JP2005527197A - Therapeutic polypeptides, nucleic acids encoding the same, and methods of use - Google Patents

Abstract

Nucleic acids encoding the novel polypeptides are disclosed herein. Polypeptides encoded by these nucleic acid sequences, and antibodies that immunospecifically bind to the polypeptides, as well as derivatives, variants, variants of the novel polypeptides, polynucleotides, or antibodies specific for the polypeptides, Or a fragment is also disclosed. Also included are recombinant methods for obtaining vectors, host cells, antibodies and polypeptides and polynucleotides, or methods of their use. The present invention further discloses therapeutic, diagnostic and research methods for the diagnosis, treatment and prevention of diseases involving any of these novel human nucleic acids and proteins.

Description

Detailed Description of the Invention

(Background technology)
Eukaryotic cells feature biochemical and physiological methods that are delicately balanced to achieve cell maintenance and proliferation under normal conditions. When such cells are components of multicellular organisms such as vertebrates, or more particularly organisms such as mammals, the regulation of biochemical and physiological methods involves sophisticated signaling pathways. . Often such signaling pathways involve extracellular signaling proteins, cellular receptors that bind to signaling proteins, and signaling components that are localized within the cell.

  Signal transduction proteins can be classified as endocrine effectors, paracrine effectors or autocrine effectors. Endocrine effectors are signaling molecules that are secreted into the circulatory system by a particular organ, which is then transported to a remote target organ or tissue. Target cells contain receptors for endocrine effectors, and when the endocrine effectors bind, a signaling cascade is induced. Paracrine effectors involve secretory cells and recipient cells in close proximity to each other, for example, two different classes of cells within the same tissue or organ. One class of cells secretes paracrine effectors, which then reach a second class of cells, for example by diffusion through the extracellular fluid. The second class of cells contains receptors for paracrine effectors, and effector binding induces a signaling cascade that induces the corresponding biochemical or physiological action. Autocrine effectors have a high degree of similarity to paracrine effectors, except that the same type of cells that secrete autocrine effectors also contain receptors. Thus, the autocrine effector binds to the receptor on the same cell and on the same adjacent cell. The binding process then causes a characteristic biochemical or physiological effect.

  Signal transduction processes for cells and tissues include, but are not limited to, induction of cell or tissue proliferation, inhibition of growth or proliferation, induction of cell or tissue differentiation or maturation, and cell or tissue differentiation or maturation. Can cause a variety of effects including suppression.

  Many pathological conditions involve dysregulation of the expression of important effector proteins. In a particular class of disease states, dysregulation appears as a reduced or suppressed level of protein effector synthesis and secretion. In other types of pathology, unregulation is manifested as increased or upregulated levels of protein effector synthesis and secretion. In the clinical setting, a subject may be suspected of suffering from an abnormality caused by increased or excessive levels of protein effector of interest. Therefore, there is a need to assay the level of protein effector of interest in a biological sample from such a subject and compare that level to that characteristic of a non-pathological condition. There is also a need to provide protein effectors as products of manufacture. Administering an effector to a subject in need thereof is useful for treating a pathological condition. Thus, there is a need for methods of treatment of pathological conditions caused by reduced or suppressed levels of protein effectors of interest. In addition, there is a need for methods of treatment of pathological conditions caused by increased or effected up-regulation of protein effectors of interest. Furthermore, there is a need for methods of treating pathological conditions caused by increased or upregulated levels of protein effectors of interest.

  An antibody is a multi-chain protein that specifically binds to a specific antigen and hardly binds to a substance that is not the same type of antigen or hardly binds at all. An antibody contains two short chains called light chains and two long chains called heavy chains. These chains constitute an immunoglobulin domain, and these domains generally have two classes: one variable domain per chain, one invariant in the light chain Domains, and three or more invariant domains in the heavy chain. The antigen-specific portion of an immunoglobulin molecule is in the variable domain; one light chain and one heavy chain variable domain bind together to form an antigen-binding portion. Antibodies that immunospecifically bind to the cognate or target antigen bind with high affinity. They are therefore useful in specifically assaying for the presence of antigen in a sample. Furthermore, they have the potential to inactivate the activity of the antigen.

  It is therefore necessary to assay the level of the protein effector of interest in a biological sample from such a subject and compare this level to a level characterized by not being in a pathological state. There is a particular need for such assays based on using antibodies that immunospecifically bind to an antigen. Furthermore, in cases where the pathological condition is elevated or arises from excessive effector levels, it is necessary to inhibit the activity of protein effectors based on the use of antibodies that immunospecifically bind to the effectors. Thus, there is a need for antibodies as production results. There is also a need for a method of treating pathological conditions caused by elevated or excessive levels of the protein of interest based on administering antibodies to a subject.

(Summary of the Invention)
The present invention is based in part on the discovery of an isolated polypeptide comprising an amino acid sequence selected from a mature form of an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, where n is an integer between 1 and 37 It is. Novel nucleic acids and polypeptides are referred to herein as NOVX or NOV1a, NOV1b, NOV2a, NOV2b, and the like. These nucleic acids and polypeptides and their derivatives, homologues, analogs and fragments are hereinafter collectively referred to as “NOVX” nucleic acid or polypeptide sequences.

  The invention is based in part on a mature variant of an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, where n is an integer between 1 and 37, where any mature amino acid is , Have changed to different amino acids. However, no more than 15% of the amino acid residues in the mature sequence have changed as such. In another embodiment, the invention comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is between 1 and 37. In other embodiments, the invention also includes a variant of an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 37, wherein in the selected sequence Any amino acid specified in is changed to a different amino acid. However, no more than 15% of the amino acid residues in the sequence have changed as such. The invention also relates to a fragment of any mature form of an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, or any other amino acid sequence selected from this group, where n is 1 and 37 An integer between. The invention includes fragments from these groups that vary by up to 15% of the residues.

  In another embodiment, the invention comprises a polypeptide that is a naturally occurring allelic variant of a sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 37. . These allelic variants include amino acid sequences that are translations of nucleic acid sequences that differ by a single nucleotide from a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 2n-1, where n is 1 and 37 Between. A variant polypeptide is altered to provide a conservative substitution if any amino acid is altered in the selected sequence.

  In another embodiment, the invention provides a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 37, and a pharmaceutical relating to a pharmaceutically acceptable carrier Including a composition. In another embodiment, the invention relates to a kit comprising the pharmaceutical composition in one or more containers.

  In another embodiment, the invention includes the use of a therapeutic agent in the manufacture of a medicament for treating a syndrome associated with a human disease, wherein the disease comprises a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 2n and Selected from the associated pathology, where n is an integer between 1 and 37, wherein the therapeutic agent is a polypeptide selected from this group.

  In another embodiment, the invention includes a method of determining the presence or amount of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, where n is an integer between 1 and 37; The method provides a sample; introducing the sample into an antibody that immunospecifically binds to the polypeptide; and determining the presence or amount of antibody bound to the polypeptide, thereby the polypeptide in the sample Related to determining the presence or amount of.

  In another embodiment, the invention provides a method for determining the presence or predisposition of a disease associated with an altered level of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 2n in a first mammalian subject. Wherein n is an integer between 1 and 37 and the method measures the level of expression of the polypeptide in the sample from the first mammalian subject; and the polypeptide in the sample Is compared to the amount of the polypeptide present in a control sample from a second mammalian subject not known to have or not predisposed to the disease, wherein A change in the expression level of the polypeptide of the first subject when compared indicates the presence or predisposition of the disease.

  In another embodiment, the invention relates to a method of identifying an agent that binds to a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 37. The method includes introducing the polypeptide into the agent; and determining whether the agent binds to the polypeptide. The agent can be a cellular receptor or a downstream effector.

  In another embodiment, the invention relates to a method of identifying a potential therapeutic agent for use in the treatment of a pathology, wherein the pathology comprises a polyamino acid sequence selected from the group consisting of SEQ ID NO: 2n. With respect to abnormal expression of peptides or abnormal physiological interactions, where n is an integer between 1 and 37 and the method expresses a polypeptide of the invention and has properties or functions attributable to the polypeptide Contacting the cell with a composition comprising a candidate substance; and determining whether the substance alters a property or function to be attributed to the polypeptide; whereby the observed change in the presence of the substance is a cell If not observed when contacted with a substance-free composition, the substance is identified as a potential therapeutic agent.

  In another embodiment, the invention relates to a screening method for a modulator of pathological activity or potential or predisposition associated with a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is 1 The method comprises administering a test compound to a test animal at increased risk of pathology associated with the polypeptide of the invention, wherein the test animal recombinantly converts the polypeptide of the invention Measuring the activity of the polypeptide in the test animal after administration of the test compound; and comparing the activity of the protein in the test animal to the activity of the polypeptide in the control animal not administered with the polypeptide. Where the change in activity of the polypeptide in the test animal relative to the control animal is the potential for pathology associated with the polypeptide of the invention. To point out that is a modulator of predisposition. Recombinant test animals can express increased levels of protein transgene or promoter-controlled transgene relative to wild-type test animals.

  In another embodiment, the invention relates to a method of modulating the activity of a polypeptide of an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 37, said method comprising poly Introducing a sufficient amount of a compound that binds to the polypeptide to modulate the activity of the peptide and a cell sample that expresses the polypeptide.

  In another embodiment, the invention relates to a method of treating or preventing a pathology associated with a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 37 And the method comprises administering the polypeptide to a subject where such treatment or prevention is desired in an amount sufficient to treat or prevent the pathology of the subject. The subject can include a human.

  In other embodiments, the invention relates to a method of treating a mammal's pathological condition, the method comprising administering to the mammal an amount of a polypeptide sufficient to alleviate the pathological condition. Wherein the polypeptide is a polypeptide having an amino acid sequence at least 95% identical to a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, or a biologically active fragment thereof, n is an integer between 1 and 37.

  In another embodiment, the invention provides an isolated nucleic acid molecule comprising a nucleic acid sequence encoding a polypeptide having an amino acid sequence selected from the group consisting of the mature form of the amino acid sequence provided in SEQ ID NO: 2n, where n is 1 An integer between 37; a mature variant of an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, where n is an integer between 1 and 37, wherein the mature form of the selected sequence Any amino acid in it has been changed to a different amino acid. However, no more than 15% of the amino acid residues in the mature sequence have changed as such; an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, where n is an integer between 1 and 37 A variant of an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, where n is an integer between 1 and 37, and any amino acid specified in the selected sequence is changed to a different amino acid; Is done. However, no more than 15% of the amino acid residues in the sequence have changed as such; a nucleic acid fragment encoding at least a portion of a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 37, or any variant of the polypeptide, where any amino acid in the selected sequence is changed to a different amino acid. However, no more than 10% of the amino acid residues in the sequence are so altered; and pertain to any complement of the nucleic acid molecule.

  In other embodiments, the invention includes an isolated nucleic acid molecule having a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of the mature form of the amino acid sequence provided in SEQ ID NO: 2n, where n is An integer between 1 and 37, wherein the nucleic acid molecule comprises the nucleotide sequence of a naturally occurring allelic nucleic acid variant.

  In another embodiment, the invention relates to an isolated nucleic acid molecule comprising a nucleic acid sequence encoding a polypeptide having an amino acid sequence selected from the group consisting of the mature form of the amino acid sequence given in SEQ ID NO: 2n, wherein n Is an integer between 1 and 37, which encodes a variant polypeptide, wherein the variant polypeptide has the polypeptide sequence of a naturally occurring polypeptide variant.

  In other embodiments, the invention includes an isolated nucleic acid molecule having a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of the mature form of the amino acid sequence provided in SEQ ID NO: 2n, where n is An integer between 1 and 37, wherein the nucleic acid molecule differs by a single nucleotide from a nucleic acid sequence selected from the group consisting of SEQ ID NO: 2n-1, where n is an integer between 1 and 37 is there.

  In other embodiments, the invention includes an isolated nucleic acid molecule having a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of the mature form of the amino acid sequence provided in SEQ ID NO: 2n, where n is An integer between 1 and 37, wherein the nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of nucleotide sequences selected from the group consisting of SEQ ID NOs: 2n-1, where n is 1 and 37 Wherein one or more nucleotides in the nucleotide sequence are selected from the group consisting of SEQ ID NO: 2n-1, where n is an integer between 1 and 37, The nucleotides are changed from those selected from the group consisting of the selected sequences. However, no more than 15% of the nucleotides will vary as such; a nucleic acid fragment of a sequence selected from the group consisting of SEQ ID NO: 2n-1, where n is an integer between 1 and 37; and where the nucleotide sequence Wherein one or more nucleotides are selected from the group consisting of SEQ ID NO: 2n-1, where n is an integer between 1 and 37, and the nucleic acid fragment is selected from the group consisting of a selected sequence From one to a different nucleotide. However, no more than 15% nucleotides change as such.

  In other embodiments, the invention includes an isolated nucleic acid molecule having a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of the mature form of the amino acid sequence provided in SEQ ID NO: 2n, where n is An integer between 1 and 37, wherein the nucleic acid hybridizes under stringent conditions to a nucleotide sequence selected from the group consisting of SEQ ID NO: 2n-1 or a complement of the nucleotide sequence; Here, n is an integer between 1 and 37.

  In another embodiment, the invention comprises an isolated nucleic acid molecule comprising a nucleic acid encoding a polypeptide comprising an amino acid sequence selected from the group consisting of the mature form of the amino acid sequence given in SEQ ID NO: 2n, where n is 1 An integer between 37 and 37, wherein the nucleic acid molecule has a nucleotide sequence, wherein any nucleotide specified in the coding sequence of the selected nucleotide sequence is selected from the group consisting of a selected sequence From different nucleotides (provided that no more than 15% of the nucleotides in the selected coding sequence have been altered as such), an isolated second polynucleotide that is the complement of the first polynucleotide. Changed to nucleotides, or any fragment thereof.

  In another embodiment, the invention comprises a vector comprising a nucleic acid molecule having a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of the mature form of the amino acid sequence provided in SEQ ID NO: 2, wherein n Is an integer between 1 and 37. The vector can have a promoter operably linked to the nucleic acid molecule. This vector can be located intracellularly.

  In another embodiment, the invention relates to a method of determining the presence or amount of a nucleic acid molecule having a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of the mature form of the amino acid sequence given in SEQ ID NO: 2n. Where n is an integer between 1 and 37, the method providing a sample; introducing the sample into a probe that binds to a nucleic acid molecule; and the presence of a probe bound to the nucleic acid molecule Or determining the amount, thereby determining the presence or amount of the nucleic acid molecule in the sample. The presence or amount of the nucleic acid molecule is used as a marker for cell or tissue type. The cell type may be cancer.

  In another embodiment, the invention provides a nucleic acid molecule having a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of the mature form of the amino acid sequence provided in SEQ ID NO: 2n in the first mammalian subject. A method for determining the presence or predisposition of a disease associated with a level of change, wherein n is an integer between 1 and 37, the method measuring the amount of nucleic acid in a sample from a first mammalian subject And comparing the amount of nucleic acid in the sample of step (a) with the amount of nucleic acid present in a control sample from a second mammalian subject known to be disease free or predisposed. Including; where a change in the level of nucleic acid present in the first subject, as compared to a control sample, indicates the presence or predisposition of the disease.

  The invention further provides an antibody that immunospecifically binds to a NOVX polypeptide. NOVX antibodies may be monoclonal, humanized or fully human antibodies. Preferably, the antibody has a dissociation constant of less than 1 × 10 −9 M for NOVX polypeptide binding thereto. More preferably, the NOVX antibody neutralizes the activity of the NOVX polypeptide.

In a further aspect, the present invention provides the use of a therapeutic agent in the manufacture of a medicament for the treatment of a syndrome associated with a human disease associated with a NOVX polypeptide. Preferably, the therapeutic agent is a NOVX antibody. Preferably, the therapeutic agent is a NOVX antibody.
In yet a further aspect, the invention provides a method for treating or preventing a NOVX-related disease, a method for treating a pathological condition in a mammal, by administering to the patient an amount of NOVX antibody sufficient to treat or prevent the disease, and Methods of treating or preventing pathologies associated with polypeptides are provided.

  Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are hereby incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative and not intended to be limiting.

  Other features and advantages of the invention will be apparent from the following invention disclosure and claims.

(Detailed description of the invention)
The present invention provides novel nucleotides and polypeptides encoded thereby. The present invention includes novel nucleic acid sequences, their encoded polypeptides, antibodies, and other related compounds. As used herein, sequences are collectively referred to as “NOVX nucleic acids” or “NOVX polynucleotides” and the corresponding encoded polypeptides are referred to as “NOVX polypeptides” or “NOVX proteins”. Unless otherwise stated, “NOVX” is meant to refer to any novel sequence disclosed herein. Table A shows a summary of NOVX nucleic acids and their encoded polypeptides.

Table A: Sequences and corresponding sequence numbers

  Table A shows the homology of NOVX polypeptides with known protein families. Thus, nucleic acids, polynucleotides, antibodies and related compounds according to the present invention corresponding to NOVX identified in the first column of Table 1 are, for example, lesions associated with known protein families identified in column 5 of Table A. And useful in therapeutic and diagnostic applications related to disease.

  Pathologies, diseases, disorders and conditions associated with NOVX sequences include, but are not limited to, for example: cardiomyopathy, atherosclerosis, hypertension, congenital heart disease, aortic stenosis, atrial septal defect Disease (ASD), vascular calcification, fibrosis, atrioventricular (AV) duct defect, arterial duct, pulmonary stenosis, lower aortic stenosis, ventricular septal defect (VSD), valve disease, tuberous sclerosis , Scleroderma, obesity, obesity-related metabolic disturbance, transplantation, osteoarthritis, rheumatoid arthritis, osteochondrosplasia, adrenoleukodystrophy, congenital adrenal hyperplasia, prostate cancer, diabetes, metabolic disorders, neoplasm Adenocarcinoma, lymphoma, uterine cancer, fertility, glomerulonephritis, hemophilia, hypercoagulability, idiopathic thrombocytopenic purpura, immunodeficiency, psoriasis, skin disease, graft-versus-host disease, AIDS, bronchial asthma , Lupus, Crohn's disease; inflammatory bowel Disease, ulcerative disease, multiple sclerosis, Albright hereditary osteodystrophy, infectious disease, anorexia, cancer-associated cachexia, cancer, neurodegenerative disorder, Alzheimer's disease, Parkinson's disease, immune disorder, hematopoiesis Disorders and various dyslipidemias, schizophrenia, depression, asthma, emphysema, allergies, metabolic syndrome X and chronic diseases and various cancers and conditions such as transplantation, neuroprotection, fertility or regeneration (in vitro and Consumable disorder associated with in vivo).

  NOVX nucleic acids and their encoded polypeptides are useful in a variety of applications and situations. Various NOVX nucleic acids and polypeptides according to the present invention are useful as novel members of a protein family according to the existence of domains and sequence relationships with said proteins. In addition, NOVX nucleic acids and polypeptides can be used to identify proteins that are members of the family to which the NOVX polypeptide belongs.

  Consistent with other known members of the protein family identified in column 5 of Table A, the NOVX polypeptides of the present invention show homology to and characterize other members of such protein families. Contains the domain. Details of sequence relatedness analysis and domain analysis for each NOVX are shown in Example A.

  NOVX nucleic acids and polypeptides can be used to screen for molecules that inhibit or promote NOVX activity or function. In particular, the nucleic acids and polypeptides according to the invention can be used as targets for the identification of small molecules that modulate or inhibit diseases associated with the protein families listed in Table A.

NOVX nucleic acids and polypeptides are also useful for detecting specific cell types. Details of expression analysis for each NOVX are shown in Example C. Accordingly, NOVX nucleic acids, polypeptides, antibodies and related compounds according to the present invention have diagnostic and therapeutic applications in the detection of various diseases having different expression in normal tissue versus diseased tissue, eg, various cancers. .
Additional uses for NOVX nucleic acids and polypeptides according to the present invention are disclosed herein.

NOVX clones NOVX nucleic acids and their encoded polypeptides are useful in a variety of applications and situations. Various NOVX nucleic acids and polypeptides according to the present invention are useful as novel members of the protein family according to the presence of domains and sequences associated with the protein. In addition, NOVX nucleic acids and polypeptides can be used to identify proteins that are members of the family to which the NOVX polypeptide belongs.

  The NOVX genes and their corresponding encoded proteins are useful for preventing, treating or alleviating medical conditions, eg, by protein therapy or gene therapy. The pathology can be diagnosed by measuring the amount of the new protein in the sample or measuring the presence of the mutation in the new gene. Based on the tissues in which the NOVX gene is most highly expressed, the specific use for each NOVX gene will be described. Use includes developing products for diagnosing or treating various diseases and disorders.

  The NOVX nucleic acids and proteins of the present invention are useful as potential diagnostic and therapeutic applications and research tools. These include serving as specific or selective nucleic acids, or proteins, diagnostic markers and / or prognostic markers. Here, the presence or amount of nucleic acids or proteins, as well as potential therapeutic applications such as: (i) protein therapeutics, (ii) small molecule targets, (iii) antibody targets (therapeutic, Diagnostic, drug targeting / cytotoxic antibodies), (iv) nucleic acids useful for gene therapy (gene delivery / gene surgery), and (v) compositions that promote tissue regeneration in vitro and in vivo, (vi) organisms Defense weapon.

  In one specific embodiment, the invention provides a mature form having an amino acid sequence selected from the group consisting of: (a) SEQ ID NO: 2n (n is an integer from 1 to 37); (b) SEQ ID NO: 2n ( n is an integer from 1 to 37), and a mature variant having an amino acid sequence selected from the group consisting of 15% of amino acid residues in the mature sequence (C) an amino acid sequence selected from the group consisting of SEQ ID NO: 2n (n is an integer from 1 to 37); (d) SEQ ID NO: 2n ( a variant having an amino acid sequence selected from the group consisting of n is an integer of 1 to 37, provided that any amino acid identified by the selected sequence comprises 15% or less of the amino acid residues in the sequence Change to a different amino acid under the condition It is; to and (e) (a) no comprising an isolated polypeptide comprising any of the fragments, the amino acid sequence selected from the group consisting of (d).

  In another particular embodiment, the present invention provides (a) a mature form having an amino acid sequence given SEQ ID NO: 2n (n is an integer from 1 to 37); (b) SEQ ID NO: 2n (n is A mature variant having an amino acid sequence selected from the group consisting of 1 to 37, wherein any amino acid in the mature form of the selected sequence is an amino acid residue in the mature sequence (C) an amino acid sequence selected from the group consisting of SEQ ID NO: 2n (n is an integer from 1 to 37); d) a variant of an amino acid sequence selected from the group consisting of SEQ ID NO: 2n (n is an integer from 1 to 37), wherein the specified amino acid in the selected sequence is an amino acid residue in the sequence Different nets on condition that 15% or less is subject to change A variant that is altered to an acid; and (e) at least a portion of a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 2n (n is an integer from 1 to 37), or a selected sequence A fragment of a nucleic acid encoding any variant of a polypeptide, wherein any amino acid of is altered to a different amino acid provided that less than 10% of the amino acid residues in the sequence are altered; and (f) a nucleic acid molecule An isolated nucleic acid molecule comprising a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of:

  In yet another particular embodiment, the present invention includes an isolated nucleic acid molecule. Wherein the nucleic acid molecule is (a) a nucleotide sequence selected from the group consisting of SEQ ID NO: 2n-1 (n is an integer of 1 to 37); (b) SEQ ID NO: 2n-1 (n is 1 to 37) A condition wherein one or more nucleotides in a nucleotide sequence selected from the group consisting of: is selected from the group consisting of the selected sequence and no more than 15% of the nucleotides are altered (C) a nucleic acid fragment having a sequence selected from the group consisting of SEQ ID NO: 2n-1 (n is an integer from 1 to 37); and (d) SEQ ID NO: 2n Whether one or more nucleotides are selected from the group consisting of selected sequences in a nucleotide sequence selected from the group consisting of -1 (n is an integer from 1 to 37) Contain different nucleic acid fragments that are modified nucleotide, a nucleotide sequence selected from the group consisting of with the proviso that more than 15% of the nucleotides undergo changes.

NOVX Nucleic Acids and Polypeptides One aspect of the invention pertains to isolated nucleic acid molecules encoding NOVX polypeptides or biologically active portions thereof. The invention also provides nucleic acid fragments sufficient for use as hybridization probes to identify nucleic acids encoding NOVX (eg, mRNA of NOVX), and PCR primers for amplification and / or mutation of NOVX nucleic acid molecules Including fragments for use as. As used herein, the term “nucleic acid molecule” refers to a DNA molecule (eg, cDNA or genomic DNA), an RNA molecule (eg, mRNA), a DNA analog or RNA analog produced using nucleotide analogs, And their derivatives, fragments and homologues. The nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA.

  The NOVX nucleic acid can encode a mature NOVX polypeptide. As used herein, a “mature” form of a polypeptide or protein disclosed in the present invention is a naturally occurring polypeptide, or precursor, or product of a proprotein. Naturally occurring polypeptides, precursors or proproteins include, by way of non-limiting example, full-length gene products encoded by the corresponding genes. Alternatively, it may be defined as a polypeptide, precursor or proprotein encoded by the ORFs described herein. A “mature” form of a product occurs, as a non-limiting example, as a result of one or more naturally occurring processing steps that can occur in a cell (eg, a host cell) that produces a gene product. Examples of such processing steps that lead to a “mature” form of a polypeptide or protein include cleavage of the N-terminal methionine residue encoded by the initiation codon of the ORF, or proteolytic cleavage of the signal peptide or leader sequence. Thus, a mature form resulting from a precursor polypeptide or protein having residues 1-N where residue 1 is the N-terminal methionine has residues 2-N remaining after removal of the N-terminal methionine. Alternatively, the mature form resulting from a precursor polypeptide or protein having residues 1-N that cleaves the N-terminal signal sequence from residues 1-residue M is from residual residues M + 1-residue N. Has a residue. Further, as used herein, a “mature” form of a polypeptide or protein can result from post-translational steps other than proteolytic cleavage events. Such further methods include, but are not limited to glycosylation, myristoylation, or phosphorylation. In general, a mature polypeptide or protein can be produced by manipulation of only one of these methods, or any combination thereof.

  As used herein, the term “probe” refers to a variable length nucleic acid sequence, preferably between at least about 10 nucleotides (nt) to about 100 nt, or depending on the particular use, eg, about 6000 nt. Point to. Probes can be used for the detection of identical, similar or complementary nucleic acid sequences. Longer probes are generally obtained from natural or recombinant sources. Longer probes are slower to hybridize than oligomer probes with higher specificity and shorter lengths. Probes can be single-stranded or double-stranded and can be designed to have specificity in PCR, membrane-based hybridization techniques, or ELISA-like techniques.

  As used herein, the term “isolated” nucleic acid molecule is a nucleic acid that is separated from other nucleic acid molecules that are present in the natural source of the nucleic acid. Preferably, an “isolated” nucleic acid does not have sequences that naturally flank the nucleic acid in the genomic DNA of the organism from which the nucleic acid is derived (ie, sequences located at the 5 ′ and 3 ′ ends of the nucleic acid). For example, in various embodiments, the isolated NOVX nucleic acid molecule is about 5 kb, 4 kb naturally adjacent to the nucleic acid molecule in the genomic DNA of the cell / tissue from which the nucleic acid is derived (eg, brain, heart, liver, spleen, etc.). It may contain nucleotide sequences of 3 kb, 2 kb, 1 kb, 0.5 kb, 0.1 kb or less, or less. Furthermore, an “isolated” nucleic acid molecule, such as a cDNA molecule, may be substantially free of other cellular material, media, or chemical precursors or other chemicals.

  A nucleic acid molecule of the present invention, for example, a nucleic acid molecule having the nucleotide sequence of SEQ ID NO: 2n-1 (where n is an integer from 1 to 37), or the complement of this nucleotide sequence, can be obtained using standard molecular biology techniques and It can be isolated using the sequence information provided in the specification. Using all or part of the nucleic acid sequence of SEQ ID NO: 2n-1 (where n is an integer from 1 to 37) as a hybridization probe, standard hybridization and cloning techniques (eg, Sambrook, et al., ( eds.), MOLECULAR CLONING: A LABORATORY MANUAL 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989; and Ausubel, et al., (eds.), CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons , New York, NY, 1993) can be used to isolate NOVX molecules.

  The nucleic acids of the invention can be amplified with appropriate oligonucleotide primers according to standard PCR amplification techniques using cDNA, mRNA, or alternatively genomic DNA as a template. The nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis. In addition, oligonucleotides corresponding to NOVX nucleotide sequences can be prepared by standard synthetic techniques, such as the use of automated DNA synthesizers.

  As used herein, the term “oligonucleotide” refers to a series of linking nucleotide residues. Short oligonucleotide sequences can be based on or designed from genomic or cDNA sequences. Short oligonucleotide sequences are then used to amplify, confirm, or reveal the presence of identical, similar, or complementary DNA or RNA in a particular cell or tissue. The oligonucleotide comprises a nucleic acid sequence of about 10 nt, 50 nt, or 100 nt in length, preferably about 15 nt to 30 nt in length. In one embodiment of the invention, the oligonucleotide comprising a nucleic acid molecule of less than 100 nt in length is at least 6 consecutive nucleotides of SEQ ID NO: 2n-1 (n is an integer from 1 to 37), or It further includes a complement. Oligonucleotides can be chemically synthesized and used as probes.

  In another embodiment, the isolated nucleic acid molecule of the invention comprises a nucleotide sequence set forth in SEQ ID NO: 2n-1 (n is an integer from 1 to 37), or a portion of this nucleotide sequence (eg, NOVX polypeptide A nucleic acid molecule that is the complement of a fragment that can be used as a probe, primer, or fragment encoding a biologically active portion of A nucleic acid molecule that is complementary to a nucleotide sequence that represents SEQ ID NO: 2n-1 (n is an integer from 1 to 37) is a nucleotide sequence that represents SEQ ID NO: 2n-1 (n is an integer from 1 to 37). It is sufficiently complementary and can hydrogen bond with the nucleotide sequence shown in SEQ ID NO: 2n-1 (where n is an integer from 1 to 37) with little or no mismatch. Thus, the nucleic acid molecule forms a stable duplex.

  As used herein, the term “complementary” refers to Watson-Crick or Hoogsteen base pairing between nucleotide units of a nucleic acid molecule, and the term “binding” refers to two polypeptides or compounds, or related polypeptides. Or means a physical or chemical interaction between compounds or combinations thereof. Binding includes ionic, non-ionic, van der Waals, hydrophobic interactions, and the like. The physical interaction can be direct or indirect. Indirect interactions may be through or due to the action of other polypeptides or compounds. Direct binding refers to an interaction that does not occur through or due to the action of another polypeptide or compound but instead takes place without other substantial chemical mediators.

  As provided herein, “fragments” are at least 6 fragments that are long enough to allow specific hybridization in the case of nucleic acids, and long enough for specific recognition of epitopes in the case of amino acids. Defined as a sequence of (contiguous) nucleic acids or a sequence of at least 4 (contiguous) amino acids, and some part of most shorter than the full length. Fragments can be derived from any contiguous portion of the selected nucleic acid or amino acid sequence.

A full-length NOVX clone is identified as containing an ATG translation start codon and an in-frame stop codon. Any disclosed NOVX nucleotide sequence lacking the ATG initiation codon therefore encodes a truncated C-terminal fragment of the respective NOVX polypeptide and extends in the 5 'direction of the disclosed sequence of the corresponding full-length cDNA. Request. Any disclosed NOVX nucleotide sequence lacking an in-frame stop codon similarly encodes a truncated N-terminal fragment of the respective NOVX polypeptide, such that the corresponding full-length cDNA extends in the 3 'direction of the disclosed sequence. Request.
A derivative is a nucleic acid or amino acid sequence generated either directly from the original compound, either by modification or by partial substitution. Analogs are nucleic acid or amino acid sequences that have a structure that is similar but not identical to the original compound, eg, they differ from a natural compound with respect to a particular component or side chain. Analogs can be synthetic, can be derived from different evolutionary origins, and can have similar or opposite metabolic activities compared to wild-type. A homologue is the nucleic acid or amino acid sequence of a particular gene derived from a different species.

  Derivatives and analogs can be full length or other than full length. Nucleic acid or protein derivatives or analogs of the present invention, in various embodiments, when compared to alignment sequences aligned over nucleic acid or amino acid sequences of the same size or by computer homology programs known in the art, A molecule comprising a region that is substantially homologous to a nucleic acid or protein of the invention with at least about 70%, 80%, or 95% identity (preferably 80-95% identity), or encoding thereof Nucleic acids include, but are not limited to, molecules that are capable of hybridizing under stringent, moderately stringent, or low stringency conditions to the complement of a sequence encoding a protein of the invention. See, for example, Ausubel, et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York, NY, 1993 and the following.

  “Homologous nucleic acid sequence” or “homologous amino acid sequence” or variants thereof refer to sequences characterized by homology at the nucleotide or amino acid level as described above. Homologous nucleotide sequences include those sequences that encode isoforms of the NOVX polypeptide. Isoforms can be expressed in different tissues of the same organism as a result of, for example, alternative splicing of RNA. Alternatively, isoforms can be encoded by different genes. In the present invention, a homologous nucleotide sequence includes a nucleotide sequence encoding a non-human species NOVX polypeptide, including but not limited to vertebrates. Thus, for example, include frogs, mice, rats, rabbits, dogs, cats, cows, horses, and other organisms. Homologous nucleotide sequences also include, but are not limited to, naturally occurring allelic variants and mutants of the nucleotide sequences set forth herein. However, homologous nucleotide sequences do not include the exact nucleotide sequence encoding human NOVX protein. Homologous nucleic acid sequences include nucleic acid sequences that encode conservative amino acid substitutions (see below) of SEQ ID NO: 2n-1 (where n is an integer from 1 to 37) as well as polypeptides having NOVX biological activity. Various biological activities of the NOVX protein are described below.

  NOVX polypeptides are encoded by the open reading frame (“ORF”) of NOVX nucleic acids. The ORF corresponds to a nucleotide that can potentially be translated into a polypeptide. A series of nucleic acids containing the ORF is not interrupted by a stop codon. The ORF representing the sequence encoding the full-length protein begins with an ATG “start” codon and ends with one of the three “stop” codons, TAA, TAG or TGA. For the purposes of the present invention, the ORF can be any portion of the coding sequence that may or may not have a start codon, a stop codon, or both. In order to consider the ORF as a good candidate for encoding a genuine cellular protein, minimal requirements are often defined, for example a series of DNAs encoding 50 amino acids or more.

  Nucleotide sequences determined from cloning of the human NOVX gene are for use in identifying and / or cloning NOVX homologues from other cell types, eg, other tissues, and NOVX homologues from other vertebrates Allows creation of probes and primers to be designed. The probe / primer typically comprises a substantially purified oligonucleotide. The oligonucleotide is at least about 12, 25, 50, 100, 150, 200, 250, 300, 350 or 400 consecutive sense strand nucleotides of SEQ ID NO: 2n-1 (n is an integer from 1 to 37) An antisense strand nucleotide sequence of SEQ ID NO: 2n-1 (n is an integer from 1 to 37); or a naturally occurring variant of SEQ ID NO: 2n-1 (n is an integer from 1 to 37) Typically includes regions of nucleotide sequences that hybridize under stringent conditions.

  Probes based on human NOVX nucleotide sequences can be used to detect transcripts or genomic sequences encoding the same or homologous proteins. In various embodiments, the probe is provided with a detectable label, for example, the label can be a radioisotope, a fluorescent compound, an enzyme, or a cofactor of the enzyme. Such probes are part of a diagnostic test kit for identifying cells or tissues that misexpress a NOVX protein, such as by measuring the level of a NOVX-encoding nucleic acid in a cell sample from a subject. For example, NOVX mRNA is detected or whether the genomic NOVX gene has been mutated or deleted.

  A “polypeptide having a biologically active portion of a NOVX polypeptide” includes mature forms as measured in a particular biological analysis and is similar, but not necessarily identical, to the activity of a polypeptide of the invention. It refers to a polypeptide that exerts no activity with or without dose dependency. A nucleic acid fragment encoding a “biologically active portion of NOVX” is a sequence of SEQ ID NOs: 2n-1 (where n is Can be prepared by isolating a portion (which is an integer from 1 to 37), expressing the NOVX protein-encoding portion (eg, by in vitro recombinant expression), and evaluating the activity of the NOVX-encoding portion.

NOVX nucleic acid and polypeptide variants The present invention further differs from the nucleotide sequence shown in SEQ ID NO: 2n-1 (where n is an integer from 1 to 37) due to the degeneracy of the genetic code, and thus SEQ ID NO: 2n-1 ( n is an integer from 1 to 37) and includes a nucleic acid molecule that encodes the same NOVX protein as encoded by the nucleotide sequence shown in FIG. In another embodiment, an isolated nucleic acid molecule of the invention has a nucleotide sequence that encodes a protein having the amino acid sequence set forth in SEQ ID NO: 2n (n is an integer from 1 to 37).

  In addition to the human NOVX nucleotide sequence shown in SEQ ID NO: 2n-1 (where n is an integer from 1 to 37), polymorphisms of the DNA sequence that result in a change in the amino acid sequence of the NOVX polypeptide are a population (eg, a human population). Those skilled in the art will appreciate that they can be present therein. Such genetic polymorphisms in the NOVX gene may exist among individuals in the population due to natural allelic variation. The terms “gene” and “recombinant gene” as used herein refer to a nucleic acid molecule comprising an open reading frame (ORF) encoding a NOVX protein, preferably a vertebrate NOVX protein. Such natural allelic variations typically result in 1-5% variation in the nucleotide sequence of the NOVX gene. Any and all such nucleotide variations that are the result of natural allelic variation and do not alter the functional activity of the NOVX polypeptide and the amino acid polymorphisms in the NOVX polypeptide obtained therefrom are intended to be within the scope of the invention. .

  In addition, nucleic acid molecules encoding NOVX proteins from other species, and thus nucleic acid molecules having a nucleotide sequence different from human SEQ ID NO: 2n-1, where n is an integer from 1 to 37 are within the scope of the present invention. It shall be in Nucleic acid molecules corresponding to natural allelic variants and homologues of the NOVX cDNA of the present invention are obtained using human cDNA or a portion thereof as a hybridization probe according to standard hybridization techniques under stringent hybridization conditions. It can be isolated based on homology with the human NOVX nucleic acids disclosed herein.

