TUMOR NECROSIS FACTOR RELATED RECEPTOR, TR6 POLYNECLEOTIDES

FIELD OF INVENTION

[0002] This invention relates to newly identified polynucleotides, polypeptides encoded by them and to the use of such polynucleotides and polypeptides, and to their production. More particularly, the polynucleotides and polypeptides of the present invention relate to Tumor Necrosis Factor Related family, hereinafter referred to as TR6. The invention also relates to inhibiting or activating the action of such polynucleotides and polypeptides.

BACKGROUND OF THE INVENTION

[0003] Many biological actions, for instance, response to certain stimuli and natural biological processes, are controlled by factors, such as cytokines. Many cytokines act through receptors by engaging the receptor and producing an intracellular response.

[0004] For example, tumor necrosis factors (TNF) alpha and beta are cytokines which act through TNF receptors to regulate numerous biological processes, including protection against infection and induction of shock and inflammatory disease. The TNF molecules belong to the “TNF-ligand” superfamily, and act together with their receptors or counter-ligands, the “TNF-receptor” superfamily. So far, nine members of the TNF ligand superfamily have been identified and ten members of the TNF-receptor superfamily have been characterized.

[0005] Among the ligands there are included TNF-α, lymphotoxin-α (LT-α, also known as TNF-β), LT-β (found in complex heterotrimer LT-α2-β), FasL, CD40L, CD27L, CD30L, 4-1BBL, OX40L and nerve growth factor (NGF)). The superfamily of TNF receptors includes the p55TNF receptor, p75TNF receptor, TNF receptor-related protein, FAS antigen or APO-1, CD40, CD27, CD30, 4-1BB, OX40, low affinity p75 and NGF-receptor (Meager, A., Biologicals, 22:291-295 (1994)).

[0006] Many members of the TNF-ligand superfamily are expressed by activated T-cells, implying that they are necessary for T-cell interactions with other cell types which underlie cell ontogeny and functions. (Meager, A., supra).

[0007] Considerable insight into the essential functions of several members of the TNF receptor family has been gained from the identification and creation of mutants that abolish the expression of these proteins. For example, naturally occurring mutations in the FAS antigen and its ligand cause lymphoproliferative disease (Watanabe-Fukunaga, R., et al., Nature 356:314 (1992)), perhaps reflecting a failure of programmed cell death. Mutations of the CD40 ligand cause an X-linked immunodeficiency state characterized by high levels of immunoglubulin M and low levels of immunoglobulin G in plasma, indicating faulty T-cell-dependent B-cell activation (Allen, R. C. et al., Science 259:990 (1993)). Targeted mutations of the low affinity nerve growth factor receptor cause a disorder characterized by faulty sensory innovation of peripheral structures (Lee, K. F. et al, Cell 69:737 (1992)).

[0008] TNF and LT-α are capable of binding to two TNF receptors (the 55- and 75-kd TNF receptors). A large number of biological effects elicited by TNF and LT-α, acting through their receptors, include hemorrhagic necrosis of transplanted tumors, cytotoxicity, a role in endotoxic shock, inflammation, immunoregulation, proliferation and anti-viral responses, as well as protection against the deleterious effects of ionizing radiation. TNF and LT-α are involved in the pathogenesis of a wide range of diseases, including endotoxic shock, cerebral malaria, tumors, autoimmuine disease, AIDS and graft-host rejection (Beutler, B. and Von Huffel, C., Science 264:667-668 (1994)). Mutations in the p55 Receptor cause increased susceptibility to microbial infection.

[0009] Moreover, an about 80 amino acid domain near the C-terminus of TNFR1 (P55) and Fas was reported as the “death domain,” which is responsible for transducing signals for programmed cell death (Tartaglia et al., Cell 74:845 (1993)).

[0010] The effects of TNF family ligands and TNF family receptors are varied and influence numerous functions, both normal and abnormal, in the biological processes of the mammalian system. There is a clear need, therefore, for identification and characterization of such receptors and ligands that influence biological activity, both normally and in disease states. In particular, there is a need to isolate and characterize novel members of the TNF receptor family.

[0011] This indicates that these receptors have an established, proven history as therapeutic targets. Clearly there is a need for identification and characterization of further receptors which can play a role in preventing, ameliorating or correcting dysfunctions or diseases, including, but not limited to, chronic and acute inflammation, arthritis, septicemia, autoimmune diseases (e.g. inflammatory bowel disease, psoriasis), transplant rejection, graft vs. host disease, infection, stroke, ischemia, acute respiratory disease syndrome, restenosis, brain injury, AIDS, Bone diseases, cancer (e.g. lymphoproliferative disorders), atheroschlerosis, and Alzheimers disease.

SUMMARY OF THE INVENTION

[0012] In one aspect, the invention relates to TR6 polypeptides and recombinant materials and methods for their production. Another aspect of the invention relates to methods for using such TR6 polypeptides and polynucleotides. Such uses include the treatment of chronic and acute inflammation, arthritis, septicemia, autoimmune diseases (e.g. inflammatory bowel disease, psoriasis), transplant rejection, graft vs. host disease, infection, stroke, ischemia, acute respiratory disease syndrome, restenosis, brain injury, AIDS, Bone diseases, cancer (e.g. lymphoproliferative disorders), atheroschlerosis, and Alzheimers disease, among others. In still another aspect, the invention relates to methods to identify agonists and antagonists using the materials provided by the invention, and treating conditions associated with TR6 imbalance with the identified compounds. Yet another aspect of the invention relates to diagnostic assays for detecting diseases associated with inappropriate TR6 activity or levels.

DESCRIPTION OF THE INVENTION

[0013] Definitions

[0014] The following definitions are provided to facilitate understanding of certain terms used frequently herein.

[0015] “TR6” refers, among others, to a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:2, or an allelic variant thereof.

[0016] “Receptor Activity” or “Biological Activity of the Receptor” refers to the metabolic or physiologic function of said TR6 including similar activities or improved activities or these activities with decreased undesirable side-effects. Also included are antigenic and immunogenic activities of said TR6.

[0017] “TR6 gene” refers to a polynucleotide comprising the nucleotide sequence set forth in SEQ ID NO:1 or allelic variants thereof and/or their complements.

[0018] “Antibodies” as used herein includes polyclonal and monoclonal antibodies, chimeric, single chain, and humanized antibodies, as well as Fab fragments, including the products of an Fab or other immunoglobulin expression library.

[0019] “Isolated” means altered “by the hand of man” from the natural state. If an “isolated” composition or substance occurs in nature, it has been changed or removed from its original environment, or both. For example, a polynucleotide or a polypeptide naturally present in a living animal is not “isolated,” but the same polynucleotide or polypeptide separated from the coexisting materials of its natural state is “isolated”, as the term is employed herein.

[0020] “Polynucleotide” generally refers to any polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA. “Polynucleotides” include, without limitation single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions. In addition, “polynucleotide” refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The term polynucleotide also includes DNAs or RNAs containing one or more modified bases and DNAs or RNAs with backbones modified for stability or for other reasons. “Modified” bases include, for example, tritylated bases and unusual bases such as inosine. A variety of modifications has been made to DNA and RNA; thus, “polynucleotide” embraces chemically, enzymatically or metabolically modified forms of polynucleotides as typically found in nature, as well as the chemical forms of DNA and RNA characteristic of viruses and cells. “Polynucleotide” also embraces relatively short polynucleotides, often referred to as oligonucleotides.

[0021] “Polypeptide” refers to any peptide or protein comprising two or more amino acids joined to each other by peptide bonds or modified peptide bonds, i.e., peptide isosteres. “Polypeptide” refers to both short chains, commonly referred to as peptides, oligopeptides or oligomers, and to longer chains, generally referred to as proteins. Polypeptides may contain amino acids other than the 20 gene-encoded amino acids. “Polypeptides” include amino acid sequences modified either by natural processes, such as posttranslational processing, or by chemical modification techniques which are well known in the art. Such modifications are well described in basic texts and in more detailed monographs, as well as in a voluminous research literature. Modifications can occur anywhere in a polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. It will be appreciated that the same type of modification may be present in the same or varying degrees at several sites in a given polypeptide. Also, a given polypeptide may contain many types of modifications. Polypeptides may be branched as a result of ubiquitination, and they may be cyclic, with or without branching. Cyclic, branched and branched cyclic polypeptides may result from posttranslation natural processes or may be made by synthetic methods. Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cystine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. See, for instance, PROTEINS-STRUCTURE AND MOLECULAR PROPERTIES, 2nd Ed., T. E. Creighton, W. H. Freeman and Company, New York, 1993 and Wold, F., Posttranslational Protein Modifications: Perspectives and Prospects, pgs. 1-12 in POSTTRANSLATIONAL COVALENT MODIFICATION OF PROTEINS, B. C. Johnson, Ed., Academic Press, New York, 1983; Seifter et al., “Analysis for protein modifications and nonprotein cofactors”, Meth Enzymol (1990) 182:626-646 and Rattan et al., “Protein Synthesis: Posttranslational Modifications and Aging”, Ann NY Acad Sci (1992) 663:48-62.

