US 5,773,579 AGrant
Lung Cancer Marker
Issue Date:1998-06-30
•12 Claims
•1 Drawing Sheets
Abstract
The present invention discloses an isolated and purified nucleic acid sequence and corresponding amino acid sequence to a novel protein specific for human lung cancer cells. This gene is expressed at a much higher level in these cells than in normal lung cells, other normal tissues and other tumor cell lines tested. Also disclosed are three additional recombinant forms of this gene and protein, in the first two cases a membrane spanning region is removed and in the third case an amino acid is changed by in vitro mutagenesis.
Metadata
Assignee
- Cytoclonal Pharmaceutics, Inc.
Inventors
- Richard M. Torczynski
- Arthur P. Bollon
Application Information
Application Number:US 7760884
Filing Date:1997-01-21
Priority Date:1994-07-19
Art Unit:187
Classifications
IPC:
C07K 1400C07H 2100
Field of Search:
53053693035023.1;24.310;240
Patent Drawings (1 sheets)
Description
TECHNICAL FIELD
The invention relates to genes and proteins specific for certain cancers and methods for their detection.
BACKGROUND OF THE INVENTION
Lung cancer is the most common form of cancer in the world. Estimates for the year 1985 indicate that there were about 900,000 cases of lung cancer worldwide. (Parkin, et al., "Estimates of the worldwide incidence of eighteen major cancers in 1985," Int J Cancer 1993; 54:594-606). For the United States alone, 1993 projections placed the number of new lung cancer cases at 170,000, with a mortality of about 88%. (Boring, et al., "Cancer statistics," CA Cancer J Clin 1993; 43:7-26). Although the occurrence of breast cancer is slightly more common in the United States, lung cancer is second behind prostate cancer for males and third behind breast and colorectal cancers for women. Yet, lung cancer is the most common cause of cancer deaths.
The World Health Organization classifies lung cancer into four major histological types: (1) squamous cell carcinoma (SCC), (2) adenocarcinoma, (3) large cell carcinoma, and (4) small cell lung carcinoma (SCLC). (The World Health Organization, "The World Health Organization histological typing of lung tumours," Am J Clin Pathol 1982; 77:123-136). However, there is a great deal of tumor heterogeneity even within the various subtypes, and it is not uncommon for lung cancer to have features of more than one morphologic subtype. The term non-small cell lung carcinoma (NSCLC) includes squamous, adenocarcinoma and large cell carcinomas.
Typically, a combination of X-ray and sputum cytology is used to diagnose lung cancer. Unfortunately, by the time a patient seeks medical help for their symptoms, the cancer is at such an advanced state it is usually incurable. Cancer Facts and Figures (based on rates from NCI SEER Program 1977-1981), New York: American Cancer Society, 1986). Routine large-scale radiologic or cytologic screening of smokers has been investigated. Studies concluded that cytomorphological screening did not significantly reduce the mortality rate from lung cancer and was not recommended for routine use. ("Early lung cancer detection: summary & conclusions," Am Rev Respir Dis 1984; 130:565-70). However, in a subpopulation of patients where the cancer is diagnosed at a very early stage and the lung is surgically resectioned, there is a 5-year survival rate of 70-90%. (Flehinger, et al., "The effect of surgical treatment on survival from early lung cancer," Chest; 1992, 101:1013-1018; Melamed, et al., "Screening for early lung cancer: results of the Memorial Sloan-Kettering Study in New York," Chest; 1984 86:44-53). Therefore, research has focused on early detection of tumor markers before the cancer becomes clinically apparent and while the cancer is still localized and amenable to therapy.
The identification of antigens associated with lung cancer has stimulated considerable interest because of their use in screening, diagnosis, clinical management, and potential treatment of lung cancer. International workshops have attempted to classify the lung cancer antigens into 15 possible clusters that may define histologic origins. (Souhami, et al., "Antigens of lung cancer: results of the second international workshop on lung cancer antigens," JNCI 1991; 83:609-612). As of 1988, more than 200 monoclonal antibodies (MAb) have been reported to react with human lung tumors. (Radosevich, et al., "Monoclonal antibody assays for lung cancer," In: Cancer Diagnosis in Vitro Using Monoclonal Antibodies. Edited by H. A. Kupchik. New York: Marcel Dekker, 1988).
MAbs for lung cancer were first developed to distinguish NSCLC from SCLC. (Mulshine, et al., "Monoclonal antibodies that distinguish nonsmall-cell from small-cell lung cancer," J Immunol 1983; 121:497-502). In most cases, the identity of the cell surface antigen with which a particular antibody reacts is not known, or has not been well characterized. (Scott, et al., "Early lung cancer detection using monoclonal antibodies," In: Lung Cancer. Edited by J. A. Roth, J. D. Cox, and W. K. Hong. Boston: Blackwell Scientific Publications, 1993).