  Thus, in another embodiment, an isolated nucleic acid molecule of the present invention is at least 6 nucleotides in length and is exact for a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 2n-1 (n is an integer from 1 to 37). Hybridizes under conditions. In another embodiment, the nucleic acid is at least 10, 25, 50, 100, 250, 500, 750, 1000, 1500, 2000 or more nucleotides in length. In yet another embodiment, the isolated nucleic acid molecule of the invention hybridizes to the coding region. As used herein, the term “hybridizes under stringent conditions” describes hybridization and washing conditions in which nucleotide sequences that are at least about 65% homologous to each other typically remain hybridized to each other. Intended.

  Homologues (i.e., nucleic acids encoding NOVX proteins from non-human species) or other related sequences (e.g., paralogs) can be converted to specific human sequences using methods well known in the art of nucleic acid hybridization and cloning. All or part of the probe is used as a probe, and can be obtained by low, medium, or high stringent hybridization.

  As used herein, the term “stringent hybridization conditions” refers to conditions under which a probe, primer or oligonucleotide hybridizes to a target sequence but not to other sequences. The exact conditions are sequence dependent and there are differences in different environments. Longer sequences hybridize specifically at higher temperatures than shorter sequences. In general, stringent conditions are selected to be about 5 ° C. lower than the melting temperature (Tm) for the specific sequence at a constant ionic strength and pH. Tm is the temperature (under a defined ionic strength, pH and nucleic acid concentration) at which 50% of the probe complementary to the target sequence hybridizes to the target sequence at equilibrium. Since the target sequence is generally present in excess at Tm, it accounts for 50% of the probe at equilibrium. Typically, the strict conditions are pH 7.0-8.3 and a salt concentration of less than about 1.0M sodium ion, typically about 0.01-1.0M sodium ion (or other salt), The temperature is at least about 30 ° C. for short probes, primers or oligonucleotides (eg, 10 nt to 50 nt) and at least about 60 ° C. for longer probes, primers and oligonucleotides. Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide.

  The exact conditions are known to those skilled in the art and can be found in Ausubel, et al., (Eds.), CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, NY (1989), 6.3.1-6.3.6. it can. Preferably, the conditions are such that sequences that are at least 65%, 70%, 75%, 85%, 90%, 95%, 98%, or 99% homologous to each other typically remain hybridized to each other. is there. Non-limiting examples of stringent hybridization include 6 × SSC, 50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA and 500 mg / ml denaturation. Hybridization is performed at 65 ° C. in a high salt buffer containing salmon sperm DNA, and then washed once or more at 50 ° C. in 0.2 × SSC, 0.01% BSA. An isolated nucleic acid molecule of the invention that hybridizes under stringent conditions to the sequence of SEQ ID NO: 2n-1 (n is an integer from 1 to 37) corresponds to a naturally occurring nucleic acid molecule. As used herein, the term “naturally-occurring” nucleic acid molecule refers to an RNA or DNA molecule having a nucleic acid sequence that occurs in nature (eg, encodes a natural protein).

  In a second embodiment, the nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 2n-1 (where n is an integer from 1 to 37), or a fragment, analog or derivative thereof, hybridizes under moderately stringent conditions. Nucleic acid sequences for soy are provided. Non-limiting examples of moderately stringent hybridization conditions include hybridization at 55 ° C. in 6 × SSC, 5 × Reinhardt solution, 0.5% SDS and 100 mg / ml denatured salmon sperm DNA, followed by 1 X Washing once or more at 37 ° C in SSC, 0.1% SDS. Other moderately stringent conditions that can be used are well known in the art. See, for example, Ausubel, et al. (Eds.), 1993, CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, NY, and Krieger, 1990; GENE TRANSFER AND EXPRESSION, A LABORATORY MANUAL, Stockton Press, NY. .

  In a third embodiment, the nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 2n-1 (n is an integer from 1 to 37), or a fragment, analog or derivative thereof, hybridizes under less stringent conditions. Nucleic acid sequences for soy are provided. Non-limiting examples of low stringency hybridization conditions include 35% formamide, 5 × SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.0%. Hybridization was performed in 2% BSA, 100 mg / ml denatured salmon sperm DNA, 10% (wt / vol) dextran sulfate at 40 ° C., followed by 2 × SSC, 25 mM Tris-HCl (pH 7.4), 5 mM EDTA, And washing once or more at 50 ° C. in 0.1% SDS. Other less stringent conditions that can be used (eg, for interspecies hybridization) are well known in the art. For example, Ausubel, et al. (Eds.), 1993, CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, NY, and Kriegler, 1990; GENE TRANSFER AND EXPRESSION, A LABORATORY MANUAL, Stockton Press, NY .; Shilo and Weinberg 1981. Proc Natl Acad Sci USA 78: 6789-6792.

Conservative mutations In addition to the naturally occurring allelic variation of the NOVX sequence that may be present in the population, a mutation is introduced into the nucleotide sequence of SEQ ID NO: 2n-1 (where n is an integer from 1 to 37). One skilled in the art further understands that changes in the amino acid sequence of the encoding NOVX protein can be made without altering the functional activity of the NOVX protein. For example, nucleotide substitutions leading to amino acid substitutions at “non-essential” amino acid residues can be made in the sequence of SEQ ID NO: 2n-1 (n is an integer from 1 to 37). “Non-essential” amino acid residues are those residues that can change the wild-type sequence of the NOVX protein without altering their biological activity, while “essential” amino acid residues are such biological activity. Need to. For example, amino acid residues that are conserved in the NOVX protein of the present invention are not expected to be particularly resistant to conversion. Amino acids for which conservative substitutions can be made are well known in the art.

  Another aspect of the invention pertains to nucleic acid molecules encoding NOVX proteins that contain changes in amino acid residues that are not essential for activity. Such NOVX protein differs from SEQ ID NO: 2n-1 (n is an integer from 1 to 37) in amino acid sequence, but still retains biological activity. In one embodiment, the isolated nucleic acid molecule comprises a nucleotide sequence that encodes a protein, wherein the protein is at least about 50% homologous to the amino acid sequence of SEQ ID NO: 2n (n is an integer from 1 to 37). Contains amino acid sequence. Preferably, the protein encoded by the nucleic acid molecule is at least about 60% homologous to SEQ ID NO: 2n (n is an integer from 1 to 37); more preferably, the protein encoded by the nucleic acid molecule is SEQ ID NO: 2n ( n is an integer from 1 to 37); more preferably at least about 80% homologous to SEQ ID NO: 2n (n is an integer from 1 to 37); and even more Preferably, it is at least about 90% homologous to SEQ ID NO: 2n (n is an integer from 1 to 37); most preferably, it is at least about 95% homologous to SEQ ID NO: 2n (n is an integer from 1 to 37). It is.

  An isolated nucleic acid molecule that encodes a NOVX protein that is homologous to the protein of SEQ ID NO: 2n (where n is an integer from 1 to 37) within the protein that encodes one or more amino acid substitutions, additions or deletions Can be created by introducing one or more nucleotide substitutions, additions or deletions into the nucleotide sequence of SEQ ID NO: 2n-1 (where n is an integer from 1 to 37).

  Mutations can be introduced into SEQ ID NO: 2n-1 (n is an integer from 1 to 37) by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Preferably, conservative amino acid substitutions are made at one or more predicted non-essential amino acid residues. A “conservative amino acid substitution” is one of the amino acid residues that is replaced with an amino acid residue having a similar side chain. Families of amino acid residues with similar side chains have been defined within the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), amino acids with acidic side chains (e.g., aspartic acid, glutamic acid), amino acids with uncharged side chains (e.g., glycine, Asparagine, glutamine, serine, threonine, tyrosine, cysteine), amino acids with nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), amino acids with beta side chains (e.g., Threonine, valine, isoleucine), as well as amino acids with aromatic side chains (eg tyrosine, phenylalanine, tryptophan, histidine). Thus, a predicted nonessential amino acid residue in a NOVX protein is replaced with another amino acid residue from the same side chain family. Alternatively, in another embodiment, mutations can be introduced randomly along all or part of a NOVX coding sequence, such as saturation mutagenesis, and the resulting mutations The body can be screened for NOVX biological activity to identify mutants that retain activity. Following mutagenesis of SEQ ID NO: 2n-1 (n is an integer from 1 to 37), the encoded protein can be expressed by any recombinant technique known in the art and the activity of the protein can be measured. .

  Amino acid family relationships can also be determined based on side chain interactions. Substituted amino acids can be fully conserved “strong” residues or fully conserved “weak” residues. The “strong” group of conserved amino acid residues can be any one of the following groups: STA, NEQK, NHQK, NDEQ, QHRK, MILV, MILF, HY, FYW, where the one letter code for amino acids Are grouped with amino acids that can be substituted for each other. Similarly, the “weak” group of conserved residues can be any one of the following: CSA, ATV, SAG, STNK, STPA, SGND, SNDEKK, NDEQHK, NEQHRK, HFY, where each Group letters represent the single letter code for amino acids.

In one embodiment, the mutant NOVX protein is (i) another NOVX protein, other cell surface protein or protein that interacts with their biological active site: the activity of forming the protein, (ii) the mutant NOVX protein May be assayed for complex formation between certain NOVX ligands, or (iii) the activity of mutant NOVX proteins that bind to intracellular target proteins or their biologically active sites; (eg, avidin protein).
In yet another embodiment, the mutant NOVX protein may be assayed for activity that modulates a particular biological function (eg, modulation of insulin secretion).

Interfering RNA
In one embodiment of the invention, NOVX gene expression can be attenuated by RNA interference. One approach that is well known in the art is gene silencing mediated by short interfering RNA (siRNA), in which at least 19 to 25 nucleotides long segments of the NOVX gene transcript A specific double-stranded NOVX-derived siRNA nucleotide sequence that is complementary and contains a 5 ′ untranslated (UT) region, ORF, or 3 ′ UT region targets the NOVX gene expression product. See, for example, PCT applications WO00 / 44895, WO99 / 32619, WO01 / 75164, WO01 / 92513, WO01 / 29058, WO01 / 89304, WO02 / 16620, and WO02 / 29858, each incorporated herein by reference. . The targeted gene may be the NOVX gene or may be an upstream or downstream modulator of the NOVX gene. Non-limiting examples of upstream or downstream modulators of the NOVX gene are, for example, kinases or phosphatases that interact with the transcription factor NOVX polypeptide that binds to the NOVX gene promoter, and polypeptides included in the NOVX regulatory pathway.

  According to the methods of the present invention, NOVX gene expression is silenced using interfering RNA. The NOVX polynucleotides of the present invention include siRNA polynucleotides. Using the NOVX polynucleotide sequence, for example, by processing the NOVX polynucleotide sequence in a cell-free system such as, but not limited to, Drosophila extract, by transcription of recombinant double-stranded NOVX RNA, or by the NOVA sequence Such NOVX siRNA can be obtained by synthesizing a nucleotide sequence homologous to. See, for example, Tuschul, Zamire, Lehmann, Bartel and Sharp (1999), Genes & Dev. 13: 3191-3197 (incorporated into the system of the present invention by reference). When synthesized, typical 0.2 micromolar scale RNA synthesis yields about 1 milligram of siRNA, sufficient for 1000 transfection experiments using a 24-well tissue culture plate format.

  The most efficient silencing is generally observed using a siRNA duplex containing a 21 nucleotide sense strand and a 21 nucleotide antisense strand paired to have a 2 nucleotide 3 ′ overhang. The The sequence of the 2 nucleotide 3 'overhang makes a further minor contribution to the specificity of siRNA target recognition. The contribution to specificity is localized to unpaired nucleotides adjacent to the first paired base. In one embodiment, the nucleotide in the 3 'overhang is a rib nucleotide. In another embodiment, the nucleotide in the 3 'overhang is a deoxyribonucleotide. Using 2'-deoxyribonucleotides in the 3 'overhang is effective as a use of ribonucleotides, but deoxyribonucleotides are often cheaper to synthesize and are most likely to be more nuclease resistant.

  The contemplated recombinant expression vector of the present invention is in an expression vector comprising a proximity regulatory sequence operably linked to a NOVX sequence in a manner that allows expression of both strands (by transcription of the DNA molecule). Contains integrated NOVX DNA molecules. An RNA molecule that is antisense to NOVX mRNA is transcribed by a first promoter (eg, the 3 ′ promoter sequence of the cloned DNA), and an RNA molecule that is the sense strand for NOVX mRNA is transcribed by a second promoter (clone Transcribed by the 5 'promoter sequence of the modified DNA). The sense and antisense strands hybridize in vivo to generate siRNA constructs for silencing the NOVX gene. Alternatively, two constructs can be used to create the sense and antisense strands of the siRNA construct. Eventually, the cloned DNA may encode a construct having a second structure, with a single transcript having sense and complementary antisense sequences from the target gene (s). In one example of this embodiment, the hairpin RNAi product is homologous to all or part of the target gene. In another example, the hairpin RNAi product is siRNA. The regulatory sequences adjacent to the NOVX sequence may be the same or different if their expression can be independently modulated or modulated temporally or positionally.

  In particular embodiments, siRNAs are transcribed intracellularly, for example by incorporating a NOVX gene template into a vector comprising an RNA pol III transcription unit derived from smaller nuclear RNA (snRNA) U6 or human RNase P RNA H1. The One example of a vector system is the GeneSuppressor ™ RNA Interference kit (commercially available from Imgenex). The U6 and H1 promoters are members of the type III class of the pol III promoter. The +1 nucleotide of the U6-like promoter is always guanosine, whereas the +1 of the H1 promoter is adenosine. The termination signal for these promoters is defined by 5 consecutive thymidines. Typically, the transcript is cleaved after the second uridine. Cleavage at this position results in a 3'UU overhang in the expressed siRNA, which is similar to the 3 'overhang of synthetic siRNA. Sequences less than 400 nucleotides in length can be transcribed by these promoters, and therefore they are ideally suited for expressing about 21 nucleotides of siRNA, eg, in an RNA stem loop transcript of about 50 nucleotides Is.

  SiRNA vectors are considered advantageous over synthetic siRNA when long term expression knockdown is required. Cells transfected with siRNA expression vectors will be stable and will undergo prolonged mRNA inhibition. In contrast, cells transfected with exogenous synthetic siRNA typically recover from mRNA suppression within 7 days or during 10 rounds of cell division. The long-term gene silencing ability of siRNA expression vectors may allow application to gene therapy.

  In general, siRNA is cleaved from longer dsRNAs by an ATP-dependent ribonuclease called DICER. DICER is a member of the RNase III family of double-stranded RNA-specific endonucleases. siRNAs assemble with cellular proteins to form an endonuclease complex. In vitro studies in Drosophila suggest that the siRNA / protein complex (siRNP) is subsequently transferred to a second enzyme complex called an RNA-induced silencing complex (RISC) that contains an endoribonuclease different from DIECR. doing. RISC uses the sequence encoded by the siRNA strand to find and destroy the complementary sequence of mRNA. Thus, the siRNA acts as a guide, limiting the ribonuclease to cleave only mRNA that is complementary to one of the two siRNA strands.

  The NOVX mRNA region to be targeted by siRNA is generally selected from the desired NOVX sequence starting from 50 to 100 nucleotides downstream of the start codon. Alternatively, the 5 'or 3' UTR and the region near the start codon can be used but are generally avoided. Because they are abundant in regulatory protein binding sites. The UTR binding protein and / or translation initiation complex may interfere with the binding of the siRNP or RISC endonuclease complex. An initial BLAST homology search for the selected siRNA sequence is performed on the available nucleotide sequence library to ensure that only one gene is targeted. The target recognition specificity by the siRNA duplex indicates that a single point mutation present in the paired region of the siRNA is sufficient to prevent degradation of the target mRNA. See Elbashir et al. 2001 EMBO J. 20 (23): 6877-88. Therefore, SNPs, polymorphisms, allelic variants or species-specific changes should be taken into account when targeting the desired gene.

  In one embodiment, a complete NOVX siRNA experiment uses the correct negative control. In general, negative control siRNA has the same nucleotide composition as NOVX siRNA, but lacks significant sequence homology to the genome. Typically, the nucleotide sequence of the NOVX siRNA is scrambled and a homology search is performed to confirm that it lacks homology with any other gene.

  Two independent NOVX siRNA duplexes can be used to knock down the target NOVX gene. This helps to control the specificity of the silencing effect. Further, by using equal concentrations of different NOVX siRNA duplexes, eg, NOVX siRNA and siRNA for NOVX gene or polypeptide regulators, the expression of two independent genes can be knocked down simultaneously. The availability of siRNA binding proteins is thought to be more limited than the target mRNA accessibility.

  Typically, the targeted NOVX region is two adenines (AA) and two thymidines (TT) separated by a spacer region of 19 (N19) residues (eg, AA ( N19) TT). Desirable spacer regions have a G / C-content of about 30-70%, more preferably about 50%. If the sequence AA (N19) TT is not present in the target sequence, another target region would be AA (N21). The sequence of the NOVX sense siRNA corresponds to (N19) TT or N21, respectively. In the latter case, if such a sequence is not essentially present in the NOVX polynucleotide, conversion of the sense siRNA to the 3 'end TT can be performed. The logical interpretation of this sequence conversion is to produce a symmetric duplex with respect to the sequence composition of the sense and antisense 3 'overhangs. Symmetric 3 'overhangs can help ensure that siRNP is formed at the appropriate equal proportion of sense and antisense target RNA-cleavage siRNP. See, for example, Elbashir, Lendeckel and Tuschl (2001). Genes & Dev. 15: 188-200 (incorporated herein by reference). It is not believed that modification of the siRNA duplex sense sequence overhang affects the recognition of the targeted mRNA. This is because the antisense siRNA strand guides target recognition.

  Alternatively, if the NOVX target mRNA does not contain the appropriate AA (N21) sequence, the sequence NA (N21) may be searched. Furthermore, the sequence of the sense strand and the antisense strand may be synthesized as 5 '(N19) TT. This is because the sequence of most nucleotides on the 3 'side of the antisense siRNA does not contribute to specificity. Unlike antisense or ribozyme methods, the secondary structure of the target mRNA is not thought to strongly influence silencing. See Harborth, et al. (2001) J. Cell Science 114: 4557-4565 (incorporated herein by reference).

  Standard nucleic acid transfection methods such as OLIGOFECTAMINE Reagent (commercially available from Invitrogen) can be used to transfect NOVX siRNA duplexes. In general, assays for NOVX gene silencing are performed about 2 days after transfection. In the absence of transfection reagent, NOVX gene silencing was not observed, allowing comparative analysis of wild type and silencing NOVX phenotypes. In a particular embodiment, about 0.84 μg siRNA duplex is usually sufficient for one well of a 24-well plate. Typically, cells are seeded the day before and transfected when approximately 50% confluent. The selection of cell culture medium and culture conditions is usually done by those skilled in the art and will vary with the choice of cell type. The efficiency of transfection depends not only on the cell type, but also on the cell passage number and confluence. The formation time and method (eg, inverted vortex) of the siRNA-liposome complex is also important. Low transfection efficiency is the biggest cause of unsuccessful NOVX silencing. It is necessary to carefully examine the transfection efficiency for the new cell line used. Preferred cells are derived from mammals, more preferably from rodents such as rats or mice, and most preferably from humans. When used for therapeutic treatment, preferably the cells are autologous, but non-autologous cell sources are also within the scope of the invention.

  For control experiments, transfection of 0.84 μg single-stranded sense NOVX siRNA did not affect NOVX silencing, and 0.84 μg antisense siRNA had a weaker silencing effect compared to 0.84 μg double-stranded siRNA. Have Control experiments further allow comparative analysis of wild type and silent NOVX phenotypes. In order to control transfection efficiency, protein targeting is typically performed. For example, targeting Lamin A / C or transfection of CMV driven EGFP expression plasmid (eg, commercially available from Clontech). In the above example, the Lamin A / C knockdown fragment in the cells is performed the next day by methods such as immunofluorescence, Western blot, Northern blot or other similar assays for protein expression or gene expression. Lamin A / C monoclonal antibody was obtained from Santa Cruz Biotechnology.

  Depending on the abundance and half-life (or turnover) of the targeted NOVX polynucleotide in the cell, a knockdown phenotype can be revealed after 1-3 days or thereafter. If a NOVX knockdown phenotype is not observed, it may be desirable to analyze whether the target mRNA (NOVX or NOVX upstream or downstream gene) was effectively destroyed by the transfected siRNA duplex. Two days after transfection, total RNA is prepared, reverse transcribed using target-specific primers, and PCR amplification is performed using primer pairs that convert at least one exon-exon junction to control pre-mRNA amplification. . RT / PCR of untargeted mRNA is also required as a control. A decrease in target protein that is an effective depletion of mRNA but cannot be detected may indicate that a large reservoir of stable NOVX protein is present in the cell. Multiple transfections at sufficiently long intervals may be required before the target protein can eventually be depleted and the phenotype can be revealed. If multiple transfection steps are required, the cells are split 2-3 days after transfection. The cells may be transfected immediately after dividing.

  The therapeutic methods of the invention contemplate administering a NOVX siRNA construct as a treatment to correct for increased or deviated NOVX expression or activity. As described above, NOVX ribopolynucleotides are obtained and processed into siRNA fragments or synthesized with NIVX siRNA. As described above, NOVX siRNA is administered to cells or tissues using known nucleic acid transfection methods. NOVX siRNA specific for the NOVX gene reduces or knocks down NOVX transcripts, which reduces NOVX polypeptide production and reduces NOVX polypeptide activity in cells or tissues.

  The present invention also encompasses a method of treating a disease or condition associated with the presence of NOVX protein in an individual, the method comprising an RNAi construct that targets mRNA of the protein to be degraded (mRNA encoding the protein). It is characterized by being administered to an individual. Special RNAi constructs include siRNA or double stranded gene transcripts that are processed into siRNA. The target protein is no longer produced by treatment, or the level of production is lower than when no treatment is performed.

If NOVX gene function does not correlate with a known phenotype, a control sample of cells or tissue from a healthy individual provides a reference standard for determining NOVX expression levels. Expression levels are detected using the described assays, eg, RT-PCR, Northern blotting, ELISA, etc. A sample of cells or tissue is collected from a diseased mammal, preferably a human subject. These cells or tissues are treated by administering NOVX siRNA to the cells or tissues by the methods described for transfection of nucleic acids into cells or tissues, and NOVX polypeptides or polypeptides in the subject sample using the described assay. Observe the change in nucleotide expression and compare to that of the control sample. This NOVX gene knockdown method provides a rapid method for determining the NOVX minus (NOVX ⁻ ) phenotype in a sample to be treated. Thus, the NOVX ^- phenotype observed in the sample to be treated serves as a marker for follow-up of the disease state being treated.

  In a special embodiment, NOVX siRNA is used for therapy. Methods for producing and using NOVX siRNA are known to those skilled in the art. An example of the method is shown below.

Generation of RNA NOVX sense RNA (ssRNA) and antisense (asRNA) are obtained using known methods such as transcription in RNA expression vectors. In the first experiment, sense and antisense RNA are each about 500 bases in length. The resulting ssRNA and asRNA (0.5 μM) were heated in 10 mM Tris-HCl (pH 7.5) containing 20 mM NaCl for 1 minute at 95 ° C., then cooled and annealed at room temperature for 12-16 hours. Let RNA is precipitated and resuspended in lysis buffer (below). To monitor annealing, RNA is electrophoresed in a 2% agarose gel in TBE buffer and stained with ethidium bromide. See, for example, Sambrook et al., Molecular Cloning. Cold Spring Harbor Laboratory Press, Plainview, NY (1989).

Lysate preparation Collect untreated rabbit reticulocyte lysate according to the manufacturer's instructions (Ambion). Incubate dsRNA in lysate at 30 ° C. for 10 minutes, then add mRNA. Thereafter, NOVX mRNA is added and the incubation is continued for another 60 minutes. The molar ratio of double stranded RNA to mRNA is about 200: 1. NOVX mRNA is radiolabeled (using known methods) and its stability is monitored by gel electrophoresis.

In experiments performed in parallel under the same conditions, double-stranded RNA is radiolabeled internally with ³² P-ATP. The reaction is stopped with 2X proteinase K buffer and deproteinized as previously described (Tuschl et al., Genes Dev., 13: 3191-3197). Products are analyzed by electrophoresis in 15% or 18% polyacrylamide sequencing gels using appropriate RNA standards. By monitoring the gel for radioactivity, the natural production of 10-25 nucleotide RNA from double stranded RNA can be examined.

  A band of double-stranded RNA of about 21 to 23 bp is eluted. The effectiveness of these 21-23 mer NOVX transcriptional repressions is assayed in vitro using the same rabbit reticulocytes as described above using 50 nanomolar double stranded 21-23 mers for each assay. These 21-23 mer sequences are then determined using standard nucleic acid sequencing methods.

Preparation of RNA Based on the sequence determined above, nucleotide RNA is chemically synthesized using Expedite RNA phosphoramidites and thymidine phosphoramidite (Proligo, Germany) 21. Synthetic oligonucleotides are deprotected and gel purified (Elbashir, Lendeckel, & Tuschl, Genes & Dev. 15, 188-200 (2001)), then a Sep-Pak C18 cartridge (Waters, Milford, Mass., USA) (Tuschl, et al., Biochemistry, 32: 11658-11668 (1993)).
These RNA (20 μM) single strands are incubated in annealing buffer at 90 ° C. for 1 minute and then at 37 ° C. for 1 hour.

Cell culture Cell cultures known in the art for regular expression of NOVX are performed using standard conditions. 24 hours prior to transfection, cells are trypsinized at approximately 80% confluence, diluted 1: 5 in fresh medium without antibiotics (1-3 × 10 ⁵ cells / ml) and transferred to 24-well plates (500 ml / well). Transfection is performed using a commercial lipofection kit, and NOVX expression is monitored using standard methods with positive and negative controls. Positive controls are cells that naturally express NOVX, and negative controls are cells that do not express NOVX. Base-paired 21 and 22 nucleotide siRNAs with an overhang 3 'mediate effective sequence-specific mRNA degradation in lysates and cell cultures. Different concentrations of siRNA are used. The effective concentration for in vitro suppression in mammalian cell culture is a final concentration of 25 nM to 100 nM. This indicates that siRNA concentrations several orders of magnitude lower than those used for conventional antisense or ribozyme gene targeting experiments are effective.

  The above methods provide methods for both inference of NOVX siRNA sequences and use of such siRNA for ion vitro suppression. In vivo suppression may be performed using the same siRNA using well-known in vivo transfection or gene therapy transfection methods.

Antisense Nucleic Acid Another aspect of the invention is capable of hybridizing to a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 2n-1 (where n is an integer from 1 to 37), or a fragment, homologue or derivative thereof. Or an isolated antisense nucleic acid molecule. An “antisense” nucleic acid comprises a nucleotide sequence that is complementary to a “sense” nucleic acid encoding a protein (eg, complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence). In particular embodiments, antisense nucleic acid molecules comprising at least about 10, 25, 50, 100, 250, or 500 nucleotides or a sequence complementary to the entire NOVX coding strand, or only a portion thereof, are provided. A nucleic acid molecule encoding a fragment, homologue, derivative and analog of NOVX protein with SEQ ID NO: 2n (n is an integer from 1 to 37), or SEQ ID NO: 2n-1 (n is an integer from 1 to 37) ) And an antisense nucleic acid complementary to the NOVX nucleic acid sequence provided.

  In one embodiment, the antisense nucleic acid molecule is antisense to a “coding region” of the coding strand of a nucleotide sequence encoding a NOVX protein. The term “coding region” refers to a region of a nucleotide sequence that includes codons translated into amino acid residues. In another embodiment, the antisense nucleic acid molecule is antisense to a “non-coding region” of the coding strand of a nucleotide sequence encoding a NOVX protein. The term “noncoding region” refers to 5 ′ and 3 ′ sequences that flank the coding region that are not translated into amino acids (ie, also referred to as 5 ′ untranslated region and 3 ′ untranslated region).

  Given the sequence of the coding strand encoding the NOVX protein disclosed herein, antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick or Hoogsteen base pairing. The antisense nucleic acid molecule can be complementary to the entire coding region of NOVX mRNA, but more preferably is an oligonucleotide that is antisense to only a portion of the coding or non-coding region of NOVX mRNA. . For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of NOVX mRNA. Antisense oligonucleotides can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 nucleotides in length. An antisense nucleic acid of the invention can be constructed using chemical synthesis or enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid (e.g., an antisense oligonucleotide) increases the biological stability of a naturally occurring nucleotide or molecule, or a double-stranded physical stability that forms between an antisense nucleic acid and a sense nucleic acid. Various modified nucleotides designed to increase can be chemically synthesized (eg, phosphorothioate derivatives and nucleotides substituted with acridine can be used).

  Examples of modified nucleotides that can be used to make antisense nucleic acids include: 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5 -Carboxymethylaminomethyl-2-thiouridine, 5- (carboxyhydroxymethyl) uracil, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosilk enosine, inosine, N6-isopentenyladenine, 1-methylguanine 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 5-methoxyuracil, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methyl Aminomethyl Lacil, 5-methoxyaminomethyl-2-thiouracil, 2-thiouracil, 4-thiouracil, beta-D-mannosyl eosin, 5′-methoxycarboxymethyluracil, 2-methylthio-N6-isopentenyladenine, uracil-5 Oxyacetic acid (v), wivetoxosin, pseudouracil, queosin, 2-thiocytosine, 5-methyl-2-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methyl ester, uracil-5-oxyacetic acid, uracil-5-oxy Acetic acid (v), 5-methyl-2-thiouracil, 3- (3-amino-3-N-2-carboxypropyl) uracil, (acp3) w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid is subcloned in the antisense orientation of the nucleic acid (ie, RNA transcribed from the inserted nucleic acid is the antisense orientation for the target nucleic acid of interest and is further described in the subsection below). Can be produced biologically using the expression vector.

  Protein expression by hybridizing or binding the antisense nucleic acid molecules of the invention to cellular mRNA and / or genomic DNA that encodes certain NOVX proteins thereby (eg, inhibiting transcription and / or translation) Is typically administered to a subject so as to inhibit or made in tissue. Hybridization can also be due to the complementarity of conventional nucleotides to form stable duplexes. Alternatively, for example, in the case of an antisense nucleic acid that binds to a DNA double strand, it can be through a specific interaction in the double-stranded major groove. An example of a route of administration of antisense nucleic acid molecules of the invention is direct injection into a tissue site. Alternatively, antisense nucleic acid molecules can be modified to selected cellular targets where they can be administered systemically. For example, for systemic administration, antisense molecules are specifically bound to receptors or antigens expressed on selected cell surfaces (e.g., linking antisense nucleic acid molecules to peptides or cell surfaces). May be modified (by antibodies that bind to receptors or antigens). Antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. In order to deliver sufficient nucleic acid molecules, vector structures that place antisense nucleic acid molecules under the control of a strong pol II or pol III promoter are preferred.

  In yet another embodiment, the antisense nucleic acid molecule of the invention is an α-anomeric nucleic acid molecule. α-anomeric nucleic acid molecules form specific double-stranded hybrids with complementary RNAs, which are opposite to normal β units and run parallel to each other. See, for example, Gaultier, et al., 1987. Nucl. Acids Res. 15: 6625-6641. Antisense nucleic acid molecules can also be 2′-o-methyl ribonucleotides (see, eg, Inoue, et al. 1987. Nucl. Acids Res. 15: 6131-6148) or chimeric RNA-DNA analogs (eg, Inoue, et al., 1987. FEBS Lett. 215: 327-330).

Ribozymes and PNA moieties Nucleic acid modifications include, by way of non-limiting example, modified bases and nucleic acids modified or derived from sugar phosphate backbones. These modifications are made at least in part to enhance the chemical stability of the modified nucleic acid so that it can be used, for example, as an antisense that binds to the nucleic acid in therapeutic applications to a subject.

  In one embodiment, the antisense nucleic acid of the invention is a ribozyme. Ribozymes are catalytically active RNA molecules with ribonuclease activity that are capable of cleaving single-stranded nucleic acids such as mRNA having a complementary region. Thus, ribozymes (eg, hammerhead ribozymes as described in Haselhoff and Gerlach 1988. Nature 334: 585-591) are used to catalytically cleave NOVX mRNA transcripts, thereby NOVX mRNA. Translation may be inhibited. Ribosomes having specificity for a nucleic acid encoding NOVX can be designed based on the nucleotide sequence of certain NOVX cDNAs disclosed herein (ie, SEQ ID NO: 2n-1 (n is an integer from 1 to 37)). . For example, a derivative of Tetrahymena L-19IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to a nucleotide sequence that can be cleaved in mRNA encoding NOVX. See, for example, Cech, et al., US Pat. No. 4,987,071, and Cech, et al., US Pat. No. 5,116,742. NOVX mRNA can also be used to select catalytic RNAs with specific ribonuclease activity from a pool of RNA molecules. See, for example, Bartel et al., (1993) Science 261: 1411-1418.

  On the other hand, NOVX gene expression is inhibited by targeting a nucleotide sequence complementary to a regulatory region of NOVX nucleic acid (eg, NOVX promoter and / or enhancer), and triple helical that blocks transcription of NOVX gene in the target cell. A structure can be formed. See, for example, Helene, 1991. Anticancer Drug Des. 6: 569-84; Helene, et al. 1992. Ann. NY Acad. Sci. 660: 27-36; Maher, 1992. Bioassays 14: 807-15. .

  In various embodiments, NOVX nucleic acids can be modified at the base moiety, sugar moiety, or phosphate backbone moiety to improve, for example, molecular stability, hybridization, or solubility. For example, the nucleic acid deoxyribose phosphate backbone can be modified to produce peptide nucleic acids. See, for example, Hyrup, et al., 1996. Bioorg Med Chem 4: 5-23. As used herein, the term “peptide nucleic acid” or “PNA” refers to a nucleic acid mimetic (eg, a DNA mimetic) that replaces the deoxyribose phosphate backbone with a pseudopeptide backbone and retains only four nucleobases. . The neutral backbone of PNA is shown to allow specific hybridization to DNA and RNA under conditions of low ionic strength. The synthesis of PNA oligomers is described in Hyrup, et al., 1996. supra; Perry-O'Keefe, et al., 1996. Proc. Natl. Acad. Sci. USA 93: 14670-14675 It can be performed using a standard solid phase peptide synthesis protocol.

NOVX PNA may be used for therapeutic and diagnostic applications. For example, PNA can be used as an antisense or antigenic agent for sequence specific modulation of gene expression, for example by inducing transcription or translational arrest or inhibiting replication. NOVX PNA can also be used, for example, as an artificial restriction enzyme that can be used in combination with single base pair mutations in genes (eg, PNA directing PCR fixation; other enzymes such as S ₁ nuclease) ( Hyrup, et al., 1996.supra); or as DNA sequence and hybridization probes or primers (Hyrup, et al., 1996, supra; see Perry-O'Keefe, et al., 1996. supra) )) Can also be used.

  In another embodiment, the PNA of NOVX is modified, eg, by attaching a lipophilic or other auxiliary group to the PNA, by generating a PNA-DNA chimera, or by liposomes or the art Can be used to enhance their stability or cellular uptake by use of other drug delivery techniques known in the art. For example, a PNA-DNA chimera of NOVX can be generated that can combine the beneficial properties of PNA and DNA. Such chimeras allow DNA recognition enzymes (eg, RNase H and DNA polymerase) to interact with the DNA moiety, while the PNA moiety provides binding high affinity and binding specificity. PNA-DNA chimeras can be joined using linkers of appropriate lengths selected for base linkage, number of linkages between nucleotide bases and orientation (see Hyrup, et al., 1996. supra). Synthesis of PNA-DNA chimeras can be performed as described in Hyrup, et al., 1996. supra and Finn, et al., 1996. Nucl Acids Res 24: 3357-3363. For example, a DNA strand can be synthesized on a solid support using standard phosphoramidite coupling chemistry. Modified nucleoside analogs, such as 5 ′-(4-methoxytrityl) amino-5′-deoxythymidine phosphoramidites, can then be used between the PNA and the 5 ′ end of the DNA. See, for example, Mag, et al., 1989. Nucl Acid Res 17: 5973-5988. The PNA monomer is then coupled stepwise to produce a chimeric molecule having a 5 ′ PNA segment and a 3 ′ DNA segment. See, for example, Finn, et al., 1996. supra. Alternatively, the chimeric molecule can be synthesized with a 5 ′ DNA segment and a 3 ′ PNA segment. See, for example, Petersen, et al., 1975. Bioorg. Med. Chem. Lett. 5: 1119-11124.

  In other embodiments, the oligonucleotides are attached to groups such as peptides (e.g., to target host cell receptors in vivo), or cell membranes (e.g., Letsinger, et al., 1989. Proc. Natl. Acad. Sci. USA 86: 6553-6556; Lemaitre, et al., 1987. Proc. Natl. Acad. Sci. 84: 648-652; Agents that facilitate transport across (see WO89 / 10134). In addition, oligonucleotides can be combined with hybridization-induced cleavage agents (see, eg, Krol, et al., 1988. BioTechniques 6: 958-976) or intercalating agents (eg, Zon, 1988. Pharm. Res. 5: 539 -549). For this purpose, oligonucleotides can be conjugated, for example, with peptides, hybridization-inducing cross-linking agents, transport agents, hybridization-inducing cleavage agents and the like.

NOVX Polypeptides Polypeptides according to the present invention include polypeptides that contain the amino acid sequence of the NOVX polypeptide whose sequence is provided in SEQ ID NO: 2n (n is an integer from 1 to 37). The present invention also provides a protein that retains its NOVX activity and physiological function while any residue thereof can be converted from the corresponding residue shown in SEQ ID NO: 2n (n is an integer from 1 to 37), Or a mutant or variant protein that still encodes a functional fragment thereof.