[0022] “Variant” as the term is used herein, is a polynucleotide or polypeptide that differs from a reference polynucleotide or polypeptide respectively, but retains essential properties. A typical variant of a polynucleotide differs in nucleotide sequence from another, reference polynucleotide. Changes in the nucleotide sequence of the variant may or may not alter the amino acid sequence of a polypeptide encoded by the reference polynucleotide. Nucleotide changes may result in amino acid substitutions, additions, deletions, fusions and truncations in the polypeptide encoded by the reference sequence, as discussed below. A typical variant of a polypeptide differs in amino acid sequence from another, reference polypeptide. Generally, differences are limited so that the sequences of the reference polypeptide and the variant are closely similar overall and, in many regions, identical. A variant and reference polypeptide may differ in amino acid sequence by one or more substitutions, additions, deletions in any combination. A substituted or inserted amino acid residue may or may not be one encoded by the genetic code. A variant of a polynucleotide or polypeptide may be a naturally occurring such as an allelic variant, or it may be a variant that is not known to occur naturally. Non-naturally occurring variants of polynucleotides and polypeptides may be made by mutagenesis techniques or by direct synthesis.

[0023] “Identity” is a measure of the identity of nucleotide sequences or amino acid sequences. In general, the sequences are aligned so that the highest order match is obtained. “Identity” per se has an art-recognized meaning and can be calculated using published techniques. See, e.g.: (COMPUTATIONAL MOLECULAR BIOLOGY, Lesk, A. M., ed., Oxford University Press, New York, 1988; BIOCOMPUTING: INFORMATICS AND GENOME PROJECTS, Smith, D. W., ed., Academic Press, New York, 1993; COMPUTER ANALYSIS OF SEQUENCE DATA, PART I, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; SEQUENCE ANALYSIS IN MOLECULAR BIOLOGY, von Heinje, G., Academic Press, 1987; and SEQUENCE ANALYSIS PRIMER, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991). While there exist a number of methods to measure identity between two polynucleotide or polypeptide sequences, the term “identity” is well known to skilled artisans (Carillo, H., and Lipton, D., SIAM J Applied Math (1988) 48:1073). Methods commonly employed to determine identity or similarity between two sequences include, but are not limited to, those disclosed in Guide to Huge Computers, Martin J. Bishop, ed., Academic Press, San Diego, 1994, and Carillo, H., and Lipton, D., SIAM J Applied Math (1988) 48:1073. Methods to determine identity and similarity are codified in computer programs. Preferred computer program methods to determine identity and similarity between two sequences include, but are not limited to, GCS program package (Devereux, J., et al., Nucleic Acids Research (1984) 12(1):387), BLASTP, BLASTN, FASTA (Atschul, S. F. et al., J Molec Biol (1990) 215:403).

[0024] As an illustration, by a polynucleotide having a nucleotide sequence having at least, for example, 95% “identity” to a reference nucleotide sequence of SEQ ID NO:1 is intended that the nucleotide sequence of the polynucleotide is identical to the reference sequence except that the polynucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence of SEQ ID NO:1. In other words, to obtain a polynucleotide having a nucleotide sequence at least 95% identical to a reference nucleotide sequence, up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence. These mutations of the reference sequence may occur at the 5 or 3 terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence.

[0025] Similarly, by a polypeptide having an amino acid sequence having at least, for example, 95% “identity” to a reference amino acid sequence of SEQ ID NO:2 is intended that the amino acid sequence of the polypeptide is identical to the reference sequence except that the polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the reference amino acid of SEQ ID NO:2. In other words, to obtain a polypeptide having an amino acid sequence at least 95% identical to a reference amino acid sequence, up to 5% of the amino acid residues in the reference sequence may be deleted or substituted with another amino acid, or a number of amino acids up to 5% of the total amino acid residues in the reference sequence may be inserted into the reference sequence. These alterations of the reference sequence may occur at the amino or carboxy terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.

[0026] Polypeptides of the Invention

[0027] In one aspect, the present invention relates to TR6 polypeptides. The TR6 polypeptides include the polypeptides of SEQ ID NOS:2 and 4; as well as polypeptides comprising the amino acid sequence of SEQ ID NO:2; and polypeptides comprising the amino acid sequence which have at least 80% identity to that of SEQ ID NO:2 over its entire length, and still more preferably at least 90% identity, and even still more preferably at least 95% identity to SEQ ID NO:2. Furthermore, those with at least 97-99% are highly preferred. Also included within TR6 polypeptides are polypeptides having the amino acid sequence which have at least 80% identity to the polypeptide having the amino acid sequence of SEQ ID NO:2 over its entire length, and still more preferably at least 90% identity, and even still more preferably at least 95% identity to SEQ ID NO:2. Furthermore, those with at least 97-99% are highly preferred. Preferably TR6 polypeptides exhibit at least one biological activity of the receptor.

[0028] The TR6 polypeptides may be in the form of the “mature” protein or may be a part of a larger protein such as a fusion protein. It is often advantageous to include an additional amino acid sequence which contains secretory or leader sequences, pro-sequences, sequences which aid in purification such as multiple histidine residues, or an additional sequence for stability during recombinant production.

[0029] Fragments of the TR6 polypeptides are also included in the invention. A fragment is a polypeptide having an amino acid sequence that entirely is the same as part, but not all, of the amino acid sequence of the aforementioned TR6 polypeptides. As with TR6 polypeptides, fragments may be “free-standing,” or comprised within a larger polypeptide of which they form a part or region, most preferably as a single continuous region. Representative examples of polypeptide fragments of the invention, include, for example, fragments from about amino acid number 1-20, 21-40, 41-60, 61-80, 81-100, and 101 to the end of TR6 polypeptide. In this context “about” includes the particularly recited ranges larger or smaller by several, 5, 4, 3, 2 or 1 amino acid at either extreme or at both extremes.

[0030] Preferred fragments include, for example, truncation polypeptides having the amino acid sequence of TR6 polypeptides, except for deletion of a continuous series of residues that includes the amino terminus, or a continuous series of residues that includes the carboxyl terminus or deletion of two continuous series of residues, one including the amino terminus and one including the carboxyl terminus. Also preferred are fragments characterized by structural or functional attributes such as fragments that comprise alpha-helix and alpha-helix forming regions, beta-sheet and beta-sheet-forming regions, turn and turn-forming regions, coil and coil-forming regions, hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate binding region, and high antigenic index regions. Other preferred fragments are biologically active fragments. Biologically active fragments are those that mediate receptor activity, including those with a similar activity or an improved activity, or with a decreased undesirable activity. Also included are those that are antigenic or immunogenic in an animal, especially in a human.

[0031] Preferably, all of these polypeptide fragments retain the biological activity of the receptor, including antigenic activity. Among the most preferred fragment is that having the amino acid sequence of SEQ ID NO:4. Variants of the defined sequence and fragments also form part of the present invention. Preferred variants are those that vary from the referents by conservative amino acid substitutions—i.e., those that substitute a residue with another of like characteristics. Typical such substitutions are among Ala, Val, Leu and Ile; among Ser and Thr; among the acidic residues Asp and Glu; among Asn and Gln; and among the basic residues Lys and Arg; or aromatic residues Phe and Tyr. Particularly preferred are variants in which several, 5-10, 1-5, or 1-2 amino acids are substituted, deleted, or added in any combination.

[0032] The TR6 polypeptides of the invention can be prepared in any suitable manner. Such polypeptides include isolated naturally occurring polypeptides, recombinantly produced polypeptides, synthetically produced polypeptides, or polypeptides produced by a combination of these methods. Means for preparing such polypeptides are well understood in the art.

[0033] Polynucleotides of the Invention

[0034] Another aspect of the invention relates to TR6 polynucleotides. TR6 polynucleotides include isolated polynucleotides which encode the TR6 polypeptides and fragments, and polynucleotides closely related thereto. More specifically, TR6 polynucleotide of the invention include a polynucleotide comprising the nucleotide sequence set forth in SEQ ID NO:1 encoding a TR6 polypeptide of SEQ ID NO:2, and polynucleotides having the particular sequences of SEQ ID NOS: 1 and 3. TR6 polynucleotides further include a polynucleotide comprising a nucleotide sequence that has at least 80% identity to a nucleotide sequence encoding the TR6 polypeptide of SEQ ID NO:2 over its entire length, and a polynucleotide that is at least 80% identical to that having SEQ ID NO:1 over its entire length. In this regard, polynucleotides at least 90% identical are particularly preferred, and those with at least 95% are especially preferred. Furthermore, those with at least 97% are highly preferred and those with at least 98-99% are most highly preferred, with at least 99% being the most preferred. Also included under TR6 polynucleotides are a nucleotide sequence which has sufficient identity to a nucleotide sequence contained in SEQ ID NO:1 to hybridize under conditions useable for amplification or for use as a probe or marker. The invention also provides polynucleotides which are complementary to such TR6 polynucleotides.

