NZ507014A - A gene encoding a novel marker for cancer - Google Patents

Abstract

A cDNA molecule that encodes a protein designated Labyrinthin (Lab) is isolated and its nucleotide sequence is determined. The protein, or peptides derived from the protein, are markers useful to define novel classes of cancers. Diagnostic assays for these cancers use antibodies to Lab or nucleotide probes that hybridise with the lab gene or a fragment therefrom. Vaccines useful either to prevent recurrence of cancers in subjects who test positive for Lab (or lab), or to prevent initial occurrence of cancer, use proteins or peptides derived from Lab. Expression of Lab via immunogenic assays is used to monitor effects of cancer treatments. Antisense molecules against lab are used in treatments. Sense molecules of lab are used to restore lost lab function in diseased normal cells, for example, gland cells.

Description

GENE ENCODING LABYRINTHIN, A MARKER FOR CANCER rnveutor: James A. Radosevich The invention relates to a gene encoding a protein and peptides therefrom that includes an epitope, a cancer associated antigen, usefbl as a marker that is not restricted, to previously defined histological classes of cancer. Antigenic peptides are useful as a vaccine for treatment and prevention of cancer, and for the preparation of new, specific, monoclonal antibodies. Antisease molecules are useful in pharmaceutical compositions asd are useful for diagnosis and treatment BACKGROUND OF TH£ INVENTION i Cancer ("cancer is k malignant tumor,11 wherein a "tumor" is an abnormal mass of tissue, that need not be jnalignant; "neoplasm" is a form of new growth) is a leading cause of death in men aadjwomen throughout the world. In the United States alone, over 1 million new cases are diagnosed each year, and over 0.5 million deaths are reported annually (Landislsf a!„ 1998). Historically, tumors are grouped and treated, j based in part by the tissues in which they arise « for example, breast cancer, colon cancer, and lung cancer, and the like, Yet, within lung cancer, for example, it is well recognized that these tumors are a very heterogeneous group of neoplasms. This is al3o true for tumors arising in other tissues. In part, because of this heterogeneity, j there are complex and inconsistent classification schemes which are used for human tumors. Previous i^ttemptaj to treat cancer have been hampered by: (1) the arbitrary classification of tumors arising within given tissues, and (2) by using microscopic methods based on how these tumors look (histological classification). Although exisftmg classifications for various tumor types have some prognostic value, almost all the classifications fail to predict responsiveness to treatments and likelihood of cure or disease course. Improved: classification schemes based on the biological constitution of these neoplasms is required to significantly alter the survival statistics of humans j who have cancer. One approach to solving these problems is to locate molecules specific to tumors, preferably antigens in molecules that axe markers for cancer cells.

I (A "marker" is defined hejrein as any property which can be used to distinguish cancer from normal tissues and fjrom other disease states.) The markers' presence is then a basis for classification. ./ iCV. VON:EPA MUEXCIIENi 01 Vlu-U9 : <j:na • . , - J iJ -nj . ,,T22- +4'j By ay9944C5:# 9 1540-1999' pctus 9& c$363' desopamd^j 1 Attorney Docket No. 21212/90J35 FCT/US99/05365 Manoclonal antibodies (MCAs) prepared by somatic cell hybridization tecjmiqucs, usually ill mice, are useful molecular probes for the detection and discrimination of cellular antigens, and therefore have great potential for detecting cancer associated antigens. These antibodies bind to specific antigens and the binding 5 is detectable by well known methods. When, binding occurs, the inference is made that a specific antigen is present. Those cancer associated antigens which are exposed to the cell surface or found in the cancer mags, are molecular targets for the immune systems (including host antibodies) of the host Recent findings suggest that cancer patients who have antibodies against their tumors, do better than those who do not 10 mount this type of immune response (Livingston et al.t 1994). Therefore, natural, induced, or administered antibodies are a promising therapeutic approach.

The humanization of non-humaaMCAs (the process by which non-human MCA reactive sites are shuttled into cloned human antibodies and expressed) results in reduced immunogenicity of the foreign antibodies without the loss of theii specific 15 binding in in vivo and in ex vivo applications. MCAs can be used as in vivo imaging agents, diagnostic tests, and for therapy (Radossvich et al,, 1988, 1990; Rosen eial., 1988).

Vaccine therapy is a well established approach directed at Inducing an immune response without exposure to the causative agent of a disease or condition. Many 20 vaccines are available, for example, w stimulate a response in a host to bacterial and viral agents. The use of tumoT associated antigens (markers) in a vaccine could prevent primary cancer occurrence, and could also provide a means to prevent recurrence of the disease.

Gene therapy is a means by whicb the genetic make-up of cells is modified to 25 express the gene of interest, There are many forms of gene therapy including-, gene replacement, antisense suppression therapy, and surrogate gene expression.

Discovering genes encoding cancer-associated, preferably cancer-specific antigens (markers) opens the door to genetic intervention against cancer cell proliferation. The accurate and consistent use of a cancer marker to differentiate cancerous fiom. normal 30 tissue, not only has diagnostic potential, but is also desirable for treatment and prognosis. Therefore, such markers have been sought.

Recent Studies have shown that the enzyme encoding human aspartyl beta-hydroxylase (HAAH) is overexptsssed in some human adenocarcinoma cell lines, and .i +49 »i'J 2.309-1 J-f," *"l DESCPAMD PCT/US99/0536S in primary hepatocellular cancers, therefore could be a marker. The gene said to encode HAAH has teen cloned and sequenced (Gronke at al% 1989, 1990; Wang er a/., 1991; Jia eta!., 1992, 1994; Korioth etal, 1994; Lavaissiere et al, 1996).

However, little is known about HAAH expression in human tumors in general (Lavaissiere etal., 1996).

Tlue study of the HAAH enzyme grew out of the study of its bovine counterpart (Gronke et al., 1989, 1990; Wang et 1991; Jia. et al., 1992). Bovine aspartyl beta-hydroxylasc is an intracellular, glycosylated protein, localized in the rough endoplasmic reticulum. The protein has been reported to have three major species of molecules; a 85 kilodalton form, and two active forms with molecular weights of 56 and 52 kilodaltons respectively (Lavaissiere et aU 1996), Using standard biochemical methods, bovine aspartyl beta-hyidroxylase (bAAH) has been purified and characterized (GronJce er al., 1990; Wang et cd1991). The activity of the enzyme has been shown to be correlated with the 52 and 56 kilodalton species which were purified.

Immunologically, a related higher molecular weight form (35-90 kilodalton) was also observed. As part of the purification, bAAH is bound to Coq A sepharose, which is consistent with the conclusion that the enzyme is glycosylated. (Subsequent reports on the DHA sequence show three possible glycosylation sites, with one site being very close to the known active enzyme domain.) The protein is very acidic in nature, and a detergent is not required to solubiKze the active fraction. The active enzyme site is dependent from the biochemically isolated bovine protein (bAAH) on the presence of histidine at position 675 (Jia er a!,, 1994).

