td>SEQ ID n</td><td> ° 24</td><td>Hs. 282326</td><td> /</td><td>NM</td><td> 004414</td><td>73-831 that</td><td>Isoform a of calcipressin 1;</td>
<td></td><td></td><td>DSCR1</td><td> /</td><td></td><td></td><td>encode the</td><td>interacts with calcineurin A and</td>
<td></td><td></td><td> 1827</td><td></td><td></td><td></td><td>SEQ ID No. 71</td><td>inhibits calcineurin-dependent signaling pathways</td>
<td>SEQ ID n</td><td> ° 25</td><td>Hs. 520794</td><td> /</td><td>NM</td><td> 006555</td><td>158-754 than</td><td>SNARE Ykt6 protein; transport</td>
<td></td><td></td><td>YKT6</td><td> /</td><td></td><td></td><td>encode the</td><td>vesicular between compartments</td>
<td></td><td></td><td> 10652</td><td></td><td></td><td></td><td>SEQ ID No. 72</td><td>secretion</td>
<td>SEQ ID n</td><td> ° 26</td><td>Hs. 509765</td><td> /</td><td>NM</td><td> 001102</td><td>184-2862 than</td><td>Actinin α1; structural constituent</td>
<td></td><td></td><td>ACTN1 / 87</td><td></td><td></td><td></td><td>encode the</td><td>of the cytoskeleton; ion fixation</td>
<td></td><td></td><td></td><td></td><td></td><td></td><td>SEQ ID No. 73</td><td>calcium</td>
<td>SEQ ID n</td><td> ° 27</td><td>Hs.113823</td><td> /</td><td>NM</td><td> 006660</td><td>73-1974 that</td><td>Protease X homolog</td>
<td></td><td></td><td>CLPX</td><td> /</td><td></td><td></td><td>encode the</td><td>ClpX casinolytic; regulator</td>
<td></td><td></td><td> 10845</td><td></td><td></td><td></td><td>SEQ ID No. 74</td><td>energy-dependent proteolysis</td>
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<td>SEQ ID No. 28</td><td>Hs.155097 / CA2 / 760</td><td>NM_000067</td><td>66-848 that encode the SEQ ID No. 75</td><td>Carbonic anhydrase II; carbonate dehydratase activity</td>
<td>SEQ ID No. 29</td><td>Hs.520714 / SNX10 / 29887</td><td>NM_013322</td><td>216-821 encoding the SEQ ID No. 76</td><td>Nexina 10 sorter; unknown function</td>
<td>SEQ ID No. 30</td><td>Hs.525061 / TDRD3 / 81550</td><td>NM_030794</td><td>258-2213 that encode the SEQ ID No. 77</td><td>Contains 3 Tudor domains; nucleic acid binding</td>
<td>SEQ ID No. 31</td><td>Hs.275775 / SEPP1 / 614</td><td>NM_005410</td><td>101-1246 that encode the SEQ ID No. 78</td><td>Selenoprotein P; space extracellular, intervenes in the defense</td>
<td>SEQ ID No. 32</td><td>Hs. 518138 / KIAA0040 / 9674</td><td>NM_014656</td><td>921-1382 encoding the SEQ ID No. 79</td><td>KIAA0040; new protein</td>
<td>SEQ ID No. 33</td><td>Hs.368912 / DPP4 / 1803</td><td>NM_001935</td><td>562-2862 that encode the SEQ ID No. 80</td><td>Dipeptidylpeptidase IV; aminopeptidase activity</td>
<td>SEQ ID No. 34</td><td>Hs.304682 / CST3 / 1471</td><td>NM_000099</td><td>76-516 encoding the SEQ ID No. 81</td><td>Inhibitory activity of cysteine proteases</td>
<td>SEQ ID No. 85</td><td>None / none / none</td><td>AL357873</td><td>New</td><td>New</td>
<td>SEQ ID No. 86</td><td></td><td>AL645465 / BQ182670</td><td>New</td><td>New</td>
Table 2: The consensus sequence of SEQ ID No. 1 and SEQ ID No. 2 cloned from a sample of mature human osteoclasts is shown
<td>Sequence identification</td><td>ORF nucleotide positions</td><td>Polypeptide sequence #</td>
<td>SEQ ID No. 83</td><td> 1-987</td><td>SEQ ID No. 48</td>
<td>SEQ ID No. 84</td><td> 1-471</td><td>SEQ ID No. 49</td>
Table 3: List of mouse orthologs for AB0326
<td>Sequence identification</td><td>Unigén / cluster of NCBI</td><td>Access number</td><td>ORF nucleotide positions</td><td>Polypeptide sequence #</td>
<td>SEQ ID No. 35</td><td>Neither / LOC620235 / 620235</td><td>XM_884636</td><td>122-1102 / similar to neural cell adhesion molecule 2 / unknown function</td><td>SEQ ID No. 82</td>
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Table 4: List of other shRNA plasmid and oligonucleotide identification sequences
<td>Sequence identification</td><td>Name</td><td>Description</td>
<td>SEQ ID No. 36</td><td>p14</td><td>Vector for STAR</td>
<td>SEQ ID No. 37</td><td>p17 +</td><td>Vector for STAR</td>
<td>SEQ ID No. 38</td><td>pCATRMAN</td><td>Vector for STAR</td>