[0035] TR6 of the invention is structurally related to other proteins of the Tumor Necrosis Factor Related family, as shown by the results of sequencing the cDNA encoding human TR6. The cDNA sequence of SEQ ID NO:1 contains an open reading frame (nucleotide numbers 94 to 1329) encoding a polypeptide of 411 amino acids of SEQ ID NO:2. The amino acid sequence of Table 1 (SEQ ID NO:2) has about 58% identity (using GAP (From GCG)) in 411 amino acid residues with DR4, the receptor for the ligand TRAIL. (Pan, G., O'Rourke, K., Chinnaiyan, A. M., Gentz, R., Ebner, R., Ni, J. and Dixit, V. M., Science 276, 111-113 (1997)). The nucleotide sequence of Table 1 (SEQ ID NO:1) has about 70% identity (using GAP (from GCG)) in 1335 nucleotide residues with DR4, the receptor for the ligand TRAIL. TR6 contains a death domain (amino acids 290 to 324 in SEQ ID NO:2) which is 64% identical to the death domain of the human Death receptor 4 (DR4) (Pan, G., O'Rourke, K., Chinnaiyan, A. M., Gentz, R., Ebner, R., Ni, J. and Dixit, V. M., Science 276, 111-113 (1997)), 35.7% identical to the death domain of the human Death receptor 3 (DR3) (A. M. Chinnaiyan, et al, Science 274 (5289), 990-992 (1996)), 32.7% identical to the death domain of human TNFR-1, and 19.6% identical to the death domain of CD95 (Fas) (1. Cascino, J. Immunol. 154 (6), 2706-2713 (1995)).

1TABLE 1a1CTTTGCGCCCACAAAATACACCGACGATGCCCGATCTACTTTAAGGGCTG51AAACCCACGGGCCTGAGAGACTATAAGAGCGTTCCCTACCGCCATGGAAC101AACGGGGACAGAACGCCOCGGCCGCTTCGGGGGCCCGGAAAAGGCACGGC151CCAGGACCCAGGGAGGCGCGGGGAGCCAGGCCTGGGCCCCGGGTCCCCAA201GACCCTTGTGCTCGTTGTCGCCGCGGTCCTGCTGTTGGTCTCAGCTGAGT251CTGCTCTGATCACCCAACAAGACCTAGCTCCCCAGCAGAGAGCGGCCCCA301CAACAAAAGAGGTCCAGCCCCTCAGAGGGATTGTGTCCACCTGGACACCA351TATCTCAGAAGACGGTAGAGATTGCATCTCCTGCAAATATgGACAGGACT401ATAGCACTCAaTGGAATGACCTCCTTTTCTGCTTGCGCTGCACCAGGTGT451GATTCAGGTGAAGTGGAGCTAAGTCCCTGCACCAGGACCAGAAACACAGT501GTGTCAGTGCGAAGAAgGCACCTTCCGGGAAGAAGATTCTCCTGAGATGT551GCCGGAAGTGCCGCACAGGGTGTCCCAgAGGGATGGTCAAGGTCGGTGAT601TGTACACCCTGGAGTGACATCGAATGTGTCCACAAAGAATCAGGCATCAT651CATAgGAGTCACAGTTGCAGCCGTAGTCTTGATTGTGGCTGTGTTTGTTT701GCaAgTCTTTACTGTGGAAgAAAGTCCTTCCTTACCTGAAAGGCATCTGC751TCAGGTGGTGGTGGGGACCCTGAGCGTGTGGACAGAAGcTCACAACGACc801TGGGGCTGAGGACAATGTCCTCAATGAGATCGTGAGTATCTTGCAGCCCA851CCCAGGTCCCTGAGCAGGAAATGGAAGTCCAGGAGCCAGCAGAGCCAACA901GGTGTCAACATGTTGTCCCCCGGGGAGTCAGAGCATCTGCTGGAACCGGC951AGAAGCTGAAAGGTCTCAGAGGAGGAGGCTGCTGGTTCCAGCAAATGAAG1001GTGATCCCACTGAGACTCTGAGACAGTGCTTCGATGACTTTGCAGACTTG1051GTGCCCTTTGACTCCTGGGAgCCgCTCATGAGGAAGTTGGGCCTCATGGA1101CAATgAGATaaaGGTGGCTAAAGCTGAGGCAGCGGGCCACAGGGACACCT1151TGTACACGATGCTGATAAAGTGGGTCAACAAAACCGGGCGAGATGCCTCT1201GTCCACACCCTGCTGGATGCCTTGGAGACGCTGGGAGAGAGACTTGCCAA1251GCAGAAGATTGAGGACCACTTGTTGAGCTCTGGAAAGTTCATGTATCTAG1301AAGGTAATGCAGACTCTGCCATGTCCTAAGTGTGATTCTCTTCAGGAAGT1351CAGACCTTCCCTGGTTTACCTTTTTTCTGGAAAAAGCCCAACTGGACTCC1401AGTCAGTAGGAAAGTGCCACAATTGTCACATGACCGGTACTGGAAGAAAC1451TCTCCCATCCAACATCACCCAGTGGATGGAACATCCTGTAACTTTTCACT1501GCACTTGGCATTATTTTTATAAGCTGAATGTGATAATAAGGACACTATGG1551AAATGTCTGGATCATTCCGTTTGTGCGTACTTTGAgATTTGGTTTGGGAT1601GTCATTGTTTTCACAGCACTTTTTTATCCTAATGTAAATGCTTTATTTAT1651TTATTTGGGCTACATTGTAAgATCCATCTACACAGTCGTTGTCCGACTTC1701ACTTGATACTATATGATATGAACCTTTTTTGGGTGGGGGGTGCGGGGCAg1751TTCACTCTGTCTCCCAGGCTGGAGTGCAATGGTGCAATCTTGGCTCACTA1801TAGCCTTGACCTCTCAGGCTCAAGCGATTCTCCCACCTCAGCCATCCAAA1851TAGCTGGGACCACAGGTGTGCACCACCACGCCCGGCTAATTTTTTGTATT1901TTGTCTAgATATAGGGGCTCTCTATGTTGCTCAGGGTGGTCTC9AATTCC1951TGGAcTCAAGCAGTCTGCCCACcTCAGAcTCCCAAAGCGGTGGAATTAGA2001GGCGTGAGCCCCCATGcTTGgCCTTACcTTTcTACTTTTATAATTCTGTA2051TGTTATTATTTTATGAACATGAAGAAACTTTAGTAAATGTACTTGTTTAC2101ATAGTTATGTGAATAGATTAGATAAACATAAAAGGAGGAGACATACAATG2151GGGGAAGAAGAAGAAGTCCCCTGTAAGATGTCACTGTcTGGGTTCCAGCC2201CTCCCTCAGATGTACTTTGGCTTCAATGATTGGCAACTTCTACAGGGGCC2251AGTCTTTTGAACTGGACAACCTTACAAGTATATGAGTATTATTTATAGGT2301AGTTGTTTACATATGAGTCGGGACCAAAGAGAACTGGATCCACGTGAAGT2351CCTGTGTGTGGCTGGTCCCTACCTGGGCAGTCTCATTTGCACCCATAGCC2401CCCATCTATGGACAGGCTGGGACAGAGGCAGATGGGTTAGATCACACATA2451ACAATAGGGTCTATGTCATATCCCAAGTGAACTTGAGCCCTGTTTGGGCT2501CAGGAGATAGAAGACAAAATCTGTCTCCCCACGTCTGCCATGGCATCAAG2551GGGGAAGAGTAGATGGTGCTtGAGAATGGTGTGAAATGGTTGCCATCTCA2601GGAGTAGATGGCCCGGCTCACTTCTGGTTATCtGTCACCCTGAGCCCAtG2651AGCTGCcTTTTAGGGTACAGATTGCCTACTTGAGGACCTTGGCCGCTCTG2701TAAGCATCTGACTCATCTCAGAAATGTCAATTCTTAAACACTGTGGCAAC2751AGGACCTAGAATGGCTGACGCATTAAGGTTTTCTTcTTGTGTCCTGTTCT2801ATTAtTGTTTTAAGACCTCAGTAACCATTTCAGCCTCTTTCCAGCAAACC2851CTTCTCCATAGTATTTCAGTCATGGAAGGATCATTTATGCAGGTAGTCAT2901TCCAGGAGTTTTTGGTCTTTTCTGTCTCAAGGCATTGTGTGTTTTGTTCC2951GGGACTGGTTTGGGTGGGACAAAGTTAGAATTGCCTGAAGATCACACATT3001CAGACTGTtGTGTCTGTGGAGTTTTAGGAGTGGGGGGTGACCTTTcTGGT3051CTTtGcACTTCCATCcTcTCCCAcTTCCATcTGGCATCCCCACGcGTTGT3101CCCcTGCAcTTcTGGAAGGCACAGGGTGCTGCTGCTTCCTGGTCTTTGCC3151TTTGCTGGGCCTTCTGTGCAGGACGCTCAGCCTCAGGGCTCAGAAGGTGC3201CAGTCCGGTCCCAGGTCCCTTGTCCCTTCCACAGAGGCCTTCcTAGAAGA3251TGCATCTAGAGTGTCAGCCTTATCAGTGTTTAAGATTTTTCTTTTATTTT3301TAATTTTTTTGAGACAGAATCTCACTCTCTCGCCCAGGCTGGAGTGCAAC3351GGTACGATCTTGGCTCAGTGCAACCTCCGCCTCCTGGGTTCAAGCGATTC3401TCGTGCCTCAGCCTCCGGAGTAGCTGGGATTGCAGGCACCCGCCACCACG3451CCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGT3501CAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCACNTTGGCCTCCGAA3551AGTGCTGGGatatacaaggcGTGAGCCACCAGCCAGGCCAAGATATTNTT3601NTAAAGNNAGCTTCCGGANGACATGAAATAANGGGGGGTTTTGTTGTTTA3651GTAACATTNGGCTTTGATATATCCCCAGGCCAAATNGCANGNGACACAGG3701ACAGCCATAGTATAGTGTGTCACTCGTGGTTGGTGTCCTTTCATGGTTcT3751GCCCTGTCAAAGGTCCCTATTTGAAATGTGTTATAATACAAACAAGGAAG3801CACATTGTGTACAAAATACTTATGTATTTATGAATCCATGACCAAATTAA3851ATATGAAACCTTATATAAAAAAAAAAAAAAAaA nucleotide sequence of a human TR6. (SEQ ID NO:1).