MAbs have been used in the immunocytochemical staining of sputum samples to predict the progression of lung cancer. (Tockman, et al., "Sensitive and specific monoclonal antibody recognition of human lung cancer antigen on preserved sputum cells: a new approach to early lung cancer detection," J Clin Oncol 1988; 6:1685-1693). In the study, two MAbs were utilized, 624H12 which binds a glycolipid antigen expressed in SCLC and 703D4 which is directed to a protein antigen of NSCLC. Of the sputum specimens from participants who progressed to lung cancer, two-thirds showed positive reactivity with either the SCLC or the NSCLC MAb. In contrast, of those that did not progress to lung cancer, 35 of 40 did not react with the SCLC or NSCLC Mab. This study suggests the need for the development of additional early detection targets to discover the onset of malignancy at the earliest possible stage.
Carcinoembryonic antigen (CEA) is a frequently studied tumor marker of cancer including lung cancer. (Nutini, et al., "Serum NSE, CEA, CT, CA 15-3 levels in human lung cancer," Int J Biol Markers 1990; 5:198-202). Squamous cell carcinoma antigen is another established serum marker. (Margolis, et al., "Serum tumor markers in non-small cell lung cancer," Cancer 1994; 73:605-609.). Other serum antigens for lung cancer include antigens recognized by MAbs 5E8, 5C7, and 1F10, the combination of which distinguishes between patients with lung cancer from those without. (Schepart, et al., "Monoclonal antibody-mediated detection of lung cancer antigens in serum," Am Rev Respir Dis 1988; 138:1434-8) Furthermore, the combination of 5E8, 5C7 and 1F10 was more sensitive, specific and accurate for identifying NSCLC when compared to results from a combination of the CEA and squamous cell carcinoma antigen tests. (Margolis, et al., Cancer 1994; 73:605-609).
Serum CA 125, initially described as an ovarian cancer-associated antigen, has been investigated for its use as a prognostic factor in NSCLC. (Diez, et al., "Prognostic significance of serum CA 125 antigen assay in patients with non-small cell lung cancer," Cancer 1994; 73:136876). The study determined that the preoperative serum level of CA 125 antigen is inversely correlated with survival and tumor relapse in NSCLC.
Despite the numerous examples of MAb applications, none has yet emerged that has changed clinical practice. (Mulshine, et al., "Applications of monoclonal antibodies in the treatment of solid tumors," In: Biologic Therapy of Cancer. Edited by V. T. Devita, S. Hellman, and S. A. Rosenberg. Philadelphia: JB Lippincott, 1991, pp. 563-588). MAbs alone may not be the answer to early detection because there has only been moderate success with immunologic reagents for paraffin-embedded tissue. Secondly, lung cancer may express features that cannot be differentiated by antibodies; for example, chromosomal deletions, gene amplification, or translocation and alteration in enzymatic activity.
After the gene to the MAb recognized surface antigen has been cloned, cytogenetic and molecular techniques may provide powerful tools for screening, diagnosis, management and ultimately treatment of lung cancer. An example of a lung cancer antigen that has been cloned is the adenocarcinoma-associated antigen. This antigen, recognized by KS1/4 MAb, is an epithelial malignancy/epithelial tissue glycoprotein from the human lung adenocarcinoma cell line UCLA-P3. (Strand, et al., "Molecular cloning and characterization of a human adenocarcinoma/epithelial cell surface antigen complementary DNA," Cancer Res 1989; 49:314-317). The antigen has been found on all adenocarcinoma cells tested and in various corresponding normal epithelial cells. Northern blot analysis indicated that transcription of the adenocarcinoma-associated antigen was detected in RNA isolated from normal colon but not in RNA isolated from normal lung, prostate, or liver. Therefore identification of adenocarcinoma-associated antigen in lung cells may prove to be diagnostic for adenocarcinoma.
The cloning of CEA and the nonspecific crossreacting antigen (NCA) has allowed the development of specific DNA probes which discriminate their expression in lung cancer at the mRNA level. (Hasegawa, et al., "Nonspecific crossreacting antigen (NCA) is a major member of the CEA-related gene family expressed in lung cancer," Br J Cancer 1993; 67:58-65). NCA is a component of the CEA gene family in lung cancer and is also recognized by anti-CEA antibodies, especially polyclonal antibodies. Because of the crossreactivity, investigations to analyze CEA and NCA separately in lung disease had been difficult. The use of DNA probes determined that lung cancer cells fall into three different types according to their CEA and/or NCA expression by Northern blot analysis. Specifically, lung cancers expressed both CEA and NCA mRNA, only NCA mRNA, or neither mRNA. CEA-related mRNA expression was always accompanied by NCA mRNA expression and there were no cases of CEA MRNA expression alone. The separate assessment of CEA and NCA expression in lung cancers may be important in determining the prognosis of lung cancers because the antigens have been described as cell-cell adhesion molecules and may play a role in cancer metastasis.
