US20040136999A1

US20040136999A1 - Melanoma antigens and methods of use

Info

Publication number: US20040136999A1
Application number: US10/754,820
Authority: US
Inventors: Theresa Strong; Robert Conry; Albert LoBuglio
Original assignee: UAB Research Foundation
Current assignee: UAB Research Foundation
Priority date: 1999-10-18
Filing date: 2004-01-09
Publication date: 2004-07-15
Also published as: WO2001029064A8; WO2001029064A2; US6677444B1; AU2114401A

Abstract

The present invention provides for isolated DNA and protein corresponding to novel melanoma tumor-associated antigens, antibodies directed towards the novel antigens of the present invention as well as methods of using the antigens for inhibiting the growth of a melanoma tumor and methods of screening compounds that inhibit the novel antigens of the present invention.

Description

CROSS-REFERENCE TO RELATED APPLICATION

This non-provisional patent application claims benefit of provisional patent application U.S. Serial No. 60/160,042 filed Oct. 18, 1999, now abandoned. [0001]

FEDERAL FUNDING LEGEND

[0002] This invention was produced in part using funds obtained through grant 5R21CA78489 from the National Institute of Health. Consequently, the federal government has certain rights in this invention.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates generally to the field of cancer. More specifically, the present invention relates to antigens specific for melanoma carcinomas.

2. Description of the Related Art

Several methods have been employed to isolate and clone tumor-associated antigens, and in general, these methods have relied upon the ability of the antigens to stimulate cytolytic T cells (1-4). These methods involve demanding techniques, including extensive manipulation and expansion of cytolytic T cells.

Furthermore, it is becoming increasingly apparent that tumor-bearing individuals also develop serological immune responses to tumor antigens. Antibodies directed towards mutated cellular genes have been described, including those reactive with mutant p53 (5, 6) and ras (7). In addition, humoral immune responses to non-mutated, aberrantly expressed tumor antigens, such as erbB-2 (8) and cathepsin D (9), have been reported.

The presence of humoral immunity to many known tumor-associated antigens suggests its use for identification of novel tumor-associated antigens. The feasibility of this strategy was demonstrated in a study by Pfreundschuh and coworkers (10, 11) who screened tumor-derived cDNA libraries with autologous patient sera and identified two known tumor antigens as well as several novel, putative tumor antigens. This technology, termed SEREX, for serological identification of antigens by recombinant expression cloning, has since been applied by many groups and has led to the substantial expansion of known tumor antigens (12).

Thus, the prior art is deficient in additional novel antigens specific to melanomas. The present invention fulfills this long-standing need and desire in the art.

SUMMARY OF THE INVENTION

Herein, the SEREX approach was used to identify melanoma antigens in patients undergoing active immunotherapy. The primary goal of identifying novel melanoma antigens is to expand the potential targets for immunotherapy. In addition, characterization of these proteins has the potential to impact on diverse areas of melanoma research including detection, diagnosis and staging, characterization of the genetic changes associated with tumorigenesis, and the principles of immune activation and tumor cell rejection.

Novel melanoma tumor-associated antigens may be useful for detection, diagnosis, and staging of melanomas. Novel melanoma tumor-associated antigens may also be useful for monitoring to detect recurrence and metastatic disease and to monitor disease burden (e.g., proteins expressed on the cell surface may provide targets for monitoring, i.e., via detection and imaging of tumors). Novel tumor-associated antigens may additionally be useful as targets for immunotherapy and intervention strategies.

One object of the present invention is to provide melanoma tumor-associated antigens and methods of using the melanoma tumor-associated antigens.

In one embodiment of the present invention, there is provided DNA encoding a melanoma tumor-associated antigen selected from the group consisting of: (a) isolated DNA as shown in SEQ ID Nos. 1-12; (b) isolated DNA which is complementary to isolated DNA of (a) above; and (c) isolated DNA differing from the isolated DNAs of (a) and (b) above in codon sequence due to the degeneracy of the genetic code.

In another embodiment of the present invention, there is provided an isolated and purified melanoma tumor-associated antigen coded for by the DNA disclosed herein.

In another embodiment of the present invention, there is provided a method for detecting mRNA coding for a melanoma tumor-associated antigen in a sample, comprising the steps of: (a) contacting a sample with an oligonucleotide probe having a sequence such as SEQ ID Nos. 1-12; and (b) detecting binding of the probe to the mRNA coding for a melanoma tumor-associated antigen in the sample.

In yet another embodiment of the present invention, there is provided a kit for detecting mRNA coding for a melanoma tumor-associated antigen, comprising: an oligonucleotide probe having a nucleotide sequence shown in SEQ ID Nos. 1-12. The kit may further comprises: a label with which to label the probe; and means for detecting the label.

In still yet another embodiment of the present invention, there is provided a method of detecting a melanoma tumor-associated antigen in a sample, comprising the steps of: (a) contacting a sample with an antibody specific for a melanoma tumor-associated antigen or a fragment thereof encoded by the DNA disclosed herein; and (b) detecting binding of the antibody to the melanoma tumor-associated antigen in the sample.

In another embodiment of the present invention, there is provided a kit for detecting a melanoma tumor-associated antigen, comprising: an antibody specific for a melanoma tumor-associated antigen or a fragment thereof encoded by the DNA disclosed herein. The kit may further comprise means to detect the antibody.

In another embodiment of the present invention, there is provided an antibody specific for a melanoma tumor-associated antigen or a fragment thereof encoded by the DNA disclosed herein.

In still yet another embodiment of the present invention, there is provided a method of screening for compounds that inhibit the activity of a melanoma tumor-associated antigen, comprising the steps of: (a) contacting a sample with a compound, wherein the sample comprises a melanoma tumor-associated antigen encoded by the DNA disclosed herein; and (b) assaying for activity of the melanoma tumor-associated antigen. Generally, a decrease in the melanoma tumor-associated antigen activity in the presence of the compound relative to the melanoma tumor-associated antigen activity in the absence of the compound is indicative of a compound that inhibits the activity of the melanoma tumor-associated antigen.

In another embodiment of the present invention, there is provided a method of inhibiting the growth of a melanoma tumor in an individual, comprising the steps of: (a) treating an individual with a therapeutic compound, wherein the therapeutic compound comprises a thereapeutic moiety and a targeting moiety, wherein the targeting moiety recognizes a melanoma tumor-associated antigen encoded by the DNA disclosed herein; wherein the therapeutic compound inhibits the growth of the melanoma tumor in the individual.

In another embodiment of the present invention, there is provided a cancer vaccine composition, comprising a vector capable of expressing a DNA molecule such as SEQ ID Nos. 1-12, and an appropriate adjuvant.

In another embodiment of the present invention, there is provided a method of vaccinating an individual against cancer, comprising the step of: (a) administering to the individual a vector capable of expressing a DNA molecule such as SEQ ID Nos. 1-12, wherein said expression elicits an immune response specific towards a melonoma-specific antigen, thereby inducing immune-mediated destruction of melanoma cells.

In another embodiment of the present invention, there is provided a method of inhibiting the growth of a melanoma tumor, comprising the steps of: (a) administering to an individual a cancer vaccine comprising a vector expressing a DNA such as SEQ ID Nos. 1-12, wherein administration of said vaccine induces an immune response, thereby inhibiting the growth of a melanoma tumor.

Other and further aspects, features, and advantages of the present invention will be apparent from the following description of the presently preferred embodiments of the invention. These embodiments are given for the purpose of disclosure.