[0036]

2

TABLE 2b

1
Met
Glu
Gln
Arg
Gly
Gln
Asn
Ala
Pro
Ala
Ala
Ser
Gly
Ala
Arg
Lys
16

17
Arg
His
Gly
Pro
Gly
Pro
Arg
Glu
Ala
Arg
Gly
Ala
Arg
Pro
Gly
Pro
32

33
Arg
Val
Pro
Lys
Thr
Leu
Val
Leu
Val
Val
Ala
Ala
Val
Leu
Leu
Leu
48

49
Val
Ser
Ala
Glu
Ser
Ala
Leu
Ile
Thr
Gln
Gln
Asp
Leu
Ala
Pro
Gln
64

65
Gln
Arg
Ala
Ala
Pro
Gln
Gln
Lys
Arg
Ser
Ser
Pro
Ser
Glu
Gly
Leu
80

81
Cys
Pro
Pro
Gly
His
His
Ile
Ser
Glu
Asp
Gly
Arg
Asp
Cys
Ile
Ser
96

97
Cys
Lys
Tyr
Gly
Gln
Asp
Tyr
Ser
Thr
Gln
Trp
Asn
Asp
Leu
Leu
Phe
112

113
Cys
Leu
Arg
Cys
Thr
Arg
Cys
Asp
Ser
Gly
Glu
Val
Glu
Leu
Ser
Pro
128

129
Cys
Thr
Thr
Thr
Arg
Asn
Thr
Val
Cys
Gln
Cys
Glu
Glu
Gly
Thr
Phe
144

145
Arg
Glu
Glu
Asp
Ser
Pro
Glu
Met
Cys
Arg
Lys
Cys
Arg
Thr
Gly
Cys
160

161
Pro
Arg
Gly
Met
Val
Lys
Val
Gly
Asp
Cys
Thr
Pro
Trp
Ser
Asp
Ile
176

177
Glu
Cys
Val
His
Lys
Glu
Ser
Gly
Ile
Ile
Ile
Gly
Val
Thr
Val
Ala
192

193
Ala
Val
Val
Leu
Ile
Val
Ala
Val
Phe
Val
Cys
Lys
Ser
Leu
Leu
Trp
208

209
Lys
Lys
Val
Leu
Pro
Tyr
Leu
Lys
Gly
Ile
Cys
Ser
Gly
Gly
Gly
Gly
224

225
Asp
Pro
Glu
Arg
Val
Asp
Arg
Ser
Ser
Gln
Arg
Pro
Gly
Ala
Glu
Asp
240

241
Asn
Val
Leu
Asn
Glu
Ile
Val
Ser
Ile
Leu
Gln
Pro
Thr
Gln
Val
Pro
256

257
Glu
Gln
Glu
Met
Glu
Val
Gln
Glu
Pro
Ala
Glu
Pro
Thr
Gly
Val
Asn
272

273
Met
Leu
Ser
Pro
Gly
Glu
Ser
Glu
His
Leu
Leu
Glu
Pro
Ala
Glu
Ala
288

289
Glu
Arg
Ser
Gln
Arg
Arg
Arg
Leu
Leu
Val
Pro
Ala
Asn
Glu
Gly
Asp
304

305
Pro
Thr
Glu
Thr
Leu
Arg
Gln
Cys
Phe
Asp
Asp
Phe
Ala
Asp
Leu
Val
320

321
Pro
Phe
Asp
Ser
Trp
Glu
Pro
Leu
Met
Arg
Lys
Leu
Gly
Leu
Met
Asp
336

337
Asn
Glu
Ile
Lys
Val
Ala
Lys
Ala
Glu
Ala
Ala
Gly
His
Arg
Asp
Thr
352

353
Leu
Tyr
Thr
Met
Leu
Ile
Lys
Trp
Val
Asn
Lys
Thr
Gly
Arg
Asp
Ala
368

369
Ser
Val
His
Thr
Leu
Leu
Asp
Ala
Leu
Glu
Thr
Leu
Gly
Glu
Arg
Leu
384

385
Ala
Lys
Gln
Lys
Ile
Glu
Asp
His
Leu
Leu
Ser
Ser
Gly
Lys
Phe
Met
400

401
Tyr
Leu
Glu
Gly
Asn
Ala
Asp
Ser
Ala
Met
Ser
End

411

b
An amino acid sequence of a human TR6. (SEQ ID NO:2).

[0037] One polynucleotide of the present invention encoding TR6 may be obtained using standard cloning and screening, from a cDNA library derived from mRNA in cells of human of human thymus stromal cells, monocytes, peripheral blood lymphocytes, primary dendritic, and bone marrow cells using the expressed sequence tag (EST) analysis (Adams, M. D., et al. Science (1991)252:1651-1656; Adams, M. D. et al., Nature, (1992)355:632-634; Adams, M. D., et al., Nature (1995) 377 Supp:3-174). Polynucleotides of the invention can also be obtained from natural sources such as genomic DNA libraries or can be synthesized using well known and commercially available techniques.

[0038] The nucleotide sequence encoding TR6 polypeptide of SEQ ID NO:2 may be identical to the polypeptide encoding sequence contained in Table 1 (nucleotide number 94 to 1329 of SEQ ID NO:1), or it may be a sequence, which as a result of the redundancy (degeneracy) of the genetic code, also encodes the polypeptide of SEQ ID NO:2.

[0039] When the polynucleotides of the invention are used for the recombinant production of TR6 polypeptide, the polynucleotide may include the coding sequence for the mature polypeptide or a fragment thereof, by itself; the coding sequence for the mature polypeptide or fragment in reading frame with other coding sequences, such as those encoding a leader or secretory sequence, a pre-, or pro- or prepro-protein sequence, or other fusion peptide portions. For example, a marker sequence which facilitates purification of the fused polypeptide can be encoded. In certain preferred embodiments of this aspect of the invention, the marker sequence is a hexa-histidine peptide, as provided in the pQE vector (Qiagen, Inc.) and described in Gentz et al., Proc Natl Acad Sci USA (1989) 86:821-824, or is an HA tag. The polynucleotide may also contain non-coding 5′ and 3′ sequences, such as transcribed, non-translated sequences, splicing and polyadenylation signals, ribosome binding sites and sequences that stabilize mRNA.

[0040] Further preferred embodiments are polynucleotides encoding TR6 variants comprising the amino acid sequence of TR6 polypeptide of Table 1 (SEQ ID NO:2) in which several, 5-10, 1-5, 1-3, 1-2 or 1 amino acid residues are substituted, deleted or added, in any combination. Among the preferred polynucleotides of the present invention is contained in Table 3 (SEQ ID NO:3) encoding the amino acid sequence of Table 4 (SEQ ID NO:4).