A partial arninn acid sequence was obtained for HAAH. DNA probes (a DNA probe is a molecule having a nucleotide sequence that is capable of binding to a specified nucleotide sequence under certain conditions) deduced from this amino -acid sequence was used to screen a bovine cDNA library (Jia et al,, 1992). (A cDNA library contains the sections of DNA that encode for gene products - for example, peptides as opposed to genomic DHA). Several overlapping cDNA sequences in the library contained a 764 amino acid open reading frame (ORF) sequence which, will be expected to encode an 85 kilodalton protein. Also present in this ORF sequence were two other possible start codons, that is, locations at which encoding begins. The most 3' start codoa was preceded by a ribosome binding site. Translation of the clone 1 ' '■ 10-99 : 0:04 ; 012 3 ./22-» pctus 390536$ Attorney Docket Ma. 21511/90185 CV. VON: UFA MUt-XCHEN 01 'l(j-Og : 0:3-1. • •„ J 0 \ , % *-U- J . -22- +49 89 2399*465: #11 potus 99 g536§: Attorney Docket No. 21511/90185 PCT/U599/05365 having this sequence resulted in a protein, that was about 85 Icilodaltons, Antiserum was raised to the membrane fraction of Iranian MG-63 calls and was used to iroraunoscresn a cDNA library made fiom MG-63 cells. Data on one clone was reported which could encode a 757 amino acid protein, and, by sequence analysis, was 5 found to have strong N-terminal homology with bAAH (Korioth et al, 1994). When this clone was used in an in vitro translation system (an artificial cocktail of normal cell cytoplasm used to convert mRNA into protein), a 56 kilodalton protein was produced. It was suggested that this was due to post-translatioual cleavage.

The HAAH enzyme is responsible for the modification of specific aspartic 10 acid residues within the epidermal growth factor-like domains of proteins. It has been hypothesized that these modified aspartic acid residues allow the epidermal growth fector-like domains to become calcium binding domains. (Gronke et aL, 1989, 1990; . Wang s tal„ 1991; Tizetal,, 1992,1994; Korioth er aL, 1994; Lavaissiera etal., 1996).

An enzyme related to HAAH, aspartyl beta-hydroxylase (AAH), was first studied because it specifically modified select aspaitic acid or asparagine residues in a group of biologically important proteins including the vitamin. K-dependsnt coagulation factors Yn, IX, and X. Other proteins like C, S, and Z also have this modification (Gronke etal.% 1989,1990; Wang et aL, 1991; Jia at a!,, 1992, 1994; 20 ' Korioth er a!,, 1994; Lavaissiere et aL, 1996). Aspartic acid and asparagine residues have been shown to be modified by HAAH in proteins containing epidermal growth factor-like domains, The function of the beta-hydroxyaspartic and beta-hydroyasparagine residues is unknown, however, it has been speculated that this modification is required for calcium binding in the epidermal growth factor EGF-liie 25 domains of selected proteins.

Antibodies were laised to human hepatocellular carcinoma FOCUS cells (Lavaissiere et al, 1990). One MCA reacted with an antigen that was highly expressed in. hepatocellular carcinomas (Lavaissiere er aL, 1996). Immune screening using this antibody and a lambda gtl 1 HepG2 library resulted in the isolation of a 30 partial cDNA, which was subsequently used to isolate a larger clone.

, A human adenocarcinoma cell line designated A549 was reported as having very high levels of HAAH activity (Lavaissiere et al., 1996). A mouse monoclonal antibody designated MCA 44-3Afr(U,S. Patent No. 4,816,402) was produced against ~ ^ V. VOX: tPA ML t.\CHli\ 0 J >10-99 : 0 = 05; al2 i 722-* +49 fig jj'joi-i-t;? it 12 p^rusmo^m DESCPAMD Attorney Docket Ho. 21 SI 1/90185 FCT/US99/05365 the human adenocarcinoma cell line A549 (A.TCC accession number CCL 185) (Radosevich et al., 1985). The antibody recognized a cell surface, non-glycosylated antigenic protein, having an estimated apparent molecular wight of 40 kDa).

The antigen was expressed by A549 cells, and was found to be a good 5 adenocarcinoma, marker; thai is, it "was frequently expressed by cancers which looked like adenocarcinomas when examined histologically (Radosevich er al., 1990a; Lee et a!,, 1985). MCA 44-3A6 is unique in that it is the first monoclonal antibody which has this binding specificity. The results from an International Workshop for Lung Cancer confirmed other related published findings on MCA 44-3 AS (StaheJ, 1994), 10 The antibody designated MCA 44-3A6 has clinical utility because it ^ differentiates antigens associated with adenocarcinomas, The normal and fetal tissue .) distribution of the antigen is restricted to some glandular tissues (Radosevich et al, 1991). Detection can occur on formalin fixed-paraffin embedded tissue (Radosevich et al, 1985, 1988, 1990a, 199Gb; Lee et a/, 1985, 1986; Piehl etal.r 1988; Combs et 15 aly 1988b, 1988c; Banner et al., 1985), The antibody has a restricted binding pattern within human pulmonary tumors (Lee et al, 1985; Banner et al,, 1985; Radosevich er al., 1990a, 1990b).

In a study of over two hundred pulmonary cancers, MCA 44-3A6 was found to react with all of the adenocarcinomas tested, many of the large cell carcinomas, as 20 ' well as with sub set? of intermediate neuroendocrine small cell lung cancers, well-;• differentiated neuroendocrine small cell carcinomas, carcinoids, but not mesotheliomas. MCA 44*3A.6 does not react with squamous cell carcinoma, ^ bronchioloalveolpx carcinoma, or small cell carcinoma (Lee et al,, 1985). MCA 44- 1 3A6 is useful in distinguishing adenocarcinomas that are metastatic to the pleura from mesothelioma (Lee et al, 1986). The antibody has selected reactivity among adenocarcinomas and in large cell carcinomas (Piehl et al., 1988; Radosevich etal., 1990b), Irj a study of over 40 cases of lung cancer comparing etiological and histological findings, MCA 44-3A6 was found to be useful in cytological diagnosis 30 and was consistent with the histological finding (Banner et al, 1985). Histology is the study of tissues (which are made of cells). Cytology is the study of cells which have been removed from the organizational context which is common referred to as tissue. Cells removed from.tissues.da nnt. always behave, the same as if they were in the tissue : ^ -fnterf >V ^ . vuivi: lif'fV I lli)\ 1)1 "•-10-90 : »,U* ; nr- 7.)0 31-1 +1-9 89 23994+65 :#jn ,s-1q-198$ "pcjus0&os36s descpamd Attorney Docket No, 21311/90163 PCT/US99/053 65 m fi , ■ from which they were derived. Fortunately, the antigen detected by MCA 44-3A6 expressed in adenocarcinoma cells in. tissue behaves in. the same ways as adenocarcinoma cells removed from tissues. This ia a very diagnostically important ■ characteristic. Similar correlations using oytologically prepared cell blocks of 5 pulmonary carcinomas, as well as ACs presenting in body fluids from other sites throughout the body were demonstrated (Lee ef al, 1985; Spagnolo er al, 1991; Combs er al, 1988c), Also, MCA 44-3A6 binds to adenocarcinomas from sites other than lung cancer. The egression of the antigen in primary and metastatic lesions was also reported (Combs et al., 1988a). The utility of the MCA antibody in 10 differentiating cancer from benign lesions in human breast tissue was also noted Q (Dudaef a]., 1991).