  In general, one NOVX variant that retains a NOVX-like function includes any variant that substitutes a residue at a particular site in the sequence with another amino acid, with another residue between two residues of the parent protein. Or further including the possibility of inserting multiple residues as well as the possibility of deleting one or more residues from the parent sequence. Any amino acid substitution, insertion or deletion is encompassed by the present invention. In preferred circumstances, the substitution is a conservative substitution as defined above.

  One aspect of the present invention relates to isolated NOVX proteins and biologically active portions thereof, or derivatives, fragments, analogs or homologues thereof. Polypeptide fragments suitable for use as an immunogen for the production of anti-NOVX antibodies can also be provided. In one embodiment, native NOVX protein may be isolated from a cell or tissue source by a suitable purification scheme using standard protein purification techniques. In another embodiment, NOVX protein is produced by recombinant DNA technology. As an alternative to recombinant expression, certain NOVX proteins or polypeptides can be chemically synthesized using standard peptide synthesis techniques.

  An “isolated” or “purified” polypeptide or protein or biologically active portion thereof is substantially free of cellular or tissue source cellular material or other contaminating protein from which the NOVX protein is derived, or chemically When synthesized, it is substantially free of chemical precursors or other chemicals. The term “substantially free of cellular material” includes a sample of NOVX protein that has separated the protein from the cellular components of the original cell from which the protein was isolated or recombinantly produced. In one embodiment, the term “substantially free of cell source” means less than about 30% (dry weight ratio) of non-NOVX protein (also referred to herein as “contaminating protein”), more preferably about Samples of NOVX protein having less than 20% non-NOVX protein, even more preferably less than about 10% non-NOVX protein, and most preferably less than about 5% non-NOVX protein are included. In recombinantly producing NOVX proteins or biologically active portions thereof, it is also preferably substantially free of medium, ie, the medium is less than about 20% of the volume of the NOVX protein specimen, more preferably It represents less than about 10%, and most preferably less than 5%.

  The term “substantially free of chemical precursors or other chemicals” includes a sample of NOVX protein where proteins are separated from chemical precursors or other chemicals involved in protein synthesis. To do. In one embodiment, the term “substantially free of chemical precursors or other chemicals” refers to less than about 30% (dry weight ratio) chemical precursors or non-NOVX chemicals, more preferably Less than about 20% chemical precursor or non-NOVX chemical, even more preferably less than about 10% chemical precursor or non-NOVX chemical, and most preferably less than about 5% chemical precursor or non-NOVX Includes specimens of NOVX protein with chemicals.

The biologically active portion of the NOVX protein comprises an amino acid sequence of NOVX protein that contains fewer amino acids than the full-length NOVX protein and exhibits at least one activity of the NOVX protein (eg, SEQ ID NO: 2n, where n is 1 to 37 The amino acid sequence derived from the amino acid sequence sufficiently homologous to (the amino acid sequence shown in the amino acid sequence of the NOVX protein). Typically, the biologically active portion includes a domain or motif having at least one activity of the NOVX protein. A biologically active portion of a NOVX protein can be a polypeptide, eg, 10, 25, 50, 100 or more amino acid residues long.
In addition, other biologically active portions lacking other regions of the protein can be prepared by recombinant techniques and evaluated for one or more of the functional activities of the native NOVX protein.

  In one embodiment, the NOVX protein has the amino acid sequence shown in SEQ ID NO: 2n (where n is an integer from 1 to 37). In other embodiments, the NOVX protein is substantially homologous to SEQ ID NO: 2n (where n is an integer from 1 to 37), and SEQ ID NO: 2n (where n is an integer from 1 to 37). Retains the functional activity of certain proteins, but still differs in amino acid sequence due to natural allelic variants or mutations as detailed below. Thus, in another embodiment, the NOVX protein comprises an amino acid sequence that is at least about 45% homologous to the amino acid sequence of SEQ ID NO: 2n (where n is an integer from 1 to 37), And n is an integer of 1 to 37).

Measuring homology between two or more sequences To determine the percentage of homology between two amino acid sequences or two nucleic acids, the sequences are aligned for optimal comparison purposes (eg, gaps of 2 In the first amino acid sequence or nucleic acid sequence for optimal alignment with the second amino acid or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid or nucleic acid sites are then compared. When a site in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding site in the second sequence, both molecules are homologous at that site (ie, as used herein, amino acids or Nucleic acid “homology” is equivalent to amino acid or nucleic acid “identity”).

  Nucleic acid sequence homology can be measured as the degree of identity between two sequences. Homology can be measured using computer programs known in the art, such as GAP software provided in the GCG program package. See Needleman and Wunsch, 1970. J Mol Biol 48: 443-453. Using the GCG GAP software with the following settings: GAP generation penalty 5.0 or GAP extension penalty 0.3, the coding region of the above similar nucleic acid sequence is SEQ ID NO: 2n-1 (where n is Preferably at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity with the CDS (encoding) portion of the DNA sequence shown in FIG. Indicates the degree.

  The term “sequence identity” refers to the extent to which two polynucleotide or polypeptide sequences are identical from residue to residue over a particular region of comparison. The term “percent of sequence identity” is used to compare two sequences that are optimally aligned over the region of comparison and to determine the number of matching sites (for example, A, in the case of nucleic acids, A, The number of sites where T, C, G, U, or I) is present in both sequences is determined, the number of matching sites is divided by the total number of sites in the comparison region (ie, window size), and the quotient is 100. Can be calculated by multiplying to obtain a percentage of sequence identity. As used herein, the term “substantial identity” means a property of a polynucleotide sequence. Here, the polynucleotide comprises at least 80% sequence identity, preferably at least 85% sequence identity, and often 90-95% sequence identity, more usually compared to the standard sequence over the comparison region. Includes sequences with at least 99% sequence identity.

Chimeric or fusion protein The present invention also provides a NOVX chimeric or fusion protein. As used herein, certain NOVX “chimeric proteins” or “fusion proteins” include certain NOVX polypeptides operably linked to non-NOVX polypeptides. “NOVX polypeptide” refers to a polypeptide having an amino acid sequence corresponding to the NOVX protein of SEQ ID NO: 2n, where n is an integer from 1 to 37, while “non-NOVX polypeptide” A polypeptide having an amino acid sequence corresponding to a protein that is not substantially homologous to the NOVX protein, for example, a protein that is the same or different from the NOVX protein. Within a NOVX fusion protein, a NOVX polypeptide may correspond to all or part of a NOVX protein. In one embodiment, a NOVX fusion protein includes at least one biologically active portion of a NOVX protein. In another embodiment, a NOVX fusion protein comprises at least two biologically active portions of a NOVX protein. In yet another embodiment, a NOVX fusion protein comprises at least three biologically active portions of a NOVX protein. Within the fusion protein, the term “operably linked” shall indicate that the NOVX polypeptide and the non-NOVX polypeptide are fused in-frame to each other. The non-NOVX polypeptide can be fused to the N-terminus or C-terminus of the NOVX polypeptide.

  In one embodiment, the fusion protein is a GST-NOVX fusion protein. Here, the NOVX sequence is fused to the C-terminus of GST (glutathione S transferase). Such fusion proteins can facilitate the purification of recombinant NOVX polypeptides.

  In another embodiment, the fusion protein is a NOVX protein containing a heterologous signal sequence at its N-terminus. In certain host cells (eg, mammalian host cells), NOVX expression and / or secretion may be enhanced through the use of heterologous signal sequences.

  In yet another embodiment, the fusion protein is a NOVX-immunoglobulin fusion protein. Here, the NOVX sequence is fused to a sequence derived from a member of the immunoglobulin protein family. A NOVX-immunoglobulin fusion protein of the invention is incorporated into a pharmaceutical composition and administered to a subject to inhibit the interaction of a NOVX ligand with a NOVX protein on the cell, thereby inhibiting NOVX-mediated in vivo. Information transmission can be suppressed. NOVX-immunoglobulin fusion proteins can be used to affect the bioavailability of certain NOVX-like ligands. Inhibition of the NOVX ligand / NOVX interaction may be therapeutically useful for the treatment of proliferation and differentiation disorders and for modulating (eg, enhancing or inhibiting) cell survival. In addition, the NOVX-immunoglobulin fusion proteins of the present invention are used to produce anti-NOVX antibodies in a subject, purify NOVX ligand, and inhibit the interaction of NOVX with a NOVX ligand in screening assays Can be identified.

  The NOVX chimeric or fusion proteins of the invention can be produced by standard recombinant DNA techniques. For example, DNA fragments encoding different polypeptide sequences can be used, for example, using blunted or staggered ends for ligation, cleavage with restriction enzymes to provide appropriate ends, appropriately filling sticky ends, desirably Ligated together in-frame according to conventional methods such as alkaline phosphatase treatment to prevent unbound and enzymatic coupling. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments is performed using anchor primers that produce complementary overhangs between two consecutive gene fragments, which are subsequently annealed and reamplified to produce a chimeric gene sequence. (See, eg, Ausubel, et al. (Eds.) CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, 1992). Moreover, many expression vectors (eg, GST polypeptides) that already encode a fusion moiety are commercially available. A nucleic acid encoding NOVX can be cloned into such an expression vector such that the fusion moiety binds in-frame to the NOVX protein.

NOVX Agonists and Antagonists The present invention also includes variants of the NOVX protein that function as either NOVX agonists (ie, mimetics) or NOVX antagonists. NOVX protein variants may be generated by mutation (eg, point mutation or truncation of the NOVX protein). NOVX protein agonists retain substantially the same biological activity or subset thereof as the naturally occurring form of NOVX protein. An agonist of NOVX protein inhibits the activity of one or more naturally occurring forms of NOVX protein by, for example, antagonistic binding to downstream or upstream members of the cellular signaling cascade, including NOVX protein Can do. Thus, specific biological effects can be exerted by treatment with variants having limited functions. In one embodiment, treatment of a subject with a variant having a subset of the biological activity of a naturally occurring form of the protein has fewer side effects in the subject than treatment with a naturally occurring form of NOVX protein.

  Variants of NOVX proteins that function as either NOVX agonists (ie, mimetics) or NOVX antagonists screen recombinant libraries of NOVX protein mutants (eg, truncation mutants) for NOVX protein agonist or antagonist activity Can be identified. In one embodiment, a NOVX variant-rich library is generated by recombinant (combinatorial) mutagenesis at the nucleic acid level and is encoded by a gene library that is rich in change. A library enriched in NOVX variants can be used, for example, to enzymatically link a mixture of synthetic oligonucleotides to a gene sequence so that a degenerate set of potential NOVX sequences can be expressed as individual polypeptides. Or alternatively as a set of larger fusion proteins (eg, for phage display) containing a set of NOVX sequences therein. There are a variety of methods that can be generated from a degenerate oligonucleotide sequence using a library of potential NOVX variants. Chemical synthesis of degenerate gene sequences can be performed with an automated DNA synthesizer, and the synthetic gene can then be ligated into an appropriate expression vector. The use of a degenerate set of genes allows the provision of a single mixture of all of the sequences that encode the desired set of potential NOVX sequences. Methods for synthesizing degenerate oligonucleotides are well known in the art. For example, Narang, 1983. Tetrahedron 39: 3; Itakura, et al., 1984. Annu. Rev. Biochem. 53: 323; Itakura, et al., 1984. Science 198: 1056; Ike, et al., 1983. See Nucl. Acids Res. 11: 477.

Polypeptide Library In addition, a fragment library of NOVX protein-encoding sequences can be used to generate a population enriched in NOVX fragments for screening and subsequent selection of NOVX protein variants. In one embodiment, a library of coding sequence fragments is subjected to nuclease treatment of a double stranded PCR fragment of a NOVX coding sequence under conditions where nicking occurs only once per molecule to denature the double stranded DNA. Forming a double-stranded DNA that can contain sense / antisense pairs from different nicking products, removing the single-stranded portion from the double helix regenerated by treatment with S ₁ nuclease, and the resulting fragment live Can be generated by linking the library to an expression vector. By this method, an expression library encoding various sized N-terminal or internal fragments of the NOVX protein can be derived.

  Various techniques are known in the art for screening gene products of recombinant (combinatorial) libraries generated by point mutations or truncations, and screening cDNA libraries for gene products having selected properties. . Such techniques are applicable to rapid screening of gene libraries generated by recombinant (combinatorial) mutagenesis of NOVX proteins. The most widely used technique applicable to high-throughput analysis to screen large gene libraries is to clone the gene library into a replicable expression vector and transform the appropriate cells with the resulting vector library, And the detection of the desired activity typically involves expressing the recombinant (combinatorial) gene under conditions that facilitate the isolation of the vector encoding the gene that detects the product. A new technique that increases the frequency of functional mutations in the library, repetitive ensemble mutagenesis (REM), can be used in combination with screening assays to identify NOVX mutants. See, for example, Arkin and Yourvan, 1992. Proc. Natl. Acad. Sci. USA 89: 7811-7815; Delgrave, et al., 1993. Protein Engineering 6: 327-331.

Anti-NOVX Antibodies Antibodies to NOVX proteins or fragments of NOVX proteins are included in the present invention. As used herein, the term “antibody” refers to an immunologically active portion of an immunoglobulin molecule and an immunoglobulin (Ig) molecule, ie, an antigen that specifically binds (and reacts immunologically) with an antigen. Refers to a molecule containing a binding site. Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, F _ab , F _{ab ′} and F _{(ab ′) 2} fragments and a F _ab expression library. In general, antibody molecules obtained from humans relate to any of the classes IgG, IgM, IgA, IgE and IgD, which differ from each other due to the nature of the heavy chain present in the molecule. Certain classes have subclasses as well, such as IgG ₁ , IgG ₂ and others. Furthermore, in humans, the L chain can be a k chain or a lambda chain. Reference herein to antibodies includes a reference to all such classes, subclasses and types of human antibody species.

  Generate isolated antibodies immunospecifically using standard techniques for polyclonal and monoclonal antibody preparation using the isolated protein of the present invention, or a portion or fragment thereof, intended for use as an antigen, as an immunogen Can do. The full-length protein may be used, or alternatively, the present invention provides an antigenic peptide fragment of an antigen for use as an immunogen. The antigenic peptide fragment comprises at least 6 amino acid residues of the amino acid sequence of the full-length protein, such as the amino acid sequence shown in SEQ ID NO: 2n (where n is an integer from 1 to 37) and The antibodies raised in this way include the epitope so as to form a specific immune complex with the full-length protein or any fragment containing the epitope. Preferably, the antigenic peptide comprises at least 10 amino acid residues, or at least 15 amino acid residues, or at least 20 amino acid residues, or at least 30 amino acid residues. Preferred epitopes encompassed by the antigenic peptides are protein regions located on the surface; these are usually hydrophilic regions.

  In certain embodiments of the invention, at least one epitope encompassed by the antigenic peptide is a NOVX region localized on the surface of the protein, eg, a hydrophilic region. Hydrophobic analysis of the human NOVX protein sequence indicates which regions of the NOVX polypeptide are particularly hydrophilic and therefore likely to encode useful surface residues for targeting antibody production. As a means to target antibody production, hydropathy plots showing hydrophilic and hydrophobic regions are well known in the art including, for example, the Kyte Doolittle or Hopp Woods methods, both with or without Fourier transforms. It can be generated by any method. For example, Hopp and Woods, 1981, Proc. Nat. Acad. Sci. USA 78: 3824-3828; Kyte and Doolittle 1982, J. Mol. Biol. 157: 105-142 (both are hereby incorporated by reference in their entirety) As a part of the book). Antibodies that are specific for one or more domains within an antigenic protein or derivative, fragment, analog or homologue thereof are also provided herein.

The term “epitope” includes all protein determinants (sites) that can specifically bind to an immunoglobulin or T cell receptor. Epitope-like determinants (sites) usually contain surface groups of chemically active molecules (eg amino acids or sugar side chains) and usually show specific charge characteristics in addition to specific three-dimensional structural characteristics . Certain NOVX polypeptides or fragments thereof have at least one antigenic epitope. Assay (e.g., to one skilled in the art known radioligand binding assays or similar assays) as measured by equilibrium binding constant _{K D} of, <1 [mu] M, preferably <100 nM, more preferably <10 nM, most preferably < 100 pM to about 1 pM, the anti-NOVX antibody of the present invention is said to specifically bind to the antigen NOVX.

  The proteins of the invention, or derivatives, fragments, analogs, homologues, or orthologs thereof can be utilized as an immunogen in the production of antibodies that immunospecifically bind to these protein components.

  Various methods known in the art can be used for the production of polyclonal or monoclonal antibodies against a protein of the invention, or derivatives, fragments, analogs, homologues, or orthologs thereof (eg, Antibodies: A Laboratory Manual). Harlow E, and Lane D, 1988, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, which is incorporated herein by reference). Some of these antibodies are discussed below.

Polyclonal antibodies For the production of polyclonal antibodies, various suitable host animals (eg rabbits, goats, mice, or other mammals) are injected once or more with natural proteins, synthetic variants thereof, or the aforementioned derivatives. And immunize. Suitable immunogenic formulations may include, for example, naturally occurring immunogenic proteins, chemically synthesized polypeptides that are representative of immunogenic proteins, or recombinantly expressed immunogenic proteins. Furthermore, the protein may be complexed with a second protein that is known to be immunogenic in the mammal to be immunized. Examples of such immunogenic proteins include, but are not limited to, keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. The formulation may further contain an adjuvant. Various adjuvants used to increase the immune response include Freund's (complete and incomplete) adjuvants, mineral gels (e.g. aluminum hydroxide), surfactants (e.g. lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions) , Dinitrophenol, etc.), adjuvants that can be used in humans, such as, but not limited to, Bacillus Calmette-Guerin and Corynebacterium parvum. Yet another example of an adjuvant that may be used may include MPL-TDM adjuvant (monophosphoryl lipid A, synthetic dicorynomycolic acid trehalose).

  Polyclonal antibodies against immunogenic proteins are isolated from mammals (eg, from blood) and known techniques, such as affinity chromatography using protein A or protein G, which provides mainly the IgG fraction in immune serum Can be used for further purification. Subsequently, or alternatively, a specific antigen that is the target of the desired immunoglobulin, or an epitope thereof, can be immobilized on a column and the immunospecific antibody can be purified by immunoaffinity chromatography. The purification of immunoglobulins is discussed, for example, by D. Wilkinson (The Scientist, published by The Scientist, Inc., Philadelphia PA, Vol. 14, No. 8 (April 17, 2000), pp. 25-28).

Monoclonal antibody As used herein, the term “monoclonal antibody” (MAb) or “monoclonal antibody composition” refers to only one molecular species of an antibody molecule comprising a characteristic light chain gene product and a characteristic heavy chain gene product. Refers to the population of antibody molecules that it contains. In particular, the complementarity determining regions (CDRs) of monoclonal antibodies are the same in all molecules of the population. Thus, MAbs contain an antigen binding site capable of immunoreacting with a particular epitope of an antigen characterized by a characteristic binding activity thereto.

  Monoclonal antibodies can be prepared using hybridoma methods, as described by Kohler and Milstein, Nature, 256: 495 (1975). In the hybridoma method, lymphocytes that produce or are capable of producing antibodies that specifically bind to an immunizing agent are typically immunized by immunizing a mouse, hamster, or other suitable host animal with the immunizing agent. To trigger. Alternatively, lymphocytes can be immunized in vitro.

The immunizing agent typically includes protein antigens, fragments thereof or fusion proteins thereof. In general, either peripheral blood lymphocytes are used if cells derived from humans are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. . The lymphocytes are then fused with an immortal cell line using a suitable fusing agent such as polyethylene glycol to generate hybridoma cells (Goding, Monoclonal Antibodies: Principles and Practice , Academic Press, (1986) pp. 59 -103). Immortal cell lines are usually transformed mammalian cells, particularly myeloma cells from rodents, cattle or humans. Usually, rat or mouse myeloma cell lines may be used. The hybridoma cells may be cultured in a suitable medium that preferably contains one or more substances that inhibit the growth or survival of unfused, immortalized cells. For example, if the parent cell lacks the enzyme hypoxanthine guanine phosphoribosyltransferase (HGPRT or HPRT), the culture medium for hybridomas typically contains hypoxanthine, a substance that prevents the growth of HGPRT-deficient cells, Contains aminopterin and thymidine (“HAT medium”).

  Preferred immortal cell lines are those that fuse efficiently, support high level expression of antibodies by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. Further preferred immortal cell lines are mouse myeloma cell lines available from, for example, the Salk Institute Cell Distribution Center, San Diego, California and the American Type Culture Collection, Manassas, Virginia. Human myeloma and mouse-human heteromyeloma cell lines are also described for the production of human monoclonal antibodies (Kozbor, J. Immunol., 133: 3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications, Marcel Dekker, Inc., New York, (1987) pp. 51-63).

  The medium in which the hybridoma is cultured can then be assayed for the presence of monoclonal antibodies directed against the antigen. Preferably, the binding specificity of monoclonal antibodies produced by hybridoma cells is measured by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunosorbent assay (ELISA). Such techniques or assays are known in the art. The binding affinity of a monoclonal antibody can be measured, for example, by Scatchard analysis of Munson and Pollard, Anal. Biochem., 107: 220 (1980). Identifying antibodies with a high degree of specificity and high binding affinity for the target antigen is a particularly important objective in the therapeutic application of monoclonal antibodies.

  After identifying the desired hybridoma cells, the clones can be subcloned by limiting dilution and grown by standard methods (Goding, 1986). Suitable culture media for this purpose can include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium. Alternatively, the hybridoma cells can be grown in vivo as ascites in a mammal.

  Monoclonal antibodies secreted by subclones are isolated or isolated from medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein-A sepharose, hydroxyapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography. It can be purified.

  Monoclonal antibodies can also be made by recombinant DNA methods as described in US Pat. No. 4,816,567. Using an oligonucleotide probe capable of specifically binding DNA encoding the monoclonal antibody of the present invention to a gene encoding the heavy and light chains of the murine antibody using conventional procedures (eg. Can be easily isolated and sequenced. The hybridoma cells of the invention serve as a preferred source of such DNA. Once isolated, the DNA is placed in an expression vector, which is then host cells such as monkey COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that would otherwise not produce immunoglobulin proteins. It can be transfected into to obtain monoclonal antibody synthesis in recombinant host cells. DNA can also be replaced, for example, by replacing coding sequences for the normal domains of human heavy and light chains in place of homologous murine sequences (US Pat. No. 4,816,567; Morrison, Nature 368, 812- 13 (1994)), or all or part of the coding sequence for a non-immunoglobulin peptide can be modified by covalent attachment to the coding sequence of the immunoglobulin. Such non-immunoglobulin polypeptides can be substituted for the normal domain of the antibody of the invention, or can be substituted for the variable domain of one antigen binding site of the antibody of the invention to produce chimeric 2 A titer antibody can be created.

Humanized antibodies Antibodies to protein antigens of the present invention further include humanized antibodies or human antibodies. These antibodies are suitable for administration to humans without causing human immune responses to the administered immunoglobulins. Humanized forms of antibodies are chimaeric immunoglobulins, immunoglobulin chains, or fragments thereof (Fv, Fab, Fab ′) that consist primarily of human immunoglobulin sequences and contain minimal sequence derived from non-human immunoglobulin. F (ab ′) ₂ or other antigen-binding subsequence of the antibody). Humanization is performed by Winter or co-workers (Jones et al., Nature, 321: 522-525 (1986); Riechmann et al., Nature, 332: 323-327 (1988); Verhoeyen et al., Science, 239 : 1534-1536 (1988)) by replacing the rodent CDR or CDR sequence with the corresponding sequence of a human antibody. (See also US Pat. No. 5,225,539). In some cases, the Fv frame residues of the human immunoglobulin can be replaced by corresponding non-human residues. Humanized antibodies may also comprise residues that are not found in the recipient antibody or in the CDR or frame sequence. In general, a humanized antibody will contain at least one, and typically substantially all of the two variable domains. Here, all or substantially all of the CDR regions correspond to the CDR regions of a non-human immunoglobulin, and all or substantially all of the frame region is of a human immunoglobulin consensus sequence. Humanized antibodies also optimally comprise the normal region (Fc) of an immunoglobulin, typically at least part of that of a human immunoglobulin (Jones et al., 1986; Riechmann et al., 1988; and Presta , Curr. Op. Struct. Biol., 2: 593-596 (1992)).

Human antibodies A fully human antibody is essentially related to an antibody molecule in which the entire L and H chain sequences, including the CDRs, originate from a human gene. Such antibodies are referred to herein as “human antibodies” or “fully human antibodies”. Human monoclonal antibodies can be prepared by trioma technology; human B cell hybridoma technology (see Kozbor, et al., 1983 Immunol Today 4: 72) and EBV hybridoma technology to produce human monoclonal antibodies (Cole, et al. , 1985 In: MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc., pp. 77-96). Humanized monoclonal antibodies can be utilized in the practice of the invention and human hybridomas can be used (see Cote, et al., 1983. Proc Natl Acad Sci USA 80: 2026-2030) or human B cells can be Can be produced by transformation with Epstein Barr virus (see Cole, et al., 1985 In: MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc., pp. 77-96).

  In addition, human antibodies can also be obtained from phage display libraries (Hoogenboom and Winter, J. Mol. Biol., 227: 381 (1991); Marks et al., J. Mol. Biol., 222: 581 (1991)). Can be produced using further techniques including: Similarly, human antibodies can be made by introducing human immunoglobulin loci into transgenic animals, eg, mice. Here, the endogenous immunoglobulin genes are partially or completely inactivated. The challenge observes human antibody production very similar to that seen in humans in all aspects, including gene rearrangement, assembly, and antibody repertoire. This approach is described, for example, in U.S. Patent Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016. Marks et al. (Bio / Technology 10, 779-783 (1992)), Lonberg et al. (Nature 368 856-859 (1994)), Morrison (Nature 368, 812-13 (1994)), Fishwild et al, (Nature Biotechnology 14, 845-51 (1996)), Neuberger (Nature Biotechnology 14, 826 (1996)), Lonberg and Huszar (Intern. Rev. Immunol. 13 65-93 (1995)). .

  Human antibodies can additionally be produced using transgenic non-human animals that have been modified to produce fully human antibodies rather than the animal's endogenous antibodies in response to challenge with antigen (PCT Publication No. WO94 / 02602). The endogenous genes encoding immunoglobulin heavy and light chains in the non-human host are disabled, and active loci encoding human immunoglobulin heavy and light chains are inserted into the genome of the host. Human genes can be incorporated, for example, using yeast artificial chromosomes containing the necessary human DNA segments. Animals that provide all the desired modifications are then obtained as offspring by crossbreeding intermediate transgenic animals that contain less than the full complement of modifications. A preferred embodiment of such a non-human animal is a mouse, designated Xenomouse® as disclosed in PCT Publication Nos. WO96 / 33735 and WO96 / 34096. This animal produces B cells that secrete fully human immunoglobulins. The antibody can be obtained directly from the animal after immunization with the immunogen of interest, eg, as a polyclonal antibody specimen, or alternatively, an immortalized B derived from an animal, such as a hybridoma producing a monoclonal antibody. It can also be obtained from cells. In addition, genes encoding immunoglobulins with human variable regions can be recovered and expressed to obtain antibodies directly, or further modified, eg, for antibodies such as single chain Fv molecules. Analogues can be obtained.

  An example of a method of producing a non-human host, exemplified as a mouse, that lacks endogenous immunoglobulin heavy chain expression is disclosed in US Pat. No. 5,939,598. It is known from at least one endogenous heavy chain locus in embryonic stem cells to prevent loci rearrangement and to prevent transcript production of rearranged immunoglobulin heavy chain loci. A segment is deleted, this deletion being brought about by a targeting vector containing a gene encoding a selectable marker, and somatic cells or embryonic cells are transformed from embryonic stem cells containing a gene encoding the selectable marker. It is obtained by a method that includes producing.

  Methods for producing antibodies of interest, such as human antibodies, are disclosed in US Pat. No. 5,916,771. It introduces an expression vector containing a nucleotide sequence encoding an H chain into one cultured mammalian host cell, and introduces an expression vector containing a nucleotide sequence encoding an L chain into yet another mammalian host cell. And fusing two cells to produce a hybrid cell. Hybrid cells express antibodies that contain heavy and light chains.

  In a further refinement of this procedure, a method for identifying clinically relevant epitopes on an immunogen and a correlated method for selecting antibodies that immunospecifically bind to the relevant epitope with high affinity are disclosed in PCT publication. No. WO99 / 53049.

_Fab fragments and single chain antibodies In accordance with the present invention, techniques can be adapted to the production of single chain antibodies specific for the antigenic proteins of the present invention (see, eg, US Pat. No. 4,946,778). In addition, the method is adapted to the construction of _Fab expression libraries (see, eg, Huse, et al., 1989 Science 246: 1275-1281), and to proteins or derivatives, fragments, analogs or homologues thereof. It may allow rapid and effective identification of monoclonal _Fab fragments with the desired specificity for. Antibody fragments containing idiotypes against protein antigens can be produced by techniques known in the art, which are (i) F _{(ab ′) 2} fragments produced by pepsin digestion of antibody molecules; (ii) F _{( ab ′) Fab} fragments obtained by reducing disulfide bridges of ₂ fragments; (iii) _Fab fragments generated by treating antibody molecules with papain and a reducing agent; and (iv) F _v fragments. It is not limited to.

Bispecific antibodies Bispecific antibodies are monoclonal antibodies, preferably human or humanized antibodies, that have binding specificities for at least two different antigens. As used herein, one of the binding specificities is for the antigenic protein of the present invention. The second binding target is any other antigen, preferably a cell surface protein or receptor or receptor subunit.

  Methods for making bispecific antibodies are known in the art. Traditionally, recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy / light chain pairs in which the two heavy chains have different specificities (Milstein and Cuello, Nature, 305 : 537-539 (1983)). Due to the random combination of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, only one of which has the correct bispecific structure. Purification of the correct molecule is usually performed by affinity chromatography. Similar methods are disclosed in WO 93/08829 published in May 1993 and Traunecker et al., EMBO J., 10: 3655-3659 (1991).

  Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin normal domain sequences. The fusion is preferably with the normal domain of an immunoglobulin heavy chain comprising at least part of the hinge, CH2 and CH3 regions. It is preferred to have a first heavy chain normal region (CH1) containing at least the site necessary for light chain binding present in one of the fusions. The DNA encoding the immunoglobulin heavy chain fusion and, if desired, the immunoglobulin light chain are inserted into separate expression vectors and transfected into a suitable host organism. For further details of bispecific antibodies see, for example, Suresh et al., Methods in Enzymology, 121: 210 (1986).

  According to another approach described in WO 96/27011, the interface between a pair of antibody molecules can be modified to maximize the percentage of heterodimer recovered from the recombinant cell medium. A preferred interface includes at least a portion of the CH3 region of the normal domain of an antibody. In this method, one or more small amino acid side chains at the interface of the first antibody molecule are replaced with larger side chains (eg tyrosine or tryptophan). The interface of the second antibody molecule by replacing a compensatory “void” of the same or similar size as the large side chain (s) by replacing the large amino acid side chain with a smaller one (eg alanine or threonine). To generate. This provides a mechanism to increase the yield of heterodimers over other undesirable end products such as homodimers.

Bispecific antibodies can be prepared as full length antibodies or antibody fragments (eg F (ab ′) ₂ bispecific antibodies). Techniques for generating bispecific antibodies from antibody fragments have been described in the literature. For example, bispecific antibody fragments can be prepared using chemical linkage. Brennan et al., Science 229: 81 (1985) describes a procedure in which intact antibodies are cleaved with proteolytic enzymes to produce F (ab ′) ₂ fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation. The resulting Fab ′ fragment is then converted to a thionitrobenzoic acid (TNB) derivative. One of the Fab′-TNBs is then reconverted to Fab′-thiol by reduction with mercaptoethylamine and mixed with an equal amount of other Fab′-TNB derivatives to produce bispecific antibodies. The resulting bispecific antibody can be used as an enzyme selective immobilization agent.

In addition, Fab ′ fragments can be recovered directly from E. coli and chemically coupled to produce bispecific antibodies. Shalaby et al., J. Exp. Med. 175: 217-225 (1992) describes the production of F (ab ′) ₂ molecules of fully humanized bispecific antibodies. Each Fab ′ fragment was secreted separately from E. coli and subjected to directed chemical coupling in vitro to form bispecific antibodies. Thus, the formed bispecific antibody can bind to cells that overexpress the ErbB2 receptor and normal human T cells and induce lytic activity of human cytotoxic lymphocytes against human breast tumor targets. did it.

Various techniques for making and isolating bispecific antibodies directly from recombinant cell media are also described. For example, bispecific antibodies are produced using leucine zippers. Kostelny et al., J. Immunol. 148 (5): 1547-1553 (1992). Leucine zippers from Fos protein and Jun protein were linked to the Fab ′ portions of two different antibodies by gene fusion. Antibody homodimers were reduced at the hinge region to form monomers and then reoxidized to form antibody heterodimers. This method can also be utilized for the production of antibody homodimers. The “diabody” technology described by Hollinger et al., Proc. Natl. Acad. Sci. USA 90: 6444-6448 (1993) provides yet another mechanism for bispecific antibody fragment production. The fragment contains a heavy chain variable region (V _H ) linked to a light chain variable region (V _L ) by a linker, but does not allow pairing between two domains on the same chain due to the short linker . Thus, the V _H and V _L domains of one fragment are forced to pair with the complementary _VL and V _H domains of another fragment, thereby forming two antigen binding sites. Another strategy for making bispecific antibody fragments by the use of single chain Fv (sFv) dimers has also been reported. See Gruber et al., J. Immunol. 152: 5368 (1994).

Antibodies having a valence of 3 or more can also be considered. For example, trispecific antibodies can be prepared. For example, Tutt et al., J. Immunol. 147: 60 (1991).
A typical bispecific antibody can bind to two different epitopes, at least one of which is derived from a protein antigen of the invention. Alternatively, the anti-antigen arm of an immunoglobulin molecule is linked to a T cell receptor molecule (e.g. CD2, CD3, CD28 or B7) or FcγRI (CD64), FcγRII (CD32) and FcγRIII (CD16) In combination with arms that bind to inducible molecules, such as the Fc receptor for IgG (Fcγ), may focus on cellular defense mechanisms against cells that express specific antigens. Bispecific antibodies can also be used to direct cytotoxic agents to cells expressing a particular antigen. These antibodies possess an antigen-binding arm and an arm that binds to a cytotoxic agent or a radionuclide chelator such as EOTUBE, DPTA, DOTA or TETA. Another bispecific antibody of interest binds to the protein antigen described herein and further binds tissue factor (TF).

Heteroconjugate antibodies Heteroconjugate antibodies are also within the scope of the present invention. A heteroconjugate antibody consists of two antibodies linked by a covalent bond. Such antibodies are, for example, for targeting cells of the immune system to unfavorable cells (US Pat. No. 4,676,980) and for the treatment of HIV infection (WO 91/00360; WO 92/003733; EP03089). ). It is believed that these antibodies can be prepared in vitro using known methods of protein synthesis chemistry, including those involving crosslinkers. For example, immunotoxins can be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose may include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in US Pat. No. 4,676,980.

Effector Functional Engineering For example, it is desirable to modify the antibodies of the present invention with respect to effector function in order to enhance the effectiveness of the antibody in the treatment of cancer. For example, cysteine residue (s) may be introduced into the Fc region, thereby allowing interchain disulfide bond formation in this region. The homodimeric antibody thus generated may have improved internalization ability and / or enhanced complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See Caron et al., J. Exp Med., 176: 1191-1195 (1992) and Shopes, J. Immunol., 148: 2918-2922 (1992). Homodimeric antibodies with enhanced anti-tumor activity can also be prepared using heterobifunctional cross-linking agents as described in Wolff et al. Cancer Research, 53: 2560-2565 (1993). Alternatively, an antibody having a dual Fc region, thereby having enhanced complement-dependent cell lysis and ADCC ability, can be engineered. See Stevenson et al., Anti-Cancer Drug Design, 3: 219-230 (1989).

Immune complexes The present invention also includes chemotherapeutic agents, toxins (e.g., enzymatically active toxins of bacterial, fungal, plant, or animal origin, or fragments thereof) or radioisotopes (i.e., radioconjugates). It relates to an immunoconjugate comprising an antibody conjugated with such a cytotoxic substance.

Chemotherapeutic agents useful for the generation of such immune complexes are described above. Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, non-binding active fragment of diphtheria toxin, endotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, avirin A chain, modesin A chain, Alphasarcin, Aleurites fordii protein, dianthin protein, Phytolaca americana protein (PAPI, PAPII and PAP-S), momoridica char anti-a inhibitor, crucine, crotin, sapaonaria officinalisc inhibitor, gelonin, Mitogelin, ristoctocin, phenomycin, enomycin and trichothecene. Various radionuclides are available for the production of radioconjugated antibodies. As examples, ²¹² Bi, ¹³¹ I, ¹³¹ In, ⁹⁰ Y and ¹⁸⁶ Re may be mentioned.

  A complex of an antibody and a cytotoxic agent is converted to a bifunctional derivative of N-succinimidyl-3- (2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), an imide ester (such as dimethyl adipimidate HCL Active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bisazide derivatives (such as bis- (p-azidobenzoyl) -hexanediamine), bisdiazonium derivatives (such as bis -(Such as p-diazonium benzoyl) -ethylenediamine), diisocyanates (such as triene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1,5-difluoro 2,4-dinitrobenzene) A variety of bifunctional protein coupling agents are used. For example, a ricin immunotoxin can be prepared as described in Vitetta et al., Science, 238: 1098 (1987). Carbon-14 labeled 1-isothiocyanatobenzyl-3-methyldiethylenetriaminepentaacetic acid (MX-DTPA) is a typical chelating agent for conjugating radionucleotides to antibodies. See WO94 / 11026.

  In another embodiment, the antibody can be conjugated to a “receptor” (such as streptavidin) for pretargeting the tumor, wherein the antibody-receptor complex is administered to the patient. The unbound complex is then removed from the blood circulation using a scavenger and then a “ligand” (eg, avidin) conjugated to the cytotoxic agent is then administered.