BRIEF DESCRIPTION OF THE DRAWINGS

The appended drawings have been included herein so that the above-recited features, advantages and objects of the invention will become clear and can be understood in detail. These drawings form a part of the specification. It is to be noted, however, that the appended drawings illustrate preferred embodiments of the invention and should not be considered to limit the scope of the invention. [0026]
FIG. 1 shows an example of a colony lift assay with a purified positive clone. Clone 3.1 was plated in a 50:50 mix with a negative control phage. Filters were lifted from the plates, incubated with serum from [0027] patient 1, and reactive plaques were detected with a labeled secondary antibody. Dark circles represent the positive plaques for clone 3.1, while negative plaques are not detected.
FIG. 2 shows the 5′ and 3′ sequences of clone 3.1 (FIG. 2A); clone 3.14 (FIG. 2B); clone 3.3T (FIG. 2C); clone 5.17 (FIG. 2D); clone 5.31 (FIG. 2G); and complete sequence of clone 5.23 (FIG. 2E); clone 5.28 (FIG. 2F).[0028]

DETAILED DESCRIPTION OF THE INVENTION

The primary goal in identifying novel melanoma antigens is to expand the potential targets for immunotherapy. In addition, characterization of tumor antigens may impact diverse areas of melanoma research, including detection, diagnosis and staging, characterization of the genetic changes associated with tumorigenesis, and the principles of immune activation and tumor cell rejection. [0029]
The tumor-associated antigens of the present invention may be useful for detection, diagnosis, and staging of melanoma. Detection and diagnosis of melanoma is currently based on visual identification of melanoma lesions, while staging is based on depth of the lesion at the time of diagnosis. While these visual guidelines have proven useful, the use of additional marker proteins and molecular characterization of melanoma lesions may provide information useful in more accurately defining the clinical course of the disease. [0030]
The tumor-associated antigens of the present invention may also be useful for disease monitoring. Metastatic melanoma can spread to a variety of sites. The identification of the tumor-associated antigens of the present invention may allow recurrence and metastatic disease to be detected and disease burden monitored (e.g., by imaging an antigen-targeted melanoma cell). [0031]
The tumor-associated antigens of the present invention may further be useful as targets in immunotherapy. Several immunotherapy approaches directed towards melanoma cancers are currently under development. The tumor-associated antigens of the present invention will provide additional and specific therapeutic targets for intervention. [0032]
The SEREX approach has been used herein to identify novel melanoma antigens in patients undergoing active immunotherapy. [0033]
The present invention is directed towards a DNA encoding a melanoma tumor-associated antigen selected from the group consisting of: (a) isolated DNA having a sequence shown in SEQ ID Nos. 1-12; (b) isolated DNA which is complementary to the isolated DNA of (a) above; and (c) isolated DNA differing from the isolated DNAs of (a) and (b) above in codon sequence due to the degeneracy of the genetic code. [0034]
The present invention is also directed towards a vector comprising the DNA disclosed herein and regulatory elements necessary for expression of the DNA in a cell, wherein the DNA encodes a melanoma tumor-associated antigen. Also included in the present invention is a vector in which the DNA is positioned in reverse orientation relative to the regulatory elements such that a melanoma tumor-associated antigen antisense mRNA is produced. Further provided are host cells transfected with the above-described vector expressing a melanoma tumor-associated antigen. Representative host cells are bacterial cells, mammalian cells, plant cells and insect cells, more preferably, the bacterial cell is [0035] E. coli.
The present invention is additionally directed towards an isolated and purified melanoma tumor-associated antigen coded for by DNA selected from the group consisting of: (a) isolated DNA selected from the group consisting of SEQ ID Nos. 1-12; (b) isolated DNA which is complementary to the isolated DNA of (a) above; and (c) isolated DNA differing from the isolated DNAs of (a) and (b) above in codon sequence due to the degeneracy of the genetic code. [0036]
The present invention is further directed towards a method for detecting mRNA coding for a melanoma tumor-associated antigen in a sample, comprising the steps of: (a) contacting a sample with an oligonucleotide probe having a nucleotide sequence shown in SEQ ID Nos. 1-12; and (b) detecting binding of the probe to the mRNA coding for a melanoma tumor-associated antigen in the sample. [0037]
The present invention is also directed towards a kit for detecting mRNA coding for a melanoma tumor-associated antigen, comprising: an oligonucleotide probe having a nucleotide sequence such as SEQ ID Nos. 1-12. The above-described kit may further comprise a label with which to label the probe; and means for detecting the label. [0038]
The present invention is still further directed towards a method of detecting a melanoma tumor-associated antigen in a sample, comprising the steps of: (a) contacting a sample with an antibody specific for a melanoma tumor-associated antigen or a fragment thereof encoded by the DNA disclosed herein; and (b) detecting binding of the antibody to the melanoma tumor-associated antigen in the sample. [0039]
The present invention is additionally directed towards a kit for detecting a melanoma tumor-associated antigen, comprising: an antibody specific for a melanoma tumor-associated antigen or a fragment thereof encoded by the DNA disclosed herein. The above-described kit may further comprise means to detect the antibody. [0040]
The present invention is further directed towards an antibody specific for a melanoma tumor-associated antigen or a fragment thereof encoded by the DNA disclosed herein. [0041]
The present invention is also directed towards a method of screening for compounds that inhibit the activity of a melanoma tumor-associated antigen, comprising the steps of: (a) contacting a sample with a compound, wherein the sample comprises a melanoma tumor-associated antigen encoded by the DNA disclosed herein; and (b) assaying for activity of the melanoma tumor-associated antigen. Typically, a decrease in the melanoma tumor-associated antigen activity in the presence of the compound relative to the melanoma tumor-associated antigen activity in the absence of the compound is indicative of a compound that inhibits the activity of the melanoma tumor-associated antigen. [0042]
The antigens reported herein may play a role in signaling growth, activating the cell cycle, down-regulating inhibitors of growth and/or promoting metastatic spread. Alternatively, the antigens reported herein may normally be expressed in melanocytes and may or may not have a direct role in tumorigenesis. [0043]
The present invention is also directed towards a method of inhibiting the growth of a melanoma tumor in an individual, comprising the steps of: (a) treating an individual with a therapeutic compound, wherein the therapeutic compound comprises a thereapeutic moiety and a targeting moiety, wherein the targeting moiety recognizes a melanoma tumor-associated antigen encoded by the DNA disclosed herein; wherein the therapeutic compound inhibits the growth of the melanoma tumor in the individual. Preferred targeting moieties are an antibody or fragment thereof, or a ligand, while preferred therapeutic moieties are a therapeutic gene or protein, a toxin, a radiolabel or a virus. [0044]
The present invention is also directed toward a cancer vaccine composition, comprising a vector capable of expressing a DNA molecule having a sequence shown in SEQ ID Nos. 1-12, and an appropriate adjuvant. [0045]
The present invention is further directed toward a method of vaccinating an individual against cancer, comprising the steps of: (a) administering to the individual a vector capable of expressing a DNA molecule shown in SEQ ID Nos. 1-12, wherein expression elicits an immune response which is specific towards a melonoma-specific antigen, thereby inducing immune-mediated destruction of melanoma cells. Typically, the individual is at risk of getting cancer, suspected of having cancer or has cancer. [0046]
The present invention is also directed toward a method of inhibiting the growth of a melanoma tumor, comprising the steps of: (a) administering a cancer vaccine to an individual comprising a vector expressing a DNA such as SEQ ID Nos. 1-12, wherein administration of the vaccine induces an immune response, thereby inhibiting the growth of a melanoma tumor. [0047]
It will be apparent to one skilled in the art that various substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention. [0048]
In accordance with the present invention, there may be employed conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook, Fritsch & Maniatis, “Molecular Cloning: A Laboratory Manual (2nd Ed.)”, (1989); “DNA Cloning: A Practical Approach,” Volumes I and II (D. N. Glover ed. 1985); “Oligonucleotide Synthesis” (M. J. Gait ed. 1984); “Nucleic Acid Hybridization” [B. D. Hames & S. J. Higgins eds. (1985)]; “Transcription and Translation” [B. D. Hames & S. J. Higgins eds. (1984)]; “Animal Cell Culture” [R. I. Freshney, ed. (1986)]; “Immobilized Cells And Enzymes” [IRL Press, (1986)]; B. Perbal, “A Practical Guide To Molecular Cloning” (1984). Therefore, if appearing herein, the following terms shall have the definitions set out below. [0049]
A “DNA molecule” refers to the polymeric form of deoxyribonucleotides (adenine,. guanine, thymine, or cytosine) in its either single stranded form or a double-stranded helix. This term refers only to the primary and secondary structure of the molecule, and does not limit it to any particular tertiary forms. Thus, this term includes double-stranded DNA found, inter alia, in linear DNA molecules (e.g., restriction fragments), viruses, plasmids, and chromosomes. DNA structure is discussed herein according to the normal convention of showing only the sequence in the 5′ to 3′ direction along the nontranscribed strand of DNA (i.e., the strand having a sequence homologous to the mRNA). [0050]
A “vector” is a replicon, such as plasmid, phage viral genome or cosmid, to which another DNA segment may be attached so as to bring about the replication of the attached segment. A “replicon” is any genetic element (e.g., plasmid, chromosome, virus) that functions as an autonomous unit of DNA replication in vivo; i.e., capable of replication under its own control. An “origin of replication” refers to those DNA sequences that participate in and/or regulate DNA synthesis. An “expression control sequence” or “regulatory elements necessary for expression” are DNA sequence(s) that control and regulate the transcription and translation of another DNA sequence. A coding sequence is “operably linked” and “under the control” of transcriptional and translational control sequences in a cell when RNA polymerase transcribes the coding sequence into mRNA, which is then translated into the protein encoded by the coding sequence. [0051]
In general, expression vectors containing promoter sequences which facilitate the efficient transcription and translation of the inserted DNA fragment are used in connection with the host. The expression vector typically contains an origin of replication, promoter(s), terminator(s), as well as specific genes which are capable of providing phenotypic selection in transformed cells. The transformed hosts can be fermented and cultured according to means known in the art to achieve optimal cell growth. [0052]
A DNA “coding sequence” is a double-stranded DNA sequence which is transcribed and translated into a polypeptide when placed under the control of appropriate regulatory sequences. The boundaries of the coding sequence are determined by a start codon at the 5′ (amino) terminus and a translation stop codon at the 3′ (carboxyl) terminus. A coding sequence can include, but is not limited to, prokaryotic sequences, cDNAs from eukaryotic mRNA, genomic DNA sequences from eukaryotic (e.g., mammalian) DNA, and even synthetic DNA sequences. A coding sequence may alternatively be transcribed in the opposite orientation (i.e., the nontranscribed strand is used as the template) to produce an antisense RNA molecule. An antisense RNA is complementary to an mRNA molecule produced from the transcribed strand. [0053]
A polyadenylation signal and transcription termination sequence will usually be located 3′ to the coding sequence. A “cDNA” is defined as copy-DNA or complementary-DNA, and is a product of a reverse transcription reaction from an mRNA transcript. An “exon” is an expressed sequence transcribed from the gene locus, whereas an “intron” is a non-expressed, usually spliced-out, sequence. [0054]
Transcriptional and translational regulatory sequences, such as promoters, enhancers, polyadenylation signals, terminators, and the like, provide for expression of a coding sequence in a host cell. A “cis-element” is a nucleotide sequence, also sometimes termed a “consensus sequence” or “motif”, that interacts with proteins that regulate expression of a specific gene locus. A “signal sequence” can also be included with the coding sequence. This sequence encodes a signal peptide, N-terminal to the polypeptide, that communicates with the host cell and directs the polypeptide to the appropriate cellular location. Signal sequences can be found associated with a variety of proteins native to prokaryotes and eukaryotes. [0055]