) The cellular localization of the antigen detected by MCA 44-3 A6 was determined, By using live cell radioimmunoassays (a radioactive antibody test directed at determining binding of the antibody to live cells), immunofluorescence, 15 and live ceil fluorescence activated cell sorter (FACS) analysis, the antigen detected by MCA 44-3A6, was shown, to be on the outside sur&ce of the cell (Radosevich, et al, 1985). Additional studies using immunogDld-electron microscopy and FACS analysis have demonstrated that this antigen is non-modulated {that is not intemalized by the cancer cell when bound by an antibody), is expressed on the extracellular 20 ' surface of the plasma membrane, and is not cell cycle specific that is, the cell makes protein all the time it is going through the process of cell replication, and also when it js not dividing (Radosevich etal., 1991). The antigen is not found in the serum of normal or tumor bearing patients, and is not shed Into the culture media by positive ' cell lines (that is, cancer cells are known to bleb off portions of their cell membranes and release them into the surrounding fluid) (Radosevich et al, 1985), Recently 3 of 27 randomly tested adenocarcinoma patients were found to have naturally occurring antibodies to the antigen. In addition, radiolabeled MCA 44-3AS was used to localize A549 tumors growing in nude mice. A doxorubicin immunoconjugate MCA 44-346 is selectively toxic in vitro (Sinkule et al, 1991).

Determination of the nucleotide and amino acid sequences of the antigen detected by MCA 44-3A6 would enhance the usefulness of this antigen in cancer diagnosis, treatment and prevention.

BRIEF SUMMARY OF THE INVENTION PCTUS 99 053651 Attorney Docket No. 21511/90183 The antigen detected by the antibody MCA 44-3 A6 as described in the Background is now designated as irLabyimth'n," A gene (designated labyrintkm\ abbreviated lab) characterized by a unique nucleotide sequence that encodes the antigen detected by MCA 44-3A6 was isolated and characterized The notation lab signifies the nucleic DNA/RNA forms; "Lab" notation refers to the protein which is encoded by the lab DNA/RNA.

The invention described herein used the antibody MCA 44-3AS as a tool to clone the gene encoding Lab. In addition, an epitope (the necessary binding site for an antibody found on the antigen) for MCA 44-3 A6 was identified on the Lab protein expressed by the clone to be PTGEPQ (standard abbreviations for amino acids). Tie epitope represents an important immunodominant sequence; that is, when injected into animals, the animals readily produce antibodies to this sequence.

An aspect of the invention is the use of lab DNA in The sense (where the normal transcription of a DNA sequence which proceeds from the 3' to the 5' end to produce a mUNA strand from the sense strand of UNA, the mENA being complementary to the DNA) expression mode for; (1) the marking of human tumors by nucleotide probes; (2) the detection of DNA and mRNA expression of Jab in cells ' and tissues; (3) the transformation of cells into a glandulax-like cell type; (4) the production of Lab antigen in viva for immunization; (5) the ex vivo expression of Lab for immunization to produce antibodies; and (6) production of Lab in vitro. Use of an antisense molecule«- for example, by production of a mRNA or DNA strand in the reverse orientation to a sense molecule - to suppress the growth of labyrinthin-exprsssmg (cancerous) cells is another aspect of the invention.

An aspect of the invention is a vector comprising a DNA molecule with a nucleotide sequence enepding at least an epitope of the Lab antigen, and suitable regulatory sequences to allow expression in a host cell.

Another aspect of the invention is an amino acid sequence deduced from the protein coding region of the lab gene. Selected regions of the sequence were found via immunological methods, to produce effects corresponding to effects from both naturally occurring (from cancer cells), chemically produced (synthetically produced peptides), and expression products of the cloned Jab gene.

Another aspect of the invention is the use of the entire deduced amino acid sequence of Lab-, peptides derived from Lab, or chemically produced (synthetic) Lab CV. VON;: EPA MI.'RNiCl 1EN 01 -99 0:08 OliJ i /2'2- descpmd] i +4 9 4ttarney Docket No. 21511/90185 # peptides, or any combination of these molecules, for use in the preparation of vaccines to prevent human cancers and/or to treat humans with cancer. For purposes of the present invention, "humans with cancer" are those persons who have the Lab antigen detected in their cell?. These preparations may also be used to prevent patients from ever having these tumors prior to their first occurrence.

Monoclonal antibodies directed to the Lab protein, or antigenic components or derivatives of Lab proteins, are useful for detection of Lab and for other purposes. Monoclonal antibodies which are made in species other than those which react with the Lab antigen can be modified by a number of molecula* cloning methods such that they retain their binding with the Labyrinthin peptides, yet are not immunogenic in humans (Sastry it al, 1989; Sambrook et al., 1990). In brief, this is done by replacing the binding site sequence of a cloned human antibody gene, with the binding site sequence of the non-human monoclonal antibody of interest These "humanized" MCAs are used as therapeutic and diagnostic reagents, in vivo, ex vivo, and in vitro.

The use of the Lab protein or antigenic peptides derived therefrom in diagnostic assays for cancer is a way to monitor patients for the presence and amount of antibody thai they have in their blood or other body fluids or tissue. This detection IS Hot limited to cancers of a class or classes previously defined, but is useful far cancer cells th4 have the Lab marker antigen. The degree of seroconversion, as measured by techniques known to those of skill in the art (for example, ELIS A (Engrail find Perlmann, 1971)] may be used to monitor treatment effects..

:CV. VON': EH,\ MUENC1 UiN u L , ; 10-90 : 0:37 : •J 12 j o r 122 PCTUS 99 05365 Attorney Docket Ho. 2151 J/90185 +4g sa 239944c,s.:.*u P, PCT/US99/0S36S -9 • 10 t ) Treatment with antisense molecules to fafi or antibodies to Lab in a pharmaceutical composition is an approach to treat patients who have Lab in, or on, their cancer cells.

BRIEF DESCRIPTION OF THE DRAWINGS FIG, 1 is the nucleic acid sequence of the lab gene (SEQ ID NQ;1).

FIG. 2 is the amino acid sequence for Lab, deduced from the lab gene (SEQ ID N0:2).

FIG, 3 is an illustration of the lab gene and how it is related to the HAAH enzyme, DETAILED DESCRIPTION OF THE INVENTION Molecular Biology of Labyrinthine To demonstrate that the epitope MCA 44-3 A6 is encoded by a protein sequence, high molecular weight DNA from the cell line A549 was isolated. This DNA was co-precipitated (via calcium) with a plasmid (pSVneo), and used to transfect a mouse cell line designated B78H1 ceils (Albino et al., 1985), This mouse cell line is negative for the expression of the epitope and was reported to have a high frequency of incorporation and expression of any human DNA sequences. If a given. B78H1 cell was in a state to take up DNA, it would be expected to have calcen up both human DNA and the plasmid DNA. The plasmid DNA makes the cell resistant to G4 IS (a normally toxic drug). Therefore, if a cell normally sensitive to G418 growth inhibitor grows in G418, it had to have taken up the plasmid, and may also have taken up one or more A549 DNA sequences, After G418 selection (a way of choosing only cells which have resistance to growth in G418 by the uptake/expression of the Neo gene on pSVneo plasmid, and therefore representing cells that were in a state to uptake other DNA at the same time), approximately 15 of lxIO5 clones were detected using imrounoselectioc. with MCA 44-3 A6. This finding is consistent with conclusion thai human A549 cells have DNA that encodes Lab and possesses the regularity sequences necessary for the expression of Lab.