<td>SEQ ID No. 39</td><td>p20</td><td>Vector for STAR</td>
<td>SEQ ID No. 40</td><td>OGS 77</td><td>Primer used for vector p14 for STAR</td>
<td>SEQ ID No. 41</td><td>OGS 302</td><td>Primer used for vector p17 + for STAR</td>
<td>SEQ ID No. 42</td><td>Human 0326.1</td><td>SiRNA sequence for SEQ ID # 1</td>
<td>SEQ ID No. 43</td><td>Human 0369.1</td><td>ShRNA sequence for SEQ ID No. 2</td>
<td>SEQ ID No. 44</td><td>Mouse 0326.1</td><td>ShRNA sequence for SEQ ID No. 35</td>
<td>SEQ ID No. 45</td><td>Mouse 0326.2</td><td>ShRNA sequence for SEQ ID No. 35</td>
<td>SEQ ID No. 46</td><td></td><td>Vector pSilencer 2.0</td>
<td>SEQ ID No. 47</td><td></td><td>Vector pd2</td>
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Table 5:
<img file="ES2397441T3_D0001.tif" />
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<img file="ES2397441T3_D0002.tif" />
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<img file="ES2397441T3_D0003.tif" />
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SEQIDNO
<img file="ES2397441T3_D0004.tif" />
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<img file="ES2397441T3_D0005.tif" />
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<img file="ES2397441T3_D0006.tif" />
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<img file="ES2397441T3_D0007.tif" />
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SEQIDNO .:
<img file="ES2397441T3_D0008.tif" />
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<img file="ES2397441T3_D0009.tif" />
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<img file="ES2397441T3_D0010.tif" />
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<img file="ES2397441T3_D0011.tif" />
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<img file="ES2397441T3_D0012.tif" />
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<img file="ES2397441T3_D0013.tif" />
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SEQIDNO. : 60
<img file="ES2397441T3_D0014.tif" />
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SEQIDNO.; 62
<img file="ES2397441T3_D0015.tif" />
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<img file="ES2397441T3_D0016.tif" />
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SEQIDNO.:16
<img file="ES2397441T3_D0017.tif" />
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<img file="ES2397441T3_D0018.tif" />
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<img file="ES2397441T3_D0019.tif" />
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<img file="ES2397441T3_D0020.tif" />
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SEQIOHO '. : 6S
<img file="ES2397441T3_D0021.tif" />
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<img file="ES2397441T3_D0022.tif" />
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<img file="ES2397441T3_D0023.tif" />
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I SEQIDNO.:67
<img file="ES2397441T3_D0024.tif" />
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<img file="ES2397441T3_D0025.tif" />
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SEQIDNO.:23 i ¢. r
<img file="ES2397441T3_D0026.tif" />
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SEQIDNO.:24
<img file="ES2397441T3_D0027.tif" />
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<img file="ES2397441T3_D0028.tif" />
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<img file="ES2397441T3_D0029.tif" />
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<img file="ES2397441T3_D0030.tif" />
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<img file="ES2397441T3_D0031.tif" />
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<img file="ES2397441T3_D0032.tif" />
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SEQIDW. -.7 7
<img file="ES2397441T3_D0033.tif" />
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<img file="ES2397441T3_D0034.tif" />
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<img file="ES2397441T3_D0035.tif" />
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<img file="ES2397441T3_D0036.tif" />