A “promoter sequence” is a DNA regulatory region capable of binding RNA polymerase in a cell and initiating transcription of a downstream (3′ direction) coding sequence. For purposes of defining the present invention, the promoter sequence is bounded at its 3′ terminus by the transcription initiation site and extends upstream (5′ direction) to include the minimum number of bases or elements necessary to initiate transcription at levels detectable above background. Within the promoter sequence will be found a transcription initiation site, as well as consensus sequences responsible for binding of RNA polymerase. Eukaryotic promoters often, but not always, contain “TATA” boxes and “CAT” boxes. Prokaryotic promoters typically contain the −10 and −35 consensus sequences, as well as Shine-Dalgarno sequences for ribosome binding. [0056]
The term “oligonucleotide” is defined as a molecule comprised of two or more deoxyribonucleotides, preferably more than three. Its exact size will depend upon many factors which, in turn, depend upon the ultimate function and use of the oligonucleotide. The term “primer” as used herein refers to an oligonucleotide, whether occurring naturally (as in a purified restriction digest) or produced synthetically, which is capable of acting as a point of initiation when placed under conditions in which synthesis of a primer extension product, which is complementary to a nucleic acid strand, is induced, i.e., in the presence of nucleotides and a polymerizing agent such as a DNA polymerase, and at a suitable temperature and pH. The primer may be either single-stranded or double-stranded and must be sufficiently long to prime the synthesis of the desired extension product in the presence of the inducing agent. The exact length of the primer will depend upon many factors, including temperature, source of primer and the method used. For example, for diagnostic applications, depending upon the complexity of the target sequence, the oligonucleotide primer typically contains 15-25 or more nucleotides, although it may contain fewer nucleotides. [0057]
Primers are selected to be “substantially” complementary to a strand of a particular target DNA sequence. This means that the primers must be sufficiently complementary to hybridize with their respective strands under the appropriate conditions. Therefore, the primer sequence need not reflect the exact sequence of the template. For example, a non-complementary nucleotide fragment may be attached to the 5′ end of the primer, with the remainder of the primer sequence being complementary to the strand. Alternatively, non-complementary bases or longer sequences can be interspersed into the primer, provided that the primer sequence has sufficient complementarity with the sequence to hybridize therewith and thereby initiate synthesis of the extension product. [0058]
As used herein, the terms “restriction endonucleases” and “restriction enzymes” refer to enzymes which cut double-stranded DNA at or near a specific nucleotide sequence. [0059]
“Recombinant DNA technology” refers to techniques for uniting two heterologous DNA molecules, usually as a result of in vitro ligation of DNAs from different organisms. Recombinant DNA molecules are commonly produced by experiments in genetic engineering. Synonymous terms include “gene splicing”, “molecular cloning”, “cloning” and “genetic engineering”. The product of these manipulations results in a “recombinant” or “recombinant molecule”. [0060]
A cell has been “transformed” or “transfected” with exogenous or heterologous DNA when such DNA has been introduced into the cell. The transforming DNA may or may not be integrated (covalently linked) into the genome of the cell. In prokaryotes, yeast, and mammalian cells for example, the transforming DNA may be maintained on an replicative episomal element such as a vector or plasmid. With respect to eukaryotic cells, a stably transformed cell is one in which the transforming DNA has become integrated into a chromosome so that it is inherited by daughter cells through chromosome replication. This stability is demonstrated by the ability of the eukaryotic cell to establish cell lines or clones comprised of a population of daughter cells containing the transforming DNA. A “clone” is a population of cells derived (by mitosis) from a single cell or ancestor. A “cell line” is a clone of a primary cell that is capable of stable growth in vitro for many generations. An organism, such as a plant or animal, that has been transformed with exogenous DNA is termed “transgenic”. [0061]
As used herein, the term “host” is meant to include not only prokaryotes, but also eukaryotes, such as yeast cells, plant cells and animal cells. A recombinant DNA molecule or gene can be used to transform a host using any of the techniques commonly known to those of ordinary skill in the art. Prokaryotic hosts may include [0062] E. coli, S. tymphimurium, Serratia marcescens and Bacillus subtilis. Eukaryotic hosts include yeasts such as Pichia pastoris, mammalian cells and insect cells, and plant cells, such as Arabidopsis thaliana and Tobaccum nicotiana.
As used herein, “fragment,” as applied to a polypeptide, will ordinarily be at least 10 residues, more typically at least 20 residues, and preferably at least 30 (e.g., 50) residues in length, but less than the entire, intact sequence. Fragments can be generated by methods known to those skilled in the art, e.g., by enzymatic digestion/cleavage of naturally occurring or recombinant protein, by recombinant DNA techniques using an expression vector that encodes a defined fragment, or by chemical synthesis. The ability of a candidate fragment to exhibit an enzyme characteristic (e.g., binding to a specific antibody, or exhibiting enzymatic or catalytic activity) can be assessed by methods described herein. Purified fragments or antigenic fragments can be used to generate new regulatory enzymes using multiple functional fragments from different enzymes, as well as to generate antibodies, by employing standard protocols known to those skilled in the art. [0063]
Generally speaking, antibodies for use in these aspects of the present invention will preferably recognize antigens that are preferentially, or specifically, expressed by melanoma tumor cells. Such antibodies will also preferably exhibit properties of high affinity, such as exhibiting a K[0064] _dof <200 nM, and preferably, of <100 nM, and will not show significant reactivity with normal tissues, such as tissues from heart, kidney, brain, liver, bone marrow, colon, breast, prostate, thyroid, gall bladder, lung, adrenals, muscle, nerve fibers, pancreas, skin, or other life-sustaining organ or tissue in the human body. These tissues are important for the purposes of the present invention from the standpoint of low reactivity with the antibody. The term “reactivity,” as used herein, refers to an antibody or antibody fragment that, when applied to the particular tissue under conditions suitable for immunohistochemistry, will elicit staining only in positive cells and not negative cells. Particularly promising antibodies contemplated for use in the present invention are those having high reactivity specific to the melanoma tumor.
A standard Northern blot assay can be used to ascertain the relative amounts of mRNA in a cell or tissue obtained from tissue in accordance with conventional Northern blot hybridization techniques known to those persons of ordinary skill in the art. Alternatively, a standard Southern blot assay may be used to confirm the presence and the copy number of a gene in accordance with conventional Southern blot hybridization techniques known to those of ordinary skill in the art. Both the Northern blot and Southern blot use a hybridization probe, e.g., radiolabelled cDNA, either containing the full-length, single stranded DNA or a fragment of the DNA sequence at least 20 (preferably at least 30, more preferably at least 50, and most preferably at least 100 consecutive nucleotides in length). The oligonucleotide hybridization probe can be labelled by any of the many different methods known to those skilled in this art. Conditions for Northern and Southern hybridizations, i.e., stringency, can be determined for that particular system empirically and/or experimentally, and defining appropriate hybridization conditions is well within the skill of the art. See, e.g., Maniatis et al., supra; DNA Cloning, Vols. I & II, supra; Nucleic Acid Hybridization, supra. [0065]
By “high stringency” is meant DNA hybridization and wash conditions characterized by high temperature and low salt concentration, e.g., wash conditions of 65° C. at a salt concentration of approximately 0.1×SSC, or the functional equivalent thereof. For example, high stringency conditions may include hybridization at about 42° C. in the presence of about 50% formamide; a first wash at about 65° C. with about 2×SSC containing 1% SDS; followed by a second wash at about 65° C. with about 0.1×SSC. [0066]
By “substantially pure DNA” is meant DNA that is not part of a milieu in which the DNA naturally occurs, by virtue of separation (partial or total purification) of some or all of the molecules of that milieu, or by virtue of alteration of sequences that flank the claimed DNA. The term therefore includes, for example, a recombinant DNA which is incorporated into a vector, into an autonomously replicating plasmid or virus, or into the genomic DNA of a prokaryote or eukaryote; or which exists as a separate molecule (e.g., a cDNA or a genomic or cDNA fragment produced by polymerase chain reaction (PCR) or restriction endonuclease digestion) independent of other sequences. It also includes a recombinant DNA which is part of a hybrid gene encoding additional polypeptide sequence, e.g., a fusion protein. Also included is a recombinant DNA which includes a portion of the nucleotides listed in SEQ ID Nos. 1-12 or which encodes an alternative splice variant of SEQ ID Nos. 1-12. [0067]
The labels most commonly employed for these studies are radioactive elements, enzymes, chemicals which fluoresce when exposed to ultraviolet light, and others. A number of fluorescent materials are known and can be utilized as labels. These include, for example, fluorescein, rhodamine, auramine, Texas Red, AMCA blue and Lucifer Yellow. A particular detecting material is anti-rabbit antibody prepared in goats and conjugated with fluorescein through an isothiocyanate. Proteins can also be labeled with a radioactive element or with an enzyme. The radioactive label can be detected by any of the currently available counting procedures. The preferred isotope may be selected from [0068] ³H, ¹⁴C, ³²P, ³⁵S, ³⁶Cl, ⁵¹Cr, ⁵⁷Co, ⁵⁸Co, ⁵⁹Fe, ⁹⁰Y, ¹²⁵I, ¹³¹I, and ¹⁸⁶Re.
Enzyme labels are likewise useful, and can be detected by any of the presently utilized colorimetric, spectrophotometric, fluorospectrophotometric, amperometric or gasometric techniques. The enzyme is conjugated to the selected particle by reaction with bridging molecules such as carbodiimides, diisocyanates, glutaraldehyde and the like. Many enzymes which can be used in these procedures are known and routinely utilized. The preferred enzymes are peroxidase, β-glucuronidase, β-D-glucosidase, β-D-galactosidase, urease, glucose oxidase plus peroxidase and alkaline phosphatase, etc. U.S. Pat. Nos. 3,654,090, 3,850,752, and 4,016,043 are referred to by way of example for their disclosure of alternate labeling material and methods. [0069]
By “degeneracy of the genetic code” is meant that some amino acids are specified by more than one codon. Accordingly, a single protein sequence could be coded for by multiple DNA sequences due to the degeneracy of the genetic code. [0070]
As used herein, “cancer vaccine” refers to a therapeutic vaccine consisting of a vector encoding an antigenic protein or a peptide fragment thereof. Immunization of an individual with such a vaccine is meant to induce an immune response to the protein or peptide, and is directed towards a method of inhibiting growth or promoting destruction of the melanoma tumor in the individual. [0071]
As used herein, “immunotherapy”, as used in the context of cancer therapy, refers to a therapeutic method achieved by manipulation of an individual's immune system to inhibit growth or promote destruction of a tumor. [0072]
As used herein, “antigen” generally refers to a protein or polypeptide which can, in certain formulations or settings, be recognized by the immune system and elicit an immune response. Although carbohydrate moieties may also act as antigens, as used herein, antigens are defined as proteins or polypeptides which may or may not be modified post-translationally. [0073]
As used herein, “tumor-associated antigen” refers to an antigen which is associated with tumor cells. Such proteins need not be expressed exclusively in or on tumor cells. Generally, tumor-associated antigens are fetal proteins aberrantly expressed in tumor cells, mutated cellular proteins which are antigenic due to the mutation, viral proteins expressed in tumor cells, normal cellular proteins highly expressed in the tumor compared to normal tissue, or normal cellular proteins which are mislocalized. [0074]
As used herein, “melanoma antigen” refers to an antigen which is expressed in melanoma cells, however, expressed need not be limited to only melanoma cells. [0075]
As used herein, “polymerase chain reaction” or “PCR” refers to an enzymatic reaction using primers specific for a DNA or cDNA sequence which results in amplification of the specified sequence. [0076]
The following examples are given for the purpose of illustrating various embodiments of the invention and are not meant to limit the present invention in any fashion: [0077]