Comparison of HAAH and Lahvrtntfym Because the DNA sequence of lab was determined as an aspect of the present invention, HAAH and lab could be compared. HAAH and the lab nucleotide sequences have some internal fragment similarities, but are different on either side of the fragment, and are related to different products. This conclusion is based in part "by the analysis and homology of the DNA sequences reported for these two genes. Specifically, the lab 5r region has no d v. VOiVhVA WUb'\C!lh'\ U1 ' 10-99 : u. .,7 . - _ ' ' +'ta pctus 99 05365 descpa^d " Attorney Docket Na. nstimiit$ " ^PCT/US99/05365 homology with HAAH. The protein coding region of lab has about a 99,6% homology with an internal segment of the proposed protein codin g region for HAAH. The 3' region has no homology with the HAAH reported sequence. Virtually all of the other data comparing HAAH and labyrinthin ^re different, for example; (I) molecular 5 weights of the pro tains, (2) cellular localization, (3) chromosome localization, (4) histological presentation in normal tissues and tumors, (5) northern blot expression, (6) immunological findings.

Although the protein coding region of lab is identical to an internal region of the sequence reported for HAAH, the 5' untranslated region of HAAH is different, and 10 part of the 5' translated protein coding region of HAAH is missing from thai found in the lab clone, From both HAAH and lab clones, the deduced protein would be expected to be very acidic in nature, and therefore would run anomalously in SDS gels. As predicted, the Lab protein migrates anomolousiy in SDS gels. What was cloned and disclosed in the present invention migrates identically to the native protein 15 found in several cell lines. Convincing evidence that the correct gene fragment encoding the antigen detected by MCA 44-3 Afi has been cloned (mRNA) is that when the recombinant protein is made, that recombinant protein should act (in this case, •have an apparent molecular weight) the same as an independent biologically derived source of that protein, Lab provided from clones has the characteristics of Lab from 20 cells, The deduced amino acid sequence encoded by HAAH requires the use of an open reading frame which would pioduca a protein that is S5-90 kolodaltDns, and does not take into account that there are several start codons and other shorter open, reading frames. The deduced HAAH protein (biochemically) is glycosylated and the reported 25 saquencehas glycosylation sites (Korioth etal, 1994; Lavaissiere eiaL, 1996). To the contrary, Lab is not glycosylated, nor does it have predicted glycosylated sites.

The deduced HAAH amino acid sequence contains a region shared by the Lab amino add sequence which is predicted to be very hydrophobic. Lab requires strong detergents in order to be soluble; HAAH does not. The increased expression of 30 HAAH (by enzyme activity measurements) in the same cell line (Af 49) which was used to clone and study lab extensively, suggests that both of these gene products may be important to the AC phenotype and that at least A549 cells make both functional HAAH and Lab. Succeasfal transections of the antisense to. lab into A549 resulted in N S *.S «. ( CV. VON ■ tlJA Ml-'t'NCHEN UI -10-9U • o ■ , 1 SJ „ +49 89 23994.+65:#lfl pctus a^osees1 descpamd Attorney Docket No, PCT7US99/05 a marked decrease in expression of lab and m the growth rate of the cells. The expression of a Sense lab construct in NIH-3T3 cells (normal mouse fibroblasts) resulted in a "marked change in phenotype, a phenotype consistent with that of AGs. Therefore, lab expression is associated with conversion of normal cells to cancerous 5 cells. Lab and HAAH have potential calcium binding domains in caramon. cDNA Library Construction and Cloning: A cDNA lambda gtl 3 phage library was constructed "losing mRNA which was isolated from actively growing A549 cells (Sambrook et al, 1990).. This aIigo(4T)-piimed cDNA was cloned into the Eco RI site using Eco RI linkers. The library has about 83% clear (containing an insert) 10 plaques with a titer of 1.2 x lQ,(Vml representing aminirnum of 1.46 x 10* independent plaques which, by Polymerase Chain. Reaction, have insert sizes ranging from 0.6 to 5 kilobases. Since Lai is a 40 kilodalton integral protein, (a protein which is embedded in the plasma membrane) the theoretical M length mKNA encoding this protein, including a potential leader sequence is estimated to be about 1.1 kilobases. 15 This library was immunoscreeaed nsing the antibody MCA 44-3A6. Eight independently derived phage stocks (identical phage which are from the same plaque) were isolated. These have all been plaque purified by repeated cycles of immunoscreening/isolation. Upon Eco RI digestion of these eight isolates, inserts of about 2kb were seen. The largest insert was isolated (2A1A1) and the Eco RI fragment 20 was cloned into the pOEM-32 plasmid.

Sequencing and Scmience Analysis; The DNA fragment designated 2A1A1 was found'to have an insert of 2442 base pairs in length (FIG. IX containing a 5' untranslated region, a ribosome binding site, and a start codon which would be expected to encode a 25S amino acid protein (FIG. 2). The 3' untranslated region is 25 remarkable in that it contains only four instability sequences; ATTTA (Xu et al., 1997). In addition there are sequences found in the very 3' end of mRNA's which result in sdenylation of the oiRNA (Sambrook er al, 1990). The lab sequence contains both a sub-optimal (ATTAAA) and optimal (AATAAA) poly-adenylation site. These are sequences found in the very 3' end of mRNA's which result in 30 adenylate on of the mRNA. This finding provides molecular data which supports the cellular and "biochemical data that has been outlined herein. (The HAAH clone has a . poly A signal, but the whole 3' region has not been sequenced) y :C.V. VON: EPA MMb\CHIv\ 01 -LO-09* 0 • '\t> • «.« LU y-ab • 312 ,22- +40 8d 23994405 »1 PCTUQ 89 05385 DESCPAMD i Attorney Docket No, 21211/901SS PCTAJS99/05365 -12.

A calcium binding site motif is noted in the Lab amino and sequence (TIG, 2), however, it is out of the known required structural context to be a binding site. In this case, the calcium limiting sequence is there, but it is not in a protein sequence context that is known, to make it work as a binding site. Homology was noted with lab and an 5 EST clone (designated #05501) which represented only a portion of the 3' untranslated region Had independently confirmed this portion of the sequence. Some internal fragment homology is also noted -with HAAH, but the 5' untranslated and pan of the 5' translated region is different (58 amino acids), as well as a major portion of the 3' coding region is missing in lab (FIG. 3).

Genomic DNA Cloning and Analysis: Using a ?CR fragment representing the protein coding region of lab as a probe, a genomic lambda FIX n library made fiom the human pulmonary fibroblast cell line \VT-38 was screened. Ten primary plaques were isolated out of approximately 1x1015 screened plaques. Using seven of these as target DNA, polymerase Chain Reaction conditions were established with primers for 15 the protein coding region, producing a 765 base pair fragment, the expected protein coding region for Jab. On Northern blots (a method used to qualitatively assess raBNA) lab only detect? one bad noted at 2.7 lalobases. The recombinant protein •made from the lab clone, when tested on Western blots (a mediod used to qualitatively define proteins) using MCA 44-3 AS, has the sgme relative mobility as the Lab protein 20 when made by A549 cells.