Immunoliposomes The antibodies disclosed herein can also be formulated as immunoliposomes. Liposome liposomes containing antibodies are described in Epstein et al., Proc. Natl. Acad. Sci. USA, 82: 3688 (1985); Hwang et al., Proc. Natl Acad. Sci. USA, 77: 4030 (1980). And U.S. Pat. Nos. 4,485,045 and 4,544,545, as known in the art. Liposome liposomes with increased circulation time are disclosed in US Pat. No. 5,013,556.

  Particularly useful liposomal liposomes can be generated by the reverse phase evaporation method with a lipid composition comprising phosphatidylcholine, cholesterol and PEG-derivatized phosphatidylethanolamine (PEG-PE). Liposome liposomes are extruded through a filter with a defined pore size to obtain liposome liposomes of the desired diameter. Fab ′ fragments of the antibodies of the present invention can be bound to liposome liposomes via a disulfide exchange reaction as described in Martin et al., J. Biol. Chem., 257: 286-288 (1982). A chemotherapeutic agent (such as doxorubicin) is optionally contained within the liposome. See Gabizon et al., J. National cancer Inst., 81 (19): 1484 (1989).

Diagnostic Applications of Antibodies Directed to the Proteins of the Invention In one embodiment, methods for screening for antibodies possessing the desired specificity are not limited, but include enzyme linked immunosorbent analysis (ELISA) and others skilled in the art. Includes known immunological intervention techniques. In a specific embodiment, the selection of antibodies that are specific for a particular domain of NOVX protein is facilitated by the generation of hybridomas that bind to fragments of NOVX protein that possess such domain. Thus, also provided herein are antibodies that are capable of specifically binding to a desired domain, derivative, fragment, analog, or homologue thereof within the NOVX protein.
Antibodies directed against the NOVX protein of the present invention may be used in methods known in the art for the localization and / or quantification of NOVX protein (eg, measuring the level of NOVX protein in an appropriate physiological sample) For use in diagnostic methods, for use in protein imaging, etc.). In certain embodiments, an antibody specific for a NOVX protein, derivative, fragment, analog or homolog thereof, comprising an antibody-derived antigen binding domain is utilized as a pharmacologically active compound (hereinafter “therapeutic” Referred to as "agent").

Antibodies specific for the NOVX proteins of the invention (eg, monoclonal or polyclonal antibodies) can be used to isolate NOVX polypeptides by standard techniques such as immunoaffinity chromatography or immunoprecipitation. Antibodies to NOVX polypeptides can facilitate the purification of naturally derived proteins from cells and recombinantly produced NOVX antigens expressed in host cells. Further, such anti-NOVX antibodies can be used to detect antigenic NOVX protein (eg, in cell lysates or cell supernatants) to assess the abundance or expression pattern of antigenic NOVX protein. it can. Antibodies directed against the NOVX protein can be used diagnostically to monitor protein levels in tissues as part of a clinical laboratory procedure, for example, to determine the effectiveness of a given treatment modality. Detection can be facilitated by coupling (ie, physically linking) the antibody to a detectable substance. Examples of detectable substances include various enzymes, combination groups, fluorescent materials, luminescent materials, bioluminescent materials and radioactive materials. Examples of suitable enzymes may include horseradish peroxidase, alkaline phosphatase, β-galactosidase and acetylcholinesterase; examples of suitable formulations may include streptavidin / biotin and avidin / biotin; Examples of umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; examples of luminescent substances include luminol Examples of bioluminescent materials may include luciferase, luciferin and aequorin, and examples of suitable radioactive materials may include ¹²⁵ I, ¹³¹ I, ³⁵ S or ³ H.

Antibody Therapies Antibodies of the invention, including polyclonal, monoclonal, humanized and fully human antibodies, can be used as therapeutic agents. Such agents are generally used for the treatment or prevention of the disease or lesion of interest. An antibody formulation, preferably one having high specificity and high affinity for its target antigen, is administered to a subject and generally has an effect due to binding to the target. Such an effect is one of two types depending on the specific nature of the interaction between a given antibody molecule and the target antigen in question. In the first case, administration of the antibody may prevent or inhibit binding of the target to the endogenous ligand to which it is bound. In this case, the antibody binds to the target and masks the naturally occurring ligand binding site where the ligand acts as an effector molecule. Thus, the receptor mediates the signaling pathway in which the ligand plays a role.

  Alternatively, the effect may be that the antibody elicits a physiological result by binding to an effector binding site on the target molecule. In this case, a target that is a receptor having an endogenous ligand that may not be present or defective in the disease or pathology is combined with an antibody as an alternative effector ligand to produce a receptor-based signaling event. Initiated by the receptor.

  A therapeutically effective amount of an antibody of the invention generally relates to the amount required to achieve a therapeutic purpose. As mentioned above, this may be a binding interaction between an antibody and its target antigen that in certain cases inhibits the function of the target and in other cases promotes a physiological response. The amount required for administration will further depend on the binding affinity of the antibody for the particular antigen and also on the rate at which the administered antibody can be removed from the free volume of the administered subject. The usual range of therapeutically effective doses of an antibody or antibody fragment of the invention can be, by way of non-limiting example, from about 0.1 mg / kg body weight to about 50 mg / kg body weight. The usual number of administrations can range, for example, from twice a day to once a week.

Pharmaceutical Compositions of Antibodies Antibodies that specifically bind to the proteins of the invention, as well as other molecules identified by the screening assays disclosed herein, are administered for the treatment of various disorders in the form of pharmaceutical compositions. obtain. The principles and considerations involved in the preparation of such compositions, as well as guidelines for component selection, are described, for example, in The Science And Practice Of Pharmacy 19th ed. (Alfonso R. Gennaro, et al., Editors) Mack Pub. Co. ., Easton, Pa .: 1995, Drug Absorption Enhancement: Concepts, Possibilities, Limitations, And Trends, Harwood Academic Publishers, Langhorne, Pa., 1994, and Peptide And Protein Drug Delivery (Advances In Parenteral Sciences, Vol. 4), Provided in 1991, M. Dekker, New York.

  If the antigenic protein is intracellular and an intact antibody is used as an inhibitor, an internalizing antibody is preferred. However, liposomes can be used to deliver antibodies or antibody fragments into cells. When using antibody fragments, the smallest inhibitory fragment that specifically binds to the binding domain of the target protein is preferred. For example, peptide molecules can be designed that retain the ability to bind to the sequence of the target protein based on the sequence of the variable region of the antibody. Such peptides can be synthesized by chemical and / or recombinant DNA techniques. See, for example, Marasco et al., Proc. Natl. Acad. Sci. USA, 90: 7889-7893 (1993). The formulation herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other. Alternatively or in addition, the composition may contain an agent that enhances its function, eg, a cytotoxic agent, cytokine, chemotherapeutic agent, or growth inhibitory agent. Such molecules are conveniently present in combination in amounts that are effective for the intended purpose.

  The active ingredients are colloidal drug delivery systems, for example in microcapsules prepared by coacervation technology or interfacial polymerization, for example in hydroxymethylcellulose or gelatin-microcapsules and poly- (methyl methacrylate) microcapsules, respectively. (E.g., liposomes, albumin spherules, microemulsions, nanoparticles and nanocapsules) or in macroemulsions.

The formulation to be used for in vivo administration must be sterile. This is easily accomplished by filtration through a sterile filtration membrane.
Sustained release formulations can be prepared. Suitable examples of sustained release formulations include solid-phase hydrophobic polymer semipermeable matrices containing antibodies, which are in the form of shaped articles such as films or microcapsules, for example. Yes. Examples of sustained release matrices include polyesters, hydrogels (eg, poly (2-hydroxyethyl-methacrylate) or poly (vinyl alcohol), polylactide (US Pat. No. 3,773,919), L-glutamic acid and Degradable lactic acid such as γ-ethyl-L-glutamate copolymer, non-degradable ethylene-vinyl acetate, LUPRON DEPOT® (injectable microspheres consisting of lactic acid-glycolic acid copolymer and leuprolide acetate) Glycolic acid copolymers include polymers such as ethylene vinyl acetate and lactic acid-glycolic acid, which can release molecules over 100 days, while certain hydrogels release proteins in a shorter period of time.

ELISA Assay The agent that detects the analyte protein is an antibody capable of binding to the analyte protein, preferably an antibody with a detectable label. The antibody may be polyclonal or more preferably monoclonal. An intact antibody or a fragment thereof (eg, F _ab or F _{(ab) 2} ) can be used. The term “label” refers to the direct labeling of a probe or antibody by coupling (ie, physically linking) a detectable substance to the probe or antibody with respect to the probe or antibody, as well as another It is intended to include indirect labeling of probes or antibodies by reactivity with drugs. Examples of indirect labeling include detection of the first antibody using a fluorescently labeled second antibody and end-labeling of the DNA probe with biotin so that it can be detected with fluorescently labeled streptavidin. The term “biological sample” is intended to include tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. Thus, the term “biological sample” can include blood fractions or components including blood and serum, plasma, or lymph. That is, the detection methods of the present invention can be used to detect analyte mRNA, protein or genomic DNA in a biological sample in vitro as well as in vivo. For example, in vitro techniques for the detection of analyte mRNA may include Northern hybridization and in situ hybridization. Analytical protein in vitro detection techniques may include enzyme-linked immunosorbent assay (ELISA), Western blot, immunoprecipitation and immunofluorescence. A technique for in vitro detection of analyte DNA may include Southern hybridization. The procedure for performing an immunoassay is described, for example, in `` ELISA: Theory and Practice: Methods in Molecular Biology '', Vol. 42, JR Crowther (Ed.) Human Press, Totowa, NJ, 1995, `` Immunoassay '', E. Diamandis and T. Christopoulus, Academic Press, Inc., San Diego, CA, 1996, and “Practice and Thory of Enzyme Immunoassays”, P. Tijssen, Elsevier Science Publishers, Amsterdam, 1985. In addition, techniques for in vivo detection of analyte proteins include introducing labeled anti-analyte protein antibodies into a subject. For example, the antibody can be labeled with a radioactive marker whose presence or localization in a subject can be detected by standard imaging techniques.

NOVX Recombinant Expression Vectors and Host Cells Another aspect of the present invention relates to vectors, preferably expression vectors, containing nucleic acids encoding NOVX proteins or derivatives, fragments, analogs or homologues thereof. As used herein, the term “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid bound thereto. One type of vector is a “plasmid”, which refers to a circular double stranded DNA loop with additional DNA segments attached to it. Another type of vector is a viral vector, where additional DNA segments can be ligated into the viral genome. Certain vectors can be autonomously amplified in the host cell into which they are introduced (eg, bacterial vectors having a bacterial origin of replication and mammalian episomal vectors). Other vectors (eg, mammalian non-episomal vectors) can be integrated into the genome of a host cell upon introduction into the host cell, thereby replicating along with the host genome. In addition, certain vectors are capable of directing the expression of genes that are operably linked to them. Such vectors are referred to herein as “expression vectors”. In general, expression vectors useful in recombinant DNA technology are often in the form of plasmids. In the present specification, “plasmid” and “vector” may be used interchangeably as the plasmid is the most commonly used form of vector. However, the present invention is intended to include other forms of expression vectors such as viral vectors with equivalent functions (eg, retroviruses, adenoviruses and adeno-associated viruses lacking replication ability).

  A recombinant expression vector of the invention comprises a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which expresses a recombinant expression virus selected based on the host cell used for expression. It is meant to include one or more regulatory sequences operably linked to the nucleic acid sequence of interest. Within a recombinant expression vector, “operably linked” means that the nucleic acid sequence of interest is capable of expressing the nucleic acid sequence (eg, in an in vitro transcription / translation system or by introducing the vector into a host cell). In this case, it is meant to be bound to a regulatory sequence (in the host cell).

  The term “regulatory sequence” is intended to include promoters, enhancers and other expression control elements (eg, polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990). Regulatory sequences include those that direct constitutive expression of nucleotide sequences in many types of host cells and those that direct expression of nucleotide sequences only in specific host cells (e.g., tissue-specific regulatory sequences). obtain. Those skilled in the art will appreciate that the design of the expression vector may depend on factors such as the choice of host cells to transform, the expression level of the desired protein, and the like. A protein or peptide comprising a fusion protein or peptide encoded by a nucleic acid as described herein (e.g., NOVX protein, mutant form of NOVX protein, fusion) by introducing an expression vector of the invention into a host cell Protein and the like).

  The recombinant expression vectors of the invention can be designed for NOVX protein expression in prokaryotic or eukaryotic cells. For example, NOVX protein can be expressed in bacterial cells such as Escherichia coli, insect cells (using baculovirus expression vectors), yeast cells or mammalian cells. Suitable host cells are further discussed in Goeddel, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.

  Protein expression in eukaryotic cells is most often performed using vectors containing constitutive or inducible promoters that direct the expression of either fusion or non-fusion proteins in Escherichia coli. Fusion vectors add a number of amino acids to the protein encoded therein, usually at the amino terminus of the recombinant protein. Such fusion vectors typically serve three purposes: (i) to increase expression of the recombinant protein; (ii) to increase the solubility of the recombinant protein; and (iii) in affinity chromatography. To help purify recombinant protein by acting as a ligand. Often, in fusion expression vectors, proteolytic cleavage sites are introduced at the junction of the fusion moiety and the recombinant protein to allow purification of the fusion protein following separation of the recombinant protein from the fusion moiety. Such enzymes, and their homologous recognition sequences, can include Factor Xa, thrombin and enterokinase. Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith and Johnson, 1988. Gene 67: 31) in which glutathione S-transferase (GST), maltose E-binding protein, or protein A is fused to a target recombinant protein, respectively. -40), pMAL (New England Biolabs, Beverly, Mass.) And pRIT5 (Pharmacia, Piscataway, NJ).

  Examples of suitable inducible non-fused E. coli expression vectors include pTrc (Amrann et al., (1988) Gene 69: 301-315) and pET11d (Studier et al., GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990) 60-89).

  One strategy to maximize protein expression in E. coli is to express the protein in a host cell that has impaired the ability to proteolytically cleave the recombinant protein. See Gottesman, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990) 119-128. Another strategy is to alter the nucleic acid sequence of the nucleic acid inserted into the expression vector so that individual codons for each amino acid are preferentially used in E. coli (eg, Wada, et al. al., 1992. Nucl. Acids Res. 20: 2111-2118). Such alteration of the nucleic acid sequences of the present invention can be made by standard DNA synthesis techniques.

  In another embodiment, the NOVX expression vector is a yeast expression vector. Examples of expression vectors in yeast Saccharomyces cerivisae include pYepSec1 (Baldari, et al., 1987. EMBO J. 6: 229-234), pMFa (Kurjan and Herskowitz, 1982. Cell 30: 933-943), pJRY88 (Schultz et al., 1987. Gene 54: 113-123), pYES2 (Invitrogen Corporation, San Diego, Calif.), And picZ (InVitrogen Corp, San Diego, Calif.).

  Alternatively, NOVX can be expressed in insect cells using baculovirus expression vectors. Baculovirus vectors that can be used for protein expression in cultured insect cells (eg, SF9 cells) include the pAc series (Smith, et al., 1983. Mol. Cell. Biol. 3: 2156-2165) and the pVL series. (Lucklow and Summers, 1989. Virology 170: 31-39).

  In yet another embodiment, the nucleic acids of the invention can be expressed in mammalian cells using mammalian expression vectors. Examples of mammalian expression vectors may include pCDM8 (Seed, 1987. Nature 329: 840) and pMT2PC (Kaufman, et al., 1987. EMBO J. 6: 187-195). When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, adenovirus 2, cytomegalovirus and simian virus 40. For other expression systems suitable for both prokaryotic and eukaryotic cells, see, for example, Chapters 16 and 17 of Sambrook, et al., MOLECULAR CLONING: A LABORATORY MANUAL. 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor See Laboratory Press, Cold Spring Harbor, NY, 1989.

  In another embodiment, the recombinant mammalian expression vector is capable of preferentially directing the expression of a nucleic acid in a particular cell type (e.g., using tissue-specific regulatory elements to express the nucleic acid). ). Tissue specific regulatory elements are known in the art. Non-limiting examples of suitable tissue specific promoters include albumin promoters (liver specific; Pinkert, et al., 1987. Genes Dev. 1: 268-277), lymphoid specific promoters (Calame and Eaton, 1988. Adv. Immunol. 43: 235-275), especially T cell receptors (Winoto and Baltimore, 1989. EMBO J. 8: 729-733) and immunoglobulins (Banerji, et al., 1983. Cell 33: 729) -740; Queen and Baltimore, 1983. Cell 33: 741-748), neuron-specific promoters (eg, neurofilament promoters; Byrne and Ruddle, 1989. Proc. Natl. Acad. Sci. USA 86: 5473-5477 ), Pancreas-specific promoters (Edlund, et al., 1985. Science 230: 912-916), and mammary gland-specific promoters (eg, whey; US Pat. No. 4,873,316 and European Application Publication No. 264, 166). For example, the developmentally regulated promoters of the mouse hox promoter (Kessel and Gruss, 1990. Science 249: 374-379) and the α-fetoprotein promoter (Campes and Tilghman, 1989. Genes Dev. 3: 537-546) Include.

  The present invention further provides a recombinant expression vector comprising a DNA molecule of the present invention cloned in an antisense orientation into the expression vector. That is, the DNA molecule is operably linked to regulatory sequences in a manner that allows expression of the RNA molecule that is antisense to NOVX mRNA (by transcription of the DNA molecule). Selecting regulatory sequences, such as viral promoters and / or enhancers, operably linked to the nucleic acid cloned into the antisense orientation that directs the sequential expression of the antisense RNA molecule in various cell types A regulatory sequence can be selected that directs tissue-specific or cell-type-specific constitutive expression of the antisense RNA. Antisense expression vectors can be in the form of recombinant plasmids, phagemids or attenuated viruses that produce antisense nucleic acids under the control of a highly efficient regulatory region whose activity is determined by the cell type into which the vector has been introduced. See, for example, Weintraub, et al., “Antisense RNA as a molecular tool for genetic analysis” Reviews-Trends in Genetics, Vol. 1 (1) 1986, for a discussion of the regulation of gene expression using antisense genes. I want.

  Another aspect of the invention pertains to host cells into which a recombinant expression vector of the invention has been introduced. The terms “host cell” and “recombinant host cell” are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell, but also to the progeny or potential progeny of such a cell. Such progeny may not actually be identical to the parent cell, as the mutations or environmental effects may cause certain modifications in later generations, but the scope of the terms used herein Still included.

  The host cell can be any prokaryotic or eukaryotic cell. For example, NOVX protein can be expressed in bacterial cells such as E. coli, insect cells, yeast or mammalian cells (Chinese hamster ovary cells (CHO) or COS cells). Other suitable host cells are well known to those skilled in the art.

  Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. As used herein, the terms “transformation” and “transfection” refer to foreign nucleic acids (eg, DNA) including calcium phosphate or calcium chloride coprecipitation, DEAE-dextran mediated transfection, lipofection, or electroporation. It shall refer to various techniques recognized in the art for introduction into a host cell. Suitable methods for transforming or transfecting host cells include MOLECULAR CLONING: A LABORATORY MANUAL.2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989) and others. Can be found in the laboratory manual.

  For stable transfection of mammalian cells, depending on the expression vector used and the transfection technique, a small fraction of the cell can incorporate foreign DNA into its genome. In order to identify and select these integrants, a selectable marker (eg, resistance to antibiotics) is generally introduced into the host cells along with the gene of interest. Various selectable markers include those that confer resistance to drugs such as G418, hygromycin and methotrexate. Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding NOVX or can be introduced on a separate vector. Cells stably transfected with the introduced nucleic acid can be identified by drug selection (eg, cells that incorporate a selectable marker survive while other cells die).

  A host cell of the invention, such as a prokaryotic or eukaryotic cell in culture, can be used to produce (ie, express) NOVX protein. Therefore, the present invention further provides a method for producing NOVX protein using the host cell of the present invention. In one embodiment, the method comprises culturing a host cell of the invention (into which a recombinant expression vector encoding NOVX protein is introduced) in a suitable medium that produces NOVX protein. Including. In another embodiment, the method further comprises isolating NOVX protein from the medium or the host cell.

Transgenic NOVX Animals The host cells of the invention can also be used to produce non-human transgenic animals. For example, in one embodiment, the host cell of the invention is a fertilized oocyte or embryonic stem cell into which a NOVX protein coding sequence is introduced. A non-human transgenic animal that uses such a host cell to introduce an exogenous NOVX sequence into the genome, or a homologous recombinant animal that alters an endogenous NOVX sequence therein Can be created. Such animals are useful for studying NOVX protein function and / or activity and for identifying and / or evaluating modulators of NOVX protein activity. As used herein, a “transgenic animal” is a non-human animal, preferably a mammal, more preferably a rat or mouse, in which one or more cells of the animal contain the transgene. It is a tooth. Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, amphibians, and the like. The transgene is incorporated into the genome of the cell from which the transgenic animal develops and remains in the genome of the mature animal, thereby coding in one or more cell types or tissues of the transgenic animal. This is an exogenous DNA that directs the expression of a modified gene product. As used herein, “homologous recombinant animal” refers to an endogenous NOVX gene introduced into the endogenous gene and animal cells, eg, animal embryo cells, prior to animal development. A non-human animal, preferably a mammal, more preferably a mouse, which has been altered by homologous recombination with an exogenous DNA molecule.

  The transgenic animal of the present invention introduces a nucleic acid encoding NOVX into the male pronucleus of a fertilized oocyte (eg, by microinjection, retroviral infection), and the oocyte is injected into a pseudopregnant female foster animal. It can be created by allowing it to occur in the body. The human NOVX cDNA sequence of SEQ ID NO: 2n-1 (where n is an integer from 1 to 37) can be introduced as a transgene into the genome of a non-human animal. Alternatively, a non-human homologue of the human NOVX gene, such as the mouse NOVX gene, can be isolated based on hybridization with human NOVX cDNA (detailed further above) and used as a transgene. Intron sequences and polyadenylation signals can also be included in the transgene to increase the expression efficiency of the transgene. Tissue specific regulatory sequences can be operably linked to the NOVX transgene to direct expression of the NOVX protein to specific cells. Methods for producing transgenic animals, particularly animals such as mice, by embryo manipulation and microinjection have become conventional in the art, for example, US Pat. No. 4,736,866; 4,870,009. And 4,873,191; and Hogan, 1986. In: MANIPULATING THE MOUSE EMBRYO, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Similar methods can be used to produce other transgenic animals. Primary transgenic animals can be identified based on the presence of NOVX transgenes in the genome and / or expression of NOVX mRNA in animal tissues or cells. The primary transgenic animals can then be used to breed additional animals carrying the transgene. In addition, a transgenic animal carrying a transgene encoding a NOVX protein can be used to breed additional transgenic animals carrying other transgenes.

  A vector containing at least part of a NOVX gene into which deletions, additions or substitutions have been introduced in order to create homologous recombinant animals, thereby altering the NOVX gene, for example functionally disrupting To prepare. The NOVX gene can be a human gene (eg, cDNA of SEQ ID NO: 2n-1 (where n is an integer from 1 to 37)), but more preferably is a non-human homologue of the human NOVX gene. For example, a homologous set suitable for altering the endogenous NOVX gene in the mouse genome using the mouse homologue of the human NOVX gene of SEQ ID NO: 2n-1 (where n is an integer from 1 to 37) Replacement vectors can be constructed. In one embodiment, the vector is designed to functionally disrupt an endogenous gene (ie, no longer encodes a functional protein; also referred to as a “knockout” vector) by homologous recombination.

  Alternatively, the vector mutates or otherwise alters the endogenous NOVX gene by homologous recombination, but still encodes a functional protein (e.g., alters the upstream regulatory region thereby changing the endogenous To alter the expression of sex NOVX protein). In a homologous recombination vector, the altered protein of the NOVX gene is bound to the endogenous NOVX gene and embryonic stem cells carried by the vector adjacent to the 5 'end or 3' end by additional nucleic acids of the NOVX gene. Allows homologous recombination to occur between NOVX genes. Yet another flanking NOVX nucleic acid is of sufficient length to allow successful homologous recombination with the endogenous gene. Typically, a few kilobases of contiguous DNA (both 5 'and 3' ends) can be included in the vector. For a description of homologous recombination vectors, see, for example, Thomas, et al., 1987. Cell 51: 503. The vector is then introduced into an embryonic stem cell line (eg, by electroporation) and cells in which the introduced NOVX gene is homologously recombined with the endogenous NOVX gene are selected. See, for example, Li, et al., 1992. Cell 69: 915.

  The selected cells are then injected into an animal (eg, mouse) blastocyst to form an aggregated chimera. See, for example, Bradley, 1987. In: TERATOCARCINOMAS AND EMBRYONIC STEM CELLS: A PRACTICAL APPROACH, Robertson, ed. IRL, Oxford, pp. 113-152. The chimeric embryo is then implanted into a suitable pseudopregnant female foster animal, and the embryo is delivered at term. Using progeny holding DNA homologously recombined in germ cells, all cells of the animal will breed animals containing homologous recombinant DNA by germline transmission of the transgene be able to. Methods for constructing homologous recombination vectors and homologous recombination animals are described in Bradley, 1991. Curr. Opin. Biotechnol. 2: 823-829; PCT International Publication No .: WO90 / 11354; WO91 / 01140; WO92 / 0968. And further described in WO 93/04169.

  In another embodiment, non-human transgenic animals can be produced that contain selected systems that allow for regulated expression of the transgene. One example of such a system is the cre / loxP recombinase system of bacteriophage P1. For a description of the cre / loxP recombinase system, see for example Lakso, et al., 1992. Proc. Natl. Acad. Sci. USA 89: 6232-6236. Another example of a recombinase system is the Saccharomyces cerevisiae FLP recombinase system. See O'Gorman, et al., 1991. Science 251: 1351-1355. If a cre / loxP recombinase system is used to regulate transgene expression, an animal containing a transgene encoding both the Cre recombinase and the selected protein is required. Such animals are, for example, “double” transgenic animals by mating two transgenic animals, one containing a transgene encoding the selected protein and the other containing a transgene encoding a recombinase. It can be provided by constructing.

Non-human transgenic animal clones described herein can also be produced according to the method described in Wilmut, et al., 1997. Nature 385: 810-813. Briefly, isolated cells from transgenic animals (e.g., somatic cells), induction, it is possible to enter the G ₀ phase exits from the growth cycle. The quiescent cells can then be fused with enucleated oocytes from the same type of animal from which the quiescent cells were isolated, for example, by use of electric pulses. The reconstituted oocyte is then cultured such that it develops into a morula or blastocyst and then introduced into a pseudopregnant female foster animal. The offspring born from this female foster animal is an animal clone that isolates cells (eg, somatic cells).

Pharmaceutical Compositions of pharmaceutical compositions suitable for administration of the NOVX nucleic acid molecules, NOVX proteins, anti-NOVX antibodies (also referred to herein as “active compounds”), and derivatives, fragments, analogs and homologs thereof of the present invention. Can be built in. Typically, such compositions comprise a nucleic acid molecule, protein or antibody and a pharmaceutically acceptable carrier. As used herein, “pharmaceutically acceptable carrier” refers to any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are compatible with pharmaceutical administration. Intended to include. Suitable carriers are described in the latest edition of Remington's pharmacology, a standard reference text in this field, which is hereby incorporated by reference. Preferred examples of such carriers or excipients include, but are not limited to, water, saline, finger solution, dextrose solution and 5% human serum albumin. Water-insoluble vehicles such as liposomes and oils are also used. Such media and agents for pharmaceutically active substances are well known in the art. Unless any conventional media or agents are compatible with the active compounds, their use in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.

  A pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration. Examples of routes of administration may include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g. inhalation), transdermal (i.e. topical), transmucosal and rectal administration. . Solutions or suspensions used for parenteral, intradermal or subcutaneous applications may include the following components: sterile vehicles such as water for injections, saline solutions, fats and oils, polyethylene glycols, glycerin , Propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid (EDTA); acetates, citric acid Buffers such as salts or phosphates and agents that adjust isotonicity such as sodium chloride or glucose. The pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple use vials made of glass or plastic.

  Pharmaceutical compositions suitable for injection may include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for preparations prepared as necessary in sterile injectable solutions or dispersions. For intravenous administration, suitable carriers may include physiological saline, bacteriostatic water, Cremophor EL® (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Protection of microbial action is achieved by various antibacterial and antifungal agents such as parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in the composition. Prolonged absorption of injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, aluminum monostearate and gelatin.

  By incorporating the active compound (eg, a NOVX protein or anti-NOVX antibody) in the required amount, together with one or a combination of the above-listed ingredients, in a suitable solvent, and then sterile sterilizing, followed by filter sterilization Can be prepared. Generally, dispersions can be prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the method of preparation involves vacuum drying and freezing to produce a powder of the active ingredient plus any further desired ingredient powder from the pre-sterile filtered solution. It is dry.

  Oral compositions generally include an inert excipient or edible carrier. They can be enclosed in gelatin capsules or compressed into tablets. For the purpose of oral therapeutic administration, the active compound can be incorporated with additives and used in the form of tablets, troches, or capsules. Oral compositions can also be prepared using a liquid carrier for use as a mouthwash, where the compound in the liquid carrier is applied orally, quickly removed, and exhaled or swallowed. Pharmaceutically compatible binding agents, and / or adjuvant materials can be included as part of the composition. Tablets, pills, capsules, troches and the like may contain any of the following ingredients or compounds with similar properties: binders such as microcrystalline cellulose, gum tragacanth or gelatin; additives such as starch or lactose, alginic acid Disintegrants such as primogel or corn starch; lubricants such as magnesium stearate or sterote; slip agents such as colloidal silicon dioxide; sweeteners such as sucrose or saccharin; or mint, methyl salicylate, orange A fragrance like perfume.

  For administration by inhalation, the compounds can be delivered in the form of an aerosol spray from a pressurized container or dispenser which contains a suitable propellant, eg, a gas such as carbon dioxide, or a nebulizer.

  Systemic administration can also be obtained by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art and may include detergents, bile salts, fusidic acid derivatives, for example, for transmucosal administration. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds are formulated into ointments, ointments, gels, or creams as generally known in the art.

  The compounds can also be prepared in the form of suppositories (eg, with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.

  In one embodiment, the active compounds are prepared with carriers that will prevent the compound from rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable and biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polyacetic acid. It will be clear to those skilled in the art how to prepare such formulations. Materials are also commercially available from Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted from infected cells with monoclonal antibodies to viral antibodies) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in US Pat. No. 4,522,811.

  It is especially advantageous to formulate oral or parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. As used herein, unit dosage form refers to a physically discrete unit suitable as a single dosage for the subject being treated; each unit together with the required pharmaceutical carrier. Contains a predetermined amount of active compound calculated to produce the desired therapeutic effect. The unit dosage form specifications of the present invention are dictated by the unique characteristics of the active compound and the particular therapeutic effect to be achieved, as well as limitations inherent in the art to formulate such active compounds for the treatment of individuals. And depends directly.

The nucleic acid molecule of the present invention can be inserted into a vector and used as a gene therapy vector. Gene therapy vectors can be obtained, for example, by intravenous injection, by local administration (see, eg, US Pat. No. 5,328,470) or by tactile injection (see, for example, Chen, et al., 1994. Proc. Natl. Acad. Sci. USA 91: 3054-3057). A pharmaceutical formulation of a gene therapy vector can include a gene therapy vector in an acceptable excipient, or can include a sustained matrix having the gene therapy vector embedded therein. Alternatively, where a complete gene therapy vector can be produced intact from a recombinant cell, such as a retrovirus vector, the pharmaceutical formulation can include one or more cells producing a gene delivery system.
The pharmaceutical formulation may be included in a container, pack or dispenser along with instructions for administration.

Screening and Detection Methods As detailed below, the isolated nucleic acid molecules of the invention are used to express NOVX protein (eg, via a recombinant expression vector in a host cell in gene therapy applications), Genetic defects in NOVX mRNA (eg, in a biological sample) or NOVX gene can be detected and NOVX activity can be modulated. In addition, NOVX protein is used to screen for drugs or compounds that modulate NOVX protein activity or expression, as well as poor or excessive production of NOVX protein, or decreased or abnormal compared to NOVX wild-type protein Diseases characterized by the production of NOVX protein types with various activities (eg; diabetes (modulating insulin release); obesity (lipid binding and transport); obesity-related metabolic disorders, metabolic syndrome X and chronic disorders And anorexia and debilitating disorders associated with various cancers, as well as infectious diseases (with antimicrobial activity) and various dyslipidemias In addition, the anti-NOVX antibodies of the present invention may be used. NOVX protein can be detected and isolated, and NOVX activity can be modulated. Can be used in methods to affect appetite, nutrient absorption and disposal of metabolic substrates in both positive and negative ways.
The invention further relates to novel agents identified in the screening assays described herein and their use for the treatments described above.

Screening assays The present invention relates to modulators, i.e. candidate or test compounds or agents (e.g. peptides, peptides) that bind to the NOVX protein or have a promoting or inhibitory effect on the expression or activity of the NOVX protein, e.g. Methods of identifying mimetics, small molecules, or other drugs (also referred to herein as “screening assays”) are provided. The invention also includes compounds identified in the screening assays described herein.

  In one embodiment, the present invention provides an assay for screening candidate or test compounds that bind to or modulate the activity of a membrane-bound NOVX protein or polypeptide or biologically active portion thereof. To do. Test compounds of the invention can be obtained from biological libraries; spatially addressable parallel solid or liquid phase libraries; synthetic library methods requiring deconvolution; “one bead one compound” library And any of a number of approaches in combinatorial libraries well known in the art, including: methods; and synthetic library methods using affinity chromatography selection. The biological library approach is limited to peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds. See, for example, Lam, 1997. Anticancer Drug Design 12: 145.

  As used herein, “small molecule” refers to a composition having a molecular weight of less than about 5 kD, most preferably less than about 4 kD. Small molecules can be, for example, nucleic acids, peptides, polypeptides, peptidomimetics, carbohydrates, lipids or other organic or inorganic molecules. Biological mixtures, such as chemical and / or fungal, bacterial, or algae extracts are known in the art and can be screened using any assay of the present invention.

  Examples of molecular library synthesis methods are described in, for example, DeWitt, et al., 1993. Proc. Natl. Acad. Sci. USA 90: 6909, Erb, et al., 1994. Proc. Natl. Acad. Sci. : 11422, Zuckermann, et al., 1994. J. Med. Chem. 37: 2678, Cho, et al., 1993. Science 261: 1303; Carrell, et al., 1994. Angew. Chem. Int. Ed. Engl. 33: 2059, Carell, et al., 1994. Angew. Chem. Int. Ed. Engl. 33: 2061, and Gallop, et al., 1994. J. Med. Chem. 37: 1233 Get a headline.

  A library of compounds can be obtained in solution (eg, Houghten, 1992. Biotechniques 13: 412-421) or on beads (Lam, 1991. Nature 354: 82-84) on a chip (Fodor, 1993. Nature 364: 555-556), bacteria (Ladner, US Pat. No. 5,223,409), spores (Ladner, US Pat. No. 5,233,409), plasmids (Cull, et al., 1992. Proc. Natl Acad. Sci. USA 89: 1865-1869) or on phage (Scott and Smith, 1990. Science 249: 386-390; Devlin, 1990. Science 249: 404-406, Cwirla, et al., 1990 Proc. Natl. Acad. Sci. USA 87: 6378-6382, Felici, 1991. J. Mol. Biol. 222: 301-310, Ladner, US Pat. No. 5,233,409).

In certain embodiments, the assay is a cell-based assay, wherein a cell-expressing cell-bound NOVX protein or biologically active portion thereof is contacted with a test compound and the test compound is present The ability to bind to NOVX protein is measured. The cell can be, for example, a mammal or a yeast cell. Measuring the ability of a test compound to bind to the NOVX protein can be accomplished, for example, by coupling the test compound with a radioisotope or enzyme label to bind the test compound to the NOVX protein or biologically active portion thereof. The measurement can be performed by detecting the labeled compound in the complex. For example, the test compound is labeled directly or indirectly with ¹²⁵ I, ³⁵ S, ¹⁴ C or ³ H and the radioisotope is detected by direct counting of radiation emission or scintillation counting. Alternatively, the test compound is enzymatically labeled, for example, with horseradish peroxidase, alkaline phosphatase, or luciferase, and the enzyme label is detected by measuring conversion of the appropriate substrate to product. In certain embodiments, the assay comprises contacting a cell expressing a membrane-bound NOVX protein or biologically active portion thereof on the cell surface with a known compound that binds to NOVX to form an assay mixture. Contacting the assay mixture with the test compound and measuring the ability of the test compound to interact with the NOVX protein, wherein measuring the ability of the test compound to interact with the NOVX protein is determined by the test Measuring the ability of a compound to bind preferentially to a NOVX protein or biologically active portion thereof compared to a known compound.

  In another embodiment, the assay is a cell-based assay, contacting a cell expressing a membrane-bound NOVX protein or biologically active portion thereof on the cell surface with a test compound, and the test compound is NOVX Measuring the ability to modulate (eg, promote or inhibit) the activity of a protein or biologically active portion thereof. Measuring the activity of a test compound that modulates the activity of NOVX or a biologically active portion thereof is, for example, by measuring the ability of a NOVX protein to bind to or interact with a NOVX target molecule. Can be achieved. As used herein, “target molecule” refers to a molecule to which a natural NOVX protein binds or interacts, for example, a cell surface molecule that expresses a protein that interacts with a certain NOVX, a second cell surface molecule A molecule in the extracellular environment, a molecule associated with the inner surface of the cell membrane or a cytoplasmic molecule. The target molecule of NOVX can be a non-NOVX molecule or some NOVX protein or polypeptide of the invention. In one embodiment, one NOVX target molecule is a signal transduction pathway that facilitates the transmission of extracellular signals (eg, signals generated by the binding of compounds to membrane-bound NOVX molecules) through and into the cell membrane. It is an ingredient. The target can be, for example, a second intracellular protein with catalytic activity or a protein that promotes the association of a downstream signal molecule with NOVX.