EXAMPLE 1

Patient Population and Clinical Trial

Nine patients with advanced stage melanoma were enrolled in a Phase Ib clinical trial (NCI Protocol T97-0005) of intratumoral injection of a recombinant canarypox virus encoding the human interleukin-12 (IL-12) gene. The recombinant virus was provided by Pasteur Merieux Connaught through an agreement with the National Cancer Institute. Patients were injected with the recombinant virus encoding IL-12 on [0078] days 1, 4, 8, and 11 and serum was collected on days 0, 18 and 43.

EXAMPLE 2

cDNA Library Construction

A cDNA expression library derived from the melanoma cell lines MEL888 and MEL624 (kindly provided by S. Rosenberg, National Cancer Institute) was synthesized in the 1-ZAP Express vector (Stratagene). Briefly, total RNA was isolated from the cells using the RNA-Stat60 reagent (TelTestB), according to the manufacturer's directions. mRNA was isolated using a 5′→3′ mRNA isolation kit. Five to seven micrograms of mRNA was reverse transcribed using an oligo dT primer with an internal XhoI site. After second strand synthesis, EcoRI adapters were added by ligation. The cDNA was passed through a size exclusion column (Pharmacia) which eliminates cDNAs smaller than 400 bp in size and the cDNA fragments cloned into the λZapExpress vector, packaged according to the manufacturer's instructions, and used to infect [0079] E. coli cells. As a preliminary characterization of the library, inserts from twenty-five randomly selected recombinant plaques were PCR amplified using T3 and T7 primers to determine insert size ranges (0.5 to 3.0 kb). The library contained 6.8×10⁶primary recombinants.

EXAMPLE 3

Immunoscreening

Table 1 shows isolated clones screened for reactivity with all patients from the study. A cDNA expression library was generated from the melanoma cell lines MEL888 and MEL624, and serum from two individuals (patients one and two) was diluted to 1:250, mixed in equal volume and used to screen the library. Recombinant plaques were plated at a density of approximately 25,000 plaques per 150 mm plate, and a total of approximately 200,000 plaques were screened. After a four hour incubation of the plates at 37° C., protein expression was induced by incubation of the plates with nitrocellulose filters saturated with isopropyl β-D-thiogalactoside (IPTG) overnight. Filters were blocked with 1% BSA in Tris-buffered saline (TBS; 20 mM Tris (pH 7.5), 150 mM NaCl) and screened with patient sera. Primary sera is preabsorped with [0080] E. coli phage lysate (Stratagene) and diluted 1:250 for screening. After incubating filters with diluted sera, the filters were washed with TBST (TBS with 0.05% Tween 20 [Sigma]) and incubated with alkaline phosphate-conjugated goat anti-human IgG (H+L) antibodies (Jackson Labs) at a dilution of 1:5,000 for 1 hour at room temperature. After washing, an NBT/BCIP colorimetric assay was used to identify positive clones. Positive plaques were purified to clonality for further study.

Isolated clones (FIG. 1) were then screened for reactivity against sera from nine patients with advanced stage melanoma who were intratumorally injected with a recombinant canarypox virus encoding the human interleukin-12 (IL-12) gene. Patients were injected with the recombinant virus encoding IL-12 on

days

1, 4, 8, and 11 and serum was collected on days 0, 18 and 43. Confirmed immunoreactive plaques were evaluated for reactivity with serum from ten normal individuals. Only those plaques which were not reactive with ten normal sera were processed further.