Lab and HAAH genes give different results in the proteins they encode.

HAAH consistently gives two bands on Northern blot analysis (2.6 and 4.3 kilobases) suggesting that the 2.6 kilobase band is due to alternate splicing - that is, the cell cuts and splices the mRNA. Also, if Iqb and HAAH are the same gene, HAAH should 25 be detected in all tissues and cancer cell lines in which Lab is found However, Lab is not seen on Northern biota of cell lines EMT5 ot QV-DB, nor is there ifnmunorsactivity in these cells; indicating that Lab mRNA is not made, and that Lab protein is not produced in these cells. Lab protein Is rarely expressed in normal cells, where both the HAAH mKHA and HAAH protein have been reported to be expressed 30 in almost every tissue studied. mRNA. Analysis: Northern blot analysis of the DNA fragment from the A549 ■ • cell line using lab cDNA as a probe identified a single band of about 2.7 kilobases.

This is expected based onxhe cDNA (2442 base pairs) and a poly-A tail of about 300 - #00^ .W>4.nn -t rt. -tjsS-rvrV - . VON :EfJA VII KNCTHEN 01 • 1U-99 : n ■ .iq . •>!.-> ,, 312 i "u~- +1-9 8J j-jyaa-io- *2<J ^ctus;9s 06365' descpamd Attorney Docket No. 21511/90185 PCI/US 99/05365 base pairs. Northerp blot analysis of the mouse cell line, EMT5, and of the human large cell carcinoma cell line, QU-DB, confirm that no transcript for lab is produced by these cells. This is consistent -with immunoassays which are negative for lab expression, on these cells.

Antisense and Sense cDNA Expression: The pksniid (pBK-CMV) (Sambrook et al, 1990) may cany either the sense or antisense MI length cDNA lab into A549 and NIH 3T3 cells, An antisense molecule can be, for example, a complementary sequence to a sense molecule that hybridizes with the sense molecule, preventing its expression. Using the MTT assay (Siddique et al, 1992) to assess the growth, rate of 10 A549 cells expressing antisense to lab, a raaricsd reduction in growth rate was noted. The antisense tnmsfected A549 cells appear to have a greater degree of contact inhibition. A detectable amount of Lab is reduced in these antisense trsnsfected cells. • NIH-3T3 cells convert from a fibroblast-l&e cell type morphology (large, thin spindle shaped) to a large, adenocarcinoma appearing cells (very round, plump) -when sense 15 expression occurs.

Chromoscm^ ^ivalfrTwrinyv The chromosome localization foe lab, using full length cDNA as a probe via lW situ hybridization (Sambrook et aln 1990) is tentatively on chromosome 2ql2-14, with possibly some reactivity to chromosomes 4 and 8.

Using the some probe (the foil length cDNA sequence of lab) and FACS sorted 20 ' chromosomes (Lebo et al, 1985) staining was also noted on chromosome 2, with weak staining on 4 and none on 8. The use of genomic clones will be of particular value in resolving these data because higher stringency hybridization, conditions than that allowable for the cDNA, can be used, thereby reducing background signals. This . is yet another proof that the correct gene was cloned and that the results are not due to 25 a paethod artifact. There may be mutations in the genomic DNA of tumors and for the present invention, DNA was cloned fcm tumor cells (A549). Therefore, a mutated gene cpuld have been cloned. However, that is not the case because the genomic DNA from a normal cell (DNA) produced the same sequence as what was cloned as described herein. Therefore, a normal gene was cloned from A549 cells. The weak 30 signals on chromosomes 4 and 8 are consistent with a pseudogene or a related gene.

For example, HAAH has been reported to be on chromosome 8ql2 by in situ hybridization, so this result on chromosome 8 could reflect the HAAH and lab sequencer homology.

:V...VU,VEPA MttiNCIlEN 01 . ,10-99 : 0:09 : 3l2 fC|Lp m 0S365, DESCPAMD, - ' +49 89 23994-4-Qfj : it2 I bzpcp Attorney Docket No. 21511/901$5 PCT/US99/05365 Protein Molecular Characterization of Labyrinthine. Previous work using Western blot apalysis (a qualitative assay to assess antigens) has shown that the Lab antigen is a 40 kilodalton (by relative mobility) protein detectable in A549 cells (Radosevich et al,, 1985), The epitope does not appear to be modulated or blocked by 5 lectins, and is selectively expressed on the ceil surface, primarily localized to the plasma membrane. (Radosevich et al,, 1985,1991). Lab is sensitive to proteases, bat not lipid or carbohydrate altering reactions (Radosevich et aL, 1985). The biochemical properties of Lab axe consistent with Lab being an integral membrane protein.

Having a deduced amino acid sequence from the lab gene of the present invention, allows further characterization of the Lab protein. Extensive computer analysis of Lab has identified a eulcaryatic leader-like sequence and theoretical cleavage site, 3 myristylatiou sequence sites, a weak membrane anchoring domain (MAD I), and a Strang membrane anchoring domain (MAD II) (FIG. 2). [(In the 15 HAAH sequence, there are 58 (theoretical) amino acids followed by a sequence homology in the Lab protein coding sequence and an additional 443 amino acid 3' to the lab sequence.)] Wb«i Lab is expressed as a fusion protein in abacterial GST fusion expression system (pGEMEX-2T) (Amereham Pharmacia Biotech, Inc., Piscataway, 20 ' New Jersey, 08854, USA), and subjected to Western blot analysis using the antibody MCA 44-3 A6, the resulting blots demonstrate that the expressed cleaved fusion protein has the same relative mobility as the protein detected in A549 cells, The deduced molecular weight for Lab is 28.8 Jdlodalpns and on Western blots it has a relative mobility identical to the form expressed by A549 cells (apparent relative 25 mobility = 40 kilodaltpns). The 55 glutamic and 27 aspartic acid residues a (82 residues combined) are almost uniformly distributed throughout the protein (255 amino acids total; 228 no leader sequence), except for the leader sequence and the strongest membrane anchoring domain (MAD II). These data suggest that Lab migrates anomalously in SDS gels, Cell lines other than A549 (for example, 30 adenocarcinomas DU-145, ATCC # HTB-81; ZR-75-1, ATCC # CR1-1504, and so forth) have an antigen detected with the same molecular weight antigen as Lab.

Neither a 85-90 kilodalton molecular weight species, nor a 52 and 56 kilodalton. molecular weight species is noted when probing' Western, blocs for Lab, ■;* rV.VON'HPA MI.'t£\CHEN 01 • • n ■ nn ■ ' °'30 • aia • W22- +49 89 23994405 :#->o §Mm pctus^OSS®. o^cf^.v Attorney Docket No. 215U/9Q185 PCT/US99/05365 -15' Enitooe Manning Using the Antibody MCA 44-3 A6 aad Vaccine Fea^WHtv nf Life: Using Polymerase Chain Reaction and the GST fusion, protein system, subclones of the protein coding region were made, and epitopes mapped the binding of MCA 44-3A6 to six amino acids (PTGEPQ) representing amino acids #117-122 of Lab ("P" 5 peptide). In order to determine this epitope, the entire coding region was divided into regions, Polymerase Chain Reaction primers were designed to amplify each region, and the subsequent expression of Polymerase Chain Reaction, products were cloned and tested by Western biot analysis using the antibody MCA 44-3A6.