3TABLE 3c1ATGACCTCCTTTTCTGCTTGCGCTGCACCAGGTGTGATTCAGGTGAAGTG51GAGCTAAGTCCCTGCACCACGACCAGAAACACAGTGTGTCAGTGCGAAGA101AgGCACCTTCCGGGAAGAAGATTCTCCTGAGATGTGCCGGAAGTGCCGCA151CAGGGTGTCCCAgAGGGATGGTCAAGGTCGGTGATTGTACACCCTGGA&T201GACATCGAATGTGTCCACAAAGAATCAGGCATCATCATAgGAGTCACAGT251TGCAGCCGTAGTCTTGATTGTGGCTGTGTTTGTTTGCaAgTCTTTACTGT301GGAAgAAAGTCCTTCCTTACCTGAAAGGCATCTGCTCAGGTGGTGGTGGG351GACCCTGAGCGTGTGGACAGAAGCTCACAACGACcTGGGGCTGAGGACAA401TGTCCTCAATGAGATCGTGAGTATCTTGCAGCCCACCCAGGTCCCTGAGC451AGGAAATGGAAGTCCAGGAGCCAGCAGAGCCAACAGGTGTCAACATGTTG501TCCCCCGGGGAGTCAGAGCATCTGCTGGAACCGGCAGAAGCTGAAAGGTC551TCAGAGGAGGAGGCTGCTGGTTCCAGCAAATGAAGGTGATCCCACTGAGA601CTCTGAGACAGTGCTTCGATGACTTTGCAGACTTGGTGCCCTTTGACTCC651TGGGAgCCgCTCATGAGGAAGTTGGGCCTCATGGACAATgAGATaaaGGT701GGCTAAAGCTGAGGCAGCGGGCCACAGGGACACCTTGTACACGATGCTGA751TAAAGTGGGTCAACAAAACCGGGCGAGATGCCTCTGTCCACACCCTGCTG801GATGCCTTGGAGACGCTGGGAGAGAGACTTGCCAAGCAGAAGATTGAGGA851CCACTTGTTGAGCTCTGGAAAGTTCATGTATCTAGAAGGTAATGCAGACT901CTGCCATGTCCTAAGTGTGATTCTCTTCAGGAAGTCAGACCTTCCCTGGT951TTACCTTTTTTCTGGAAAAAGCCCAACTGGACTCCAGTCAGTAGGAAAGT1001GCCACAATTGTCACATGACCGGTACTGGAAGAAACTCTCCCATCCAACAT1051CACCCAGTGGATcA partial nucleotide sequence of a human TR6. (SEQ ID NO:3).

[0041]

4

TABLE 4d

1
DLLFCLRCTR
CDSGEVELSP
CTTTRNTVCQ
CEEGTFREED
SPEMCRKCRT

51
GCPRGMVKVG
DCTPWSDIEC
VHKESGIIIG
VTVAAVVLIV
AVFVCKSLLW

101
KKVLPYLKGI
CSGGGGDPER
VDRSSQRPGA
EDNVLNEIVS
ILQPTQVPEQ

151
EMEVQEPAEP
TGVNMLSPGE
SEHLLEPAEA
ERSQRRRLLV
PANEGDPTET

201
LRQCFDDFAD
LVPFDSWEPL
MRKLGLMDNE
IKVAKAEAAG
HRDTLYTMLI

251
KWVNKTGRDA
SVHTLLDALE
TLGERLAKQK
IEDHLLSSGK
FMYLEGNADS

301
AMS*

d
A partial amino acid sequence of a human TR6. (SEQ ID NO:4).

[0042] The present invention further relates to polynucleotides that hybridize to the herein above-described sequences. In this regard, the present invention especially relates to polynucleotides which hybridize under stringent conditions to the herein above-described polynucleotides. As herein used, the term “stringent conditions” means hybridization will occur only if there is at least 95% and preferably at least 97% identity between the sequences.

[0043] Polynucleotides of the invention, which are identical or sufficiently identical to a nucleotide sequence contained in SEQ ID NO:1 or a fragment thereof, including that of SEQ ID NO:3, may be used as hybridization probes for cDNA and genomic DNA, to isolate full-length cDNAs and genomic clones encoding TR6 and to isolate cDNA and genomic clones of other genes that have a high sequence similarity to the TR6 gene. Such hybridization techniques are known to those of skill in the art. Typically these nucleotide sequences are 80% identical, preferably 90% identical, more preferably 95% identical to that of the referent. The probes generally will comprise at least 15 nucleotides. Preferably, such probes will have at least 30 nucleotides and may have at least 50 nucleotides. Particularly preferred probes will range between 30 and 50 nucleotides.

[0044] In one embodiment, to obtain a polynucleotide encoding TR6 polypeptide comprises the steps of screening an appropriate library under stringent hybridization conditions with a labeled probe having the SEQ ID NO:1 or a fragment thereof, including that of SEQ ID NO:3, and isolating full-length cDNA and genomic clones containing said polynucleotide sequence. Such hybridization techniques are well known to those of skill in the art. Thus in another aspect, TR6 polynucleotides of the present invention further include a nucleotide sequence comprising a nucleotide sequence that hybridize under stringent condition to a nucleotide sequence having SEQ ID NO:1 or a fragment thereof, including that of SEQ ID NO:3. Also included with TR6 polypeptides are polypeptide comprising amino acid sequence encoded by nucleotide sequence obtained by the above hybridization condition. Stringent hybridization conditions are as defined above or alternatively conditions under overnight incubation at 42° C. in a solution comprising: 50% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 microgram/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1×SSC at about 65° C.

[0045] The polynucleotides and polypeptides of the present invention may be employed as research reagents and materials for discovery of treatments and diagnostics to animal and human disease.

[0046] Vectors, Host Cells, Expression

[0047] The present invention also relates to vectors which comprise a polynucleotide or polynucleotides of the present invention, and host cells which are genetically engineered with vectors of the invention and to the production of polypeptides of the invention by recombinant techniques. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention.

[0048] For recombinant production, host cells can be genetically engineered to incorporate expression systems or portions thereof for polynucleotides of the present invention. Introduction of polynucleotides into host cells can be effected by methods described in many standard laboratory manuals, such as Davis et al., BASIC METHODS IN MOLECULAR BIOLOGY (1986) and Sambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989) such as calcium phosphate transfection, DEAE-dextran mediated transfection, transvection, microinjection, cationic lipid-mediated transfection, electroporation, transduction, scrape loading, ballistic introduction or infection.

[0049] Representative examples of appropriate hosts include bacterial cells, such as streptococci, staphylococci, E. coli, Streptomyces and Bacillus subtilis cells; fungal cells, such as yeast cells and Aspergillus cells; insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, HeLa, C127, 3T3, BHK, HEK 293 and Bowes melanoma cells; and plant cells.

[0050] A great variety of expression systems can be used. Such systems include, among others, chromosomal, episomal and virus-derived systems, e.g., vectors derived from bacterial plasmids, from bacteriophage, from transposons, from yeast episomes, from insertion elements, from yeast chromosomal elements, from viruses such as baculoviruses, papova viruses, such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and retroviruses, and vectors derived from combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, such as cosmids and phagemids. The expression systems may contain control regions that regulate as well as engender expression. Generally, any system or vector suitable to maintain, propagate or express polynucleotides to produce a polypeptide in a host may be used. The appropriate nucleotide sequence may be inserted into an expression system by any of a variety of well-known and routine techniques, such as, for example, those set forth in Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL (supra).

[0051] For secretion of the translated protein into the lumen of the endoplasmic reticulum, into the periplasmic space or into the extracellular environment, appropriate secretion signals may be incorporated into the desired polypeptide. These signals may be endogenous to the polypeptide or they may be heterologous signals.

[0052] If the TR6 polypeptide is to be expressed for use in screening assays, generally, it is preferred that the polypeptide be produced at the surface of the cell. In this event, the cells may be harvested prior to use in the screening assay. If TR6 polypeptide is secreted into the medium, the medium can be recovered in order to recover and purify the polypeptide; if produced intracellularly, the cells must first be lysed before the polypeptide is recovered.

[0053] TR6 polypeptides can be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Most preferably, high performance liquid chromatography is employed for purification. Well known techniques for refolding proteins may be employed to regenerate active conformation when the polypeptide is denatured during isolation and or purification.

[0054] Diagnostic Assays

[0055] This invention also relates to the use of TR6 polynucleotides for use as diagnostic reagents. Detection of a mutated form of TR6 gene associated with a dysfunction will provide a diagnostic tool that can add to or define a diagnosis of a disease or susceptibility to a disease which results from under-expression, over-expression or altered expression of TR6. Individuals carrying mutations in the TR6 gene may be detected at the DNA level by a variety of techniques.