	TABLE 1


	Patients Day 43	Patient 1

	1	2	3	4	5	6	7	8	9	Day 18	0

3.1	+	−	−	−	−	−	−	−	−	+	−
3.14	+	−	−	−	−	−	−	−	−	+	−
5.16	+	−	−	−	−	−	−	−	−	+	−
5.17	+	+	−	−	−	−	−	−	−	+	−
5.23	+	−	−	−	−	−	−	−	−	+	−
5.28	+	−	−	−	−	−	−	−	−	+	−
5.31	+	−	−	−	−	−	−	−	−	+	−
3.3T	−	−	−	−	+	−	−	−	+	n/a	n/a

Isolated clones were screened for reactivity with all patients from the study. [0082]

EXAMPLE 4

Isotype Analysis

Upon plaque purification, the isotype of the reactive antibodies were determined using human isotype specific antibodies (Southern Biotech), according to the recommended procedure. Isotype analysis demonstrated the presence of predominantly IgG antibodies, consistent with a mature, T[0083] _n-dependent immune response.

EXAMPLE 5

Isolation of Plasmid DNA and DNA Sequence Analysis

Plasmid DNA containing cDNA inserts of interest were isolated from purified plaques by in vivo excision using a helper phage system (ExAssist, Stratagene). For single clone excision, approximately 10[0084] ⁵phage particles were used to infect XL-1-Blue MRF cells in the presence of the helper phage and the cells were incubated for 3 hours at 37° C. To isolate the excised phagemid which are packaged as filamentous phage particles, the culture was heated to 70° C. for 20 min, spun at 1000×g for 15 min and the supernatant collected. These phage were used to infect XLOR cells (Stratagene) and the cells were plated on selective media. These cells do not permit growth of the helper phage and only allow propagation of the phagemid. Single colonies were grown in liquid culture and DNA isolated by standard miniprep procedures.

Partial DNA sequence of each insert was determined using an automated DNA sequencer and vector specific primers. Partial DNA sequences were used in BLAST searches through the National Center for Biotechnology Information database to identify sequences which matched previously described genes or expressed sequence tags (ESTs) (Table 2).

TABLE 2


Melanoma tumor-associated antigen homology

Clone & Identifier	Homology with:	Reference

3.1 (SEQ ID No. 1 & 2)	KIAA0663	13
(=3.8 = 3.16)	(GenBank Accession No.
	AB014563)
3.14 (SEQ ID No. 3 & 4)	Drosophila disc large protein	14
	(GenBank Accession No.
	U13896)
3.3T (SEQ ID No. 5 & 6)	Ubiquilin; DA41	15
	(GenBank Accession No.
	AF176069, HRIHFB2157)
5.17 (SEQ ID No. 7 & 8)	KIAA0555	16
	(GenBank Accession No.
	AB011127)
5.23 (SEQ ID No. 9)	EST: qu76c08.x1;	17
	NCI-CGAP-ES02
	(GenBank Accession No.
	AI354862)
5.28 (SEQ ID No. 10)	Various ESTs;
	Similarity with TR: G581223
5.31 (SEQ ID No. 11 & 12)	RING3*	18
	(GenBank Accession No.
	X96670)

The positive clones, derived from plaques that bound sera from patients intratumorally injected with a recombinant virus expressing IL-12, represent putative antigens specific to melanoma tumors. [0086]