The DNA fragment representing the positive Western blot result was then 10 further subdivided. Polymerase Chain Reaction products were generated and cloned, ^ expressed, and tested via Western blot, Constructs were made in this way both from 1 the 5' end and the 3' end. and the intervals of the number of amino acids were reduced upon each round. This respited in the last round representing a one' amino acid difference from the previous round (in both directions), such that one could deduce 15 the exact binding site of the MCA 44-3 AS. This demonstrates that at least these six amino acids are exposed to the external cell surface. To further prove the point, the DNA encoding only these six amino acids have been cloned and the fusion protein is positive by Western blot analysis. Synthetically prepared "P'f peptide can be specifically detected by MCA 44-3 A6, and the synthetic peptide was immunogenic in 20 ' 5 of 5 mice tested. Computer analysis/modeling also predicted that this epitope would be very immunogenic using computer assisted analysis (GCG programs) (Genetics Computer Group, Madison, WI53703), ^ Vaccine Preparation,: A vaccine is a preparation of antigens), which when ' given to a host, results in the host producing antibodies against the amigen(s), The host reisponse results in the host being immune to the disease to which the vaccine was directed. Vaccine treatment therefore, prevents the clinical presentation of a disease, without the hast being exposed to the disease causing agents. Lai has all the J W SKV A VN >S V% 0, l,„-99 ni,, tMC-ISSS1 PCTUS S'905365 DESCPAMD ' - Attorney Dock# No. 2l 511/901 $5 PCT/US99/05365 characteristics of a preferred cancer vaccine. The lab gene is frequently expressed by tumors which look like adenocarcinomas, is expressed an the outside of the cells, is expressed by all of Che cells within a given cancer, is expressed ai all times by these cancer cells, and is infrequently expressed by normal cells. Lab protein (peptides) can 5 be produced by any number of methods using molecular cloning techniques, and can be produced in large quantities, thus n^Jring it a practical antigen to use as a vaccine.

After fte Lab protein has been purified so that it is suitable fbr injection into humans, it is administered to individuals intradermally, subcutaneously, or by other routes, so as in challenge the immune system to produce antibodies against this protein 10 (peptides). » The use of mol ecular mod eling and computer assisted analysis GC G pro grains (Genetics Crystal Group, Madison, WI S3 703) allows the identification of small portions of a molecule, slightly larger than an epitope (six to seven amino acids fbr proteins), which are expected to be on the surface of a protein molecule. In addition, 15 the degree of lay drophobicity or hydiophilic ity of a given sequence, and how immunogenic the sequence would be in animals, can be determined (Genetics Crystal Group, Madison, WI 53703). After denning which sequences meet these criteria, the peptides are synthetically made, or produced by a number of standard methods. One or more of these peptides can then be formulated to be used as a vaccine, and 20 administered to the host as outlined above, as a vaccine.

A vaccine comprising a molecule having an amino acid sequence selected from the group of sequences encoded by the cDNA of FIG. 1, sequences of FIG. 2, encoded by the cDNA, the peptides APPHDNPVED (SEQ ED NO:6), EEQQEVPPDT (SEQ ID NO:7), DGPTGEPQQE (SEQ ID NO;8), and EQENPDSSEPV (SEQ ID 25 NO:9), and any fragments or combinations thereof.

A given vaccine may be administered once to a host, or may be administered many times, In order for some patient? to recognize a given vaccine, an adjuvant may also need to be administered with the peptides. Adjuvants are nonspecific immune stimulators which heighten the immune readiness and aid in the conversion of the 30 host from not having detectable serum antibodies to having very high titer serum antibodies. It is this high level (titer) of antibodies, which effectively protects the host from the diseases or conditions to which the antibodies are directed.

:CV. VO\:EHA MUE\CHE\ 01 ; '10-99 : 0:40 : 012 ~t0~1$93 d 72l2-> +4 9 8u 2usw4io #04. pcjus m 05365; dsscpamd Attorney Docket No, 2151 !/'Pdl&5 PCT/US99.-053 63 Functional Studies: Studies directed si understanding the csllulax functions of Lab are extensions of cell locaikation/oharacicrization studies (Siddique etal., 1992). Changes in levels of Lab in response to extracellular exposure to various response to extracellular exposure to various cations (Cpf*. Mg^, Cu"~, and Fe+t) were 5 undertaken. Lab expression in. A549 cells was only modulated by Ca*+, Using the highly specific fluorescent Furs-2/AM Ca^ method, of measuring cytosolic Ci**, (Molecular Probes Inc., Eugene, OR 97402) it was demonstrated that; (1) the internal Ca^ concentration Is higher In A549 cells than in QU-DB cells; and (2) that the A549 cdl line responds to various external Ca7* levels (Siddique et aL, 1992). Since pH 10 can. modulate intracellular free Ca^ levels, external pH manipulations should result in changes-in the expression levels of Lab. Extracellular pH changes (in the presence of normal Ca* concentrations) result in: (1) a parallel change in intracellular pH as measured by SNARF-1 AM/FACS, (Molecular Probes Inc., Eugene, OR 97402); (2) transcript levels increase for Lab (when compared to GAPDH expression via Northern 15 blot)? and that (3) Lab protein also increases (using Western/Slot blot analysis). The intracellular changes in pH (due to external changes) for A549 cells axe identical to those reported for normal cells, The increased expression of lab is also not due to cell ■death (as measured by MTT assays) (Siddique et al, 1992), In addition, incubation of recombinant Lab at various pH solutions does not alter immimoreactivity. 20 Preliminary data suggests that when these experiments are conducted on A549 ceils grown in reduced Ca~", the induced expression of lab is blunted.

Methods of Diagnosing Cancer Calls in a Sample of Cells; Biological samples from a subject are used to determine whether cancer cells are present in the subject.

Examples of suitable samples include blood and biopsy material. One method of 25 diagnosis is to expose DNA form cells in the sample to a labeled probe that is capable of hybridizing to the lab gene, or a fragment thereof, under stringent conditions- for example, fix ssc; 0.05x blotto; 50% form amide; 42°C (Sambrook ef al„ 1990). Of course, the hybridizing conditions are altered to achieve optimum sensitivity and specificity depending on the nature of the biological sample, type of cancer, method of 30 probe preparation, and method of tissue preparation.

After contacting the sample with the probe, the next step is determining whether the probe has hybridized with nucleotide sequences of the DNA from the Attorney Docket No, 21511/90185 PCT/US99/05365 sample, from which the presence of the lab gene is inferred, said presence being diagnostic of cancer.

Another diagnostic method is to obtain monoclonal antibodies preferably labled, either antibodies already existing, or new ones directed to the antigenic peptides that are aspects of the present invention, and contact a sample with, these to detect the Lab antigen. These monoclonal antibodies are useful in the development of very specific assays for the detection of Lab antigen, and allow the tests to be carried out in many different formats; resulting in a. broader application in science and medicine.