[0056] Nucleic acids for diagnosis may be obtained from a subject's cells, such as from blood, urine, saliva, tissue biopsy or autopsy material. The genomic DNA may be used directly for detection or may be amplified enzymatically by using PCR or other amplification techniques prior to analysis. RNA or cDNA may also be used in similar fashion. Deletions and insertions can be detected by a change in size of the amplified product in comparison to the normal genotype. Point mutations can be identified by hybridizing amplified DNA to labeled TR6 nucleotide sequences. Perfectly matched sequences can be distinguished from mismatched duplexes by RNase digestion or by differences in melting temperatures. DNA sequence differences may also be detected by alterations in electrophoretic mobility of DNA fragments in gels, with or without denaturing agents, or by direct DNA sequencing. See, e.g., Myers et al., Science (1985) 230:1242. Sequence changes at specific locations may also be revealed by nuclease protection assays, such as RNase and S1 protection or the chemical cleavage method. See Cotton et al., Proc Natl Acad Sci USA (1985) 85:4397-4401. In another embodiment, an array of oligonucleotides probes comprising TR6 nucleotide sequence or fragments thereof can be constructed to conduct efficient screening of e.g., genetic mutations. Array technology methods are well known and have general applicability and can be used to address a variety of questions in molecular genetics including gene expression, genetic linkage, and genetic variability. (See for example: M. Chee et al., Science, Vol 274, pp 610-613 (1996)).

[0057] The diagnostic assays offer a process for diagnosing or determining a susceptibility to chronic and acute inflammation, arthritis, septicemia, autoimmune diseases (e.g. inflammatory bowel disease, psoriasis), transplant rejection, graft vs. host disease, infection, stroke, ischemia, acute respiratory disease syndrome, restenosis, brain injury, AIDS, Bone diseases, cancer (e.g. lymphoproliferative disorders), atheroschlerosis, and Alzheimers disease, through detection of mutation in the TR6 gene by the methods described.

[0058] In addition, chronic and acute inflammation, arthritis, septicemia, autoimmune diseases (e.g. inflammatory bowel disease, psoriasis), transplant rejection, graft vs. host disease, infection, stroke, ischemia, acute respiratory disease syndrome, restenosis, brain injury, AIDS, Bone diseases, cancer (e.g. lymphoproliferative disorders), atheroschlerosis, and Alzheimers disease, can be diagnosed by methods comprising determining from a sample derived from a subject an abnormally decreased or increased level of TR6 polypeptide or TR6 mRNA. Decreased or increased expression can be measured at the RNA level using any of the methods well known in the art for the quantitation of polynucleotides, such as, for example, PCR, RT-PCR, RNase protection, Northern blotting and other hybridization methods. Assay techniques that can be used to determine levels of a protein, such as an TR6, in a sample derived from a host are well-known to those of skill in the art. Such assay methods include radioimmunoassays, competitive-binding assays, Western Blot analysis and ELISA assays.

[0059] Chromosome Assays

[0060] The nucleotide sequences of the present invention are also valuable for chromosome identification. The sequence is specifically targeted to and can hybridize with a particular location on an individual human chromosome. The mapping of relevant sequences to chromosomes according to the present invention is an important first step in correlating those sequences with gene associated disease. Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be correlated with genetic map data. Such data are found, for example, in V. McKusick, Mendelian Inheritance in Man (available on line through Johns Hopkins University Welch Medical Library). The relationship between genes and diseases that have been mapped to the same chromosomal region are then identified through linkage analysis (coinheritance of physically adjacent genes). The differences in the cDNA or genomic sequence between affected and unaffected individuals can also be determined. If a mutation is observed in some or all of the affected individuals but not in any normal individuals, then the mutation is likely to be the causative agent of the disease.

[0061] The 3′ untranslated region of TR6 matches the 295 bp nucleotide sequence of a mapped EST (Genbank ID: D20151). This EST has been mapped by the Whitehead Institute to chromosome 8, 97.68 cR from the top of the Chromosome 8 linkage group

[0062] Antibodies

[0063] The polypeptides of the invention or their fragments or analogs thereof, or cells expressing them can also be used as immunogens to produce antibodies immunospecific for the TR6 polypeptides. The term “immunospecific” means that the antibodies have substantiall greater affinity for the polypeptides of the invention than their affinity for other related polypeptides in the prior art.

[0064] Antibodies generated against the TR6 polypeptides can be obtained by administering the polypeptides or epitope-bearing fragments, analogs or cells to an animal, preferably a nonhuman, using routine protocols. For preparation of monoclonal antibodies, any technique which provides antibodies produced by continuous cell line cultures can be used. Examples include the hybridoma technique (Kohler, G. and Milstein, C., Nature (1975) 256:495-497), the trioma technique, the human B-cell hybridoma technique (Kozbor et al., Immunology Today (1983) 4:72) and the EBV-hybridoma technique (Cole et al., MONOCLONAL ANTIBODIES AND CANCER THERAPY, pp. 77-96, Alan R. Liss, Inc., 1985).

[0065] Techniques for the production of single chain antibodies (U.S. Pat. No. 4,946,778) can also be adapted to produce single chain antibodies to polypeptides of this invention. Also, transgenic mice, or other organisms including other mammals, may be used to express humanized antibodies.

[0066] The above-described antibodies may be employed to isolate or to identify clones expressing the polypeptide or to purify the polypeptides by affinity chromatography.

[0067] Antibodies against TR6 polypeptides may also be employed to treat chronic and acute inflammation, arthritis, septicemia, autoimmune diseases (e.g. inflammatory bowel disease, psoriasis), transplant rejection, graft vs. host disease, infection, stroke, ischemia, acute respiratory disease syndrome, restenosis, brain injury, AIDS, Bone diseases, cancer (e.g. lymphoproliferative disorders), atheroschlerosis, and Alzheimers disease, among others.

[0068] Vaccines

[0069] Another aspect of the invention relates to a method for inducing an immunological response in a mammal which comprises inoculating the mammal with TR6 polypeptide, or a fragment thereof, adequate to produce antibody and/or T cell immune response to protect said animal from chronic and acute inflammation, arthritis, septicemia, autoimmune diseases (e.g. inflammatory bowel disease, psoriasis), transplant rejection, graft vs. host disease, infection, stroke, ischemia, acute respiratory disease syndrome, restenosis, brain injury, AIDS, Bone diseases, cancer (e.g. lymphoproliferative disorders), atheroschlerosis, and Alzheimers disease, among others. Yet another aspect of the invention relates to a method of inducing immunological response in a mammal which comprises, delivering TR6 polypeptide via a vector directing expression of TR6 polynucleotide in vivo in order to induce such an immunological response to produce antibody to protect said animal from diseases.

[0070] Further aspect of the invention relates to an immunological/vaccine formulation (composition) which, when introduced into a mammalian host, induces an immunological response in that mammal to a TR6 polypeptide wherein the composition comprises a TR6 polypeptide or TR6 gene. The vaccine formulation may further comprise a suitable carrier. Since TR6 polypeptide may be broken down in the stomach, it is preferably administered parenterally (including subcutaneous, intramuscular, intravenous, intradermal etc. injection). Formulations suitable for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation instonic with the blood of the recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents or thickening agents. The formulations may be presented in unit-dose or multi-dose containers, for example, sealed ampoules and vials and may be stored in a freeze-dried condition requiring only the addition of the sterile liquid carrier immediately prior to use. The vaccine formulation may also include adjuvant systems for enhancing the immunogenicity of the formulation, such as oil-in water systems and other systems known in the art. The dosage will depend on the specific activity of the vaccine and can be readily determined by routine experimentation.

[0071] Screening Assays

[0072] We have now discovered that TL2 of SEQ ID NO:5 (otherwise known as TRAIL, Immunity (6):673-682 (1995)) is a ligand of TR6. Thus, the TR6 polypeptide of the present invention, and one of its ligands, TL2 may be employed in a screening process for compounds which bind the receptor, or its ligand, and which activate (agonists) or inhibit activation of (antagonists) the receptor polypeptide of the present invention, or its ligand TL2. Thus, polypeptides of the invention may be used to assess the binding of small molecule substrates and ligands in, for example, cells, cell-free preparations, chemical libraries, and natural product mixtures. These substrates and ligands may be natural substrates and ligands or may be structural or functional mimetics. See Coligan et al., Current Protocols in Immunology 1(2):Chapter 5 (1991).