EXAMPLE 6

Uses

Novel tumor-associated antigens may be useful for detection, diagnosis, and staging of melanoma. Detection and diagnosis of melanoma is currently based on visual identification of melanoma lesions, while staging is based on depth of the lesion at the time of diagnosis. While these visual guidelines have proven quite useful, the use of additional marker proteins and the molecular characterization of melanoma lesions may prove more accurate in defining the clinical course of the disease. [0087]
Novel tumor-associated antigens may also be useful for disease monitoring. Metastatic melanoma can spread to a variety of sites. The identification of novel tumor antigens may allow recurrence and metastatic disease to be detected and disease burden monitored. Antigenic proteins expressed on the cell surface may provide targets for detection and imaging of metastatic disease. [0088]
Tumor-associated antigens may additionally be useful as novel targets for immunotherapy. Several immunotherapeutical approaches to melanoma are currently under development, and tumor-associated antigens may provide additional therapeutic targets for intervention. [0089]
The following references were cited herein: [0090]
1. van der Bruggen, P et al. [0091] Science 254:1643-1647, 1991.
2. Kawakami, Y et al. [0092] Proc. Natl. Acad. Sci. USA 91:3515-3519, 1994
3. Toso, J F et al. [0093] Cancer Res. 56:16-20, 1996.
4. Robbins, P F et al. [0094] Cancer Res. 54:3124-3126, 1994.
5. Schlichtholz, B et al. [0095] Cancer Res. 52: 6380-6384, 1992.
6. Lubin, R et al. [0096] Cancer Res. 53:5872-5876, 1993.
7. Stauss, H J [0097] J Natl Cancer Inst. 87:820-821, 1995.
8. Disis, M L et al. [0098] Cancer Res. 54:16-20, 1994.
9. Chinni S et al. [0099] Clin Cancer Res. 3:1557-1564, 1997.
10. Sahin, et al. [0100] Proc. Natl Acad Sci. USA 92:11810-11813, 1995.
11. Tureci, O et al. [0101] Cancer Res 56:4766-4772, 1996.
12. Old, L O & Chen, Y T. [0102] J. Exp. Med. 187:1163-1167, 1998.
13. Ishikawa, K et al. [0103] DNA Res. 5:169-176, 1998.
14. Lu, R A et al. [0104] Proc. Natl. Acad. Sci. USA 91:9818-22, 1994.
15. Hanaoka, E et al. [0105] J. Human Genet. 45:188-191, 2000.
16. Ishikawa, K et al. [0106] DNA Res. 5:31-19, 1998.
17. Natl. Cancer Institute; Cancer Genome Anatomy Project. [0107]
18. Thorpe, K L et al. [0108] Immunogenetics 44:391-6, 1996.
Any patents or publications mentioned in this specification are indicative of the levels of those skilled in the art to which the invention pertains. Further, these patents and publications are incorporated by reference herein to the same extent as if each individual publication was specifically and individually indicated to be incorporated by reference. [0109]
One skilled in the art will appreciate readily that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those objects, ends and advantages inherent herein. The present examples, along with the methods, procedures, treatments, molecules, and specific compounds described herein are presently representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the invention. Changes therein and other uses will occur to those skilled in the art which are encompassed within the spirit of the invention as defined by the scope of the claims. [0110]
1 12 1 586 DNA Unknown mat_peptide 5,8,17,38,45,68,95,465,470,472,476,506,507, 514,540,552,564, 5′ end of clone 3.1 encoding a melanoma tumor-associated antigen; n = unknown 1 atggnatntg tttgaancct attttgaaac cttgccanct cgaantaacc 50 ctcataaggg caacaaanct ggagctcgcg cgcctgcagg tcganactag 100 tggttccaaa gaattcggca cgagcctaat caaggagaag actgctattt 150 ttttttctat tccacatgta ccaaaggcga cagctgccca ttccgtcact 200 gtgaagctgc aataggaaat gaaactgttt gcacattatg gcaagaaggg 250 cgctgttttc gacaggtgtg caggtttcgg cacatggaga ttgataaaaa 300 acgcagtgaa attccttgtt attgggaaaa tcagccaaca ggatgtcaaa 350 aattaaactg cgctttccat cacaatagag gaccgatatg ttgatggcct 400 tttcctacct ccgagcaaaa ctgtgttgcc cactgtgcct gagtcaccag 450 aagaggaaag tgaangctan cncaantttc agttcaagct ggaacaaaat 500 tggctnntcc aatnccaaat cccttcccct taaacctggn ggaaaccgtt 550 antgaaaagt tagnaaattt tcccgaaaat tgttct 586 2 615 DNA Unknown 3′ end of clone 3.1 encoding a melanoma tumor-associated antigen 2 cgcctggaaa agggtaagta acccagggac ggagccttgg gtaaagtgtg 50 tcatccccca attggcccaa cgtaagcagt gagatgccgc tgtgtcattg 100 ccgctgtgaa cctcagtcca caggtcctac aggaccccca gccaaaaagg 150 cagctgtggc tgttgtcccg cttgtcttga ggcaaatcag tcctgtgcct 200 gaagcagaaa atcctagagc agtcttgtgc tgcctccaac ccagtccttt 250 cagattcctc acccccagag gtgtctggcc ctcctcatcc caatgagcat 300 gaaaactgcc gactcagctt tgcctcaaca ggaaagcccc cactcttgtg 350 gaggatgatt ttagaaacta atatgggaga tttcaggagg caaattggaa 400 gctgagattg acctggatct gggaaaatga aatgaccttt gcttgagcta 450 tcaaaatgat tatagctgaa ggtggtagtg aggacccttt aaaaaaaaaa 500 tcgccaaaaa ctggcttagt ttcattattg aactttacct gagatgatct 550 tttttagtta gaatttgccc caatcaaaga accttgaatt atccaaaaaa 600 aaaaaaaaaa aaaaa 615 3 574 DNA Unknown mat_peptide 8,9,21,29,52,473,515,545,573 5′ end of clone 3.14 encoding a melanoma tumor-associated antigen; n = unknown 3 ggggtatnnt ttgaaccttc nttctccant taaccctcat aagggaacaa 50 anctggactc gcgcgcctgc aggtcgacac tagtggatcc aaagaattcg 100 gcacgagttt atcttagccg gaggacctgc tgatctaagt ggagagctca 150 gaaaaggaga tcgtattata tcggtaaaca gtgttgacct cagagctgct 200 agtcatgagc aggcagcagc tgcattgaaa aatgctggcc aggctgtcac 250 aattgttgca caatatcgac ctgaagaata cagtcgtttt gaagctaaaa 300 tacatgattt acgggagcag atgatgaata gtagtattag ttcagggtca 350 ggttttcaaa tggttcctga ggttttttgt tgttgtccgt gttgttactg 400 ttgttcttgt catcaggttt gattttggtc cttgcccttt ccttctagtt 450 ctccttttat taataggaaa ggnaggcaaa agcccccatt tatgtggggg 500 ggttttcccc ttaanacagc ttttcattcc acctggttct gcacntaaaa 550 ttggccccaa aatcttcatt ggng 574 4 528 DNA Unknown 3′ end of clone 3.14 encoding a melanoma tumor-associated antigen 4 accgtgttga actaaaactt ttcgggccca tttttaaatg gggttttcag 50 ggcccgtttt caaaaggttc ctaaggtttt tgttgtgccc gggttgtaac 100 tggttgttct gtcatcaggt ttgattttgg gcccttgccc tttccttcta 150 gttctccttt tattaatagg aaggcaggca aaagccccat ttatgtggtg 200 ttttcccctc agacagcttt catccactgc tctgcactag aattgcacaa 250 atcttcatgg tgagcaattt taagaaatgt tagtaaaagg tagaaattat 300 ttcacaaatc agtttctctg gtccttcata ttaataataa tatttggctt 350 cccattgctc tttggagttg tttattaaat atgtgttttt gacaacctcc 400 tcattagttt cttaaatgag tactggtttg taaagaatta tcaacattat 450 ccattccatt tatgaagaag aggagaacag ctaataaact gtattgaaat 500 ccaaaaaaaa aaaaaaaaaa aaaaaaaa 528 5 547 DNA Unknown mat_peptide 4,5,26,183,216,223,231,250,252,271,315,342,351, 356,357,358,360,367,370,372,374,386,394,395,402, 409,416,420,421,435,444,461,467,482,493,495,499, 500,517,527 5′ end of clone 3.3T encoding a melanoma tumor-associated antigen; n = unknown 5 aggnnggagc actcagctcg aaattnaccc tcactaaagg gaacaaaagc 50 tggagctcgc gcgcctgcag gtcgacacta gtggatccaa agaattcggc 100 accaggaaat ccagaaatta gtcatatgtt gaataatcca gatataatga 150 gacaaacgtt ggaacttgcc aggaatccag cantgatgca ggagatgatg 200 aggaaccagg accgancttt gancaaccta naaagcatcc cagggggatn 250 tnatgcttta aggcgcatgt ncacagatat tcatgaacca atgctgagtg 300 ctgcacaaaa acaanttggg gggaaaccat ttgcttcctt gngaacaaat 350 natccnnngn ggaaggnagn cnanccttcc cgtccngaaa tttnnattcc 400 cntcccatnc cttggncccn naactcccaa atttntaaat ttcnacggcc 450 tgcacctggg ngggcantcg gttcctgcca gnggcctttt ggnanatann 500 ctgccaaatt ggcccgngag agaactnttt tttcaacaca caaaatg 547 6 413 DNA Unknown 3′ end of clone 3.3T encoding a melanoma tumor-associated antigen 6 ttttccgtga gaaacattca gttaaacaca gggggggatc accagctaat 50 aaagggtatg ggtcccctca tacagcattt tgtttttaaa aaatggattt 100 atttttgtaa cgggtttaaa ctttaaaaac ccgctttatt tcatttgctt 150 tgggaattgg cgttaaacca accccaatta gccttttaag ggggctaaag 200 gggggtttcg gaattttttt ttcggaggga ataagggaag gagatcttgc 250 attaatggat ttttaaaacc cccctttaaa gtgggggacc agattttgtc 300 ctgcatctgt ccagttattt gctttttaaa catagcctat ggtagtaatt 350 tatgtagaat aaaagcatta aaaagaagca aatcatttgc tctctaaaaa 400 aaaaaaaaaa aaa 413 7 616 DNA Unknown mat_peptide 4,5,11,453,481,498,501,531,552,568,569,571,572, 586,588,591,595,602,614 5′ end of clone 5.17 encoding a melanoma tumor-associated antigen; n = unknown 7 aggnntaggt naccctacta aagggaacaa aagctggagc tcgcgcgcct 50 gcaggtcgac actagtggat ccaaagaatt cggcacgagc cgactcggtc 100 acaaggaaaa tggattcagt ttgcatctct ccctccttta aacagcttct 150 ccgggtctca gcatggtatc aaagcttgaa agagagaaga ctcaagaagc 200 gaagaggatt cgtgagctgg agcagcgcaa gcacacggtg ctggtgacag 250 aactcaaagc caagctccat gaggagaaga tgaaggagct gcaggctgtg 300 agggagaacc ttatcaagca gcacgagcag gaaatgtcaa ggacggtgaa 350 ggtacgtgat ggaagaagat ccagaggctc aagtctgctc tctgtgctct 400 ccgcgacggc agcagtgacc aaagtaagga cagcgctacc attgaggccc 450 ggnaaggagg cccgaaacct gtttgaccca nacgccttaa gctttacngg 500 naaattgcgg acctgaaacg gccaaaagcc ngggggccaa aggttttgcc 550 antttgatcc caaggccnna nnttttatag tgggcntnga nggcnttatc 600 cncaaacctt taanat 616 8 510 DNA Unknown 3′ end of clone 5.17 encoding a melanoma tumor-associated antigen 8 gtacccccga aaagggttta cccttaaggg caattgttcc ccccccccct 50 aagggttcca aagttaagat tccccctgaa cggctaaggg ttttaaagcc 100 ttattcaagg tttcttactt gccagttcct accaaaccct gtaaaatctc 150 caataatgct gcatttaatg aaacatggta tatgtcaaat cagaagagaa 200 gaactataaa catatattgt gtaaagaaaa agttcagcaa tggaactagt 250 tttgcagatc aagcaaagat gtgtcttggg catggaacca aagttacaat 300 gaaatattca acccctgctg tgcagggggg tcattttaat gtaacaccac 350 accccatgga aacactagtc ctgataataa acatcatttt aaaagatcaa 400 