Measuring the ability of a NOVX protein to bind to or interact with a NOVX target molecule can be accomplished by one of the methods described above that measure direct binding. In one embodiment, measuring the ability of a NOVX protein to bind or interact with a NOVX target molecule can be accomplished by measuring the activity of the target molecule. For example, detecting the activity of the target molecule, detecting the induction of the target cellular second messenger (ie intracellular Ca ²⁺ , diacylglycerol, IP ₃ etc.), detecting the target catalytic / enzyme activity against the appropriate substrate Detecting the induction of a receptor gene (including a NOVX-responsive regulatory element operably linked to a nucleic acid encoding a detectable marker, such as luciferase), or a cellular response, such as a cell Can be measured by detecting cell survival, cell differentiation, or cell proliferation.

  In yet another embodiment, the assay of the present invention is a cell-free assay, wherein a NOVX protein or biologically active portion thereof is contacted with a test compound, and the test compound is NOVX protein or a biological thereof Measuring the ability to bind to an active moiety. Binding of the test compound to the NOVX protein can be measured either directly or indirectly as described above. In one such embodiment, the assay comprises contacting the NOVX protein or biologically active portion thereof with a known compound that binds NOVX to form an assay mixture, contacting the assay mixture with the test compound. And measuring the ability of a test compound to interact with a NOVX protein, wherein measuring the ability of a test compound to interact with a NOVX protein includes determining that the test compound is a NOVX protein or organism thereof. Measuring the ability to bind preferentially to a chemically active moiety compared to a known compound.

  In yet another embodiment, the assay contacts a NOVX protein or biologically active protein thereof with a test compound, and the test compound modulates the activity of the NOVX protein or biologically active protein thereof ( A cell-free assay that involves measuring the ability to (eg promote or inhibit). Measuring the ability of a test compound to modulate the activity of NOVX can be achieved, for example, by one of the methods described above for measuring direct binding to the NOVX protein binding activity to a target molecule of NOVX. it can. In yet another embodiment, measuring the ability of a test compound to modulate the activity of a NOVX protein can be achieved by measuring the ability of the NOVX protein to modulate an additional NOVX target molecule. For example, the catalytic / enzymatic activity of the target molecule against the appropriate substrate can be measured as described above.

  In yet another embodiment, the cell-free assay comprises contacting the NOVX protein or biologically active portion thereof with a known compound that binds to the NOVX protein to form an assay mixture, wherein the assay mixture is a test compound. And measuring the ability of the test compound to interact with the NOVX protein, wherein measuring the ability of the test compound to interact with the NOVX protein is the target of the NOVX with the NOVX protein. Measuring the ability to bind preferentially to a molecule or modulate its activity.

The cell-free assay of the present invention can be used for both soluble or membrane-bound NOVX proteins. In the case of cell-free assays involving membrane-bound NOVX protein, it is desirable to utilize a solubilizing agent so that the membrane-bound NOVX protein is maintained in solution. Examples of such solubilizers include n-octyl glucoside, n-dodecyl glucoside, n-dodecyl maltoside, octanoyl-N-methylglucamide, decanoyl-N-methylglucamide, Triton® X- 100, Triton® X-114, Thesit®, non-ionic surfactants such as isotridecipoly (ethylene glycol ether) _n , N-dodecyl-N, N-dimethyl-ammonio-1-propanesulfonate , 3- (3-chloroamidopropyl) dimethylaminol-1-propanesulfonate (CHAPS), or 3- (3-chloroamidopropyl) dimethylaminiol-2hydroxy-1-propanesulfonate (CHAPSO).

In two or more embodiments of the above assay of the invention, the NOVX protein or its target molecule can be immobilized to facilitate separation of the complex form from the uncomplexed form of one or both proteins, as well as the assay. Can adapt to automation. Binding of the test compound to the NOVX protein or the interaction of the NOVX protein with the target molecule in the presence and absence of the candidate compound can be accomplished in any container suitable for containing the reactants. Examples of such containers may include microtiter plates, test tubes, and microcentrifuge tubes. In one embodiment, a fusion protein can be provided that adds a domain that allows one or both proteins to be bound to a matrix. For example, GST-NOVX fusion protein or GST-target fusion protein is adsorbed onto a microtiter plate derivatized with glutathione Sepharose beads (Sigma Chemical, St. Louis, MO) or glutathione, which is then tested or tested The compound and either non-adsorbed target protein or NOVX protein are bound and the mixture is incubated under conditions that promote complex formation (eg, physiological conditions with respect to salt and pH). After incubation, the beads or microtiter plate holes are washed to remove any unbound components, in the case of beads, the matrix is immobilized, and the complex is measured directly or indirectly, eg as described above. . Alternatively, the complex can be dissociated from the matrix and the level of NOVX protein binding or activity measured using standard techniques.

  Other techniques for immobilizing proteins on a matrix can also be used in the screening assays of the invention. For example, either the NOVX protein or its target molecule can be immobilized utilizing the binding of biotin and streptavidin. A biotinylated NOVX protein or target molecule is prepared from biotin-NHS (N-hydroxy-succinimide) using techniques well known in the art (eg, biotinylated kit, Pierce Chemicals, Rockford, Ill.) To prepare streptavidin Can be immobilized in holes in a 96-well plate coated with (Pierce Chemical). Alternatively, an antibody that is reactive with the NOVX protein or target molecule but does not interfere with the binding of the NOVX protein to the target protein is derivatized into a hole in the plate to bind the unbound target or NOVX protein to the antibody. Can be captured in the hole. Methods for detecting such complexes include, in addition to those described above for GST-immobilized complexes, immunodetection of complexes using antibodies that react with NOVX proteins or target molecules, and NOVX proteins or target molecules. Mention may be made of enzyme binding assays that rely on detecting the relevant enzyme activity.

  In another embodiment, a modulator of NOVX protein expression is identified by a method of contacting a cell with a candidate compound and measuring the expression of NOVX mRNA or protein in the cell. The expression level of NOVX mRNA or protein in the presence of the candidate compound is compared to the expression level of NOVX mRNA or protein in the absence of the candidate compound. Candidate compounds can then be identified as modulators of NOVX mRNA or protein based on this comparison. For example, when the expression of NOVX mRNA or protein is greater in the presence of the candidate compound (ie, statistically significantly higher) in the presence of the candidate compound, the candidate compound is used as a promoter of NOVX mRNA or protein expression. Identify. Alternatively, when the expression of NOVX mRNA or protein is less in the presence of the candidate compound (ie, statistically significantly less) in the presence of the candidate compound, the candidate compound is treated with NOVX mRNA or protein expression. Identify as an inhibitor. The level of expression of NOVX mRNA or protein in the cell can be measured by the methods described herein for detecting NOVX mRNA or protein.

  In yet another embodiment of the invention, the NOVX protein is a two-hybrid assay or a three-hybrid assay (eg, US Pat. No. 5,283,317, Zervos, et al., 1993. Cell 72: 223-232, Madura, et al., 1993). J. Biol. Chem. 268: 12046-12054, Bartel, et al., 1993. Biotechniques 14: 920-924, Iwabuchi, et al., 1993. Oncogene 8: 1693-1696, and Brent WO 94/10300. Can be used to identify other proteins that bind or interact with NOVX to modulate NOVX activity (“NOVX binding protein” or “NOVX-bp”). Such NOVX binding proteins are also involved, for example, in signal amplification by NOVX proteins as elements upstream or downstream of the NOVX pathway.

The two-hybrid system is based on the modular nature of most transcription factors consisting of separable DNA binding and activation domains. Briefly, the assay utilizes two different DNA constructs. In one construct, the gene encoding NOVX is fused to a gene encoding the DNA binding domain of a known transcription factor (eg, GAL-4). In other constructs, DNA from a DNA sequence library encoding an unidentified protein ("prey" or "sample") is fused to a gene encoding the activation domain of a known transcription factor. If the “bait” and “prey” proteins can interact in vivo to form a NOVX-dependent complex, the DNA binding and activation domains of transcription factors can be drawn closer together. This proximity allows transcription of a reporter gene (eg, LacZ) operably linked to a transcriptional regulatory site responsive to the transcription factor. Reporter gene expression can be detected, cell colonies containing functional transcription factors can be isolated and used to obtain cloned genes that encode proteins that interact with NOVX.
The invention further relates to novel agents identified by the aforementioned screening assays and their use in the treatments described herein.

Detection Assays A portion or fragment of the cDNA identified herein (and the corresponding complete gene sequence) can be used in various ways as a polynucleotide reagent. By way of example, and without limitation, these sequences: (i) map each gene on the chromosome; thus locate the gene region associated with the genetic disease; (ii) from a trace biological sample Can be used to help identify individuals (tissue typing); and (iii) forensic identification of biological samples. Some of these applications are described in the following subsections.

Chromosome mapping Once a sequence (or part of a sequence) of a gene is isolated, this sequence can be used to map the position of the gene on the chromosome. This method is called chromosome mapping. Thus, using a portion or fragment of the NOVX sequence of SEQ ID NO: 2n-1 (where n is an integer from 1 to 37), or a fragment or derivative thereof, the position of the NOVX gene on the chromosome is Can be mapped. Mapping NOVX sequences to the chromosome is an important first step in correlating these sequences with genes associated with disease.

  Briefly, the NOVX gene can be mapped to a chromosome by preparing PCR primers (preferably 15-25 bp long) from the NOVX sequence. Computer analysis of NOVX sequences can be used to quickly select primers that span no more than two exons in genomic DNA, thus complicating the amplification process. These primers can then be used for PCR screening of somatic cell hybrids containing individual human chromosomes. Those hybrids containing the human gene corresponding to the NOVX sequence produce an amplified fragment.

  Somatic cell hybrids are prepared by fusing somatic cells from different mammals (eg, human and mouse cells). As hybrids of human and mouse cells grow and divide, they gradually delete human chromosomes in a random order, but retain mouse chromosomes. Mouse cells cannot grow because they lack specific enzymes, but human cells retain one human chromosome containing the gene encoding the required enzyme by using a medium that can grow. A panel of hybrid cell lines can be established by using various media. Each cell line in the panel contains a single human chromosome or a small number of human chromosomes, and a complete set of mouse chromosomes, allowing individual genes to be easily mapped to specific human chromosomes. See, for example, D'Eustachio, et al., 1983. Science 220: 919-924. Somatic cell hybrids containing only fragments of human chromosomes can also be produced by using human chromosomes with translocations and deletions.

  PCR mapping of somatic cell hybrids is a rapid procedure that maps a specific sequence to a specific chromosome. Using a single thermal cycler, it is possible to associate three or more sequences per day. By designing oligonucleotide primers with NOVX sequences, a detailed localization site specification can be achieved using a panel of fragments from specific chromosomes.

  Fluorescence in situ hybridization (FISH) of DNA sequences to metaphase chromosome spreads can further be used to provide precise chromosomal locations in one step. Chromosome spreads can be generated using cells that are blocked at metaphase by chemicals that disrupt the spindle, such as colcemid. Chromosomes can be briefly treated with trypsin and then Giemsa stained. A pattern of light and dark bands appears on each chromosome so that the chromosomes can be individually identified. FISH technology can be used with DNA sequences as short as 500 or 600 bases. However, clones larger than 1000 bases are more likely to bind to specific chromosomal locations with signal intensity sufficient for simple detection. Preferably 1000 bases, and more preferably 2000 bases are sufficient to obtain good results in a reasonable time. For a review of this technology, see Verma, et al., HUMAN CHROMOSOMES: A MANUAL OF BASIC TECHNIQUES (Pergamon Press, New York 1988).

  Use individual chromosome mapping reagents to label a single chromosome or a single site on that chromosome, or use a panel of reagents to label multiple sites and / or multiple chromosomes Can do. Reagents corresponding to non-coding regions of the gene are actually preferred for mapping purposes. The coding region is more likely to be conserved within the gene family, thus increasing the chance of cross-hybridization during chromosomal mapping.

  Once a sequence is mapped to a precise chromosomal location, the physical location of the sequence on the chromosome can be correlated with genetic map data. Such data is found, for example, in McKusick, Mendelian Inheritance in Man (available online through Hopkins University Welch Medical Library). The relationship between genes mapped to the same chromosomal site and the disease is then analyzed by the association analysis described in, for example, Egel and et al., 1987. Nature, 325: 783-787 (physically adjacent genes). ).

  In addition, DNA sequence differences between individuals suffering from and not affected by diseases associated with the NOVX gene can be measured. If the mutation is observed in some or all of the affected individuals but not in any of the unaffected individuals, the mutation is likely a causative agent for a particular disease. Comparison of affected and unaffected individuals is generally first detected by using visible structural changes in the chromosome, such as deletions or translocations visible from the chromosome spread, or using PCR based on its DNA sequence With the search for possible structural changes. Finally, complete sequencing of genes from several individuals can be performed to confirm the presence of the mutation and to distinguish the mutation from the polymorphism.

Tissue typing The NOVX sequences of the invention can also be used to identify individuals from trace biological samples. In this technique, an individual's genomic DNA is digested with one or more restriction enzymes and probed on a Southern blot to produce a unique band for identification. The sequences of the present invention are useful as yet another DNA marker for RFLP (restriction fragment length polymorphism, described in US Pat. No. 5,272,057).

  Furthermore, the sequences of the present invention may be used to provide yet another technique for measuring the actual base-by-base DNA sequence of a selected portion of an individual's genome. Thus, using the NOVX sequence described herein, two PCR primers can be prepared from the 5 'and 3' ends of the sequence. These primers can then be used to amplify the individual's DNA and subsequently sequence it.

  Since each individual has a characteristic set of such DNA due to allelic differences, a panel of corresponding DNA sequences from individuals prepared in this manner may provide identification of the characteristic individual. The sequences of the present invention can be used to obtain such identification sequences from individuals and tissues. The NOVX sequences of the present invention characteristically represent portions of the human genome. Allelic variation occurs to some extent in the coding regions of these sequences and to a greater extent in the non-coding regions. It is believed that allelic variation between individual humans occurs at a frequency of about 1 in 500 bases. Many of the allelic variations are due to single nucleotide polymorphisms (SNPs), including restriction fragment length polymorphisms (RFLP).

  Each of the sequences described herein can be used to some extent as a standard by which DNA from individuals can be compared for identification purposes. Since more genetic polymorphisms occur in non-coding regions, fewer sequences are required to identify individuals. Non-coding sequences can reasonably provide an unambiguous identification of an individual with a panel of perhaps 10 to 1000 primers, each resulting in a 100 base non-coding amplified sequence. If a predicted coding sequence such as the sequence of SEQ ID NO: 2n-1 (where n is an integer from 1 to 37) is used, the number of more suitable primers for unambiguous individual identification is 500-2000.

Predictive Medicine The present invention also relates to the field of predictive medicine, using diagnostic assays, prognostic assays, pharmacogenomics, and clinical trial monitoring for prognostic (predictive) purposes, thereby prophylactically treating an individual. Accordingly, one aspect of the present invention is to measure NOVX protein and / or nucleic acid expression and NOVX activity in the context of a biological sample (eg, blood, serum, cells, tissue), thereby causing an individual to become abnormal Relates to a diagnostic assay for determining whether or not one is suffering from or at risk of developing a disorder associated with the expression or activity of NOVX. Disorders include metabolic disorders, diabetes, obesity, infectious diseases, anorexia, cancer-related cachexia, cancer, neurodegenerative disorders, Alzheimer's disease, Parkinson's disease, immune disorders, and hematopoietic disorders, and various different fats May include metabolic disorders associated with blood pressure, obesity, metabolic syndrome X and debilitating diseases associated with chronic diseases and various cancers. The invention also provides a prognostic (predictive) assay to determine whether an individual is at risk for developing a disorder associated with NOVX protein, nucleic acid expression or activity. For example, certain NOVX gene mutations can be assayed in a biological sample. Such assays are used for prognostic or predictive purposes, thereby prophylacticizing individuals prior to the development of a disorder characterized or associated with NOVX protein, nucleic acid expression or biological activity. Can be treated.

  Another aspect of the present invention is a method for measuring NOVX protein, nucleic acid expression or activity in an individual, thereby selecting an appropriate therapeutic or prophylactic agent for that individual (referred to herein as “pharmacogenomics”). Provided). Pharmacogenomics allows the selection of an agent (e.g., a drug) for therapeutic or prophylactic treatment of an individual based on the individual's genotype (e.g., examining an individual's genotype to identify an individual's specific drug) Measure ability to respond to).

Yet another aspect of the invention relates to monitoring the effect of a drug (eg, drug, compound) on NOVX expression or activity in clinical trials.
These and other agents are described in detail in the following sections.

Diagnostic Assays An exemplary method for detecting the presence or absence of NOVX in a biological sample is to obtain a biological sample from a test subject, and to use the biological sample as a NOVX protein or a nucleic acid encoding NOVX protein. Involves contacting a compound or agent capable of detecting (eg, mRNA, genomic DNA) to allow the presence of NOVX to be detected in a biological sample. An agent for detection of NOVX mRNA or genomic DNA is a labeled nucleic acid probe capable of hybridizing to NOVX mRNA or genomic DNA. The nucleic acid probe is, for example, a full-length NOVX nucleic acid such as the nucleic acid of SEQ ID NO: 2n-1 (where n is an integer from 1 to 37), or at least 15, 30, 50, 100, 250 or 500 nucleotides in length. And part of an oligonucleotide sufficient to specifically hybridize to NOVX mRNA or genomic DNA under stringent conditions. Other suitable probes for use in the diagnostic assays of the invention are described herein.

The agent for detecting NOVX protein is an antibody capable of binding to NOVX protein, preferably an antibody with a detectable label. The antibody may be polyclonal, or more preferably monoclonal. Intact antibodies, or fragments thereof (eg, Fab or F (ab ′) ₂ ) can be used. The term “label” with respect to a probe or antibody refers to directly labeling a probe or antibody by coupling (ie, physically linking) a detectable substance to the probe or antibody, as well as another directly labeled one. Indirect labeling of the probe or antibody by reactivity with one reagent. Examples of indirect labeling may include detecting the first antibody using a fluorescently labeled second antibody and end-labeling the DNA probe with biotin so that it can be detected with fluorescently labeled streptavidin. . The term “biological sample” includes tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. That is, the detection methods of the invention can be used to detect NOVX mRNA, protein, or genomic DNA in a biological sample in vitro and in vivo. For example, in vitro techniques for detection of NOVX mRNA can include Northern hybridization and in situ hybridization. In vitro techniques for detecting NOVX protein may include enzyme linked immunoassay (ELISA), Western blot, immunoprecipitation, and immunofluorescence. In vitro techniques for detecting NOVX genomic DNA may include Southern hybridization. Further, in vivo techniques for detecting NOVX protein include introducing labeled anti-NOVX antibodies into the subject. For example, the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques.

  In one embodiment, the biological sample contains protein molecules from the test subject. Alternatively, the biological sample can contain mRNA molecules from the test subject or genomic DNA molecules from the test subject. A preferred biological sample is a peripheral blood leukocyte sample isolated from a subject by conventional means.

  In another embodiment, the method comprises obtaining a control biological sample from a control subject, using the control sample as a compound or agent capable of detecting NOVX protein, mRNA or genomic DNA, and NOVX protein, mRNA or genome. Further contacting to detect the presence of DNA in the biological sample and comparing the presence of NOVX protein, mRNA or genomic DNA in the control sample to NOVX protein, mRNA or genomic DNA in the test sample Accompany.

  The invention also includes a kit for detecting the presence of NOVX in a biological sample. For example, the kit: a labeled compound or agent capable of detecting NOVX protein or mRNA in a biological sample; means for measuring the amount of NOVX in the sample; and means for comparing the amount of NOVX in the sample with a standard Can be included. The compound and drug can be packaged in a suitable container. The kit may further comprise instructions for use of the kit for detecting NOVX protein or nucleic acid.

Prognostic Assays Further, the diagnostic methods described herein can be used to identify subjects who have or are at risk of developing a disease or disorder associated with abnormal NOVX expression or activity. For example, using the assays described herein, such as previous diagnostic assays and the following assays, to identify subjects who have or are at risk of developing a disorder related to NOVX protein, nucleic acid expression or activity Can do. Alternatively, prognostic assays can be utilized to identify subjects having or at risk for developing a disease or disorder. Thus, the present invention provides a method for identifying a disease or disorder associated with aberrant NOVX expression or activity that obtains a test sample from a subject and detects aberrant NOVX protein or nucleic acid (eg, mRNA, genomic DNA). Wherein the presence of NOVX protein or nucleic acid is a diagnosis for a subject having or at risk of developing a disease or disorder associated with abnormal NOVX expression or activity. As used herein, “test sample” refers to a biological sample obtained from a subject of interest. For example, the test sample can be a biological fluid (eg, serum), a cell sample, or a tissue.

  In addition, the prognostic assays described herein can be used to treat agents (eg, agonists, antagonists, peptidomimetics, proteins, peptides) to treat diseases or disorders associated with abnormal NOVX expression or activity. , Nucleic acids, small molecules, or other pharmaceutical candidates) can be determined. For example, such methods can be used to determine whether a subject's disease is effectively treated with a drug. Thus, the present invention provides a method for obtaining a test sample and determining whether an agent can effectively treat a disorder associated with abnormal NOVX expression or activity that detects NOVX protein or nucleic acid. (For example, where the presence of NOVX protein or nucleic acid becomes a diagnosis for a subject who can be administered an agent to treat a disorder associated with abnormal NOVX expression or activity).

  The method of the invention may also be used to detect genetic damage in a NOVX gene, such that the subject with the damaged gene is at risk for a disorder characterized by abnormal cell growth and / or differentiation Can decide. In various embodiments, these methods are genetically characterized in at least one change that affects the integrity of a gene encoding a NOVX protein, or misexpression of a NOVX gene, in a cell sample from a subject. Includes detection of the presence or absence of damage. For example, such genetic damage may include (i) deletion of one or more nucleotides from a NOVX gene; (ii) addition of one or more nucleotides to a NOVX gene; (iii) Substitution of one or more nucleotides of a NOVX gene, (iv) movement of a NOVX gene on a chromosome, (v) changes in mRNA transcript level of a NOVX gene, (vi) methylation pattern of genomic DNA (Vii) the presence of a non-wild type splicing pattern of an mRNA transcript of a NOVX gene, (viii) a non-wild type level of a NOVX protein, (ix) an allele deficiency of a NOVX gene And (x) confirmation of the presence of at least one inappropriate post-translational modification of a NOVX protein. There are a number of assay techniques known in the art that can be used to detect damage to certain NOVX genes described herein. A preferred biological sample is a peripheral blood leukocyte sample isolated from a subject by conventional means. However, any biological sample containing nucleated cells including, for example, buccal mucosa cells can be used.

  In certain embodiments, damage detection is in a polymerase chain reaction (PCR) such as anchor PCR or RACE PCR (see, eg, US Pat. Nos. 4,683,195 and 4,683,202) or Alternatively, Ligation Chain Reaction (LCR) (eg, Landegran, et al., 1988. Science 241: 1077-1080, and Nakazawa, et al., 1994. Proc. Natl. Acad. Sci. USA 91: 360 With the use of probes / primers in (see -364), but the latter may be particularly useful for the detection of point mutations in the NOVX gene (Abravaya, et al., 1995. Nucl. Acids Res. 23: 675-682). See). This method involves collecting a cell sample from a patient, isolating nucleic acid (eg, genome, mRNA or both) from the sample cells, and under conditions such that hybridization and amplification of the NOVX gene (if present) occurs. Contacting the nucleic acid sample with one or more primers that specifically hybridize to a NOVX gene, and detecting the presence or absence of the amplification product, or detecting the size of the amplification product, and length with the control sample A step of comparing the lengths. PCR and / or LCR are desirably used as a preliminary amplification step in conjunction with any technique used to detect mutations described herein.

  Further amplification methods include: self-retaining sequence replication (see Guatelli, et al., 1990. Proc. Natl. Acad. Sci. USA 87: 1874-1878), transcription amplification system (Kwoh, et al., 1989). Proc. Natl. Acad. Sci. USA 86: 1173-1177); Qβ replicase (see Lizardi, et al, 1988. BioTechnology 6: 1197), or any other nucleic acid amplification method followed by one skilled in the art May include detection of amplified molecules using well-known techniques. These detection schemes are particularly useful for the detection of such molecules if only a small number of nucleic acid molecules are present.

  In yet another embodiment, mutations in certain NOVX genes from sample cells can be identified by changes in restriction enzyme cleavage patterns. For example, sample and control DNA is isolated, amplified (optionally), treated with one or more restriction endonucleases, and fragment sizes are measured and compared by gel electrophoresis. Differences in fragment size between sample and control DNA indicate mutations in the sample DNA. In addition, sequence specific ribozymes (see, eg, US Pat. No. 5,493,531) can be used to assess the presence of specific mutations by the generation or disappearance of ribozyme cleavage sites.

  In other embodiments, genetic mutations in NOVX are identified by hybridizing sample and control nucleic acids, eg, DNA or RNA, to a high density array containing hundreds or thousands of oligonucleotide probes. can do. See, for example, Cronin, et al., 1996. Human Mutation 7: 244-255, Kozal, et al., 1996. Nat. Med. 2: 753-759. For example, genetic variations in NOVX can be identified in a two-dimensional array containing DNA probes that generate light as described in Cronin, et al., Supra. Briefly, the first hybridization array of probes is used to scan a long stretch of DNA in a sample and a control to create a series of overlapping probe linear arrays to determine base changes between sequences. Can be identified. This step allows the identification of point mutations. This is followed by a second hybridization that allows the characterization of a particular mutation by using a smaller special probe array that is complementary to all the mutants or mutations detected. Each mutation array consists of a set of parallel probes, one complementary to the wild type gene and the other complementary to the mutant gene.

  In yet another embodiment, the NOVX gene is directly sequenced using any of a variety of sequencing reactions known in the art, and the NOVX sequence of the sample is compared with the corresponding wild type (control) sequence. Mutations can be detected by comparison. Examples of sequencing reactions are based on the technique developed by Maxim and Gilbert, 1977. Proc. Natl. Acad. Sci. USA 74: 560 or Sanger, 1977. Proc. Natl. Acad. Sci. USA 74: 5463 You can list things. Sequencing by mass spectrometry (eg PCT International Publication No. WO 94/16101; Cohen, et al., 1996. Adv. Chromatography 36: 127-162 and Griffin, et al., 1993. Appl. Biochem. Biotechnol. 38: It can also be envisaged that any of a variety of automated sequencing methods, including 147-159) can be utilized in performing a diagnostic assay (see, eg, Naeve, et al., 1995. Biotechniques 19: 448).

Other methods for detecting mutations in the NOVX gene may include methods for detecting mismatched bases in RNA / RNA or RNA / DNA heteroduplexes using protection from cleaving agents. See, for example, Myers, et al., 1985. Science 230: 1242. In general, the art of “mismatch cleavage” is formed by hybridizing (labeled) RNA or DNA containing a wild type NOVX sequence with RNA or DNA of a potential mutant obtained from a tissue sample. Begin by providing a heteroduplex. The duplex is treated with an agent that cleaves the single-stranded region of the duplex present due to base mismatches between the control and sample strands. For example, the RNA / DNA duplex is treated with RNase, DNA / DNA hybrids treated with _{S 1} nuclease may process the mismatched regions enzymatically. In other embodiments, either DNA / DNA or RNA / DNA duplexes can be treated with hydroxylamine or osmium tetroxide and piperidine to digest mismatched regions. After processing the mismatch region, the resulting material is then separated by size on a denaturing polyacrylamide gel to determine the site of mutation. See, for example, Cotton, et al., 1988. Proc. Natl. Acad. Sci. USA 85: 4397, Saleeba, et al., 1992. Methods Enzymol. 217: 286-295. In one embodiment, control DNA or RNA may be labeled for detection.

  In yet another embodiment, the mismatch cleavage reaction recognizes mismatched base pairs in double-stranded DNA in a defined system to detect and map point mutations in NOVX cDNA obtained from a sample of cells. One or more proteins (so-called “DNA mismatch repair” enzymes) are used. For example, E. coli mutY enzyme cleaves G / A mismatch A and thymidine DNA glycosidase from HeLa cells cleaves G / T mismatch T. See, for example, Hsu, et al., 1994. Carcinogenesis 15: 1657-1662. According to an exemplary embodiment, a probe based on a NOVX sequence, eg, a wild type NOVX sequence, is hybridized with cDNA or other DNA product from the test cell (s). This duplex is treated with a DNA mismatch repair enzyme, and if a cleavage product is present, it can be detected from an electrophoresis protocol or the like. See, for example, US Pat. No. 5,459,039.

  In other embodiments, changes in electrophoretic mobility are used to identify mutations in the NOVX gene. For example, single strand conformation polymorphism (SSCP) can be used to detect electrophoretic mobility differences between mutant and wild type nucleic acids. For example, Orita, et al., 1989. Proc. Natl. Acad. Sci. USA: 86: 2766, Cotton, 1993. Mutat. Res. 285: 125-144, Hayashi, 1992. Genet. Anal. Tech. Appl. 9: See 73-79. Allows single-stranded DNA fragments of sample and control NOVX nucleic acids to be denatured and renatured. The secondary structure of single-stranded nucleic acids varies from sequence to sequence, and the resulting change in electrophoretic mobility makes it possible to detect even single base changes. DNA fragments can be labeled or detected with a labeled probe. The sensitivity of the assay can be increased by using RNA (rather than DNA) whose secondary structure is more sensitive to sequence changes. In one embodiment, the subject method utilizes heteroduplex analysis to separate duplex helical duplex molecules based on changes in electrophoretic mobility. See, for example, Keen, et al., 1991. Trends Genet. 7: 5.

  In yet another embodiment, the migration of mutant or wild type fragments in a polyacrylamide gel containing a gradient of denaturing agent is assayed using denaturing concentration gradient gel electrophoresis (DGGE). See, for example, Myers, et al., 1985. Nature 313: 495. When using DGGE as an analytical method, DNA is modified to ensure that it is not completely denatured, for example by adding a GC clamp of high melting point GC-enriched DNA of approximately 40 bp by PCR. In a further embodiment, temperature gradients are used instead of denaturing gradients to identify differences in mobility of control and sample DNA. See, for example, Rosenbaum and Reissner, 1987. Biophys. Chem. 265: 12753.

  Examples of other techniques for detecting point mutations may include, but are not limited to, selective oligonucleotide hybridization, selective amplification, or selective primer extension. For example, an oligonucleotide primer centered on a known mutation is prepared and then hybridized with the target DNA under conditions that allow hybridization only when a perfect match is found. See, for example, Saiki, et al., 1986. Nature 324: 163, Saiki, et al., 1989. Proc. Natl. Acad. Sci. USA 86: 6230. When attaching oligonucleotides to the hybridizing membrane and hybridizing to labeled target DNA, such allele-specific oligonucleotides hybridize to PCR amplified target DNA or a number of different mutants. .

  Alternatively, allele specific amplification techniques based on selective PCR amplification may be used in conjunction with the present invention. Oligonucleotides used as primers for specific amplification allow the mutation of interest to be centered in the molecule (as amplification depends on differential hybridization; see, eg, Gibbs, et al., 1989. Nucl. Acids Res. 17: 2437-2448) or, under appropriate conditions, mismatches can prevent or reduce polymerase extension (see, eg, Prossner, 1993. Tibtech. 11: 238) held at the 3 ′ extreme end of one primer. It may be. In addition, it is desirable to introduce new restriction sites in the region of the mutation in order to create detection based on cleavage. See, for example, Gasparini, et al., 1992. Mol. Cell probe s 6: 1. In certain embodiments, it is anticipated that amplification may also be performed using Taq ligase for amplification. See, for example, Barany, 1991. Proc. Natl. Acad. Sci. USA 88: 189. In such cases, ligation occurs only when there is a perfect match at the 3 'end of the 5' end sequence, and the presence of a known mutation at a particular site is detected by examining the presence or absence of amplification. Enable.

  The methods described herein can be performed, for example, by utilizing a prepacked diagnostic kit that includes at least one probe nucleic acid or antibody reagent described herein. This can be conveniently used, for example, in the clinical setting to diagnose a patient who exhibits symptoms or symptoms of a disease or disorder involving the NOVX gene or has a family history.

  In addition, any cell type or tissue that expresses NOVX, preferably peripheral blood leukocytes, may be utilized in the prognostic assays described herein. However, any biological sample containing, for example, nucleated cells of buccal mucosa cells may be used.

Pharmacogenomics An agent or modulator that has a promoting or inhibitory effect on NOVX activity (eg, NOVX gene expression) as identified by the screening assays described herein is administered to the individual to treat the disorder (prophylactically or therapeutically). Can be treated). Disorders include, but are not limited to, for example, the diseases, disorders and conditions described above, and in particular, diseases, disorders and conditions associated with homologs of the NOVX protein as summarized in Table A. Along with such treatment, an individual's pharmacogenomics (ie, a study of the relationship between an individual's genotype and the individual's response to a foreign compound or drug) may be considered. Differences in therapeutic drug metabolism can result in severe toxicity or treatment failure by altering the relationship between pharmacologically active drug dose and blood concentration. Thus, the pharmacogenomics of an individual allows for the selection of an effective agent (eg, drug) for prophylactic or therapeutic treatment based on consideration of the individual's genotype. Such pharmacogenomics can further be used to determine the appropriate dose and method of treatment. Accordingly, the activity (s) of NOVX protein, the expression of NOVX nucleic acids, or the content of NOVX gene mutations in an individual can be measured, thereby selecting the agent (s) appropriate for the therapeutic or prophylactic treatment of the individual.

  Pharmacogenomics deals with clinically significant genetic variation in response to drugs due to altered drug distribution and abnormal effects in affected individuals. See, for example, Eichelbaum, 1996. Clin. Exp. Pharmacol. Physiol., 23: 983-985; Linder, 1997. Clin. Chem., 43: 254-266. In general, two types of pharmacogenetic abnormalities can be distinguished. Genetic abnormalities that transmit as a single factor that changes the way the drug acts on the body (altered drug action) or genetic abnormalities that transmit as a single factor that changes the way the body acts on the drug (altered drug metabolism) There is. These pharmacogenetic abnormalities can occur as either rare defects or polymorphisms. For example, glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common hereditary enzyme disorder, in which the main clinical complications are oxidant drugs (antimalarials, sulfonamides) , Analgesics, nitrofurans) hemolysis after ingestion or after eating broad beans.

  In an exemplary embodiment, the activity of a drug's metabolic enzyme is a major determinant of both the intensity and duration of the drug's action. The discovery of genetic polymorphisms in drug metabolizing enzymes (eg, N-acetyltransferase 2 (NAT2) and cytochrome pregnancy band precursor protein enzymes CYP2D6 and CYP2C19) Provide an explanation of whether the expected effect of the drug is not achieved or if it shows excessive drug response and severe toxicity. These polymorphisms are expressed in the population population in two phenotypes: a high metabolic group (EM) and a low metabolic group (PM). The abundance of PM varies between different populations. For example, the gene encoding CYP2D6 is highly polymorphic and several mutations identify PMs that result in the absence of functional CYP2D6. The hypometabolic group of CYP2D6 and CYP2C19 very frequently experience excessive drug response and side effects when receiving standard doses. If the metabolite is an active therapeutic component, PM does not show a therapeutic response, as demonstrated by the analgesic action of codeine mediated by the metabolite morphine produced by CYP2D6. The exact opposite is the so-called ultrafast metabolic group that does not respond to standard doses. Recently, the molecular basis of the ultrafast metabolic group is confirmed to be due to CYP2D6 gene amplification.

  Thus, an individual's NOVX protein activity, NOVX nucleic acid expression, or mutation content of the NOVX gene can be measured, thereby selecting an appropriate agent (s) for therapeutic or prophylactic treatment of the individual . In addition, pharmacogenetic studies can be used to apply genotyping of polymorphic alleles encoding drug metabolizing enzymes to the identification of individual drug responsiveness phenotypes. In applying this knowledge to dosage and drug selection, adverse effects or treatment failures may be observed when treating a subject with a NOVX modulator, such as a modulator identified by one of the exemplary screening assays described herein. Avoiding and thus enhancing therapeutic or prophylactic efficiency.

Monitoring the effects of clinical trials Monitoring the impact of a drug (eg, drug, compound) on NOVX expression or activity (eg, activity that modulates abnormal cell growth and / or differentiation) is a fundamental drug screen. It can be applied not only to clinical trials. For example, screening assays as described herein can reduce the effectiveness of agents determined to increase NOVX gene expression, increase protein levels, or upregulate NOVX activity, to reduce NOVX gene expression, protein levels, or lower It can be monitored in clinical trials of subjects exhibiting controlled NOVX activity. Alternatively, the efficacy of an agent that has been determined to decrease NOVX gene expression, protein levels, or down-regulate NOVX activity is compared to the clinical efficacy of a subject exhibiting increased NOVX gene expression, protein levels, or upregulated NOVX activity. Can be monitored in the test. In such clinical trials, expression or activity of NOVX, and preferably other genes associated with, for example, cell proliferation or immune disorders, may be used as a “readout” or marker of immune responsiveness of specific cells. .

  By way of non-limiting example, a gene comprising NOVX that is modulated in a cell by treatment with an agent (eg, a compound, drug or small molecule) that modulates NOVX activity (eg, identified in a screening assay described herein) Can be identified. Thus, to examine the effects of drugs on cell proliferation disorders, for example, in clinical trials, cells can be isolated and RNA prepared and the expression levels of NOVX and other genes thought to be associated with the disorder can be analyzed. The amount of protein produced by gene expression levels (ie gene expression patterns) by Northern blot analysis or RT-PCR as described herein, or alternatively by one of the methods described herein. Or by measuring the activity level of NOVX or other genes. In this manner, gene expression patterns serve as markers that indicate the cellular physiological response to the drug. Thus, this response state can be measured before and during treatment of an individual with a drug at various times.

  In one embodiment, the invention is an agent (e.g., agonist, antagonist, protein, peptide, peptidomimetic, nucleic acid, small molecule, or other drug candidate identified in the screening assays described herein). A method is provided for monitoring the effectiveness of treating a subject, comprising: (i) obtaining a pre-dose sample from a subject prior to drug administration; (ii) NOVX protein, mRNA, or in a pre-dose sample; Detecting the expression level of genomic DNA, (iii) obtaining one or more post-administration samples from the subject, and (iv) the level of expression or activity of NOVX protein, mRNA, or genomic DNA in the post-administration sample (V) one or more samples after administration of the level of expression or activity of NOVX protein, mRNA, or genomic DNA in the sample prior to administration The comparison with NOVX protein, mRNA or genomic DNA,, and comprising the step of changing the administration of the agent to a subject according to (vi) it. For example, to increase NOVX expression or activity to a higher level than detected, ie, to increase the effectiveness of the drug, increased administration of the drug is desirable. Alternatively, in order to reduce NOVX expression or activity to a lower level than detected, ie, reduce the effectiveness of the drug, reduced administration of the drug is desirable.