[0073] TR6 polypeptides are responsible for many biological functions, including many pathologies. Accordingly, it is desirous to find compounds and drugs which stimulate TR6 on the one hand and which can inhibit the function of TR6 or remove TR6 expressing cells on the other hand. Antagonists, or agents which remove TR6 expressing cells, may be employed for a variety of therapeutic and prophylactic purposes for such conditions as chronic and acute inflammation, arthritis, septicemia, autoimmune diseases (e.g. inflammatory bowel disease, psoriasis), transplant rejection, graft vs. host disease, infection, stroke, ischemia, acute respiratory disease syndrome, restenosis, brain injury, AIDS, Bone diseases, cancer (e.g. lymphoproliferative disorders), atheroschlerosis, and Alzheimers disease. Agonists can be employed for therapeutic and prophylactic purposes for such conditions responsive to activation of T cells and other components of the immune system, such as for treatment of cancer and AIDS. However, agonists can also be employed for inappropriate stimulation of T cells and other components of the immune system which leads to down modulation of immune activity with therapeutic or prophylactic application for conditions such, as chronic and acute inflammation, arthritis, septicemia, autoimmune diseases (e.g. inflammatory bowel disease, psoriasis), transplant rejection, graft vs. host disease, infection, stroke, ischemia, acute respiratory disease syndrome, restenosis, brain injury, , Bone diseases,, atheroschlerosis, and Alzheimers disease.

[0074] Candidate compounds may be identified using assays to detect compounds which inhibit binding of TL2 to TR6 in either cell-free or cell based assays. Suitable cell-free assays may be readily determined by one of skill in the art. For example, an ELISA format may be used in which purified TR6, or a purified derivative of TR6, containing the extracellular domain of TR6, is immobilized on a suitable surface, either directly or indirectly (e.g., via an antibody to TR6) and candidate compounds are identified by their ability to block binding of purified TL2 to TR6. The binding of TL2 to TR6 could be detected by using a label directly or indirectly associated with TL2. Suitable detection systems include the streptavidin horseradish peroxidase conjugate, or direct conjugation by a tag, e.g., fluorescein. Conversely, purified TL2 may be immobilized on a suitable surface, and candidate compounds identified by their ability to block binding of purified TR6 to TL2. The binding of TR6 to TL2 could be detected by using a label directly or indirectly associated with TR6. Many other assay formats are possible that use the TR6 protein and its ligands.

[0075] Suitable cell based assays may be readily determined by one of skill in the art. In general, such screening procedures involve producing appropriate cells which express the receptor polypeptide of the present invention on the surface thereof. Such cells include cells from mammals, yeast, Drosophila or E. col. Cells expressing the receptor (or cell membrane containing the expressed receptor) are then contacted with a known ligand, such as TL2, or test compound to observe binding, or stimulation or inhibition of a functional response. The assays may simply test binding of a candidate compound wherein adherence to the cells bearing the receptor is detected by means of a label directly or indirectly associated with the candidate compound or in an assay involving competition with a labeled competitor, such as the ligand TL2. Further, these assays may test whether the candidate compound results in a signal generated by activation of the receptor or its ligand (e.g. TL2) using detection systems appropriate to the cells bearing the receptor or its ligand and fusion proteins thereof at their surfaces. Typical fusion partners include fusing the extracellular domain of the receptor or ligand with the intracellular tyrosine kinase domain of a second receptor. Inhibitors of activation are generally assayed in the presence of a known agonist, such as the ligand TL2, and the effect on activation by the agonist by the presence of the candidate compound is observed. Standard methods for conducting such screening assays are well understood in the art.

[0076] Examples of potential TR6 antagonists include antibodies or, in some cases, oligonucleotides or proteins which are closely related to the ligand of the TR6, e.g., a fragment of the ligand TL2, or small molecules which bind to the receptor, or its ligand, but do not elicit a response, so that the activity of the receptor is prevented. Examples of potential TR6 agonists include antibodies that bind to TR6, its ligand, such as TL2, or derivatives thereof, and small molecules that bind to TR6. These agonists will elicit a response mimicking all or part of the response induced by contacting the native ligand.

[0077] The nucleotide sequence of TL2 (SEQ ID NO:5) (published by Immunex Research and Development Corporation, Seattle, Wash. as TNF-related apoptosis-inducing ligand (TRAIL) TWiley S R, et al. Immunity (6):673-682 (1995)) is as follows.

51CCTCACTGACTATAAAAGAATAGAGAAGGAAGGGCTTCAGTGACCGGCTG51CCTGGCTGACTTACAGCAGTCAGACTCTGACAGGATCATGGCTATGATGG101AGGTCCAGGGGGGACCCAGCCTGGGACAGACCTGCGTGCTGATCGTGATC151TTCACAGTGCTCCTGCAGTCTCTCTGTGTGGCTGTAACTTACGTGTACTT201TACCAACGAGCTGAAGCAGATGCAGGACAAGTACTCCAAAAGTGGCATTG251CTTGTTTCTTAAAAGAAGATGACAGTTATTGGGACCCCAATGACGAAGAG301AGTATGAACAGCCCCTGCTGGCAAGTCAAGTGGCAACTCCGTCAGCTCGT351TAGAAAGATGATTTTGAGAACCTCTGAGGAAACCATTTCTACAGTTCAAG401AAAAGCAACAAAATATTTCTCCCCTAGTGAGAGAAAGAGGTCCTCAGAGA451ATAGCAGCTCACATAACTGGGACCAGAGGAAGAAGCAACACATTGTCTTC501TCCAAACTCCAAGAATGAAAAGGCTCTGGGGCGCAAAATAAACTCCTGGG551AATCATCAAGGAGTGGGGATTCATTCCTGAGCAACTTGCACTTGAGGAAT601GGTGAACTGGTCATCCATGAAAAAGGGTTTTACTACATCTATTCCCAAAC651ATACTTTCGATTTCAGGAGGAAATAAAAGAAAACACAAAGAACGACAAAC701AAATGGTCCAATATATTTACAAATACACAAGTTATCCTGACCCTATATTG751TTGATGAAAAGTGCTAGAAATAGTTGTTGGTCTAAAGATGCAGAATATGG801ACTCTATTCCATCTATCAAGGGGGAATATTTGAGCTTAAGGAAAATGACA851GAATTTTTGTTTCTGTAACAAATGAGCACTTGATAGACATGGACCATGAA901GCCAGTTTTTTCGGGGCCTTTTTAGTTGGCTAACTGACCTGGAAAGAAAA951AGCAATAACCTCAAAGTGACTATTCAGTTTTCAGGATGATACACTATGAA1001GATGTTTCAAAAAATCTGACCAAAACAAACAAACAGAAAACAGAAAACAA1051AAAAACCTCTATGCAATCTGAGTAGAGCAGCCACAACCAAAAAATTCTAC1101AACACACACTGTTCTGAAAGTGACTCACTTATCCCAAGAAAATGAAATTG1151CTGAAAGATCTTTCAGGACTCTACCTCATATCAGTTTGCTAGCAGAAATC1201TAGAAGACTGTCAGCTTCCAAACATTAATGCAATGGTTAACATCTTCTGT1251CTTTATAATCTACTCCTTGTAAAGACTGTAGAAGAAAGCGCAACAATCCA1301TCTCTCAAGTAGTGTATCACAGTAGTAGCCTCCAGGTTTCCTTAAGGGAC1351AACATCCTTAAGTCAAAAGAGAGAAGAGGCACCACTAAAAGATCGCAGTT1401TGCCTGGTGCAGTGGCTCACACCTGTAATCCCAACATTTTGGGAACCCAA1451GGTGGGTAGATCACGAGATCAAGAGATCAAGACCATAGTGACCAACATAG1501TGAAACCCCATCTCTACTGAAAGTGCAAAAATTAGCTGGGTGTGTTGGCA1551CATGCCTGTAGTCCCAGCTACTTGAGAGGCTGAGGCAGGAGAATCGTTTG1601AACCCGGGAGGCAGAGGTTGCAGTGTGGTGAGATCATGCCACTACACTCC1651AGCCTGGCGACAGAGOGAGACTTGGTTTCAAAAAAAAAAAAAAAAAAAAA1701CTTCAGTAAGTACGTGTTATTTTTTTCAATAAAATTCTATTACAGTATGT1751CAAAAAAAAAAAAAAAAAA

[0078] The amino acid sequence of TL2 (SEQ ID NO:6) (published by Immunex Research and Development Corporation, Seattle, Wash. as TNF-related apoptosis-inducing ligand (TRAIL) TWiley S R, et al. Immunity (6):673-682 (1995)) is as follows:

61MetAlaMetMetGluValGlnGlyGlyProSerLeuGlyGlnThrCys1617ValLeuIleValIlePheThrValLeuLeuGlnSerLeuCysValAla3233ValThrTyrValTyrPheThrAsnGluLeuLysGlnMetGlnAspLys4849TyrSerLysSerGlyIleAlaCysPheLeuLysGluAspAspSerTyr6465TrpAspProAsnAspGluGluSerMetAsnSerProCysTrpGlnVai8081LysTrpGlnLeuArgGlnLeuValArgLysMetIleLeuArgThrSer9697GluGluThrIleSerThrValGlnGluLysGlnGlnAsnIleSerPro112113LeuValArgGluArgGlyProGlnArgValAlaAlaHisIleThrGly128129ThrArgGlyArgSerAsnThrLeuSerSerProAsnSerLysAsnGlu144145LysAlaLeuGlyArgLysIleAsnSerTrpGluSerSerArgSerGly160161HisSerPheLeuSerAsnLeuHisLeuArgAsnGlyGluLeuValIle176177HisGluLysGlyPheTyrTyrIleTyrSerGlnThrTyrPheArgPhe192193GlnGluGluIleLysGluAsnThrLysAsnAspLysGlnMetValGln208209TyrIleTyrLysTyrThrSerTyrProAspProIleLeuLeuMetLys224225SerAlaArgAsnSerCysTrpSerLysAspAlaGluTyrGlyLeuTyr240241SerIleTyrGlnGlyGlyIlePheGluLeuLysGluAsnAspArgIle256257PheValSerValThrAsnGluHisLeuIleAspMetAspHisGluAla272273SerPhePheGlyAlaPheLeuValGlyEnd281