aacaaacaaa caaaaaaaac aagggtgggt ggggagtgaa gcacgaggaa 450 tacctatgaa gagctattta caataaaatg tttcatttga aaaaaaaaaa 500 aaaaaaaaaa 510 9 3512 DNA Unknown prim_transcript complete sequence of clone 5.23 encoding a melanoma tumor-associated antigen 9 ggacaacagc tggagctcgc gcgcctgcag gtcgacacta gtggatccaa 50 agaattcggc acgagagaaa gtaaggaaaa gttcagggta tagaaatagc 100 tattcagtga ctttgtattt ttacttgtgc tcttaagaac ctttattcat 150 gtaatgcaaa gtaatttgtg ttgaagttga acttgtgaga aaatatatag 200 tacctaatgc attctcattt ggaatatgtg atctgtagaa atggaaatat 250 ttttatttat tttactgttt ttataggagg ttcgtaaagt gaatgaaagc 300 atcaagataa tcacccattg agaaaatgtg ttgatacaat acttaaaaag 350 tgccctacag agtatcagga aaaaatgggt aggaacatgg atgattatga 400 agattttgat gaaaagcata gtatctatcc agtgaaaaaa gtctggtaaa 450 actgccataa acaggggact ttgctaatta taagtatttt actaatgatg 500 atttttaatt agacttctaa tcattgctca taaaaaaagg aatttttagt 550 gaatgtgtat ttaaaacttc ctttaatccc gtccttatca ttctttgaaa 600 tattttatct ctgtgtatac cagcaggggt attattggcg tttggggagg 650 gagaattctt cactgagcat aactgttaca ttatataaaa ctgttacatc 700 attttggaac attaatattc tcagcctgac ccagtaaatg ccctagcact 750 ttcccattgt tatgacaatc caaacatgct ccctagtgga gagttgaacc 800 actgttggat cagaacactg ccaggtctac ccccattctc ttttttaggt 850 gatttattca gttcagagac accgtcgaac tcaagtacaa tggcagattc 900 ttttggaaca agcattttat ctagaagatg tagcaaaaaa tgaaactagt 950 gctactcatc agtttgttca cacctttcaa tcgccagagc cagaaaatcg 1000 atttatccaa tatttttata atcctacatt tggtatgtaa tttgatataa 1050 atttcaaact ttaatgatga aaagttttct gtagaaagaa gttatgtatt 1100 ttcaccaatg caaagttgaa ttttatttgt attatttgat ttataccatg 1150 tgatattaag tatctggtaa catttcccca aaataactgt tttacttatc 1200 atataacata taatccatca gtttccactg ttacttcaca aataataaaa 1250 attctattaa aaaacatgta tacatcaagc atatttttta taatgcataa 1300 tatatacaat tatgcattgc ttaatgactg ggattactct gagaaatgta 1350 ttgttaggca atttcatcac tgcatgagca tcatagggta tgtactaaac 1400 ctagatggta tagtacaggt aggcaaatat gggtattggc ttattactcc 1450 taaggctaca aaacctatac agcatggtta ctgtacctga aagtggtagg 1500 cagttgtaca ccagggtttt tggtttttaa acttgaaaaa tatttttaaa 1550 agccgttgta atttttgggg atcacccttt ttttgcaccc tctttggccg 1600 ggaggtgtat tgacccctat gtcctttaaa aatagaaatt tagtattttt 1650 cttccagctt tggttttttt ttatttgaac tatattttgg ttaattcctc 1700 ttgatattaa cctttatagt ttttcaggaa attagttaaa atccgttgta 1750 ttttatggtc cccatttagc gtccttcatg ggtggaagtt tttatgtgac 1800 acaaggctga taaaaaggtt aaatttttaa gttattttct caccaggctg 1850 gggttttttc ttcagtcttg aacaaacaac tgaaatttgg cttaagtaag 1900 tcctccttga tattaaccat ttattagtct taattataaa accctatact 1950 ttgtaggtta tcattttttc tccttttttg ctaaatttat gggcaatccc 2000 ttccaagtat ttgtcaaatt tagtgtgaag aaacttaaaa gcaaggtacc 2050 aaaagtgtca tagtattaaa acttctattt accttattta ttttaaaaaa 2100 attgttatat tcacttgatt tctccctttg catgtttggt tttgagtatg 2150 aagacttaat ggctataaca aatatctcag aaaactcctt taacaaaaat 2200 ccttcctaat taaatgaagg aatgatgtgt tatctgtttt cattcattca 2250 acaaatattt gggtacatta gtgctatgta ttattgggtg ctgggtagct 2300 tggtatatat cagtttaaaa agacagaaat tcctgccctt gtggagtgag 2350 aaaaacagac aataaacata taaaggcata aagattctga ataggcagtt 2400 gattatagaa attgaaattc aagggaggag tctgaattgc agatatgaat 2450 tagggtacca tcaatgtgta gggaaccatg gggtcaggat aaaatcaata 2500 aagaagtaat tgagatagag aaaagagaaa agtctgagga ccaagcctga 2550 ggcactccag aatttagaga ttaggtggat gagaagtaac tagcagaaaa 2600 gactagaaaa ggaggggcca gtgagatagg aaaattagga caatgaagtg 2650 ttttgaggaa aagagtatat aaagtacctt ttcaaatgtt gcacatagat 2700 taaggatcat atatattaag acctgaccat tggattttag agaagtgagg 2750 ggagaggata aaaaagtctg actgtaattt aaaagaaata agaagaggag 2800 caattggaga cagactagaa aactctaaaa atgttttcct tataaaaggg 2850 aacagagaaa aggggtagta gctgaaagag gattgggggc atagtcaaga 2900 gaaattatca catgtaatta gtaaatgata taatagaatt tgaggccagg 2950 cgcggtggct cacacctgta atcccagcac tttgggaggc cgaggcggca 3000 gatcacaagg tcaagagatt gagaccatcc tggccaacat ggtgaaaccc 3050 cgtctctact aaaaatacaa aaattagctg ggcgtggtgg tgcgtgcctg 3100 tagtcccagc tactcgggag gctgaggcag gagaatcctt gaacaggagg 3150 cggaggttgc agtgagccga gattgtgcca tgcactccag cctacctgta 3200 gtcccagcta ctcgggaggc tgaggcagga gaatcacttg aacccaggag 3250 gtggaggttg cagtgagccg agattgcgcc actgcactcc agcctacctg 3300 tagtcccagc tacttgggag atgaggcagg agaatcgctt gaacccggga 3350 ggcagaggtt gcagtgagcc aagattgcac cactacactc cagcctgggg 3400 acagaatgag actccgtcaa aaaaaaaaaa aaaaactcga gagtacttct 3450 agagcggccg cgggcccatc gattttccac ccgggtgggg taccaggtaa 3500 gtgtacccgt cg 3512 10 2634 DNA Unknown prim_transcript complete sequence of clone 5.28 encoding a melanoma tumor-associated antigen 10 ggacgccgct ggagctccgc gcctgcaggt cgacactagt ggatccaaag 50 aattcggcac cagcctgcag gtactgctgc tcgtgcctcc ggctccggcc 100 cctgagcgat ggtcctttcc ttctgccacg gcgggatcgg gcactcaccc 150 agttgcaagt gcgagcacta tggagtagcg cagggtctcg agctgtggcc 200 gtggacttag gcaacaggaa attagaaata tcttctggaa agctggccag 250 atttgcagat ggctctgctg tagtacagtc aggtgacact gcagtaatgg 300 tcacagcggt cataaaacaa aaccttcccc ttcccagttt atgcctttgg 350 tggttgacta cagacaaaaa gctgctgcag caggtagaat tcccacaaac 400 tatctgagaa gagaggttgg tacttctgat aaagaaattc taacaagtcg 450 aataatagat cgttcaatta ggaccgctct ttccagctgg ctacttctat 500 gatacacagg ttctgtgtaa tctgttagca gtagatggtg taaatgagcc 550 tgatgtccta gcaattaatg gcgcttcgta gccctctcat tatcagatat 600 tccttggaat ggacctgttg gggcagtacg aataggaata attgatggag 650 aatatgttgt taacccaaca agaaaagaaa tgtcttctag tactttaaat 700 ttagtggttg ctggagcacc taaaagtcag attgtcatgt tggaagcctc 750 tgcagagaac attttacagc aggacttttg ccatgctatc aaagtgggag 800 tgaaatatac ccaacaaata attcagggca ttcagcagtt ggtaaaagaa 850 actggtgtta ccaagaggac acctcagaag ttatttaccc cttcgccaga 900 gattgtgaaa tatactcata aacttgctat ggagagactc tatgcagttt 950 ttacagatta cgagcatgac aaagtttcca gagatgaagc tgttaacaaa 1000 ataagattag atacggagga acaactaaaa gaaaaatttc cagaagcccg 1050 atccatatga aataatagaa tccttcaatg ttgttgcaaa ggaagttttt 1100 agaagtattg ttttgaatga atacaaaagg tgcgatggtc gggatttgac 1150 ttcacttagg aatgtaagtt gtgaggtaga tatgtttaaa acccttcatg 1200 gatcagcatt atttcaaaga ggacaaacac aggtgctttg taccgttaca 1250 tttgattcat tagaatctgg tattaagtca gatcaagtta taacagctat 1300 aaatgggata aaagataaaa atttcatgct gcactacgag tttcctcctt 1350 atgcaactaa tgaaattggc aaagtcactg gtttaaatag aagagaactt 1400 gggcatggtg ctcttgctga gaaagctttg tatcctgtta ttcccagaga 1450 ttttcctttc accataagag ttacatctga agtcctagag tcaaatgggt 1500 catcttctat ggcatctgca tgtggcggaa gtttagcatt aatggattca 1550 ggggttccaa tttcatctgc tgttgcaggc gtagcaatag gattggtcac 1600 caaaaccgat cctgagaagg gtgaaataga agattatcgt ttgctgacag 1650 atattttggg aattgaagat tacaatgtga catggacttc aaaatagctg 1700 gcacttaata aaggaataac tgcattacag gctgatatta aattacctgg 1750 aataccaata aaaattgtga tggaggctat tcaacaagct tcagtggcaa 1800 aaaaggagat attacagatc atgaacaaaa ctatttcaaa acctcgagca 1850 tctagaaaag aaaatggacc tgttgtagaa actgttcagg ttccattatc 1900 aaaacgagca aaatttgttg gacctggtgg ctataactta aaaaaacttc 1950 aggctgaaac aggtgtaact attagtcagg tggatgaaga aacgttttct 2000 gtatttgcac caacacccag tgctatgcat gaggcaagag acttcattac 2050 tgaaatctgc aaggatgatc aggagcagca attagaattt ggagcagtat 2100 ataccgccac aataactgaa atcagagata ctggtgtaat ggtaaaatta 2150 tatccaaata tggctgcggt actgcttcat aacacacaac ttgatcaacg 2200 aaagattaaa catcctactg ccctaggatt agaagttggc caagaaattc 2250 aggtgaaata ctttggacgt gacccagccg atggaagaat gaggctttct 2300 cgaaaagtgc ttcagtcgcc agctacaacc gtggtcagaa ctttgaatgc 2350 agaagtagta ttgtaatggg agaacctatt tccagtcatc atctaattct 2400 cagtgatttt ttttttttaa agagaattct agaattctat tttgtctagg 2450 gtgatgtgct gtagagcaac attttagtag tatcttccat tgtgtagatt 2500 tctatataat ataaatacat tttaattatt tgtactaaaa aaaaaaaaaa 2550 aaaactcgag agtacttcta gagcgggccg cgggcccatc gattttccac 2600 ccgggggggt accaggtaag tgtcccggct cacc 2634 11 673 DNA Unknown mat_peptide 3,4,5,6,16,21,580,590,654,668 5′ end of clone 5.31 encoding a melanoma tumor-associated antigen; n = unknown 11 ggnnnntttg tttatnacac nccagctcga aattaaccct cactaaaggg 50 aacaaaagct ggagctcgcg cgcctgcagg tcgacactag tggatccaaa 100 gaattcggca cgaggtgtta ccagtgccca tcaggtgcct gccgtctctt 150 ctgtgtcaca cacagccctg tatactcctc cacctgagat acctaccact 200 gtcctcaaca ttccccaccc atcagtcatt tcctctccac ttctcaagtc 250 cttgcactct gctggacccc cgctccttgc tgttactgca gctcctccag 300 cccagcccct tgccaaggta tgatctgtgg atttcctctg ggcagcaggg 350 aggcaagggt cttaagtaaa gtgggcttgg agtgacaggt tccctatctt 400 gtttctttct gcagaaaaaa ggcgtaaagc ggaaagcaga tactaccacc 450 cctacaccta cagccatctt ggctcctggt tctccagcta gccctcctgg 500 gagtcttgag cctaaggcag cacggcttcc cctatgcgta gagagagtgg 550 tcgcccatca agcccccacg caaagacttn ctgactctan caacaacacc 600 agactctaag aaaggaaagc tttagaacag ttaaacattg caatggattt 650 tgangagtac tctctaanaa cat 673 12 593 DNA Unknown 3′ end of clone 5.31 encoding a melanoma tumor-associated antigen 12 ttgaaaataa tgatgggagt tttttgtcat gtgtgtgcaa ctcaacgagg 50 tctcctgtct gacagtgtaa attggagcta tatcacttgg gggctgggag 100 tagggcctgt ttatcagcat agttttgagt ttggcctctt tctaggatga 150 tttgagttcc gttatgccaa gatgccagat gaaccactag aaccagggcc 200 tttaccagtc tctactgcca tgccccctgg cttggccaaa tcgtcttcag 250 agtcctccag tgaggaaagt agcagtgaga gctcctctga ggaagaggag 300 gaggaagatg aggaggacga ggaggaagaa gagagtgaac ctcagactca 350 gaggaagaaa gggctcatcg cttagcagaa ctacaggaac aggtattttg 400 tcactcttga aagtttttat tgggtaagag gttcatgccc tttgtcctca 450 ttttttcttc ttgttatttt atctttattt actttttcca cttcatgttt 500 tttttccttt agcttcgggc agtacatgaa caactggctg ctctgtccca 550 gggtccaata tccaagccca agaggaaaaa aaaaaaaaaa aaa 593