The current invention is useful in that it describes a new gene which is expressed on the surface of tumors, which-was not previously reported. This gene is oot tissue specific, and therefore will allow the detection of tumors regardless of the organ in which they arise. Likewise, the use of this gene to produce a vaccine for these tumors, will have a very broad application. Diagnostic tests will also have this broad tissue use, making the detection of Lab/lab a "pan-marker" for cancer, in particular for what have been designated previously, adenocarcinomas. <CY. VON: HI'A .V1Ul£\CHL\ 0 1 "j-10-49 : n-ji • Jy °-4' • 312 t .722- +4.0 89 2:3994- -10-189? PCTJS'SS 05365 DESCPAMD Attorney Docket No, 215l\/$0lh ' PCT/US99/05365 DOCUMENTS CITED Albino, AP, Qraf, LH, Kontor, RRS, et al. DNA-mediated transfer of human melanoma cell surface glycoprotein gp!30: Identification of transfectants by erythrocyte resetting. Mol. Cell. Biol. 5:692-697, 1985.

Banner BF, Gould YE, Radosevich JA, et aL Application of monoclonal antibody 44-3A6 in the cytodiaenosia and classification of pulmonary carcinomas.

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Brown, DT and Moore, M. Monoclonal antibodies against two human lung carcinoma cell link. Br. J. Can. 46:794-801, 1980.

Combs SG, Hidvegi DF, Ma Y, et al. Pleomorphic Carcinoma of the ^ Pancreas; A rare case report of combined histological features of pleomorphic ) _ adenocarcinoma and giant cell tumor of the pancreas. Diag, Cytopathal. 4:316-322, 1938a, Combs SG, Radosevich JA, Ma Y, et al. Expression of the Antigenic 15 Determinant Recognized by the Monoclonal Antibody 44-3 A6 on Select Human Adenocarcinomas and Normal Human Tissues. TmnorBiol, 9:116-122, 1988b.

Combs SG, Radosevich JA, and ST Rosen. Cytologicai expression of the • adenocarcinoma antigen marker in human body fluids, Tumor Biol. 9:116-122, 1988c.

' Di*da RB, August CZ, Radosevich JA and ST Rosen. Monoclonal Antibody 44-3 A6 as a Marker for Differentiation of Breast Cancer. Tumor Biol. 12:254-260, 1992.

^ Engvall, E arid Perlmann, P. Enzyme linked immunosorbent assay (ELISA): ) Quantitative assay of IgG. Imimmocheraistry. 8:87-874,1971.

Gronke RS, VanDusen WJ, Garsky VM, Jacobs JW, Sardana MK, Stem AM, and PA Friedman. Aspartyl beta hydroxylase: In vitro hydraxylarion of a synthetic * peptide based on the structure of the first growth factor-like domain of human factor IX. PNAS. 86:3609-3613,1989.

Gronke R£> WelschDJ, VanDusen "W7, Garsky VM, Sardana MK, Stem AM, 30 and PA Friedman. Partial purification and characterization of bovine liver aspartyl beta hydroxylase. J.Biol. Chem. 365-8558-8565, 1990, <yv. VON: Ui MUK\CHE\ 01 1-10-90: 0:4o ; 31., .< ■ 31 - - 7++9 89 213994-4G5:#27 PCTUS &9 05385 DESCPAMD *" Attorney Docket No. 215'lj/9Q]M3' " ' PCT/US99/05365 Jia S, VanDusen WJ, Diehi RE, KohnNE, Dixon RAF, Ellison KO, Stem AM, and PA Friedman. cDHA cloning and expression of bovine aspartyl (aspajageinyl) beta-hydroxylase. J. Biol. Chem, 267:14322-14327,1992.

Jia S, McGinns K, Van Dusen WJ, Burks CJ, Kua A, Griffin PR, Sardana 5 MK, Ellison KO, Stem AM, and PA Friedman. A fully active catalytic domain of bovine aspartyl (asparagmyl) beta-hydioxylase expressed in Escherichia coli: Characterization and evidence for the identification, of an. active-site region in vertebrate alph-ketoghitarata-dependem dioxygenases. PNAS 91:7227-7231,1994.

Korioth F, Gieffers C, and J Ftey. Cloning and characterization, of the human 10 gene encoding aspartyl beta-hydroxylase. Gene 150:395-399,1994.

Landis, SH, Murray T, Bolden S, an4 PA Wingo. Cancer Statistics, 1998, CA ) 44:6-9.

Lavaissiere L, Jia S, Nishiyama M, de la Monte S, Stren AM, Wands JR, and PA Friedman. Overexpression of human aspartyl (asparaginyl) beta-hydioxylase in 15 hepatocellular carcinoma and cholangiocarcinoraa. J. Clin. Invest. 98:1313-1323, 1996.

Lebo E.V, Tolan DR, Bruce 3D, Cheng MC, and YW Kan. Spot blot analysis of sorted chromoaomes assigns a fructose intolerance gene locus to chromosome 9. Cytometry. 6:476-483,1985.

Lee I, Radosevich JA, Rosen ST, et al, Imroimohistochemistry of lung • • carcinomas using monoclonal antibody 44-3A6. Can. Res. 45:5813-5817, 1985.

Lee I, Radosevich JA, Chelfec G, et al. Malignant Mesotheliomas: Improved Differential Diagnosis From Lung Adenocarcinomas Using Monoclonal Andbcides • ) 44-3A6 and 624A12. Amer, J. Path. 123:497-507, 1986.

Livingston PO, Wong GYC, Adluri S, Tao Y, Padevan M, Parents R, Hanlon C, Calves MJ, HtUing F, Bitter G, Oettgen, HP, and LJ Old. Improved survival in AJCC stage m melanoma pataitns with GM2 antibodies: A randomized trial of adjuvant vaccination with GM2 ganglioside. J, Clin. Oncol, 12:1036-1044, 1994.

Piehl MR, Gould VE, Radosevich JA, et al. Ixrantoohiatochemical 30 identification of Exocrine an4 Neuroendocrine Subsets of Large Cell Lung Carcinomas. Path. Res. and Prac, 183:675-682, 1988. \0n li \ ml'enchgn oj ^-ki-qg : 0-^- ..... * < 0 1. ju1~ +'v9 89 2u994-m35: #->8 %ss'% .. %-.**%<• 5- V •• ifyfi ~10?1». PCJUS m 05365 DESCPAMD Attorney Docket No, 21511/90lis PCT/US99/0S365 Radosevich JA, Ma Y, Lee I, et al. Monoclonal antibody 44-3A6 as a. probe for a novel antigen found Human lung carcinomas with glandular differentiation. Can. Res. 45:5805-5812, 1985.

Radosevich JA, Lee I, Gould YE, and ST Rosea Monoclonal antibody assays 5 for lung cancer. In: In vitro diagnosis of human tumora using monoclonal antibodies. Kupchick HZ and N Rose (Eds.) Marcel Dekker £101419,198S.

Radosevich JA, Combs SG, and ST Rosen, lamohistocheaaical analysis of lung cancer differentiation markers. In: Lung Cancer Differentiation. Lung Biology in Health and Disease, L'Enfant C, Bernal S, and Baylin S. (Eds.) Marcel Dekker, 10 1990a.