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OB'OÍlQIOSg
<img file="ES2397441T3_D0037.tif" />
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<img file="ES2397441T3_D0038.tif" />
ES 2 397 441 T3 se ·· OMaioas
<img file="ES2397441T3_D0039.tif" />
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<img file="ES2397441T3_D0040.tif" />
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<img file="ES2397441T3_D0041.tif" />
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<img file="ES2397441T3_D0042.tif" />
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<img file="ES2397441T3_D0043.tif" />
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<img file="ES2397441T3_D0044.tif" />
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SEQIDNO. : 46
<img file="ES2397441T3_D0045.tif" />
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<img file="ES2397441T3_D0046.tif" />
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<img file="ES2397441T3_D0047.tif" />
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<img file="ES2397441T3_D0048.tif" />
100
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<img file="ES2397441T3_D0049.tif" />
101
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References
PATENTS:
US Patent No. 5,712 127 Malek et al., January 27, 1998
US Patent No. 6,498,024, Malek et al., December 24, 2002
US Patent Application No. 11/000 958 filed December 2, 2003, published under number US 2005/0153333 A1 on July 14, 2005 and entitled "Selective Terminal Tagging of Nucleic Acids"
US Patent No. 6,617,434 Duffy, September 9, 2003
US Patent No. 6,451,555 Duffy, September 17, 2002
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| NZ599193A | New Zealand | A | |
| US8900579B2 | United States of America | B2 | |
| AU2010305281C1 | Australia | C1 | |
| JP2014231514A | Japan | A | |
| CA2775793C | Canada | C | |
| US2015044722A1 | United States of America | A1 | |
| US2015110785A1 | United States of America | A1 | |
| US9040246B2 | United States of America | B2 | |
| JP5723858B2 | Japan | B2 | |
| US9067984B2 | United States of America | B2 | |
| JP2015143241A | Japan | A | |
| JP5855569B2 | Japan | B2 | |
| JP5875643B2 | Japan | B2 | |
| US2016068836A1 | United States of America | A1 | |
| JP2016040324A | Japan | A | |
| CN102803293B | China | B | |
| US9388242B2 | United States of America | B2 | |
| RU2596392C2 | Russian Federation | C2 | |
| US2016289325A1 | United States of America | A1 | |
| CN106046160A | China | A | |
| JP2016204379A | Japan | A | |
| JP6047772B2 | Japan | B2 | |
| AU2014200123B2 | Australia | B2 | |
| US9617337B2 | United States of America | B2 | |
| US9695419B2 | United States of America | B2 | |
| US2017260529A1 | United States of America | A1 | |
| JP6224182B2 | Japan | B2 | |
| CA2785046C | Canada | C | |
| BR112012007860A2 | Brazil | A2 | |
| USRE47672E | United States of America | E | |
| EP1994155B2 | European Patent Office (EPO) | B2 | |
| DK1994155T4 | Denmark | T4 | |
| FI1994155T4 | Finland | T4 | |
| ES2397441T5 | Spain | T5 |
Numbers
- Publication
- 2397441
- Publication, DOCDB
- 2397441
- Publication, EPODOC
- ES2397441T
- Application
- 7710624
- Application, DOCDB
- 07710624
- Application, EPODOC
- ES20070710624T
Titles2
- Spanish
- Secuencias polinucleotídicas y polipeptídicas implicadas en el proceso de remodelación ósea
- English
- Polynucleotide and polypeptide sequences involved in the bone remodeling process
Classification
- CPC, 37
- C07K14/51
- A61K38/00
- C12Q1/6883
- C12Q2600/158
- G01N33/5044
- G01N2500/00
- G01N2800/10
- G01N2800/108
- C12Q2600/136
- C12Q2600/178
- A61P1/02
- A61P13/12
- A61P15/00
- A61P15/08
- A61P19/00
- A61P19/02
- A61P19/08
- A61P19/10
- A61P29/00
- A61P3/00
- A61P3/14
- A61P35/00
- A61P3/04
- A61P43/00
- A61P5/14
- A61P5/18
- A61P5/24
- A61P5/38
- C07K14/47
- A61K39/39533
- C07K16/18
- C07K2317/54
- C07K2317/55
- C12N15/113
- C12N2310/11
- C12N2310/12
- C12N2310/14
- IPC, 6
- A61P19 08
- C07K14 705
- A61K31 7088
- A61K38 17
- A61K39 395
- A61K48 00