Methods of Treatment The present invention provides both prophylactic and therapeutic methods for treating subjects at risk (susceptibility) or having a disease associated with abnormal NOVX expression or activity. Disorders include, but are not limited to, for example, the diseases, disorders and conditions described above, and in particular, diseases, disorders and conditions associated with homologs of the NOVX protein as summarized in Table A.
These treatments are discussed in further detail below.

Diseases and Disorders Therapeutic agents that antagonize (i.e. reduce or inhibit) activity of diseases and disorders characterized by increased levels (as compared to subjects not suffering from the disease or disorder) or biological activity Can be treated with. A therapeutic that antagonizes activity may be administered in a therapeutic or prophylactic manner. The therapeutic agents that can be used include: (i) the aforementioned peptides, or analogs, derivatives, fragments or homologues thereof; (ii) antibodies to the aforementioned peptides; (iii) nucleic acids encoding the aforementioned peptides; (iv) Antisense nucleic acids and nucleic acids that are “dysfunctional” used to “knock out” the endogenous function of the aforementioned peptides by homologous recombination (ie, heterologous into the coding sequence of the coding sequence for the aforementioned peptide) (See, eg, Capecchi, 1989. Science 244: 1288-1292); or (v) a modulator that alters the interaction of the aforementioned peptide and its binding partner (ie, further of the invention Inhibitors, agonists, antagonists) including but not limited to mimetics of other peptides or antibodies specific for the peptides of the invention.

  Diseases and disorders characterized by decreased levels (as compared to subjects not afflicted with the disease or disorder) or biological activity can be treated with therapeutic agents that increase activity (ie, are agonists). A therapeutic agent that upregulates activity may be administered in a therapeutic or prophylactic manner. The therapeutic agents that can be utilized can include, but are not limited to, the aforementioned peptides, or analogs, derivatives, fragments, or homologues thereof; or agonists that increase bioavailability.

  Increased or decreased levels are obtained from patient tissue samples (e.g., from biopsy tissue) and assayed in vitro for RNA or peptide levels, expressed peptide (or mRNA for the aforementioned peptides) structure and / or activity By doing so, it can be easily detected by quantifying the peptide and / or RNA. Methods well known in the art include to detect immunoassays (eg Western blot analysis, immunoprecipitation followed by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis, immunocytochemistry, etc.) and / or mRNA expression. Hybridization assays such as, but not limited to, Northern assays, dot blots, in situ hybridization, and the like.

Prophylactic methods In one aspect, by administering to a subject an agent that modulates abnormal NOVX expression or at least some NOVX activity, the present invention provides a method for treating a disease or disorder associated with abnormal NOVX expression or activity in a subject. Provide a way to prevent. Identifying a subject at risk for a disease caused or contributed to by aberrant NOVX expression or activity, eg, by any of diagnostic or prognostic assays or combinations thereof as described herein Can do. A prophylactic agent may be administered prior to the appearance of symptoms characteristic of NOVX abnormalities so as to prevent or alternatively delay the progression of the disease or disorder. Depending on the type of NOVX abnormality, for example, an agent that is a NOVX agonist or NOVX antagonist may be used to treat the subject. Appropriate agents can be determined based on the screening methods described herein. The prophylactic methods of the present invention are further discussed in the following subsections.

Therapeutic Methods Another aspect of the invention relates to methods of modulating NOVX expression or activity for therapeutic purposes. The modulating method of the present invention comprises contacting a cell with an agent that modulates one or more activities of NOVX protein activity associated with the cell. An agent that modulates NOVX protein activity can be an agent described herein, such as a nucleic acid or protein, a naturally-occurring ligand of a NOVX protein, a peptide, an NOVX peptide mimetic, or a small molecule. In one embodiment, the agent promotes one or more NOVX protein activities. Examples of such facilitating agents may include active NOVX proteins and nucleic acid molecules encoding NOVX introduced into cells. In another embodiment, the agent inhibits one or more NOVX protein activities. Examples of such inhibitory agents may include antisense NOVX nucleic acid molecules and anti-NOVX antibodies. These adjustment methods can be performed in vitro (eg, by culturing cells with the agent) or alternatively, in vivo (eg, by administering the agent to the subject). Thus, the present invention provides a method of treating an individual suffering from a disease or disorder characterized by abnormal expression or activity of certain NOVX proteins or nucleic acid molecules. In one embodiment, the method comprises a combination of agents (e.g., agents identified in the screening assays described herein) or combinations of agents that modulate NOVX expression or activity (e.g., upregulate or downregulate). With administration. In another embodiment, the method involves administering a NOVX protein or nucleic acid molecule as a treatment to compensate for decreased or abnormal NOVX expression or activity.

  In situations where NOVX is abnormally down-regulated and / or increased NOVX activity appears to have a beneficial effect, it is desirable to promote NOVX activity. One example of such a situation is when the subject has a disorder characterized by abnormal cell proliferation and / or differentiation (eg, cancer or an immune related disease). Another example of such a situation is when the subject has a gestational disorder (eg, preeclampsia).

Measuring the biological effect of a therapeutic agent In various embodiments of the invention, appropriate in vitro or in vivo assays are performed to indicate the effect of a particular therapeutic agent and treatment of the tissue affected by its administration. Determine whether or not.

  In various specific embodiments, an in vitro assay is performed on a representative type (s) of cells involved in a patient's disorder to determine whether the administered therapeutic agent has the desired effect on the cell type. Can be measured. The compounds used for treatment can be tested in a suitable animal model system including, without limitation, rats, mice, chickens, cows, monkeys, rabbits, etc. prior to testing in human subjects. Similarly, for in vivo studies, any animal model system known in the art can be used prior to administration to a human subject.

Prophylactic and therapeutic uses of the compositions of the invention The NOVX nucleic acids and proteins of the invention are useful for potential prophylactic and therapeutic applications associated with various disorders. Disorders include, but are not limited to, for example, the diseases, disorders and conditions described above, and in particular, diseases, disorders and conditions associated with homologs of the NOVX protein as summarized in Table A.

  By way of example, a cDNA encoding a NOVX protein of the invention can be useful for gene therapy, and the protein can be useful when administered to a subject in need thereof. By way of non-limiting example, the compositions of the present invention are effective for the treatment of subjects suffering from diseases, disorders, conditions and the like, including but not limited to those listed herein. You will have a trial.

Both novel nucleic acids encoding NOVX proteins and NOVX proteins of the invention, or fragments thereof, may also be useful in diagnostic applications to assess the presence or amount of nucleic acids or proteins. A further use may be as an antibacterial molecule (ie, certain peptides have been found to have antibacterial properties). These substances are further useful for the production of antibodies that immunospecifically bind to the novel substances of the invention for use in therapeutic or diagnostic methods.
The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.

(Example 1)
NOV1 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 1A.

  The following sequence relationship shown in Table 1B is obtained by sequence comparison of the aforementioned protein sequences.

  Further analysis of the NOV1a protein resulted in the following properties shown in Table 1C.

  A search of NOV1a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 1D.

  A BLAST search of the public sequence database revealed that the NOV1a protein has homology to the proteins shown in the BLASTP data in Table 1E.

  PFam analysis predicts that the NOV1a protein contains the domains shown in Table 1F.

（実施例2)

(Example 2)

  NOV2 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 2A.

  The following sequence relationship shown in Table 2B is obtained by sequence comparison of the aforementioned protein sequences.

  Further analysis of the NOV2a protein resulted in the following properties shown in Table 2C.

  A search of the NOV2a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 2D.

  A BLAST search of the public sequence database revealed that the NOV2a protein has homology to the proteins shown in the BLASTP data in Table 2E.

  PFam analysis predicts that the NOV2a protein contains the domains shown in Table 2F.

(実施例3)

(Example 3)

  NOV3 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 3A.

  Further analysis of the NOV3a protein resulted in the following properties shown in Table 3B.

  Searching for the NOV3a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 3C.

  A BLAST search of the public sequence database revealed that the NOV3a protein has homology with the proteins shown in the BLASTP data of Table 3D.

  PFam analysis predicts that the NOV3a protein contains the domains shown in Table 3E.

(実施例4)

(Example 4)

  NOV4 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 4A.

  The following sequence relationship shown in Table 4B is obtained by sequence comparison of the aforementioned protein sequences.

  Further analysis of the NOV4a protein resulted in the following properties shown in Table 4C.

  A search of NOV4a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 4D.

  A BLAST search of the public sequence database revealed that the NOV4a protein has homology to the proteins shown in the BLASTP data in Table 4E.

  PFam analysis predicts that the NOV4a protein contains the domains shown in Table 4F.

(実施例5)

(Example 5)

  NOV5 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 5A.

  Further analysis of the NOV5a protein resulted in the following properties shown in Table 5B.

  Searching for NOV5a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 5C.

  A BLAST search of the public sequence database revealed that the NOV5a protein has homology to the proteins shown in the BLASTP data of Table 5D.

  PFam analysis predicts that the NOV5a protein contains the domains shown in Table 5E.

(実施例6)

(Example 6)

  NOV6 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 6A.

  Further analysis of the NOV6a protein resulted in the following properties shown in Table 6B.

  A search for NOV6a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 6C.

  A BLAST search of the public sequence database revealed that the NOV6a protein has homology to the proteins shown in the BLASTP data in Table 6D.

  PFam analysis predicts that the NOV6a protein contains the domains shown in Table 6E.

(実施例7)

(Example 7)

  NOV7 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 7A.

  Further analysis of the NOV7a protein resulted in the following properties shown in Table 7B.

  A search of NOV7a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 7C.

  A BLAST search of the public sequence database revealed that the NOV7a protein has homology to the proteins shown in the BLASTP data in Table 7D.

  PFam analysis predicts that the NOV7a protein contains the domains shown in Table 7E.

(実施例8)

(Example 8)

  NOV8 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 8A.

  Further analysis of the NOV8a protein resulted in the following properties shown in Table 8B.

  Searching for NOV8a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 8C.

  A BLAST search of the public sequence database revealed that the NOV8a protein has homology to the proteins shown in the BLASTP data in Table 8D.

  PFam analysis predicts that the NOV8a protein contains the domains shown in Table 8E.

(実施例9)

(Example 9)

  NOV9 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 9A.

Further analysis of the NOV9a protein resulted in the following properties shown in Table 9B.

  A search of NOV9a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 9C.

  A BLAST search of the public sequence database revealed that the NOV9a protein has homology with the proteins shown in the BLASTP data of Table 9D.

  PFam analysis predicts that the NOV9a protein contains the domains shown in Table 9E.

(実施例10)

(Example 10)

  NOV10 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 10A.

  The following sequence relationship shown in Table 10B is obtained by sequence comparison of the aforementioned protein sequences.

  Further analysis of the NOV10a protein resulted in the following properties shown in Table 10C.

  A search of the NOV10a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 10D.

  A BLAST search of the public sequence database revealed that the NOV10a protein has homology to the proteins shown in the BLASTP data in Table 10E.

  PFam analysis predicts that the NOV10a protein contains the domains shown in Table 1F.

(実施例11)

(Example 11)

  NOV11 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 11A.

  Further analysis of the NOV11a protein resulted in the following properties shown in Table 11B.

  A search of the NOV11a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 11C.

  A BLAST search of the public sequence database revealed that the NOV11a protein has homology to the proteins shown in the BLASTP data of Table 11D.

  PFam analysis predicts that the NOV11a protein contains the domains shown in Table 11E.

(実施例12)

(Example 12)

  NOV12 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 12A.

  Further analysis of the NOV12a protein resulted in the following properties shown in Table 12B.

  A search of the NOV12a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 12C.

  A BLAST search of the public sequence database revealed that the NOV12a protein has homology with the proteins shown in the BLASTP data of Table 12D.

  PFam analysis predicts that the NOV12a protein contains the domains shown in Table 12E.

(実施例13)

(Example 13)

  NOV13 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 13A.

  The following sequence relationship shown in Table 13B is obtained by sequence comparison of the aforementioned protein sequences.

  Further analysis of the NOV13a protein resulted in the following properties shown in Table 13C.

  Searching for the NOV13a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 13D.

  A BLAST search of the public sequence database revealed that the NOV13a protein has homology to the proteins shown in the BLASTP data in Table 13E.

  PFam analysis predicts that the NOV13a protein contains the domains shown in Table 13F.

(実施例14)

(Example 14)

NOV14 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 14A.

  The following sequence relationship shown in Table 14B is obtained by sequence comparison of the aforementioned protein sequences.

  Further analysis of the NOV14a protein resulted in the following properties shown in Table 14C.

  A search of the NOV14a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 14D.

  A BLAST search of the public sequence database revealed that the NOV14a protein has homology to the proteins shown in the BLASTP data in Table 14E.

  PFam analysis predicts that the NOV14a protein contains the domains shown in Table 14F.

(実施例15)

(Example 15)

  NOV15 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 15A.

  The following sequence relationship shown in Table 15B is obtained by sequence comparison of the aforementioned protein sequences.

  Further analysis of the NOV15a protein resulted in the following properties shown in Table 15C.

  A search of the NOV15a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 15D.

  A BLAST search of the public sequence database revealed that the NOV15a protein has homology to the proteins shown in the BLASTP data in Table 15E.

  PFam analysis predicts that the NOV15a protein contains the domains shown in Table 15F.

(実施例16)

(Example 16)

  NOV16 clones were analyzed and the nucleotide and encoded polypeptide sequences are shown in Table 16A.

  The following sequence relationship shown in Table 16B is obtained by the sequence comparison of the aforementioned protein sequences.

  Further analysis of the NOV16a protein resulted in the following properties shown in Table 16C.

  A search of the NOV16a protein against the Geneseq database, a patent database containing sequences published in patents and patent publications, resulted in several homologous proteins shown in Table 16D.

  A BLAST search of the public sequence database revealed that the NOV16a protein has homology to the proteins shown in the BLASTP data in Table 16E.

（実施例B）:NOVXクローンの配列決定法および同定
1.GeneCalling(商標)技術:これはCuraGenで開発され、Shimketsら「Gene expression analysis by transcript profiling coupled to a gene database query」Nature Biotechnology 17: 198-803 (1999)に記載された、2つ以上のサンプル間の遺伝子発現の差のプロファイリングを実施する特許方法である。cDNAは種々のドナー由来の複数の組織種、正常状態および病的状態、生理的状態、ならびに発達段階に相当する種々のヒトサンプルから得た。サンプルは、全組織、一次細胞または組織培養した一次細胞または細胞株として得た。細胞および細胞株は、遺伝子発現を調節する生物因子または化学薬品、例えば、成長因子、ケモカインまたはステロイドで処理しておいてもよい。次いで、このような由来のcDNAを最大120対までの制限酵素で消化し、各対の制限酵素に特異的なリンカー-アダプター対を適当な末端に連結した。制限消化による特有のcDNA遺伝子断片の混合物が生じる。限定PCR増幅を、一方のプライマーがビオチン化され、他方が蛍光標識されている、リンカー・アダプター配列と相同なプライマーで実施する。二重標識された物質を単離し、蛍光標識された一本鎖をキャピラリーゲル電気泳動によって分離する。コンピューターアルゴリズムで、各制限消化について実験群および対照群から得た電気泳動図を比較する。これとさらなる配列由来情報を用い、種々の遺伝子データベースを用いて発現に差のある各遺伝子断片の同一性を予測する。遺伝子断片の同一性は、さらなる、遺伝子特異的競合PCRによって、またはこの遺伝子断片の単離および配列決定によって確認する。 PFam analysis predicts that the NOV16a protein contains the domains shown in Table 16F.

Example B: NOVX clone sequencing and identification
1.GeneCalling (TM) technology: This was developed at CuraGen and was developed by Shikkets et al., `` Gene expression analysis by transcript profiling coupled to a gene database query '' Nature Biotechnology 17: 198-803 (1999). A patented method for profiling differences in gene expression between samples. cDNA was obtained from a variety of human samples representing multiple tissue types from different donors, normal and pathological conditions, physiological conditions, and developmental stages. Samples were obtained as whole tissues, primary cells or tissue cultured primary cells or cell lines. Cells and cell lines may be treated with biological factors or chemicals that regulate gene expression, such as growth factors, chemokines or steroids. The cDNAs derived from such were then digested with up to 120 pairs of restriction enzymes and linker-adapter pairs specific for each pair of restriction enzymes were ligated to the appropriate ends. Restriction digestion results in a mixture of unique cDNA gene fragments. Limited PCR amplification is performed with primers homologous to the linker-adapter sequence, one primer being biotinylated and the other fluorescently labeled. The doubly labeled material is isolated and the fluorescently labeled single strand is separated by capillary gel electrophoresis. A computer algorithm compares the electropherograms obtained from the experimental and control groups for each restriction digest. Using this and further sequence-derived information, the identity of each gene fragment with different expression is predicted using various gene databases. The identity of the gene fragment is confirmed by further, gene-specific competitive PCR or by isolation and sequencing of this gene fragment.

  2. SeqCalling ™ technology: cDNA was obtained from multiple human species corresponding to multiple tissue types from different donors, normal and pathological states, physiological states, and developmental stages. Samples were obtained as whole tissues, primary cells or tissue cultured primary cells or cell lines. Cells and cell lines may be treated with biological factors or chemicals that regulate gene expression, such as growth factors, chemokines or steroids. Such derived cDNA was then sequenced using CuraGen's patented SeqCalling technology. Sequence traces were evaluated manually and edited for correction as needed. The cDNA sequences from all samples were assembled together, sometimes including public human sequences, and a consensus sequence for each assembly was obtained using a bioinformatics program. Each assembly is included in the CuraGen database. A sequence was included as a component of an assembly if the degree of identity with another component was at least 95% over 50 bp. Each assembly corresponds to a gene or part thereof and contains information about variants such as spliced single nucleotide polymorphisms (SNPs), insertions, deletions and other sequence variants.

3.PathCalling (TM) technology:
NOVX nucleic acid sequences are derived from laboratory screening of cDNA libraries by a two-hybrid approach. A cDNA fragment covering either the full-length DNA sequence or part of the sequence or both is sequenced. In silico predictions are based on sequences available in the CuraGen patent sequence database or publicly available human sequence databases and are provided with either full-length DNA sequences or some of them.

Laboratory screening was performed using the methods summarized below:
cDNA libraries were obtained from a variety of human samples representing multiple tissue types from different donors, normal and pathological conditions, physiological conditions, and developmental stages. Samples were obtained as whole tissues, primary cells or tissue cultured primary cells or cell lines. Cells and cell lines may be treated with biological factors or chemicals that regulate gene expression, such as growth factors, chemokines or steroids. The cDNA derived from this was then cloned in an orientation into an appropriate two-hybrid vector (Gal4 activation domain (Gal4-AD) fusion). Such cDNA libraries as well as those commercially available from Clontech (Palo Alto, Calif.) Were then obtained from E. coli and the CuraGen patent yeast strain (the entire text of which is incorporated herein by reference). In U.S. Pat. Nos. 6,057,101 and 6,083,693).

  Screening multiple Gal4-AD fusion cDNA libraries using Gal4 binding domain (Gal4-BD) fusions from CuraGen's patented human sequence library, so that each of the Gal4-AD fusions is an individual cDNA A yeast hybrid diploid containing was selected. Each sample was amplified using polymerase chain reaction (PCR) using non-specific primers at the cDNA insertion boundary. Such PCR products were sequenced and sequence traces were manually evaluated and edited for correction as needed. The cDNA sequences from all samples were assembled together, sometimes including public human sequences, and a consensus sequence for each assembly was obtained using a bioinformatics program. Each assembly is included in the CuraGen database. A sequence was included as a component of an assembly if the degree of identity with another component was at least 95% over 50 bp. Each assembly corresponds to a gene or part thereof and contains information about variants such as spliced single nucleotide polymorphisms (SNPs), insertions, deletions and other sequence variants.

  Physical clone: The cDNA fragment obtained by the screening procedure covering the entire open reading frame is cloned as recombinant DNA into the pACT2 plasmid (Clontech) used for the construction of the cDNA library. This recombinant plasmid is inserted into the host and selected by yeast hybrid diploids generated during the screening procedure by conjugation of both CuraGen patent yeast strains N106 ′ and YULH (US Pat. Nos. 6,057,101 and 6,083,693). .

  4. RACE: The putative cDNA sequence of the present invention was isolated or completed using techniques based on polymerase chain reaction such as rapid amplification of cDNA ends (RACE). Usually, multiple clones were sequenced from one or more human samples to derive the sequence of the fragments. Different human tissue samples from different donors were used for the RACE reaction. The sequences resulting from these procedures were included in the SeqCalling assembly process described in the previous section.

  5. Exon binding: NOVX target sequences identified in the present invention were subjected to an exon binding process to confirm the sequence. PCR primers were designed by starting with the most upstream sequence available for the forward primer and the most downstream sequence available for the reverse primer. In either case, the sequence proceeds inward from each end to the coding sequence until a unique or highly selective suitable sequence is encountered, or in the case of a reverse primer, until a stop codon is reached. I investigated. Such primers can be based on in silico predictions of full-length cDNA, part of the DNA or protein sequence of the target sequence (one or more exons), or post-translation of putative exons with closely related human sequences from other species Designed by homology. These primers are then pooled into the following pools of human cDNA: adrenal gland, bone marrow, brain-amygdala, brain-cerebellum, brain-hippocampus, brain-substantia nigra, brain-thalamus, brain-whole, fetal brain, fetal kidney, fetus PCR amplification based on liver, fetal lung, heart, kidney, lymphoma-Raji, breast, pancreas, pituitary, placenta, prostate, salivary gland, skeletal muscle, small intestine, spinal cord, spleen, stomach, testis, thyroid, trachea, uterus Used for. Usually, the resulting amplicon is gel purified, cloned and sequenced until redundancy is high. The PCR product obtained from exon binding was cloned into the pCR2.1 vector from Invitrogen. The resulting bacterial clone has an insert that covers the entire open reading frame cloned into the pCR2.1 vector. Sequences obtained from all clones were assembled using themselves, using other fragments in the CuraGen database, and using publicly available ESTs. Fragments and ESTs were included as assembly components if the degree of identity with another component of the assembly was at least 95% over 50 bp. In addition, sequence traces were manually evaluated and edited for correction as needed. These procedures provide the sequences reported herein.

  6. Physical clones: exons predicted by homology and intron / exon boundaries determined using standard genetic rules. Exons were further selected and refined by multiple BLAST (eg, tBlastN, BlastX, and BlastN) searches and, in some cases, similarity measurements using GeneScan and Grail. In order to further define and complete the gene sequence, expression sequences from both public and patent databases were also added when available. The DNA sequence was then manually corrected for obvious mismatches, resulting in the sequence encoding the full-length protein.

  A PCR product obtained by exon ligation covering the entire open reading frame was cloned into the pCR2.1 vector from Invitrogen to prepare a clone for expression and screening purposes.

Example C: Quantitative expression analysis of clones in various cells and tissues Quantitative expression of various clones was derived from various normal and pathological derived cells, cell lines and tissues using real-time quantitative PCR (RTQ PCR) Evaluation was performed using a microtiter plate containing the RNA samples. RTQ PCR was performed on an Applied Biosystems ABI PRISMO® 7700 or ABI PRISM® 7900 HT Sequence Detection System. Assembling various collections of samples on the plate, panel 1 (including normal tissue and cancer cell lines), panel 2 (including samples from normal and cancer source tissues), panel 3 (cancer cell lines Panel 4 (including cells and cell lines from normal tissues and cells associated with inflammatory conditions), panel 5D / 5I (including human tissues and cell lines with an emphasis on metabolic disease) ), AI Comprehensive Panel (including samples from normal tissues and autoinflammatory diseases), Panel CNSD.01 (including samples from normal and affected brains) and CNS Neurodegeneration panel (including normal brain and (Including samples from the brain of Alzheimer's disease).

  The integrity of the RNA from all samples was determined in terms of quality by visual assessment of agarose gel electropherograms using 28S and 18S ribosomal RNA staining intensity ratios as a guide (2: 1-2.5: 1 28s: 18s) and degradation products Control with respect to the absence of low molecular weight RNA that would suggest Samples are controlled against genomic DNA contamination by performing RTQ PCR reactions in the absence of reverse transcriptase using probe and primer sets designed to amplify over the length of a single exon.

  Initially, this RNA sample was normalized to a reference nucleic acid such as constantly expressed genes (eg, β-actin and GAPDH). Standardized RNA (5 μl) was converted to cDNA and analyzed by RTQ-PCR using one-step RT-PCR Master Mix reagent (Applied Biosystems; catalog number 4309169) and gene-specific primers according to the manufacturer's instructions.

  In other cases, non-standardized RNA samples are converted to single-stranded cDNA (sscDNA) using Superscript II (Invitrogen; catalog number 18064-147) and random hexamers according to the manufacturer's instructions. did. Reactions containing up to 10 ug of total RNA were performed in a volume of 20 μl and incubated at 42 ° C. for 60 minutes. This reaction can be scaled up to 50 μg total RNA in a final volume of 100 μl. The sscDNA sample was then normalized to the reference nucleic acid described above using a 1 × TaqMan® Universal Master mix (Applied Biosystems; catalog number 4324020) according to the manufacturer's instructions.

  Probes and primers were designed for each assay according to Applied Biosystems Primer Express software package (Apple Computer Macintosh Power PC version 1) or a similar algorithm using the target sequence as input. The default settings were used for the reaction conditions, the following parameters were set, and then primers were selected: primer concentration = 250 nM, primer melting temperature (Tm) range = 58-60 ° C, optimal primer Tm = 59 ° C, maximum primer Difference = 2 ° C, probe does not contain 5'G, probe Tm must be 10 ° C higher than primer Tm, amplicon size 75bp to 100bp. Selected probes and primers (see below) were synthesized by Synthegen (Houston, TX, USA). The probe was purified twice by HPLC to remove unbound dye and assessed by mass spectrometry to confirm binding of the reporter and quencher dye to the 5 'and 3' ends of the probe, respectively. Final concentrations were 900 nM for forward and reverse primers and 200 nM for probes.

  PCR conditions: When working with RNA samples, standardized RNA from each tissue and cell line was spotted in each well of either a 96-well or 384-well PCR plate (Applied Biosystems). A PCR cocktail can be a single gene-specific probe and primer set, or two multiplexed probe and primer sets (a set specific to the target clone and another gene-specific set multiplexed for the target probe) Was included. The PCR reaction was set up using TaqMan® One-Step RT-PCR Master Mix (Applied Biosystems, catalog number 4133803) according to the manufacturer's instructions. Reverse transcription at 48 ° C for 30 minutes, followed by the following amplification / PCR cycle: 95 ° C for 10 minutes, followed by 40 cycles of 95 ° C for 15 seconds, 60 ° C for 1 minute. The results are based on the CT value using a log scale (the given sample passes the fluorescence threshold) with respect to the difference in RNA concentration between the given sample and the sample with the lowest CT value represented by 2 for ΔCT force. Cycle). The relative expression percentage is then obtained by taking the reciprocal of this RNA difference and multiplying by 100.

  When handling sscDNA samples, standardized sscDNA was used as described above for RNA samples. PCR reactions containing one or two sets of probes and primers were set up as described above using a 1 × TaqMan® Universal Master mix (Applied Biosystems; catalog number 4324020) according to the manufacturer's instructions. PCR amplification was performed as follows: 95 ° C for 10 minutes, then 95 ° C for 15 seconds, 60 ° C for 1 minute for 40 cycles. Results were analyzed and processed as described above.

Panels 1, 1.1, 1.2, and 1.3D
Panels 1, 1.1, 1.2 and 1.3D plates contain two control wells (genomic DNA control and chemical control) and 94 wells containing cDNA from various samples. The samples in these panels are classified into two classes: samples from cultured cell lines and samples from primary normal tissues. Cell lines include the following types of cancer: lung cancer, breast cancer, melanoma, colon cancer, prostate cancer, prostate cancer, CNS cancer, squamous cell carcinoma (squamous cell carcinoma), ovarian cancer, liver cancer, renal cancer, gastric cancer and pancreatic cancer. The cell lines used in these panels are widely available through the American Type Culture Collection (ATCC), a treasure trove of cultured cell lines, and were cultured using conditions recommended by the ATCC. The normal tissue found in these panels consists of samples from all major organ systems of a single adult individual or fetus. These samples include the following organs: adult skeletal muscle, fetal skeletal muscle, adult heart, fetal heart, adult kidney, fetal kidney, adult liver, fetal liver, adult lung, fetal lung, various regions of the brain, spleen, bone marrow, Derived from lymph node, pancreas, salivary gland, pituitary, adrenal gland, spinal cord, thymus, stomach, small intestine, colon, bladder, trachea, breast, ovary, uterus, placenta, prostate, testis and fat.

The following abbreviations are used in the results of panels 1, 1.1, 1.2 and 1.3D:
ca. = carcinoma,
* = Established by metastasis,
met = metastasis,
s cell var = small cell variant,
non-s = non-sm = non-small,
squam = squamous,
pl.eff = pl effusion = pleural effusion,
glio = glioma,
astro = astrocytoma, and
neuro = neuroblastoma.

General screening panel v1.4, v1.5, v1.6 and v1.7
Panels 1.4, 1.5, 1.6 and 1.7 contain two control wells (genomic DNA control and chemical control) and 88-94 wells containing cDNA from various samples. The samples in panels 1.4, 1.5, 1.6 and 1.7 are divided into two classes: samples from cultured cell lines and samples from primary normal tissues. The cell lines are derived from the following types of cancer: lung cancer, breast cancer, melanoma, colon cancer, prostate cancer, CNS cancer, squamous cell carcinoma, ovarian cancer, liver cancer, kidney cancer, stomach cancer and pancreatic cancer. The cell lines used in panels 1.4, 1.5, 1.6 and 1.7 are widely available through the American Type Culture Collection (ATCC), a treasure trove of cultured cell lines, and were cultured using the conditions recommended by the ATCC. The normal tissue found in panels 1.4, 1.5, 1.6 and 1.7 consists of a pool of samples from all major organ systems of 2-5 different adult individuals or fetuses. These samples include the following organs: adult skeletal muscle, fetal skeletal muscle, adult heart, fetal heart, adult kidney, fetal kidney, adult liver, fetal liver, adult lung, fetal lung, various regions of the brain, spleen, bone marrow, Derived from lymph node, pancreas, salivary gland, pituitary, adrenal gland, spinal cord, thymus, stomach, small intestine, colon, bladder, trachea, breast, ovary, uterus, placenta, prostate, testis and fat. Abbreviations as described for panels 1, 1.1, 1.2, and 1.3D.

Panel 2D, 2.2, 2.3 and 2.4
Panels 2D, 2.2, 2.3, and 2.4 plates generally work closely with two control wells and the National Cancer Institute's Cooperative Human Tissue Network (CHTN) or National Disease Research Initiative (NDRI) Included are 94 test samples consisting of RNA or cDNA obtained by a relevant physician or isolated from human tissue obtained from Ardais or Clinomics. These tissues are derived from human malignancies, and where indicated, many malignant tissues contain “corresponding edges” obtained from non-cancerous tissue just adjacent to the tumor. These are referred to as normal adjacent tissues, and are indicated as “NAT” in the following results. Tumor tissue and “corresponding edges” have been evaluated by two independent pathologists (by surgical pathologists and also NDRI / CHTN / Ardais / Clinomics pathologists). Non-corresponding RNA samples from tissues without malignant tumors (normal tissues) were also obtained from Ardais or Clinomics. This analysis provides an overall histopathological assessment of the extent of tumor differentiation. In addition, most samples include an initial surgical pathology report that provides information about the clinical stage of the patient. These corresponding edges are taken from the tissue surrounding the surgical field (ie, nearest neighbor) (referred to as “NAT” in Table RR from the term normal neighbor cell). In addition, RNA and cDNA samples were obtained from various human tissues obtained from autopsy performed on elderly or suddenly-dead victims (eg accidents). These tissues were confirmed not to be ill and were purchased from various commercial sources such as Clontech (Palo Alto, CA), Research Genetics, and Invitrogen.

HASS panel v 1.0
The HASS panel v 1.0 plate consists of 93 cDNA samples and 2 controls. Specifically, 81 of these samples were derived from cultured human cancer cell lines that were subjected to serum starvation, acidosis and anoxia for different periods of time, and controls for these treatments, 3 samples were human primary cells and 9 samples were Malignant brain cancer (4 medulloblastomas and 5 glioblastomas), and 2 are controls. Human cancer cell lines are obtained from ATCC (American Type Culture Collection), and are classified into the following tissue groups: breast cancer, prostate cancer, bladder carcinoma, pancreatic cancer, and CNS cancer cell lines. All these cancer cells are cultured under standard recommended conditions. The treatments used (serum starvation, acidosis and anoxia) have been published in scientific papers so far. Human primary cells were obtained from Clonetics (Walkersville, MD) and grown in the culture medium and conditions recommended by Clonetics. Malignant brain cancer samples are obtained as part of a collaborative study (Henry Ford Cancar Center) and evaluated by pathologists before CuraGen receives the samples. RNA was prepared from these samples using standard procedures. Genomic and chemical control wells have already been described.

ARDAIS panel v1.0
The ARDAIS panel v1.0 plate contains 22 test samples consisting of RNA isolated from human tissue, generally obtained by two control wells and a physician in close cooperation with Ardais. The tissue originates from human lung malignacies (Lung adenocacinoma or lung squamous cell carcinoma), and if indicated, many malignant samples are just adjacent to the tumor "Corresponding edge" obtained from non-cancerous lung tissue. These corresponding edges are taken from the tissue surrounding the surgical field (ie, closest adjacent) (called “NAT” from the term normal adjacent cells) in the following results. Tumor tissue and "corresponding edges" have been evaluated by independent pathologists (surgical pathologists and also Ardais pathologists). Non-compliant malignant and non-malignant RNA samples from the lung were also obtained from Ardais. Further information from Ardais provides an overall histopathological assessment of the extent and stage of tumor differentiation. In addition, most samples include an initial surgical pathology report that provides information about the clinical stage of the patient.

ARDAIS prostate v1.0
The ARDAIS panel v1.0 plate contains 68 test samples consisting of RNA isolated from human tissue, generally obtained by two control wells and a physician in close cooperation with Ardais. The tissue is derived from human prostate malignacies, and where indicated, many malignant samples contain “corresponding edges” obtained from non-cancerous prostate tissue just adjacent to the tumor. These corresponding edges are taken from the tissue surrounding the surgical field (ie, closest adjacent) (called “NAT” from the term normal adjacent cells) in the following results. Tumor tissue and "corresponding edges" have been evaluated by independent pathologists (surgical pathologists and also Ardais pathologists). RNA from non-compliant malignant and non-malignant samples from the lung was also obtained from Ardais. Further information from Ardais provides an overall histopathological assessment of the extent and stage of tumor differentiation. In addition, most samples include an initial surgical pathology report that provides information about the clinical stage of the patient.

Panel 3D, 3.1 and 3.2
Panels 3D, 3.1, and 3.2 plates consist of 94 cDNA samples and 2 control samples. Specifically, 92 of these samples are derived from cultured human cancer cell lines, 2 samples are derived from human primary cerebellar tissue, and 2 is a control. Human cell lines are generally obtained from ATCC (American Type Culture Collection), NCI, or German Tumor cell bank, and the following tissue groups: squamous cell carcinoma of the tongue, breast cancer, prostate cancer, melanoma, epidermoid carcinoma (epidermoid carcinoma), sarcomas, bladder carcinoma, pancreatic cancer, kidney cancer, leukemias / lymphomas, ovary / uterine / cervical cancer, stomach cancer, colon cancer, lung cancer And CNS cancer cell lines. In addition, there are two independent cerebellar samples. All of these cells were cultured under standard recommended conditions and RNA was extracted using standard procedures. The cell lines in panels 3D, 3.1, 3.2, 1, 1.1, 1.2, 1.3D, 1.4, 1.5 and 1.6 are the most common cell lines used in the scientific literature.

Panels 4D, 4R, and 4.1D
Panel 4 is a sample of RNA (panel 4R) or cDNA (panel 4D / 4.1D) isolated from various human cell lines or tissues associated with inflammatory symptoms in a 96 well plate (control well 2, test sample 94) including. Total RNA from control normal tissues such as colon and lung (Stratagene, La Jolla, CA) and thymus and kidney (Clontech) were used. Liver tissue from cirrhosis patients and kidney-derived total RNA from lupus patients were obtained from BioChain (Biochain Institute, Inc., Hayward, Calif.). Intestinal tissue for RNA preparation from patients diagnosed with Crohn's disease and ulcerative colitis was obtained from National Disease Research Interchange (NDRI) (Philadelphia, PA).

  Astrocytes, lung fibroblasts, skin fibroblasts, coronary artery smooth muscle cells, bronchiole epithelium, bronchial epithelium, skin microvascular endothelial cells, lung microvascular endothelial cells, human pulmonary aortic endothelial cells, human umbilical vein endothelial cells All were purchased from Clonetics (Walkersville, MD) and grown on the media provided by Clonetics for these cell types. These primary cell types were activated for 6 and / or 12-14 hours with various cytokines or combinations of cytokines as indicated. The following cytokines were used; about 1-5 ng / ml IL-1β, about 5-10 ng / ml TNFα, about 20-50 ng / ml IFNγ, about 5-10 ng / ml IL-4, about 5- 10 ng / ml IL-9, about 5-10 ng / ml IL-13. Endothelial cells were sometimes starved for various periods of time by culturing in the basic medium of Clonetics containing 0.1% serum.