^ Radosevich JA, Noguchi M, Rosen ST, Y Shimosato. Iromunocytocheirnical analysis of human adenocarcinomas and bronchiolo alveolar carcinomas of the lung using this monoclonal antibody 44-3A6. Tumor Biology. 11:151485, 1990b.

Radosevich JA, Combs SG, and ST Rosen. Expression of MCA 44-3A6 in 15 human fetal development. Tumor Biology 12:321-329,1991A Radosevich JA, Siddique FS, Rosen ST, and WJ Kabat, Cell Cycle and EM Evaluation of the Adenocarcinoma Antigen Recognized by the Monoclonal Antibody 44-3A6, Br. J. Can, 63:86-87,1991.

Rosen ST, Mulshine JL, Cuttitta F, and PG Abrams. Biology of Lung Cancer. 20 ' Marcel Dekker, Inc. New York, NY, Vol, 37,1988.

Sambrook J, Fritsch EF, and T Maniatis. Molecular cloning: a laboratory manual. 2nd Ed. Cold Spring Harbor Lab. Press, 1990.

^ Sastry L, Alting-Mees M, Huse WD, Short JM, Hay BN, Janda KD, Benkovis ) S J, and Lemer. Cloning of the immunological repertoire in Escherichia coli for generation of monoclonal catalytic antibodies: Construction of a heavy chain, variable region-specific cDNA library. PNAS- 86:5728-5732,1989.

Siddique FS, Iqbal Z, and JA Radosevich. Changes in the expression of the tumor-associated Antigen recognized by monoclonal antibody 44-3A6 in A549 calls due to calcium. Tumor Biol, 13:142-151, 1992.

Sinkuls J, Rosen ST, and JA Radosevich. MCA 44-3 A6 Doxorubicin (Adriamydn) Immunoconjugates: Comparative in In Vitro Anti-Tumor Efficacy of Different Conjugation Methods. Tumor Biol. 12:198-206,1991, •A RC\. VON - LI'A VII.'ONCHENI 01 15-10-90 * • ,, JS .«'• «9 89.a3WIHTfi:»-B t5-10-199«, ' PCTUS990§36$ DESCPAMD Attorney Docket No, PCT/US99/05365 * Spagnolo DV, Witaker D, Carrello S, et al. The us« of monoclonal antibody 44*<3A6 in cell blocks in the dianosis of Lung carcinoma, carcinomas metastatic to lung and pleura, and pleural malignant mesothelioma. Am, J. Clin. Path. 95:322-329, 1991.

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I 23

Claims (11)

WHAT WE CLAIM IS: 1

1. Use of a DNA molecule with a nucleotide sequence as shown in FIG. 1 or a sequence showing at least about 70% homology to the nucleotide sequence in FIG. 1, for the diagnosis of cancer.

2. A cDNA molecule with a nucleotide sequence as shown in FIG. 1.

3. A cDNA molecule with a nucleotide sequence showing at least 70% homology to the nucleotide sequence in FIG. 1

4. A segment of the cDNA molecule of claim 2, wherein the segment extends from the start codon (ATG) to the stop codon TAA in the nucleotide sequence and includes 765 base pairs.

5. A segment of a cDNA sufficient to encode an epitope in a protein designated Lab detectable by the antibody MCA 44-3A6.

6. An isolated amino acid sequence encoded by the cDNA of either claim 2, 3,4 or 5.

7. A method to diagnose cancer cells in a sample of cells, said method comprising: a. contacting the sample of cells with a labelled probe that is capable of hybridizing to a cDNA molecule with a nucleotide sequence as shown in FIG. 1 or a fragment thereof, under stringent conditions; b. determining whether the probe has hybridized with nucleotide sequences in the sample; and c. inferring the presence of the sequence if the probe has hybridized, said presence being diagnostic of cancer. INTELLECTUAL PROPERTY office of n.z. " 1 MAY 2003 RECEIVED 24

8. Use of a molecule having an amino acid sequence selected from the group of sequences encoded by the cDNA of FIG. 1, sequences encoded by the cDNA of FIG. 2, the peptides APPEDNPVED, EEQQEVPPDT, DGPTGEPQQE, and EQENPDSSEPV, and any fragment or combinations thereof, in a vaccine.

9. An isolated molecule with an amino acid sequence selected from the group consisting of APPEDNPVED, EEQQEVPPDT, DGPTGEPQQE and EQENPDSSEPV.

10. An isolated molecule with the amino acid sequence PTGEPQ.

11. An isolated peptide selected from the group consisting of all sequences that are between 5 and 20 amino acids in length, aligned as are the amino acids in FIG 2, wherein the position of the first amino acid of the sequence of n amino acids is selected from the group consisting of position 1 to n-5 to n-20.

12. An isolated antibody directed to a peptide having an amino acid sequence selected from the sequence of claim 6, 8, 9, 10 or 11, excluding monoclonal antibody 44-3 A6.

13. The antibody of claim 12, further defined as a monoclonal antibody.

14. An isolated antibody produced in mammals against an amino acid sequence encoded by the DNA molecule of claim 2, 3,4 or 5 or a fragment thereof containing an epitope, excluding monoclonal antibody 44-3 A6.

15. A method to attenuate the effects of expression of the cDNA molecule of claim 2, 3, 4 or 5 said method comprising: a. obtaining an antisense molecule to the cDNA molecule or its expression product and INl omcFAifR0PERTY OFFICE OF N.Z. ~7 may 2003 RECEIVED 25 070 16. 17. 18. 19. 20. 21. 22. % 23. 24. 25. b. hybridizing the antisense molecule to the cDNA molecule or its expression The method of claim 15, wherein the antisense molecule is at least 100 nucleotides in length. An isolated genomic DNA molecule from which the cDNA of claim 2 or 3 is derived. A vector comprising the isolated cDNA molecule of claim 2, 3, 4 or 5. A vector comprising a cDNA molecule that encodes a molecule with an amino acid sequence in accord with claims 6, 8,9,10 or 11. A use as claimed in claim 1 substantially as herein described or exemplified with reference to the accompanying drawings. A cDNA molecule as claimed in claim 2 or 3 substantially as herein described or exemplified with reference to the accompanying drawings. A segment as claimed in claim 4 or 5 substantially as herein described or exemplified with reference to the accompanying drawings. An isolated amino acid sequence as claimed in claim 6 substantially as herein described or exemplified with reference to the accompanying drawings. A method as claimed in claim 7 substantially as herein described or exemplified with reference to the accompanying drawings. A use as claimed in claim 8 substantially as herein described or exemplified with reference to the accompanying drawings. product.

26. An isolated molecule as claimed in claim 9 or 10 substantially as herein described or exemplified with reference to the accompanying drawings.

27. An isolated peptide as claimed in claim 11 substantially as herein described or exemplified with reference to the accompanying drawings.

28. An isolated antibody as claimed in claim 12 or 14 substantially as herein described or exemplified with reference to the accompanying drawings.

29. A method as claimed in claim 15 substantially as herein described or exemplified with reference to the accompanying drawings.

30. An isolated genomic DNA molecule as claimed in claim 17 substantially as herein described or exemplified with reference to the accompanying drawings.

31. A vector as claimed in claim 18 or 19 substantially as herein described or exemplified with reference to the accompanying drawings. ~7 MAY 2003