[0079] Prophylactic and Therapeutic Methods

[0080] This invention provides methods of treating abnormal conditions such as, chronic and acute inflammation, arthritis, septicemia, autoimmune diseases (e.g. inflammatory bowel disease, psoriasis), transplant rejection, graft vs. host disease, infection, stroke, ischemia, acute respiratory disease syndrome, restenosis, brain injury, AIDS, Bone diseases, cancer (e.g. lymphoproliferative disorders), atheroschlerosis, and Alzheimers disease, related to both an excess of and insufficient amounts of TR6 activity.

[0081] If the activity of TR6 is in excess, several approaches are available. One approach comprises administering to a subject an inhibitor compound (antagonist) as hereinabove described along with a pharmaceutically acceptable carrier in an amount effective to inhibit activation by blocking binding of ligands to the TR6, or by inhibiting a second signal, and thereby alleviating the abnormal condition. In another approach, soluble forms of TR6 polypeptides still capable of binding the ligand in competition with endogenous TR6 may be administered. Typical embodiments of such competitors comprise fragments of the TR6 polypeptide.

[0082] In still another approach, expression of the gene encoding endogenous TR6 can be inhibited using expression blocking techniques. Known such techniques involve the use of antisense sequences, either internally generated or separately administered. See, for example, O'Connor, J Neurochem (1991) 56:560 in Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988). Alternatively, oligonucleotides which form triple helices with the gene can be supplied. See, for example, Lee et al., Nucleic Acids Res (1979) 6:3073; Cooney et al., Science (1988) 241:456; Dervan et al., Science (1991) 251:1360. These oligomers can be administered per se or the relevant oligomers can be expressed in vivo.

[0083] For treating abnormal conditions related to an under-expression of TR6 and its activity, several approaches are also available. One approach comprises administering to a subject a therapeutically effective amount of a compound which activates TR6, i.e., an agonist as described above, in combination with a pharmaceutically acceptable carrier, to thereby alleviate the abnormal condition. Alternatively, gene therapy may be employed to effect the endogenous production of TR6 by the relevant cells in the subject. For example, a polynucleotide of the invention may be engineered for expression in a replication defective retroviral vector, as discussed above. The retroviral expression construct may then be isolated and introduced into a packaging cell transduced with a retroviral plasmid vector containing RNA encoding a polypeptide of the present invention such that the packaging cell now produces infectious viral particles containing the gene of interest. These producer cells may be administered to a subject for engineering cells in vivo and expression of the polypeptide in vivo. For overview of gene therapy, see Chapter 20, Gene Therapy and other Molecular Genetic-based Therapeutic Approaches, (and references cited therein) in Human Molecular Genetics, T Strachan and A P Read, BIOS Scientific Publishers Ltd (1996). Another approach is to administer a therapeutic amount of TR6 polypeptides in combination with a suitable pharmaceutical carrier.

[0084] Formulation and Administration

[0085] Peptides, such as the soluble form of TR6 polypeptides, and agonists and antagonist peptides or small molecules, may be formulated in combination with a suitable pharmaceutical carrier. Such formulations comprise a therapeutically effective amount of the polypeptide or compound, and a pharmaceutically acceptable carrier or excipient. Such carriers include but are not limited to, saline, buffered saline, dextrose, water, glycerol, ethanol, and combinations thereof. Formulation should suit the mode of administration, and is well within the skill of the art. The invention further relates to pharmaceutical packs and kits comprising one or more containers filled with one or more of the ingredients of the aforementioned compositions of the invention.

[0086] Polypeptides and other compounds of the present invention may be employed alone or in conjunction with other compounds, such as therapeutic compounds.

[0087] Preferred forms of systemic administration of the pharmaceutical compositions include injection, typically by intravenous injection. Other injection routes, such as subcutaneous, intramuscular, or intraperitoneal, can be used. Alternative means for systemic administration include transmucosal and transdermal administration using penetrants such as bile salts or fusidic acids or other detergents. In addition, if properly formulated in enteric or encapsulated formulations, oral administration may also be possible. Administration of these compounds may also be topical and/or localized, in the form of salves, pastes, gels and the like.

[0088] The dosage range required depends on the choice of peptide, the route of administration, the nature of the formulation, the nature of the subject's condition, and the judgment of the attending practitioner. Suitable dosages, however, are in the range of 0.1-100 μg/kg of subject. Wide variations in the needed dosage, however, are to be expected in view of the variety of compounds available and the differing efficiencies of various routes of administration. For example, oral administration would be expected to require higher dosages than administration by intravenous injection. Variations in these dosage levels can be adjusted using standard empirical routines for optimization, as is well understood in the art.

[0089] Polypeptides used in treatment can also be generated endogenously in the subject, in treatment modalities often referred to as “gene therapy” as described above. Thus, for example, cells from a subject may be engineered with a polynucleotide, such as a DNA or RNA, to encode a polypeptide ex vivo, and for example, by the use of a retroviral plasmid vector. The cells are then introduced into the subject.

EXAMPLES

[0090] The examples below are carried out using standard techniques, which are well known and routine to those of skill in the art, except where otherwise described in detail. The examples illustrate, but do not limit the invention.

Example 1

[0091] Two ESTs (EST#1760054 and EST#1635744) with sequence similarity to the human TNF receptor were discovered in a commercial EST database. Analysis of the two nucleotide sequences (3,466 bp and 2,641 bp respectively), revealed each was a partial sequence of the complete cDNA sequence, overlapping, with 100% identity, 2,226 bp at the nucleotide level. Together, the two sequences encompassed the complete predicted cDNA sequence of 3,881 bp, and encoded an open reading frame for a novel member of the TNF receptor superfamily and named TR6. The predicted protein is 411 amino acids long with a hydrophobic membrane spanning region indicating that at least one form of TR6 is expressed as a membrane bound protein. Comparison of TR6 protein sequence, with other TNF receptor family proteins indicates that it has two of the cysteine-rich repeats characteristic of the extracellular domains of this family, and an intracellular death domain.

[0092] Northern Blot of TR6

[0093] Various tissues and cell lines were screened for mRNA expression by Northern blot. RNA was prepared from cells and cell lines using Tri-Reagent (Molecular Research Center Inc., Cincinnati, Ohio), run in denaturing agarose gels (Sambrook et al., Molecular Cloning: a laboratory manual, 2nd Ed. Cold Spring Harbor Lab Press, New York (1989)) and transfered to Zeta-probe nylon membrane (Biorad, Hercules, Calif.) via vacuum blotting in 25 mM NaOh for 90 min. After neutralization for 5-10 minutes with 1M tris-HCl, pH 7.5 containing 3M NaCl, the blots were prehybridized with 50% formamide, 8% dextran sulfate, 6XSSPE, 0.1% SDS and 100 mg/ml of sheared and dentured salmon sperm DNA for at least 30 min. At 42° C. cDNA probes were labeled with 32P-CTP by random priming (Statagene, La Jolla, Calif.), briefly denatured with 0.25M NaOH and added to the prehybridization solution. After a further incubation for at least 24 h at 42° C., the blots were washed in high stringency conditions and exposed to X-ray film.

[0094] Very high expression of TR6 RNA was detected in aortic endothelial cells. High expression was also detected in monocytes. Low expression was detected in bone marrow and CD4+ activated PBLs. Very low, but detectable levels of TR6 RNA was expressed in CD19+PBLs, CD8+PBLs (both activated and unstimulated), and unstimulated CD4+PBLs.

[0095] In hematopoietic cell lines, low levels of TR6 RNA was expressed in HL60 (promyelocyte), KG1a (promyeloblast) and KG1 (myeloblast) cell lines. Very low but detectable levels of TR6 RNA was expressed in U937 (monoblast) and THP-1 (monocyte) cell lines.

[0096] The major RNA form is 3.8 kb in size.

	Number	Date	Country
Parent	08853684	May 1997	US
Child	08916625	Aug 1997	US

TUMOR NECROSIS FACTOR RELATED RECEPTOR, TR6 POLYNECLEOTIDES

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