Mononuclear cells were prepared from the blood of CuraGen employees using Ficoll. LAK cells from these cells were DMEM 5% FCS (Hyclone), 100 μM non-essential amino acids (Gibco / Life Technologies, Rockville, MD), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5 × 10 ⁻⁵ M (Gibco) And 4-6 days in culture with 10 mM Hepes (Gibco) and interleukin 2. Cells are then active for 6 hours with 10-20 ng / ml PMA and 1-2 μg / ml ionomycin, 5-10 ng / ml IL-12, 20-50 ng / ml IFNγ and 5-10 ng / ml IL-18 Made it. In some cases, mononuclear cells were treated with DMEM 5% FCS (Hyclone), 100 μM non-essential amino acid (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5 × 10 ⁻⁵ M (Gibco), and about 5 μg / ml. The cells were cultured in 10 mM Hepes (Gibco) containing PHA (phytohemagglutinin) or PWM (pokeweed mitogen) for 4-5 days. Samples were taken at 24, 48 and 72 hours for RNA preparation. MLR (mixed lymphocyte reaction) samples were collected from two donors, mononuclear cells were isolated using Ficoll, and the isolated mononuclear cells were identified as DMEM 5% FCS (Hyclone), 100 μM non-essential amino acids ( Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol (5.5 × 10 ⁻⁵ M) (Gibco), and 10 mM Hepes (Gibco) at a final concentration of approximately 2 × 10 ⁶ cells / ml 1: 1. Got in. MLRs were cultured and samples were taken at various time points ranging from 1-7 days for RNA preparation.

Monocytes were isolated from mononuclear cells using CD 14 Miltenyi beads, positive VS selection column and Vario Magnet according to the manufacturer's instructions. Monocytes are DMEM 5% fetal calf serum (FCS) (Hyclone, Logan, UT), 100 μM non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5 × 10 ⁻⁵ M (Gibco), and 10 mM. Differentiated into dendritic cells by culturing with Hepes (Gibco), 50 ng / ml GMCSF and 5 ng / ml IL-4 for 5-7 days. Macrophages are DMEM 5% FCS (Hyclone), 100 μM non-essential amino acid (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5 × 10 ⁻⁵ M (Gibco), 10 mM Hepes (Gibco) and 10% AB human serum Alternatively, it was prepared by culturing monocytes with about 50 ng / ml MCSF for 5-7 days. Monocytes, macrophages and dendritic cells were also stimulated with 100 ng / ml lipopolysaccharide (LPS) for 6 and 12-14 hours. Dendritic cells were also stimulated with 10 μg / ml anti-CD40 monoclonal antibody (Pharmingen) for 6 and 12-14 hours.

CD4 lymphocytes, CD8 lymphocytes and NK cells were also isolated from mononuclear cells using CD4, CD8 and CD56 Miltenyi beads, positive VS selection column and Vario Magnet according to the manufacturer's instructions. CD45RA and CD45RO CD4 lymphocytes were isolated by depleting mononuclear cells of CD8, CD56, CD14 and CD19 cells using CD8, CD56, CD14 and CD19 Miltenyi beads and positive selection. CD45RO CD4 lymphocytes were then isolated using CD45RO beads along with the remaining cells that were CD45RA CD4 lymphocytes. CD45RA CD4, CD45RO CD4 and CD8 lymphocytes were added to DMEM 5% FCS (Hyclone), 100 μM nonessential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5x10 ^-5 (Gibco), and 10 mM Hepes (Gibco ) And play at 10 ⁶ cells / ml on Falcon 6-well tissue culture plates coated overnight with 0.5 μg / ml anti-CD28 (Pharmingen) and 3 ug / ml anti-CD3 (OKT3, ATCC) in PBS. Tinged. The cells were harvested for RNA preparation after 6 and 24 hours. To prepare chronically activated CD8 lymphocytes, we activated the isolated CD8 lymphocytes on anti-CD28 and anti-CD3 coated plates for 4 days, then harvested the cells and transferred them to DMEM Enlarged with 5% FCS (Hyclone), 100 μM non-essential amino acid (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5 × 10 ⁻⁵ M (Gibco), and 10 mM Hepes (Gibco), and IL-2. The expanded CD8 cells were then activated again for 4 days on plates conjugated with anti-CD3 and anti-CD28 and expanded as before. RNA was isolated 6 and 24 hours after the second activation and 4 days after the second expansion culture. Isolated NK cells are: DMEM 5% FCS (Hyclone), 100 μM non-essential amino acid (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5 × 10 ⁻⁵ M (Gibco), and 10 mM Hepes (Gibco) and IL Cultured at -2 for 4-6 days, after which RNA was prepared.

Tonsils were obtained from NDRI to obtain B cells. The tonsils were finely cut with a sterilized scissors and then sieved. The tonsil cells were then sedimented and with DMEM 5% FCS (Hyclone), 100 μM non-essential amino acid (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5 × 10 ⁻⁵ M (Gibco), and 10 mM Hepes (Gibco) And resuspended at 10 ⁶ cells / ml. To activate the cells, we used 5 μg / ml PWM or about 10 μg / ml anti-CD40 (Pharmingen) and 5-10 ng / ml IL-4. Cells were harvested at 24, 48 and 72 hours for RNA preparation.

To prepare primary and secondary Th1 / Th2 and Tr1 cells, 6-well Falcon plates were coated overnight with 10 μg / ml anti-CD28 (Pharmingen) and 2 μg / ml OKT3 (ATCC) and then washed twice with PBS. Cord blood CD4 lymphocytes (Poietic Systems, German Town, MD) with DMEM 5% FCS (Hyclone), 100 μM non-essential amino acid (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5 × 10 ^-5 M (Gibco) And 10 mM Hepes (Gibco) and IL-2 (4 ng / ml) at 10 ⁵ to 10 ⁶ cells / ml. IL-12 (5 ng / ml) and anti-IL4 (1 μg / ml) were used to target Th1, while IL-4 (5 ng / ml) and anti-IFNγ (1 μg / ml) were used to target Th2, 5 ng / ml of IL-10 was used to direct Tr1. After 4-5 days, activated Th1, Th2 and Tr1 lymphocytes were washed once with DMEM, DMEM 5% FCS (Hyclone), 100 μM non-essential amino acid (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5 × Expansion was with 4-5 days with ^10-5 M (Gibco), 10 mM Hepes (Gibco) and IL-2 (1 ng / ml). Thereafter, activated Th1, Th2 and Tr1 lymphocytes were restimulated with anti-CD28 / OKT3 and cytokines for 5 days after addition of anti-CD95L (1 μg / ml) to prevent apoptosis, as described above. After 4-5 days, Th1, Th2 and Tr1 lymphocytes were washed and then expanded again with IL-2 for 4-7 days. Activated Th1 and Th2 lymphocytes were thus maintained for up to 3 cycles. After 6 and 24 hours of 4 and 4 days of second and third activation on plates bound with anti-CD3 and anti-CD28 mAbs, and second and third expansion cultures with interleukin 2, RNA was primary and Prepared from secondary Th1, Th2 and Tr1.

The following white blood cell lines: Ramos, EOL-1, and KU-812 were obtained from ATCC. EOL cells were further differentiated by culturing for 8 days with 0.1 mM dbcAMP at 5 × 10 ⁵ cells / ml, changing the medium every 3 days and adjusting the cell concentration to 5 × 10 ⁵ cells / ml. I let you. For culturing these cells, we used DMEM or RPMI (recommended by ATCC) with 5% FCS (Hyclone), 100 μM non-essential amino acid (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5. × 10 ⁻⁵ M (Gibco), 10 mM Hepes (Gibco) was added and used. RNA was prepared from either resting cells or cells activated with 10 ng / ml PMA and 1 μg / ml ionomycin for 6 and 14 hours. Keratinocyte strain CCD106 and airway epithelial tumor strain NCI-H292 were also obtained from ATCC. Both were cultured in DMEM 5% FCS (Hyclone), 100 μM non-essential amino acid (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5 × 10 ⁻⁵ M (Gibco), and 10 mM Hepes (Gibco). CCD1106 cells are activated with approximately 5 ng / ml TNFα and 1 ng / ml IL-1β for 6 and 14 hours, NCI-H292 cells are the following cytokines: 5 ng / ml IL-4, 5 ng / ml IL-9, 5 ng / ml Activation with IL-13 and 25 ng / ml IFNγ for 6 and 14 hours.

For these cell lines and blood cells, RNA was prepared by lysing to approximately 10 ⁷ cells / ml with Trizol (Gibco BRL). Briefly, 1/10 volume of bromochloropropane (Molecular Research Corporation) was added to the RNA sample, vortexed and after 10 minutes at room temperature, the tube was spun at 14,000 rpm in a Sorvall SS34 rotor. The aqueous phase was collected and placed in a 15 ml Falcon Tube. An equal amount of isopropanol was added, and the mixture was allowed to stand at −20 ° C. overnight. The precipitated RNA was precipitated with a Sorvall SS34 rotor at 9,000 rpm for 15 minutes and washed with 70% ethanol. The pellet was redissolved in 300 μl RNase free water and 35 μl buffer (Promega), 5 μl DTT, 7 μl RNAsin and 8 μl DNase were added. The tube was incubated at 37 ° C. for 30 minutes to remove contaminating genomic DNA, extracted once with phenol chloroform, and precipitated again with 1/10 volume of 3M sodium acetate and 2 volumes of 100% ethanol. RNA was precipitated and placed in water without RNase. RNA was stored at -80 ° C.

AI comprehensive panel v1.0
The AI Comprehensive Panel v1.0 plate contains two control wells and 89 test samples consisting of cDNA isolated from surgical and autopsy human tissues obtained from Backus Hospital and Clinomics (Frederick, MD). Total RNA was extracted from tissue samples obtained from Backus Hospital in the CuraGen facility. Total RNA from other tissues was obtained from Clinomics.

  Joint tissues including synovial fluid, synovium, bone and cartilage were obtained from patients undergoing total knee or hip replacement at Backus Hospital. Tissue samples were immediately snap frozen in liquid nitrogen to ensure that the isolated RNA was of optimum quality and did not degenerate. Additional samples of joint tissue from osteoarthritis and rheumatoid arthritis were obtained from Clinomics. Normal control tissues were provided by Clinomics and were obtained during autopsy of trauma victims.

  Surgical samples of psoriatic tissue and adjacent counterpart tissue were provided as total RNA by Clinomics. Two male and two female patients between 25-47 years old were selected. None of the patients were taking prescription drugs when the samples were isolated.

  Surgical samples of the affected colon obtained from patients with ulcerative colitis and Crohn's disease and adjacent counterpart tissues were obtained from Clinomics. Intestinal tissue from 3 women and 3 male patients with Crohn's disease between 41 and 69 years old was used. Two patients were not prescribed medication, while others were taking dexamethasone, phenobarbital, or tylenol. Ulcerative colitis tissue was obtained from 3 male and 4 female patients. Four of the patients were taking lebvid and two were taking phenobarbital.

  Total RNA from autopsy anatomical lung tissue obtained from trauma victims without disease or suffering from emphysema, asthma or COPD was purchased from Clinomics. All pulmonary emphysema patients in the 40-70 year range are smokers, and this age range focuses on patients with emphysema associated with tobacco and has chosen to avoid patients with alpha-1 antitrypsin deficiency . Asthmatic patients ranged from 36 to 75 years and excluded smokers to avoid patients who could also have COPD. COPD patients ranged between 35 and 80 years and included both smokers and non-smokers. Most patients were taking corticosteroids and bronchodilators.

The following abbreviations are used in the labels used to identify tissues in the AI Comprehensive Panel v1.0 panel:
AI = autoimmunity
Syn = synovial fluid
Normal = no obvious disease
Rep22 / Rep20 = Individual patient
RA = rheumatoid arthritis
Provided by Backus = Backus Hospital
OA = osteoarthritis
(SS) (BA) (MF) = Individual patient
Adj = adjacent organization
Match control = adjacent tissue
-M = male
-F = Female
COPD = chronic obstructive pulmonary disease

AI.05 Chondrosarcoma
AI.05 chondrosarcoma plates consist of SW1353 cells that have been subjected to treatment with cytokines (eg, IL1β) known to induce serum starvation and MMP (1, 3 and 13) synthesis. These treatments include: IL-1β (10 ng / ml), IL-1β + TNF-α (50 ng / ml), IL-1β + oncostatin (50 ng / ml) and PMA (100 ng / ml) . SW1353 cells were obtained from ATCC (American Type Culture Collection) and were all cultured under standard recommended conditions. SW1353 cells were plated in 6 well plates at 3 × 10 ⁵ cells / ml (DMEM medium-10% FBS). Treatment was done in triplicate for 6 and 18 hours. Supernatants were collected for analysis of MMP1, 3 and 13 production and for RNA extraction. RNA was prepared from these samples using standard procedures.

Panel 5D and 5I
Panels 5D and 5I contain two control wells and various cDNAs isolated from human tissues and cell lines with emphasis on metabolic disease. Metabolic tissues were obtained from patients participating in the Gestational Diabetes study. Cells were obtained during various stages in the differentiation of adipocytes derived from human mesenchymal stem cells. Human islets were also obtained.

In gestational diabetes studies, subjects are gestational diabetics who have undergone conventional (selective) caesarean section, or are young (18-40 years) or healthy women. When the surgical incision after infant delivery was repaired / closed, a small sample (<1 cc) of exposed metabolic tissue was removed by the obstetrician during each surgical level of termination. The biopsy material was rinsed with sterilized saline within 5 minutes from the time of extraction, and the water was absorbed and snap frozen. The tissue was then snap frozen in liquid nitrogen and stored individually in sterile screw-cap tubes and kept on dry ice for shipping or for collection by CuraGen. The metabolic tissues of interest include uterine wall (smooth muscle), visceral fat, skeletal muscle (straight muscle) and subcutaneous fat. The patient summary is as follows:
Patient 2: Diabetic Latin American, overweight, not taking insulin regularly Patient 7-9: Non-diabetic white and obese (BMI> 30)
Patient 10: Diabetes Latin American, overweight, insulin overuse Patient 11: Non-diabetic African American overweight, Patient 12: Diabetes Latin American overuse insulin

Adipocyte differentiation was induced in donor progenitor cells obtained from Osirus (a division of Clonetics / BioWhittaker) in triplicate, except for donor 3U, which had only two replicas. Clonetics scientists identified human mesenchymal stem cells (HuMSCs) for CuraGen based on the published protocol found in Mark F. Pittenger et al., Multilineage Potential of Adult Human mesenchymal Stem Cell Science Apr 2 1999: 143-147. Separated, propagated and differentiated. Clonetics provided Trizol lysates or frozen pellets suitable for mRNA isolation and double stranded cDNA generation. The outline of each donor is as follows:
Donor 2 and 3U: Mesenchymal stem cells, undifferentiated fat Donor 2 and 3AM: Fat, in the middle of differentiation Donor 2 and 3AD: Fat, differentiated fat

  Human cell lines are mostly obtained from ATCC (American Type Culture Collection), NCI or German Tumor cell bank, and the following tissue groups: renal proximal tubules, uterine smooth muscle cells, small intestine, liver HepG2 cancer Classified as cells, primary cardiac stromal cells, and adrenocortical adenoma cells. All of these cells were cultured under standard recommended conditions and RNA was extracted using standard procedures. All samples were treated with CuraGen to obtain single stranded cDNA.

  Panel 51 contained all the samples described so far and further added a 58-year-old female patient's islet from the University of Miami School of Medicine Diabetes Research Institute. The island tissue was processed into total RNA from an external source and delivered to CuraGen for addition to panel 51.

The following abbreviations are used in the labels used for tissue identification in 5D and 51 panels:
GO fat = omental fat
SK = skeletal muscle
UT = uterus
PL = placenta
AD = differentiated fat
AM = fat during differentiation
U = undifferentiated stem cell

Panel CNSD 01
Panel CNSD 01 plate contains 94 control samples consisting of 2 control wells and cDNA isolated from autopsy dissected human brain tissue obtained from Harvard Brain Tissue Resource Center. The brain is removed from the donor calvaria 4-24 hours after death, sectioned by a neuroanatomist, and frozen at −80 ° C. in liquid nitrogen vapor. All brains are sectioned and examined by neuropathologists to confirm the diagnosis of clearly related neuropathology.

  Disease diagnosis is taken from patient records. The panel includes the following diagnoses: two brains from each of Alzheimer's disease, Parkinson's diseas, Huntington's disease, Progressive Supernuclear Palsy, Depression, and `` A “normal control” is included. Within each of these brains, the following areas are shown: zonal gyrus, temporal pole, pallidum, substantia nigra, Broadman area 4 (primary motor zone), Broadman area 7 (parietal cortex) ), Broadman area 9 (frontal cortex), and Broadman area 17 (occipital cortex). Not all patients show all brain areas; for example, Huntington's disease is characterized by neurodegeneration in the pallidal bulb, so this area from patients identified as Huntington's disease It is impossible to get. Similarly, Parkinson's disease is characterized by substantia nigra degeneration, making it more difficult to obtain this area. Normal control brains were examined for neuropathology and found to have no pathology consistent with neurodegeneration.

The following abbreviations are used in the labels used to identify tissues in the CNS panel:
PSP = progressive supranuclear palsy
Sub Nigra = Black
Glob Palladus = Tanyukyu
Temp Pole = temporal pole
Cing Gyr = Zonal gyrus
BA 4 = Broadman Field 4

Panel CNS Neurodegeneration V1.0
Panel CNS Neurodegenerative V1.0 plates include two control wells and Harvard Brain Tissue Resource Center (McLean Hospital) and Human Brain and Spinal Fluid Resource Center Included are 47 test samples consisting of cDNA isolated from autopsy human brain tissue obtained from (VA Greater Los Angeles Healthcare System). The brain is removed from the donor calvaria 4-24 hours after death, sectioned by a neuroanatomist, and frozen at −80 ° C. in liquid nitrogen vapor. All brains are sectioned and examined by neuropathologists and diagnoses are confirmed for clearly related neuropathologies.

  Disease diagnosis is taken from patient records. This panel includes brains from six Alzheimer's disease (AD) patients and brains from “normal controls” that did not show signs of dementia before death. The eight normal control brains are of two types: non-pathological controls such as dementia and Alzheimer's disease (controls) and no dementia but severe pathological signs such as Alzheimer's disease (specifically 0-3 Senile plaque mass rated as stage 3; 0 = no signs of plaque, 3 = severe AD senile plaque mass). Within each of these brains, the following areas are shown: hippocampus, temporal cortex (Broadman area 21), parietal cortex (Broadman area 7), and occipital cortex (Broadman area 17). These regions were chosen to encompass all stages of neurodegeneration in AD. The hippocampus is an early and severe area of neuronal loss in AD; the temporal cortex is known to show neurodegeneration after the hippocampus in AD; the parietal cortex exhibits moderate neuronal cell death at the end of the disease Shown; the occipital cortex is left behind in AD, thus serving as a “control” area within AD patients. Not all brain areas are shown in all patients.

The following abbreviations are used in the labels used to identify tissues in the CNS neurodegenerative V1.0 panel:
AD = Alzheimer's disease brain; at autopsy, patient was demented and showed AD-like pathology
Control = control brain; non-demented patient without neuropathology
Control (Path) = control brain; patients with non-dementia but severe AD-like pathology
SupTemporal Ctx = Upper temporal cortex
InfTemporal Ctx = Inferior temporal cortex

Panel CNS neurodegeneration V2.0
Panel CNS Neurodegenerative V1.0 plates include two control wells and Harvard Brain Tissue Resource Center (McLean Hospital) and Human Brain and Spinal Fluid Resource Center Included are 47 test samples consisting of cDNA isolated from autopsy human brain tissue obtained from (VA Greater Los Angeles Healthcare System). The brain is removed from the donor calvaria 4-24 hours after death, sectioned by a neuroanatomist, and frozen at −80 ° C. in liquid nitrogen vapor. All brains are sectioned and examined by neuropathologists and diagnoses are confirmed for clearly related neuropathologies.

  Disease diagnosis is taken from patient records. This panel includes brains from 16 Alzheimer's disease (AD) patients and brains from “normal controls” that did not show signs of dementia before 29 deaths. 29 normal control brains are of two types: 14 dementia and non-pathological controls such as Alzheimer's disease (control) and 15 dementia but no severe pathological signs such as Alzheimer's disease (more details Senile plaque mass evaluated as level 3 on a 0-3 scale; 0 = no signs of plaque, 3 = severe AD senile plaque mass). For all samples obtained from the Harvard Brain Tissue Resource Center, select tissue from the temporal cortex (Broadman area 21), and from the two samples (Samples 1 and 2) obtained from the Human Brain and Spinal Fluid Resource Center. And each sample in the panel corresponds to a lower and upper scalp pool of one individual patient. The temporal cortex was chosen to show neuronal loss at an intermediate stage of the disease. Selecting a region affected early in Alzheimer's disease (e.g., hippocampus or olfactory cortex) examines gene expression after loss of vulnerable neurons, and genes involved in the actual neurodegenerative process There is a possibility of losing sight.

The following abbreviations are used in the labels used to identify tissues in the CNS neurodegenerative V2.0 panel:
AD = Alzheimer's disease brain; at autopsy, patient was demented and showed AD-like pathology
Control = control brain; non-demented patient without neuropathology
AH3 = control brain; patients with non-dementia but severe AD-like pathology
Inf & Sup Temp Ctx Pool = Pool of the lower and upper scalp of a given individual

A. CG126472-02: TEM7.
The expression of gene CG126472-02 was evaluated using primer-probe set Ag4727 and listed in Table AA. The results of RTQ-PCR performed are shown in Tables AB, AC, AD, AE and AF.

Table AA Probe name Ag4727

Table AB CNS neurodegeneration v1.0

Table AC General Screening Panel v1.4

Table AD Panel 3D

Table AE Panel 4.1D

Table AF General Oncology Screening Panel v_2.4

CNS neurodegeneration v1.0 Summary: Ag4727 Two experiments with identical probes and primers gave very consistent results. In this panel, the expression of this gene is confirmed at a low level in the brain of an independent population. This gene appears to be slightly down-regulated in the temporal cortex of Alzheimer's disease patients. Thus, up-regulation of this gene or its protein product, or treatment with an agonist specific for this receptor, may be useful in reversing dementia, memory loss and neuronal death associated with this disease.

General Screening Panel v1.4 Summary: Ag4727 The highest expression of this gene is found in brain cancer cell lines (CT = 28). This gene is widely expressed in this panel, with moderate expression seen in colon and gastric cancer cell lines. This expression profile suggests a role for this gene in cell survival and proliferation. This regulation of the gene product may be useful in the treatment of cancer.

  In tissues with metabolic function, this gene is expressed at moderate to low levels in the pituitary gland, fat, adrenal gland, pancreas, thyroid, fetal liver and adult and fetal skeletal muscle and heart. This widespread expression in these tissues indicates that this gene product may play a role in normal neuroendocrine and metabolic functions, and the unregulated expression of this gene is such as obesity and diabetes Suggests that it may cause neuroendocrine or metabolic diseases.

  Interestingly, this gene is expressed at a much higher level in the fetal kidney (CT = 29) compared to the level of expression in the adult kidney (CT = 32). This finding suggests that the expression of this gene can be used to distinguish between fetal and adult sources of this tissue. Furthermore, the relative overexpression of this gene in the fetal kidney suggests that this protein product may enhance kidney growth or development in the fetus and thus may act in regenerative capacity even in adults. To do. Thus, therapeutic modulation of the protein encoded by this gene may be useful in the treatment of kidney related diseases.

  This gene is also expressed at moderate to low but significant levels in the CNS, including the hippocampus, thalamus, substantia nigra, amygdala, cerebellum and cerebral cortex. Thus, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurological diseases such as Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, stroke and epilepsy.

Panel 3D Summary: Ag4727 The highest expression of this gene is found in the cerebellum (CT = 30). Medium level expression is seen in several cancer cell lines in this panel, consistent with panel 1.4. See that panel for a discussion of this.

Panel 4.1D Summary: Ag4727 The highest expression of this gene is found in the thymus (CT = 27.8), and a moderate level of expression is found in the normal lung. Therefore, the protein encoded by this gene may play an important role in T cell development. Therefore, therapeutic regulation of the expression or function of this gene can be used to regulate immune function (T cell development) and may be important for immune reconstitution after organ transplantation, AIDS treatment or chemotherapy .

General Oncology Screening Panel v2.4 Summary: Ag4727 This gene is widely expressed in this panel and is most highly expressed in lung cancer (CT = 32.6). Furthermore, this gene is more highly expressed in lung and kidney cancer than the corresponding normal adjacent tissue. Therefore, the expression of this gene may be used as a marker for these cancers. Furthermore, therapeutic modulation of the expression or function of this gene product may be useful in the treatment of lung and kidney cancer.

B. CG170490-01: Ubiquitin-protein ligase E3 component N-Recognin (RECOGNIN)
The expression of the gene CG170490-01 was evaluated using the primer-probe set Ag6130 and listed in Table BA. The results of RTQ-PCR performed are shown in Tables BB, BC and BD.

Table BA Probe name Ag6130

Table BB CNS neurodegeneration v1.0

Table BC General Screening Panel v1.5

Table BD Panel 4.1D

CNS neurodegeneration v1.0 Summary: Ag6130 In this panel, the expression of this gene is confirmed at low levels in the brain of an independent population.

General Screening Panel v1.5 Summary: Ag6130 The highest expression of this gene is detected in the brain cancer U-118-MG cell line (CT = 27.6). Medium level expression of this gene is also found in clusters of cancer cell lines derived from pancreatic cancer, stomach cancer, colon cancer, lung cancer, liver cancer, kidney cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, melanoma and brain cancer. It can be seen. Therefore, the expression of this gene could potentially be used as a marker for detecting the presence of these cancers. In addition, the therapeutic regulation of the expression or function of this gene is effective in the treatment of pancreatic cancer, stomach cancer, colon cancer, lung cancer, liver cancer, kidney cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, melanoma and brain cancer It can be.

  In tissues with metabolic or endocrine function, this gene is expressed at moderate levels in the pancreas, fat, adrenal gland, thyroid, pituitary, skeletal muscle, heart, liver and gastrointestinal tract. Thus, therapeutic modulation of the activity of this gene may prove useful in the treatment of endocrine / metabolism related diseases such as obesity and diabetes.

  In addition, this gene is expressed at moderate levels in all areas of the central nervous system examined, including the amygdala, hippocampus, substantia nigra, thalamus, cerebellum, cerebral cortex and spinal cord. Thus, therapeutic modulation of this gene product may be useful in the treatment of central nervous system diseases such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

  Interestingly, this gene is expressed at significantly higher levels in the fetus (CT = 28.7) compared to adult liver (CT = 33). This finding suggests that the expression of this gene can be used to distinguish between fetus and adult liver. Furthermore, the relative overexpression of this gene in fetal tissue suggests that this protein product may enhance liver growth or development in the fetus and thus may act in regenerative capacity even in adults. To do. Thus, therapeutic modulation of the protein encoded by this gene may be useful in the treatment of liver related diseases.

Panel 4.1D Summary: Ag6130 The highest expression of this gene is detected in activated secondary Tr1 cells (CT = 29.9). This gene is expressed at moderate to low levels in a wide range of cell types that are important in immune responses in health and disease. These cells include T cells, B cells, endothelial cells, macrophage / monocytes and peripheral blood mononuclear cell family members, as well as epithelial and fibroblast types from lung and skin, and colon, lung, thymus and A normal tissue corresponding to the kidney may be mentioned. This broad pattern of expression suggests that this gene product may be involved in these and other cell types and tissue homeostasis processes. This pattern is consistent with the expression profile of the general screening panel v1.5, suggesting a role for this gene product in cell survival and proliferation. Thus, modulation of this gene product with functional therapeutics results in functional changes associated with these cell types and also includes asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis and osteoarthritis May result in improvement of symptoms in patients suffering from autoimmunity and inflammatory diseases such as.

C. CG170667-02: Putative neural cell adhesion molecule The expression of the gene CG170667-02 was evaluated using the primer-probe sets Ag6137 and Ag6161, and listed in Tables CA and CB. The results of performing RTQ-PCR are shown in Tables CC and CD.

Table CA Probe name Ag6137

Table CB Probe name Ag6161

Table CC CNS Neurodegeneration v1.0

Table CD General Screening Panel v1.5

CNS neurodegeneration v1.0 Summary: Ag6137 In this panel, the expression of this gene is confirmed at a low level in the brain of an independent population.

General Screening Panel v1.5 Summary: Ag6137 The highest expression of this gene is detected in liver cancer cell lines (CT = 28.2). Medium to low expression of this gene is detected in several cancer cell lines derived from pancreatic cancer, brain cancer, colon cancer, kidney cancer, breast cancer and ovarian cancer. Therefore, the expression of this gene could potentially be used as a marker for detecting the presence of these cancers. Furthermore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of pancreatic cancer, brain cancer, colon cancer, kidney cancer, breast cancer and ovarian cancer.

  In tissues with metabolic or endocrine function, this gene is expressed at low levels in the pancreas, thyroid, pituitary, fetal heart, liver and gastrointestinal tract. Thus, therapeutic modulation of the activity of this gene may prove useful in the treatment of endocrine / metabolism related diseases such as obesity and diabetes.

  In addition, this gene is expressed at low levels in all areas of the central nervous system examined, including the amygdala, hippocampus, substantia nigra, thalamus, cerebellum, cerebral cortex and spinal cord. Thus, therapeutic modulation of this gene product may be useful in the treatment of central nervous system diseases such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

D.CG170791-01: Acetyl-CoA transporter (ACATN)
The expression of the gene CG170791-01 was evaluated using the primer-probe set Ag6214 and listed in Table DA. The results of RTQ-PCR are shown in Table DB and DC.

Table DA Probe name Ag6214

Table DB CNS Neurodegeneration v1.0

Table DC Panel 4.1D

CNS neurodegeneration v1.0 Summary: Ag6214 Low expression of this gene is found in the temporal cortex of control patients (CT = 34.2). Thus, therapeutic modulation of this gene or its protein product may be useful in the treatment of neurological diseases such as epileptic seizures, Alzheimer's disease, schizophrenia and amnesia.

Panel 4.1D Summary: Ag6214 Low expression of this gene is detected primarily in TNFα + IL-β activated HPAEC and bronchial epithelium and TNFα activated dermal fibroblasts. Thus, therapeutic modulation of this gene or its protein product may be useful in the treatment of autoimmune and inflammatory diseases including psoriasis, chronic obstructive pulmonary disease, asthma, allergies and emphysema.

E.CG171174-01: Novel plasma membrane protein The expression of the gene CG171174-01 was evaluated using the primer-probe set Ag6166 and listed in Table EA. The results of RTQ-PCR runs are shown in Tables EB, EC and ED.

Table EA Probe name Ag6166

Table EB CNS neurodegeneration v1.0

Table EC General Screening Panel v1.5

Table ED Panel 4.1D

CNS neurodegeneration v1.0 Summary: Ag6166 In this panel, the expression of this gene is confirmed at a low level in the brain of an independent population. It can be seen that this gene is slightly up-regulated in the temporal cortex of Alzheimer's disease patients. The receptor blockade may be useful in treating the disease and reducing neuronal death.

General Screening Panel v1.5 Summary: Ag6166 The highest expression of this gene is detected in the cerebellum (CT = 27). This gene is expressed at moderate levels in all areas of the central nervous system examined, including the amygdala, hippocampus, substantia nigra, thalamus, cerebellum, cerebral cortex and spinal cord. Thus, therapeutic modulation of this gene product may be useful in the treatment of central nervous system diseases such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

  Medium level expression of this gene is also found in clusters of cancer cell lines derived from pancreatic cancer, stomach cancer, colon cancer, lung cancer, liver cancer, kidney cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, melanoma and brain cancer. It can be seen. Therefore, the expression of this gene could potentially be used as a marker for detecting the presence of these cancers. In addition, the therapeutic regulation of the expression or function of this gene is effective in the treatment of pancreatic cancer, stomach cancer, colon cancer, lung cancer, liver cancer, kidney cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, melanoma and brain cancer It can be.

  In tissues with metabolic or endocrine function, this gene is expressed at moderate to low levels in the pancreas, fat, adrenal gland, thyroid, pituitary, skeletal muscle, heart, liver and gastrointestinal tract. Thus, therapeutic modulation of the activity of this gene may prove useful in the treatment of endocrine / metabolism related diseases such as obesity and diabetes.

  Interestingly, this gene is expressed at fairly high levels in the fetus (CT = 30) compared to adult liver (CT = 34.8). This finding suggests that the expression of this gene can be used to distinguish between fetus and adult liver. Furthermore, the relative overexpression of this gene in fetal tissue suggests that this protein product may enhance liver growth or development in the fetus and thus may act in regenerative capacity even in adults. To do. Thus, therapeutic modulation of the protein encoded by this gene may be useful in the treatment of liver related diseases.

Panel 4.1D Summary: Ag6166 The highest expression of this gene is detected in TNFα-treated mysterious fibroblasts (CT = 33.3). Low expression of this gene is found in a wide range of cell types that are important in immune responses in healthy and diseased states. These cells include T cells, B cells, endothelial cells, activated monocytes and members of the peripheral blood mononuclear cell family, and epithelial and fibroblast types from lung and skin. Expression of this gene is upregulated in LPS-stimulated monocytes, activated Ramos B cells, activated naive and memory T cells, and activated polarized T cells. Thus, modulation of this gene product with functional therapeutics results in functional changes associated with these cell types and also includes asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis and osteoarthritis May result in improvement of symptoms in patients suffering from autoimmunity and inflammatory diseases such as.

F. CG172921-01: Interleukin-5 receptor α chain The expression of the gene CG172921-01 was evaluated using the primer-probe sets Ag5894 and Ag6187 and listed in Tables FA and FB. The results of RTQ-PCR are shown in Tables FC and FD. Note that CG172921-01 corresponds to a full-length physical clone.

Table FA Probe name Ag5894

Table FB Probe name Ag6187

Table FC AI Comprehensive Panel v1.0

Table FD panel 4.1D

AI Comprehensive Panel v1.0 Summary: The highest expression of Ag5894 is seen in RA bone derived samples (CT = 30.9). In addition, moderate levels of expression are seen in clusters of RA-derived samples. Thus, the expression of this gene could be used in this panel to distinguish RA-derived samples from other samples and as a marker for RA. Furthermore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of RA.

Panel 4.1D Summary: Ag5894 / Ag6187 Two experiments with two different probes and primer sets gave very consistent results. Detectable expression is limited to resting neutrophils (CT = 31-33). In neutrophils activated by TNF-α + LPS, this expression is reduced to background levels (CT = 40). This expression profile suggests that this gene is produced by resting neutrophils but not by activated neutrophils. Therefore, this gene product may reduce the activation of these inflammatory cells, such as Crohn's disease, ulcerative colitis, multiple sclerosis, chronic obstructive pulmonary disease, asthma, emphysema, rheumatoid arthritis, lupus erythematosus or It can be useful as a protein therapeutic to reduce or eliminate symptoms in psoriasis patients.

G.CG176203-01: Novel membrane protein The expression of the gene CG176203-01 was evaluated using the primer-probe set Ag6370 and listed in Table GA. The results of RTQ-PCR performed are shown in Tables GB and GC.

Table GA Probe name Ag6370

Table GB General Screening Panel v1.6

Table GC Panel 4.1D

General Screening Panel v1.6 Summary: Ag6370 The highest expression of this gene is detected in the ovarian cancer SK-OV-3 cell line (CT = 27.7). Medium level expression of this gene is also found in clusters of cancer cell lines derived from pancreatic cancer, stomach cancer, colon cancer, lung cancer, liver cancer, kidney cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, melanoma and brain cancer. It can be seen. Therefore, the expression of this gene could potentially be used as a marker for detecting the presence of these cancers. In addition, the therapeutic regulation of the expression or function of this gene is effective in the treatment of pancreatic cancer, stomach cancer, colon cancer, lung cancer, liver cancer, kidney cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, melanoma and brain cancer It can be.

  In tissues with metabolic or endocrine function, this gene is expressed at moderate levels in the pancreas, fat, adrenal gland, thyroid, pituitary, skeletal muscle, heart, fetal liver and gastrointestinal tract. Thus, therapeutic modulation of the activity of this gene may prove useful in the treatment of endocrine / metabolism related diseases such as obesity and diabetes.

  In addition, this gene is expressed at moderate levels in all areas of the central nervous system examined, including the amygdala, hippocampus, substantia nigra, thalamus, cerebellum, cerebral cortex and spinal cord. Thus, therapeutic modulation of this gene product may be useful in the treatment of central nervous system diseases such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

  Interestingly, this gene is expressed at a much higher level in the fetus (CT = 29.3) compared to adult liver (CT = 40). This finding suggests that the expression of this gene can be used to distinguish between fetus and adult liver. Furthermore, the relative overexpression of this gene in fetal tissue suggests that this protein product may enhance liver growth or development in the fetus and thus may act in regenerative capacity even in adults. To do. Thus, therapeutic modulation of the protein encoded by this gene may be useful in the treatment of liver related diseases.

Panel 4.1D Summary: Ag6370 The highest expression of this gene is detected in lung microvascular endothelial cells (CT = 29.3). This gene is expressed at moderate to low levels in a wide range of cell types important in immune responses in health and disease. These cells correspond to T cells, B cells, endothelial cells, macrophage / monocytes and peripheral blood mononuclear cell family members, as well as lung and skin derived epithelial and fibroblast types, and lung and kidney Normal tissue is mentioned. This broad pattern of expression suggests that this gene product may be involved in these and other cell types and tissue homeostasis processes. This pattern is consistent with the expression profile of the general screening panel v1.6, suggesting a role for this gene product in cell survival and proliferation. Thus, modulation of this gene product with functional therapeutics results in functional changes associated with these cell types and also includes asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis and osteoarthritis May result in improvement of symptoms in patients suffering from autoimmunity and inflammatory diseases such as.

H.CG50691-02: CRIM1 homologue The expression of gene CG50691-02 was evaluated using primer-probe sets Ag155 and Ag7290 and listed in Tables HA and HB. The results of RTQ-PCR are shown in Tables HC, HD, HE, HF and HG.