Claims

What is claimed is:

1. An isolated DNA encoding a melanoma tumor-associated antigen selected from the group consisting of:

(a) isolated DNA comprises of sequence selected from the group consisting of SEQ ID Nos. 1-12;

(b) isolated DNA which is complementary to the isolated DNA of (a) above; and

(c) isolated DNA differing from the isolated DNAs of (a) and (b) above in codon sequence due to the degeneracy of the genetic code.

2. A vector comprising the DNA of claim 1 and regulatory elements necessary for expression of said DNA in a cell.

3. The vector of claim 2, wherein said DNA encodes a melanoma tumor-associated antigen.

4. The vector of claim 2, wherein said DNA is positioned in reverse orientation relative to said regulatory elements such that a melanoma tumor-associated antigen antisense mRNA is produced.

5. A host cell transfected with the vector of claim 2, said vector expressing a melanoma tumor-associated antigen.

6. The host cell of claim 5, wherein said cell is selected from group consisting of bacterial cells, mammalian cells, plant cells and insect cells.

7. The host cell of claim 6, wherein said bacterial cell is E. coli.

8. Isolated and purified melanoma tumor-associated antigen encoded for by the DNA of claim 1.

9. A method for detecting mRNA coding for a melanoma tumor-associated antigen in a sample, comprising the steps of:

(a) contacting a sample with an oligonucleotide probe specific for a melanoma tumor-associated antigen, wherein said probe comprises of sequence selected from the group consisting of SEQ ID Nos. 1-12; and

(b) detecting binding of said probe to said mRNA coding for said melanoma tumor-associated antigen in said sample.

10. A kit for detecting mRNA coding for a melanoma tumor-associated antigen, comprising:

an oligonucleotide probe specific for a melanoma tumor-associated antigen, wherein said probe comprises of sequence selected from the group consisting of SEQ ID Nos. 1-12.

11. The kit of claim 10, further comprising:

a label with which to label said probe; and

means for detecting said label.

12. A method of detecting a melanoma tumor-associated antigen in a sample, comprising the steps of:

(a) contacting a sample with an antibody, wherein said antibody is specific for a melanoma tumor-associated antigen or a fragment thereof encoded by the DNA of claim 1; and

(b) detecting binding of said antibody to said melanoma tumor-associated antigen in said sample.

13. A kit for detecting a melanoma tumor-associated antigen, comprising:

an antibody, wherein said antibody is specific for a melanoma tumor-associated antigen or a fragment thereof encoded by the DNA of claim 1.

14. The kit of claim 13, further comprising:

means to detect said antibody.

15. An antibody, wherein said antibody is specific for a melanoma tumor-associated antigen or a fragment thereof encoded by the DNA of claim 1.

16. A method of screening for compounds that inhibit the activity of a melanoma tumor-associated antigen, comprising the steps of:

(a) contacting a sample with a compound, wherein said sample comprises a melanoma tumor-associated antigen encoded by the DNA of claim 1; and

(b) assaying for activity of said melanoma tumor-associated antigen, wherein a decrease in said melanoma tumor-associated antigen activity in the presence of said compound relative to said melanoma tumor-associated antigen activity in the absence of said compound is indicative of a compound that inhibits the activity of said melanoma tumor-associated antigen.

17. A method of inhibiting the growth of a melanoma tumor in an individual, comprising the steps of:

(a) administering to an individual a therapeutic compound, wherein said therapeutic compound comprises a thereapeutic moiety and a targeting moiety, wherein said targeting moiety recognizes a melanoma tumor-associated antigen encoded by the DNA of claim 1, wherein said therapeutic compound inhibits the growth of said melanoma tumor in said individual.

18. The method of claim 17, wherein said targeting moiety is selected from the group consisting of an antibody or fragment thereof and a ligand.

19. The method of claim 17, wherein said therapeutic moiety is selected from the group consisting of a therapeutic gene or protein, a toxin, a radiolabel and a virus.

20. A cancer vaccine composition, comprising a vector capable of expressing a DNA molecule selected from the group consisting of SEQ ID Nos. 1-12, and an appropriate adjuvant.

21. A method of vaccinating an individual against cancer, comprising the steps of:

administering to said individual a vector capable of expressing a DNA molecule selected from the group consisting of SEQ ID Nos. 1-12, wherein said expression elicits an immune response specific towards a melonoma-specific antigen, thereby inducing immune-mediated destruction of melanoma cells.

22. The method of claim 21, wherein said individual is at risk of getting cancer, suspected of having cancer or has cancer.

23. A method of inhibiting the growth of a melanoma tumor, comprising the steps of:

administering the cancer vaccine of claim 20 to an individual, wherein administration of said vaccine induces an immune response, thereby inhibiting the growth of a melanoma tumor.