Table HA Probe name Ag155

Table HB Probe name Ag7290

Table HC Ardais Prostate 1.0

Table HD CNS neurodegeneration v1.0

Table HE General Screening Panel v1.7

Table HF Panel 1

Table HG Panel 4.1D

Ardais Prostate 1.0 Summary: The highest expression of this gene encoding the Ag7290 putative CRIM1 protein is found in normal tissues adjacent to prostate carcinoma (CT = 29.9). Furthermore, this gene is widely expressed at low levels in most samples of this panel, suggesting a role for this protein in cell survival and / or proliferation.

CNS neurodegeneration v1.0 Summary: Ag7290 This panel shows no difference in the expression of this gene in Alzheimer's disease. However, this profile confirms low level expression of this gene in the brain. See panel 1.7 for a discussion of this gene in the central nervous system.

General Screening Panel v1.7 Summary: Ag7290 The highest expression of this gene is found in ovarian cancer cell lines (CT = 26.2). This gene is widely expressed in this panel, with moderate to high expression in brain cancer, colon cancer, stomach cancer, lung cancer, breast cancer, ovarian cancer, prostate cancer and melanoma cancer cell lines. This expression profile suggests a role for this gene in cell survival and proliferation. This gene encodes a novel protein with homology to cysteine-rich motor neuron protein 1 (CRIM1) that can interact with growth factors involved in motor neuron differentiation and survival (Kolle, G .; Georgas Holmes, GP; Little, MH; Yamada, T .: CRIM1, a novel gene encoding a cysteine-rich repeat protein, is developmentally regulated and implicated in vertebrate CNS development and organogenesis.Mech. Dev. 90: 181- 193, 2000. PubMed ID: 10642437).
The Crim1 gene is an IGF-binding protein motif and multiple, similar to that of the chordin and short gastrulation (sog) proteins associated with the TGFβ superfamily member, bone morphogenetic protein (BMP) It encodes a putative transmembrane protein containing the VWFC domain. In chodin, such repeats are entrusted to their dorsalizing activity and binding to bone morphogenetic protein (BMP). Chordins are BMP antagonists that dorsalize early vertebrate embryonic tissues by binding to ventralized TGFβ-like bone morphogenetic proteins and trapping them in potential complexes. Scott et al. (Scott, IC; Blitz, IL; Pappano, WN; Imamura, Y .; Clark, TG; Steiglitz, BM; Thomas, CL; Maas, SA; Takahara, K .; Cho, KWY; Greenspan, DS: Mammalian BMP-1 / Tolloid-related metalloproteinase, including novel family member mammalian Tolloid-like 2, have differential cyclic activities and distributions of expression relevant to patterning and skeletogenesis.Dev. Biol. 213: 283-300, 1999.) We have shown that RLL1 counteracts chordal dorsalization when overexpressed in Xenopus embryos. It suggests that BMP1 is a major chodin antagonist in early mammalian embryogenesis and in prenatal and postnatal skeletal formation. It also binds directly to BMP-4 and BMP-2, Interfere with the binding. Bone metastasis is a common clinical problem in patients with breast cancer, prostate cancer and other cancers. The formation of these lesions is a site-specific process determined by multiple cellular and molecular interactions between cancer cells and the bone microenvironment. Bone morphogenetic protein (BMP) has been found to be one of the important factors in the prognosis of bone tumors. Overexpression of BMP2, BMP4, and BMP6 is seen in most metastatic osteosarcoma or prostate cancer (Guo, W., Gorlick, R., Ladanyi, M., Meyers, PA., Huvos, AG., Bertino , JR., And Healey, JH., 1999, Expression of bone morphogenetic protein and receptors in sarcomas.Clinical Orthopaedics and Related Research 365: 175-183; Hamdy, F., Autzen, P., Robinson, MC., Wilson Horne , CH., Neal, DE. And Robson CN., 1997, Immunolocalization and messenger RNA expression of bone morphogenetic protein -6 in human benign and malignant prostatic tissue.Cancer Research 57: 4427-4431). Suggest a close relationship between metastases. BMP-2, -4, and -6 may be part of the cause of osteoblastic changes in metastatic lesions secondary to prostate cancer.

  Kolle et al. (2000) suggested that CRIM1 may be involved in motor neuron survival by interacting with various growth factors. Georgas K et al. (Georgas K, Bowles J, Yamada T, Koopman P, Little MH, 2000, Characterisation of Crim1 expression in the developing mouse urogenital tract reveals a sexually dimorphic gonadal expression pattern.Dev Dyn 219 (4): 582-7) Crim1 also demonstrated a striking male-specific expression pattern in the fetal gonad, indicating that its expression is strongest in Sertoli cells of the developing testis.

  CG50691-02 and CG50691-03 (see below) correspond to two novel splicing variants of CRIM1, with deletion of internal 58aa (exon 2) or 65aa (exon 14). The encoded protein contains either all characteristic domains similar to the parent CRIM1 or those lacking the VWFC cysteine rich repeat domain. Thus, it is expected that splicing variants may have similar or altered biological functions as the parent protein that may be involved in the BMP pathway during organogenesis or cancer development. Thus, regulation of this gene product may be useful in the treatment of cancer, specifically the cancers listed above, including prostate cancer.

  In tissues with metabolic function, this gene is expressed at moderate levels in the pituitary gland, fat, adrenal gland, pancreas, thyroid and adult and fetal skeletal muscle, heart and liver. This widespread expression in these tissues indicates that this gene product may play a role in normal neuroendocrine and metabolic functions, and the unregulated expression of this gene is such as obesity and diabetes Suggests that it may cause neuroendocrine or metabolic diseases.

  This gene is also expressed at moderate levels in the CNS including the hippocampus, thalamus, substantia nigra, amygdala, cerebellum and cerebral cortex. Thus, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurological diseases such as Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, stroke and epilepsy.

  Furthermore, this gene is expressed at a much higher level (CT = 27) in the kidney compared to expression in the fetal counterpart (CT = 30). Thus, the expression of this gene can be used to distinguish between fetal and adult sources of this tissue.

Panel 1 Summary: The highest expression of Ag155 is found in the placenta (CT = 20.74). Overall, the expression profile is consistent with the results in panel 1.7. See that panel for a discussion of this gene.

Panel 4.1D Summary: Ag7290 highest expression is seen in IL1-b treated samples from HUVEC (CT = 30.2). Overall, this transcript is expressed at moderate levels in endothelial cells, including samples from HPAEC, HUVEC and embryonic and dermal microvascular ECs. Fibroblasts also express this transcript. Therapies designed with the protein encoded by this transcript may be important in regulating endothelial function, including the major components of inflammation during leukocyte extravasation, asthma, IBD and psoriasis. is there.

I. CG50691-03: CRIM1 homologue The expression of the gene CG50691-03 was evaluated using the primer-probe sets Ag155 and Ag7303 and listed in Tables IA and IB. The results of RTQ-PCR runs are shown in Tables IC, ID, IE and IF.

Table IA Probe name Ag155

Table IB Probe name Ag7303

Table IC CNS neurodegeneration v1.0

Table ID General Screening Panel v1.7

Table IE panel 1

Table IF panel 4.1D

CNS neurodegeneration v1.0 Summary: Ag7303 In this panel, the expression of this gene is confirmed at a low level in the brain of an independent population. This gene appears to be slightly upregulated in the temporal cortex of Alzheimer's disease patients. Thus, therapeutic modulation of the expression or function of this gene reduces neuronal death and may be useful in the treatment of this disease.

General Screening Panel v1.7 Summary: Ag7303 The highest expression of this gene is seen in kidney cancer cell lines (CT = 23.5). This gene is widely expressed in this panel, with high to moderate expression seen in brain cancer, colon cancer, stomach cancer, lung cancer, prostate cancer, breast cancer, ovarian cancer and melanoma cancer cell lines. This expression profile suggests a role for this gene in cell survival and proliferation. This regulation of the gene product may be useful in the treatment of cancer.

  In tissues with metabolic functions, this gene is expressed at high to medium levels in the pituitary gland, fat, adrenal gland, pancreas, thyroid and adult and fetal skeletal muscle, heart and liver. This widespread expression in these tissues indicates that this gene product may play a role in normal neuroendocrine and metabolic functions, and the unregulated expression of this gene is such as obesity and diabetes Suggests that it may cause neuroendocrine or metabolic diseases.

  This gene is also expressed at high to medium levels in the CNS including the hippocampus, thalamus, substantia nigra, amygdala, cerebellum and cerebral cortex. Thus, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurological diseases such as Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, stroke and epilepsy.

  This gene encodes a novel splicing variant of CRIM1. See CG50691-02 for further discussion of this gene.

Panel 1 Summary: The highest expression of Ag155 is found in the placenta (CT = 20.74). Overall, the expression profile is consistent with the results in panel 1.7. See that panel for a discussion of this gene.

Panel 4.1D Summary: Ag7303 The highest expression of this gene is seen in untreated lung microvascular endothelial cells (CT = 30). This transcript is also expressed in clusters of samples from HPAEC, HUVEC, lung and dermal microvascular EC and lung and dermal fibroblasts. Thus, treatments designed with the protein encoded by this transcript may be important in regulating endothelial function, including the major components of inflammation during leukocyte extravasation, asthma, IBD and psoriasis There is sex.

J.CG50691-04: Cysteine-rich repeat-containing protein S52 precursor The expression of the gene CG50691-04 was evaluated using primer-probe sets Ag155 and Ag8164 and listed in Tables JA and JB. The results of RTQ-PCR performed are shown in Tables JC, JD, JE and JF.

Table JA Probe name Ag155

Table JB Probe name Ag8164

Table JC CNS Neurodegeneration v1.0

Table JD Oncology Cell Line Screening Panel v3.2

Table JE Panel 1

Table JF Panel 4.1D

CNS neurodegeneration v1.0 Summary: Ag8164 This profile confirms low level expression of this gene in the brain. Thus, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurological diseases such as Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, stroke and epilepsy.

Oncology cell line screening panel v3.2 Summary: Ag8164 highest expression is seen in colon cancer cell lines (CT = 30). Furthermore, this gene is expressed at moderate to low levels in many samples of this panel, suggesting a role for this gene in cell survival and proliferation.

Panel 1 Summary: The highest expression of Ag155 is found in the placenta (CT = 20.74). Overall, the expression profile is consistent with the results in panel 1.7. See that panel for a discussion of this gene.

Panel 4.1D Summary: Ag8164 The highest expression of this gene is seen in untreated lung microvascular endothelial cells (CT = 31.1). This transcript is also expressed in clusters of samples from HPAEC, HUVEC, lung and dermal microvascular EC and lung and dermal fibroblasts. Thus, treatments designed with the protein encoded by this transcript may be important in regulating endothelial function, including the major components of inflammation during leukocyte extravasation, asthma, IBD and psoriasis There is sex.

K.CG51905-01 and CG51905-03: 28804279.0.7
Expression of the genes CG51905-01 and CG51905-03 was evaluated using primer-probe sets Ag2814 and Ag203 and listed in Tables KA and KB. The results of RTQ-PCR performed are shown in Tables KC, KD and KE. Note that CG51905-03 corresponds to a full-length physical clone of the CG51905-01 gene, which confirms the prediction of the gene sequence.

Table KA Probe name Ag2814

Table KB Probe name Ag203

Table KC Panel 1

Table KD Panel 1.3D

Table KE Panel 4D

Panel 1 Summary: Ag203 The highest expression of this gene is detected in the thymus (CT = 29.9). Thus, this gene or its protein product may play an important role in T cell development. Small molecule therapeutics or antibody therapeutics designed against the protein encoded by this gene can be used to regulate immune function (T-cell development) and immunity after organ transplantation, AIDS treatment or chemotherapy May be important for reconstruction.

  Medium to low expression of this gene is also detected in cancer cells from a small number of ovarian cancer, lung cancer, kidney cancer and brain cancer. Thus, therapeutic modulation of this gene or its protein product may be useful in the treatment of ovarian cancer, lung cancer, kidney cancer and brain cancer.

  Low expression of this gene is also found in lymph nodes, pancreas and colon. See panel 1.3D for further discussion of this gene.

Panel 1.3D Summary: Ag2814 The highest expression of this gene is mainly found in fetal skeletal muscle (CT = 32.6). Interestingly, this gene is expressed at fairly high levels in the fetus when compared to adult skeletal muscle (CT = 40). This finding suggests that the expression of this gene can be used to distinguish between fetal and adult skeletal muscle. Furthermore, the relative overexpression of this gene in fetal skeletal muscle suggests that this protein product may enhance muscle growth or development in the fetus and thus may act in regenerative capacity even in adults. To do. Thus, therapeutic modulation of the GPCR encoded by this gene may be useful in the treatment of muscle related diseases. More specifically, treatment of weak or dystrophic muscle with the protein encoded by this gene may restore muscle mass or function.

  Low expression of this gene is also found in some of the tissues with metabolic or endocrine functions, including placenta, fetal liver, colorectal area and stomach. Thus, therapeutic modulation of this gene or its protein product may be useful in the treatment of endocrine / metabolism related diseases such as obesity and diabetes.

  Furthermore, this gene is expressed at considerably higher levels in the fetus (CT = 34.6) compared to adult liver (CT = 40). This finding suggests that the expression of this gene can be used to distinguish between fetus and adult liver. Furthermore, the relative overexpression of this gene in fetal tissue suggests that this protein product may enhance liver growth or development in the fetus and thus may act in regenerative capacity even in adults. To do. Thus, therapeutic modulation of the protein encoded by this gene may be useful in the treatment of liver related diseases.

Panel 4D Summary: Ag203 / Ag2814 Two experiments with different probe-primer sets are in good agreement. The highest expression of this gene is detected in activated primary Th2 cells and activated Ramos B cells (CT = 32-32.6). Low expression of this gene is also associated with activated primary TH1 and Tr1, activated secondary Th1, Th2 and Tr1 cells, activated memory T cells, activated PBMC cells, activated B lymphocytes, activated peripheral airway epithelium, Found in basophils, mucosal epidermal cells, dermal fibroblasts, thymus and kidney. Thus, modulation of this gene product with functional therapeutics results in functional changes associated with these cell types and also includes asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis and osteoarthritis May result in improvement of symptoms in patients suffering from autoimmunity and inflammatory diseases such as.

L.CG52414-01: Romboid (3541612.0.88)
The expression of gene CG52414-01 was evaluated using primer-probe sets Ag2648, Ag2786, Ag2787 and Ag913 and listed in Tables LA, LB, LC and LD. The results of RTQ-PCR are shown in Tables LE, LF, LG, LH, LI, LJ and LK.

Table LA Probe name Ag2648

Table LB Probe name Ag2786

Table LC Probe name Ag2787

Table LD Probe name Ag913

Table LE AI

Table LF CNS Neurodegeneration v1.0

Table LG General Screening Panel v1.6

Table LH Oncology Cell Line Screening Panel v3.2

Table LI Panel 1.3D

Table LJ Panel 2D

Table LK Panel 4D

AI Comprehensive Panel v1.0 Summary: Ag2787 The highest expression of this gene is detected in matched control samples of ulcerative colitis (CT = 28). Medium to low level expression of this gene is also observed in normal and orthoarthitis / rheumatoid arthritis and adjacent bone, cartilage, synovial and synovial fluid samples, normal lung, COPD lung, emphysema, atopy Detected in samples from sexual asthma, asthma, allergy, Crohn's disease (normal correspondence control and affected area), ulcerative colitis (normal correspondence control and affected area), and psoriasis (normal correspondence control and affected area). Thus, therapeutic modulation of this gene product can ameliorate symptoms / symptoms associated with autoimmunity and inflammatory diseases including psoriasis, allergies, asthma, inflammatory bowel disease, rheumatoid arthritis and osteoarthritis.

CNS neurodegeneration v1.0 Summary: Ag2648 / Ag2786 / Ag2787 The three experiments with different probe-primer sets are in good agreement. In this panel, the expression of this gene is confirmed at a low level in the brain of an independent population. However, in this experiment, no differential expression of this gene was detected between Alzheimer's autopsy brain and non-demented controls. See panel 1.3D for a discussion of the potential role of this gene in the treatment of central nervous system disorders.

General Screening Panel v1.6 Summary: Ag913 The highest expression of this gene is detected in the renal cancer TK-10 cell line (CT = 26.9). Medium to high expression of this gene is found in several cancer cell lines derived from pancreatic cancer, stomach cancer, colon cancer, lung cancer, liver cancer, kidney cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, melanoma and brain cancer It can be seen. In addition, this gene shows extensive expression in this panel, which correlates with the expression seen in panel 1.3D. See panel 1.3D for further discussion of this gene.

  Interestingly, this gene is expressed at significantly higher levels in the fetus (CT = 30-32.5) compared to adult lung and liver (CT = 35-40). This finding suggests that the expression of this gene can be used to distinguish fetuses from adult lungs and liver. Furthermore, the relative overexpression of this gene in fetal tissue may enhance the growth and development of lungs and liver in the fetus in the fetus and thus may act in regenerative capacity even in adults I suggest that. Thus, therapeutic modulation of the protein encoded by this gene may be useful in the treatment of lung and liver related diseases.

Oncology Cell line screening panel v3.2 Summary: Ag2648 The highest expression of this gene is detected in pancreatic cancer SU86.86 cells (CT = 30). Moderate expression of this gene is derived from lung, bone marrow, epidermis, vulva, bone, bladder, pancreas, kidney, B and T cells, leukocytes, lymphoma, cervix, stomach, colon, lung and brain Of cancer cell lines. This expression pattern correlates with that seen in panel 1.3D. See panel 1.3D for further discussion of this gene.

Panel 1.3D Summary: Ag2648 / Ag2786 / Ag2787 The three experiments with different probe-primer sets are in good agreement. The highest expression of this gene is detected in the renal cancer A498 cell line (CT = 28-28.9). Medium level expression of this gene is also seen in clusters of cancer cell lines derived from pancreatic cancer, stomach cancer, colon cancer, lung cancer, liver cancer, kidney cancer, breast cancer, ovarian cancer, prostate cancer, melanoma and brain cancer. Therefore, the expression of this gene could potentially be used as a marker for detecting the presence of these cancers. In addition, the therapeutic regulation of the expression or function of this gene is effective in the treatment of pancreatic cancer, stomach cancer, colon cancer, lung cancer, liver cancer, kidney cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, melanoma and brain cancer It can be.

  In tissues with metabolic or endocrine function, this gene is expressed at moderate to low levels in the pancreas, fat, adrenal gland, thyroid, pituitary, skeletal muscle, heart, liver and gastrointestinal tract. Thus, therapeutic modulation of the activity of this gene may prove useful in the treatment of endocrine / metabolism related diseases such as obesity and diabetes.

  Furthermore, this gene is expressed at moderate to low levels in all areas of the central nervous system examined, including the amygdala, hippocampus, substantia nigra, thalamus, cerebellum, cerebral cortex and spinal cord. Thus, therapeutic modulation of this gene product may be useful in the treatment of central nervous system diseases such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

Panel 2D Summary: Ag2648 / Ag2786 / Ag2787 The three experiments with different probe-primer sets are in good agreement. The highest expression of this gene is detected in bladder and kidney cancer (CT = 26.4-28). High to moderate expression of this gene is also detected in cancer and normal samples from the colon, prostate, liver, lung, kidney, breast, thyroid, ovary and stomach. Interestingly, the expression of this gene is higher in cancer samples, especially gastric cancer, bladder cancer, breast cancer, kidney cancer and colon cancer compared to adjacent normal tissue. Thus, this gene can be used as a diagnostic marker for detecting the presence of these cancers. In addition, this gene encodes a putative protease belonging to the rhomboid family that activates growth factor ligands (Urban et al. Cell 2001 Oct 19; 107 (2): 173-82). Thus, this gene may play a role in tumor cell proliferation and invasion by activating growth factors such as TGFα and EGF that mediate cell growth and invasion. Targeting the protease encoded by this gene with a human monoclonal antibody that results in inhibition of the activity of this protein, preferably its putative protease activity, is preferably a tumor of the colon, stomach, kidney, ovary and bladder It has a therapeutic effect on and leads to a decrease in tumor cell growth, proliferation and invasion.

Panel 4D Summary: Ag2648 / Ag2786 / Ag2787 The three experiments with different probe-primer sets are in good agreement. The highest expression of this gene is detected in LPS activated macrophages and monocytes (CT = 27-28.5). This gene is expressed at high to medium levels in a wide range of cell types important in immune responses in healthy and diseased states. These cells include T cells, B cells, endothelial cells, macrophage / monocytes and peripheral blood mononuclear cell family members, as well as epithelial and fibroblast types from lung and skin, and colon, lung, thymus and A normal tissue corresponding to the kidney may be mentioned. Expression of this gene is promoted in activated endothelial cells, peripheral airway epithelia and fibroblasts. The broad pattern of expression suggests that this gene product may be involved in these and other cell types and tissue homeostatic processes. Thus, modulation of this gene product with functional therapeutics results in functional changes associated with these cell types and also includes asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis and osteoarthritis May result in improvement of symptoms in patients suffering from autoimmunity and inflammatory diseases such as.

Example D: Identification of single nucleotide polymorphisms in NOVX nucleic acid sequences Variant sequences are also included in this application. Variant sequences may include single nucleotide polymorphisms (SNPs). SNPs are sometimes referred to as “cSNPs” to indicate that the nucleotide sequence containing the SNPs occurs as cDNA. SNPs can occur in several ways. For example, a SNP can be by substitution of one nucleotide for another at the polymorphic site. Such substitutions can be either transitions or transitions. SNPs can also result from nucleotide deletions or nucleotide insertions compared to a reference allele. In this case, a polymorphic site is a site where one allele has a gap relative to a particular nucleotide of another allele. SNPs that occur within a gene can result in an alteration of the amino acid encoded by the gene at the position of the SNP. Intragenic SNPs may also be silent as a result of the degeneracy of the genetic code if the codon containing the SNP encodes the same amino acid. SNPs that occur outside of a gene region or in introns within a gene do not change any amino acid sequence of the protein, but may result in altered regulation of expression patterns. Examples include changes in temporal expression, physiological response regulation, cell type expression regulation, expression intensity, and stability of the transcribed message.

  The SeqCalling assembly obtained by the exon binding process was selected and extended using the following criteria. Genomic clones having a region with 98% identity to all or part of the initial sequence or extended sequence were identified by BLASTN search using appropriate sequences to query the human genomic database. Since this identity indicates that these clones contain the genomic locus of these SeqCalling assemblies, the resulting genomic clones were selected for further analysis. These sequences were analyzed for similarity to putative coding regions and known DNA and protein sequences. Programs used for these analyzes include Rail, Genscan, BLAST, HMMER, FASTA, Hybrid, and other appropriate programs.

  Some additional genomic regions may be identified by mapping selected SeqCalling assemblies to those regions. Such SeqCalling sequences may overlap with regions defined by homology or exon prediction. These may also be included because the location of the fragment was in the vicinity of the genomic region identified by similarity or exon prediction included in the original predicted sequence. The sequence identified in this way may be assembled manually and then extended with one or more additional sequences obtained from the CuraGen human SeqCalling database. SeqCalling fragments suitable for inclusion were identified by the CuraTools ™ program SeqExtend or by identification of SeqCalling fragments that map to the appropriate region of the analyzed genomic clone.

  Then, to derive the final sequence disclosed herein, the region defined by the procedure is manually integrated, eg, from a base that was miscalled in the original fragment, or a predicted exon junction, An obvious discrepancy that could arise from the discrepancy between the EST position and the sequence similarity region was corrected. If necessary, the SeqCalling assembly and the process of identifying and analyzing genomic clones were repeated to derive a full-length sequence (Alderborn et al., Determination of Single Nucleotide Polymorphisms by Real-time Pyrophosphate DNA Sequencing. Genome Research. 10 (8) 1249-1265, 2000).

  Although variants are reported individually, all combinations of variants or any combination of selected subsets are included as contemplated NOVX embodiments of the present invention.

Table SNP1: CG172318-01 SNP variant (NOV7a)

Table SNP2: SNP variant of CG170791-01 (NOV5a)

Table SNP3: SNP variant of CG176203-01 (NOV11a)

Table SNP4: SNP variant of CG176213-01 (NOV12a)

Table SNP5: SNP variant of CG50691-02 (NOV13c)

Table SNP6: SNP variant of CG52414-01 (NOV15b)

Table SNP7: SNP variant of CG52552-04 (NOV16b)

Example E: Inhibition of NOV15 CG52414-01 expression using antisense in ovarian tumor-derived cell lines
Five oligonucleotides were designed and synthesized as mixed backbone oligonucleotides containing 5 'and 3' terminal modified phosphorothioate segments and a centrally located 2'-O-methyl RNA oligonucleotide segment. The purity of the oligonucleotide was confirmed by mass spectrometry. The oligonucleotide sequence of CG52414-01 is:
SEQ ID NO: 138: AS1: 5'CCCTCCCAGUCGCCGCTGAC3 '(complementary to the sequence located in the 5'UTR of LIV-1)
SEQ ID NO: 139: AS2: 5′TTCAGGCGGCCGAGCGCAT3 ′ (complementary to the sequence around the ATG start codon)
SEQ ID NO: AS3: 5′AGGTCACGCUGGCACGAGGC 3 ′ (complementary to the 3 ′ sequence of AS2)
SEQ ID NO: 141: AS4: 5′GCCCUUGAUCUCGCAGTCCA3 ′ (complementary to the middle sequence of SLPI ORF)
SEQ ID NO: 142: AS5: 5′AGCGGUCAGUGCAGCACCTG3 ′ (complementary to the sequence flanking the 3 ′ stop codon).

  OVCAR-5 cells were seeded and cultured at 10,000 cells / well in 96-well plates with complete medium 24 hours prior to transfection to reach 50% confluency on the day of transfection. Oligonucleotides were diluted to 100 and 400 nM with Optimen and mixed with Oligofectamine (Invitrogen) according to the manufacturer's instructions. Cells were washed with serum free medium. The mixture of oligo and liposomes was then added to the cells. Serum was added back to the cells after a 4 hour incubation period. The number of viable cells 72 hours after transfection was measured using Promega's CellTiter 96 Aqueous Non-Radioactive Cell Proliferation Assay kit. Briefly, 20 μl of the combined MTS solution was diluted with 100 μl complete medium and added to each well of a 96 well plate. After 1 hour incubation at 37 ° C., the absorbance at 490 nm was recorded using an ELISA plate reader.

  Inhibition of CG52414-01 expression by antisense compounds AS1, AS2, AS3, AS4, AS5, alone or in combination, inhibited OVCAR-5 cell proliferation (FIG. 1).

Example F NOV15 CG52414 related pathway materials and methods
PathCalling ™ Technology The sequence of accession number CG52414-01 was derived by laboratory screening of a cDNA library by a two-hybrid approach. A cDNA fragment covering the full length of the DNA sequence or part or both of the sequence was cloned. In silico prediction was based on sequences available in CuraGen's patent sequence database or publicly available human sequence databases, and provided either full-length DNA sequences or some of them.

  Laboratory screening was performed using the following method. cDNA libraries were obtained from a variety of human samples representing multiple tissue types from different donors, normal and pathological conditions, physiological conditions, and developmental stages. Samples were obtained as whole tissues, primary cells or tissue cultured primary cells or cell lines. Cells and cell lines may be treated with biological factors or chemicals that regulate gene expression, such as growth factors, chemokines or steroids. The cDNA derived from this was then cloned in an orientation into an appropriate two-hybrid vector (Gal4 activation domain (Gal4-AD) fusion). Such a cDNA library, as well as a cDNA library commercially available from Clontech (Palo Alto, Calif.), Was then obtained from the CuraGen patent yeast strain from E. coli (US Pat.No. 6,057,101, which is incorporated herein by reference in its entirety). And disclosed in US Pat. No. 6,083,693).

  Screening multiple Gal4-AD fusion cDNA libraries using Gal4 binding domain (Gal4-BD) fusions from CuraGen's patented human sequence library, so that each of the Gal4-AD fusions is an individual cDNA A yeast hybrid diploid containing was selected. Each sample was amplified using polymerase chain reaction (PCR) using non-specific primers at the cDNA insertion boundary. Such PCR products were sequenced and sequence traces were manually evaluated and edited for correction as needed. The cDNA sequences from all samples were assembled together, sometimes including public human sequences, and a consensus sequence for each assembly was obtained using a bioinformatics program. Each assembly is included in the CuraGen database. A sequence was included as a component of an assembly if the degree of identity with another component was at least 95% over 50 bp. Each assembly corresponds to a gene or part thereof and contains information about variants such as spliced single nucleotide polymorphisms (SNPs), insertions, deletions and other sequence variants.

  Physical clone: The cDNA fragment obtained by the screening procedure covering the entire open reading frame is cloned as recombinant DNA into the pACT2 plasmid (Clontech) used for the construction of the cDNA library. This recombinant plasmid is inserted into the host and selected by yeast hybrid diploids generated during the screening procedure by conjugation of both CuraGen patent yeast strains N106 ′ and YULH (US Pat. Nos. 6,057,101 and 6,083,693). .

  Add protein pair interactions to CuraGen's PathCalling ™ protein interaction database. This database allows for the discovery of new drug targets based on their interactions and / or their presence in pathologically relevant signaling pathways. The protein interactions are then analyzed using bioinformatic tools within GeneScape ™, which provide a means to visualize binary protein interactions, protein complex formation, and complete cellular signaling pathways. The specific interactions that make up a specific complex may also be useful for therapeutic drop intervention by using recombinant protein or antibody therapy, small molecule drugs or gene therapy approaches. Protein interactions identified by digging the PathCalling ™ database can be screened in vitro and in vivo to provide expression, functional, biochemical and phenotypic information. The assay can be used alone but is not limited to the following techniques: RTQ-PCR, recombinant protein transfection, co-immunoprecipitation and mass spectrometry, FRET, affinity chromatography, immunohistochemistry or immune cells Can be used in combination with chemistry, gene CHIP hybridization, antisense (i.e. knockdown, knockup), GeneCalling experiments, and / or biochemical assays (phosphorylation, dephosphorylation, protease, etc.) Good.

  The protein CG52414-01 (romboid-like), tousled-like kinase 1 and the zinc finger ZNK263 protein interact to form a protein complex, which forms to propagate cellular signals, or as a result It is understood that this complex can be constituted, and this has a physiological link with disease pathology.

Other Embodiments Although specific embodiments have been disclosed in detail herein, this has been done by way of example only for purposes of illustration and is intended to limit the scope of the appended claims below. Not what you want. Specifically, the inventors consider that various substitutions, changes, and modifications may be made to the present invention without departing from the spirit and scope of the invention as defined in the claims. Selection of the nucleic acid starting material, the clone of interest, or the type of library would be a common problem for those skilled in the art having knowledge of the embodiments described herein. Other aspects, advantages, and modifications are considered to be within the scope of the following claims. The claims set forth are intended to be representative of the invention disclosed herein. Other, unclaimed inventions are also contemplated. Applicants reserve the right to pursue such inventions in later claims.

OVCAR-5 cell growth inhibition by antisense knockdown of CG52414-01.

Claims (45)

  A polypeptide comprising an isolated mature amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer from 1 to 37.   An isolated polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer from 1 to 37.   An isolated polypeptide comprising an amino acid sequence that is at least 95% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer from 1 to 37.   38. An isolated polypeptide comprising an amino acid sequence comprising one or more conservative substitutions in an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer from 1 to 37.   The polypeptide of claim 1, wherein the polypeptide is naturally occurring.   A composition comprising the polypeptide of claim 1 and a carrier.   A kit comprising the composition of claim 6 in one or more containers.   Use of a therapeutic agent in the manufacture of a medicament for treating a syndrome associated with a human disease, wherein the disease is selected from a pathology associated with the polypeptide of claim 1 and the therapeutic agent is the polypeptide of claim 1. Uses that contain. A method for determining the presence or amount of a polypeptide of claim 1 in a sample comprising:
(A) providing the sample;
(B) introducing the sample into an antibody that immunospecifically binds to the polypeptide, and then (c) determining the presence or amount of antibody bound to the polypeptide, thereby determining the polypeptide in the sample. Determine the presence or quantity,
A method involving that. A method for determining the presence or predisposition of a disease associated with an altered level of expression of a polypeptide of claim 1 in a first mammalian subject comprising:
a) measuring the level of expression of the polypeptide in the sample from the first mammalian subject, and then b) determining the expression of the polypeptide in the sample of step (a) that is free of or predisposed to the disease Comparing the expression of the polypeptide present in a control sample from a second mammalian subject, known not to,
Wherein the change in the level of expression of the polypeptide in the first subject when compared to the control sample is indicative of the presence or predisposition of the disease. A method of identifying an agent that binds to the polypeptide of claim 1 comprising:
(A) introducing the polypeptide into the agent and then (b) determining whether the agent binds to the polypeptide.   12. The method of claim 11, wherein the agent is a cellular receptor or a downstream effector. A method of identifying a potential therapeutic agent in the treatment of a pathology, wherein the pathology is associated with abnormal expression or abnormal physiological interaction of the polypeptide of claim 1;
(A) providing a cell that expresses the polypeptide of claim 1 and has properties or functions attributable to the polypeptide;
(B) contacting the cell with a composition comprising a candidate substance, and then (c) determining whether the substance alters a property or function to be attributed to the polypeptide;
By performing the above steps, if a change observed in the presence of the substance is not observed when cells are contacted with the composition in the absence of the substance, the substance is identified as a potential therapeutic agent. The way that is. A method of screening for modulators of pathological activity or potential or predisposition associated with a polypeptide of claim 1 comprising the following steps:
(A) administering a test compound to a test animal at increased risk of pathology associated with the polypeptide of claim 1, wherein the test animal recombinantly expresses the polypeptide of claim 1; ,
(B) After the administration of the compound of step (a), the activity of the polypeptide in the test animal is measured, and then (c) the activity of the polypeptide in the test animal is determined as a control not administered with the polypeptide. A change in the activity of the polypeptide in the test animal relative to the control animal compared to the activity of the polypeptide in the animal is a modulator of pathological activity or potential or predisposition to which the test compound is associated with the polypeptide of claim 1. A method that points out that there is.   The test animal expresses the test protein transgene, or expresses the transgene under the control of a promoter at an increased level relative to the wild type test animal, and the promoter 15. The method of claim 14, which is not the gene's native gene promoter.   A method of modulating the activity of the polypeptide of claim 1, wherein a cell sample expressing the polypeptide of claim 1 is combined with a sufficient amount of the compound that binds to the polypeptide to modulate the activity of the polypeptide. A method comprising contacting.   A method of treating or preventing a pathology associated with the polypeptide of claim 1, wherein the subject in whom such treatment or prevention is desired is in an amount sufficient to treat or prevent the pathology in the subject. Administering a peptide.   18. The method of claim 17, wherein the subject is a human.   A method of treating a mammalian pathological condition comprising administering to a mammal an amount of a polypeptide sufficient to alleviate the pathological condition, said polypeptide consisting of SEQ ID NO: 2n A polypeptide having an amino acid sequence selected from the group or a biologically active fragment thereof, wherein n is an integer from 1 to 37.   An isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 2n-1, wherein n is an integer from 1 to 37.   21. The nucleic acid molecule of claim 20, wherein the molecule exists in nature.   A nucleic acid molecule which differs from a nucleic acid sequence selected from the group consisting of SEQ ID NO: 2n-1 by a single nucleotide, wherein n is an integer from 1 to 37.   An isolated nucleic acid molecule encoding a mature form of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer from 1 to 37.   An isolated nucleic acid molecule comprising a nucleic acid selected from the group consisting of SEQ ID NO: 2n-1, wherein n is an integer from 1 to 37.   21. The nucleic acid molecule of claim 20, wherein said nucleic acid molecule hybridizes under stringent conditions to a nucleotide sequence selected from the group consisting of SEQ ID NO: 2n-1, or a complement of said nucleotide sequence, wherein n is 1 to 37 A numerator that is an integer.   21. A vector comprising the nucleic acid molecule of claim 20.   27. The method of claim 26, comprising a promoter operably linked to the nucleic acid molecule.   27. A cell comprising the vector of claim 26.   An antibody that immunospecifically binds to the polypeptide of claim 1.   30. The antibody of claim 29 which is a monoclonal antibody.   30. The antibody of claim 29 which is a humanized antibody. A method for determining the presence or amount of a nucleic acid molecule of claim 20 in a sample comprising:
(A) providing the sample; (b) introducing the sample into a probe that binds to the nucleic acid molecule; and (c) determining the presence or amount of the probe that binds to the nucleic acid molecule, A method by which the presence or amount of nucleic acid in a sample is determined.   35. The method of claim 32, wherein the presence or amount of the nucleic acid molecule is used as a marker for cell or tissue type.   34. The method of claim 33, wherein the cell or tissue type is cancerous. A method for determining the presence or predisposition of a disease associated with an altered level of expression of a nucleic acid molecule of claim 20 in a first mammalian subject comprising:
a) measuring the level of expression of the nucleic acid in the sample from the first mammalian subject, and then b) determining the level of expression of the nucleic acid in the sample of step (a) as having no or predisposition to the disease Comparing the level of expression of nucleic acid present in a control sample from a second mammalian subject, known not to, wherein the level of expression of nucleic acid in the first subject when compared to the control sample A method wherein the change is indicative of the presence or predisposition of the disease.   A method for producing the polypeptide of claim 1, comprising culturing the cell under conditions that lead to expression of the polypeptide, wherein the cell is selected from the group consisting of SEQ ID NO: 2n-1. A method comprising a vector comprising an isolated nucleic acid molecule comprising a sequence, wherein n is an integer from 1 to 37.   37. The method of claim 36, wherein the cell is a bacterial cell.   37. The method of claim 36, wherein the cell is an insect cell.   37. The method of claim 36, wherein the cell is a yeast cell.   38. The method of claim 36, wherein the cell is a mammalian cell.   A method for producing the polypeptide of claim 2, comprising culturing the cell under conditions that lead to expression of the polypeptide, wherein the cell comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO: 2n-1. A method comprising a vector containing a isolated nucleic acid molecule, wherein n is an integer from 1 to 37.   42. The method of claim 41, wherein the cell is a bacterial cell.   42. The method of claim 41, wherein the cell is an insect cell.   42. The method of claim 41, wherein the cell is a yeast cell. 42. The method of claim 41, wherein the cell is a mammalian cell.

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