Another method to detect the presence of an antigen gene or its mRNA in specific cells or to localize an antigen gene to a specific locus on a chromosome is in situ hybridization. In situ hybridization uses nucleic acid probes that recognize either repetitive sequences on a chromosome or sequences along the whole chromosome length or chromosome segments. By tagging the probes with radioisotopes or color detection systems, chromosome regions can be identified within the cell. Investigations using in situ hybridization have demonstrated numerical chromosomal abnormalities in samples from human tumors, including bladder, neuroectodermal, breast, gastric and lung cancer tumors. (Kim, et al., "Interphase cytogenetics in paraffin sections of lung tumors by non-isotopic in situ hybridization. Mapping Genotype/phenotype heterogeneity," Am J Pathol 1993; 142:307-317).
Fluorescence in situ hybridization (FISH) allows cells to be stained so that genetic aberrations resulting in changes in gene copy number or structure can be quantitated by fluorescence microscopy. In this technique, a chemically labeled single-stranded nucleic acid probe homologous to the target nucleic acid sequence is annealed to denatured nucleic acid contained in target cells. The cells may be mounted on a microscope slide, in suspension or prepared from paraffin-embedded material. Treating the chemically modified probes with a fluorescent ligand makes the bound probe visible. FISH has been used for (1) detection of changes in gene copy number and gene structure; (2) detection of genetic changes, even in low frequency subpopulations; and (3) detection and measurement of the frequency of residual malignant cells. (Gray, et al., "Molecular cytogenetics in human cancer diagnosis," Cancer 1992; 69:1536-1542).
Other molecular markers for lung cancer include oncogenes and tumor suppressor genes. Dominant oncogenes are activated by mutation and lead to deregulated cellular growth. Such genes code for proteins that function as growth factors, growth factor receptors, signal transducing proteins and nuclear proteins involved in transcriptional regulation. Amplification, mutation, and translocations have been documented in many different cancer cells and have been shown to lead to gene activation or overexpression.
The ras family of oncogenes comprises a group of membrane associated GTP-binding proteins thought to be involved in signal transduction. Mutations within the ras oncogenes, resulting in sustained growth stimulation, have been identified in 15 to 30% of human NSCLC. (Birrer, et al., "Application of molecular genetics to the early diagnosis and screening of lung cancer," Cancer 1992; 52suppl; 2658s-2664s). Patients with tumors containing ras mutations had decreased survival compared with patients whose tumors had no ras mutations. Polymerase chain reaction (PCR) amplification of ras genes can be analyzed to determine the presence of mutations by several methods: (a) differential hybridization of .sup.32 P-labeled mutated oligonucleotides; (b) identification of new restriction enzyme sites created by the activating mutation; (c) single-strand conformational polymorphisms; and (d) nucleic acid sequencing. These methods combined with PCR technology could allow detection of an activated ras gene from sputum specimens.
Another family of dominant oncogenes, the erb B family, has been found to be abnormally expressed in lung cancer cells. This group codes for membrane-associated tyrosine kinase proteins and contains erb B1, the gene coding for the epidermal growth factor (EGF) receptor, and erb B2 (also called Her-2/neu). The erb B1 gene has been found to be amplified in NSCLC (up to 20% of squamous cell tumors), while the EGF receptor has been shown to be overexpressed in many NSCLC cells (approximately 90% of squamous cell tumors, 20 to 75% of adenocarcinomas, and rarely in large cell or undifferentiated tumors). (Birrer, et al., Cancer 1992: 52 suppl; 2658s-2664s). Amplification of the related oncogene erb B2 (Her-2/neu) occurs infrequently in lung cancer but is a negative prognostic factor in breast cancer. However, overexpression of the erb B2 protein product, p185.sup.neu, occurs in some NSCLC and may be related to poor prognosis. (Kern, et al., "p185.sup.neu expression in human lung adenocarcinomas predicts shortened survival," Cancer Res 1990; 50:5184-5191).
A third family of dominant oncogenes involved in lung cancer is the myc family. These genes encode nuclear phosphoproteins, which have potent effects on cell growth and which function as transcriptional regulators. Unlike ras genes, which are activated by point mutations in lung cancer cells, the myc genes are activated by overexpression of the cellular myc genes, either by gene amplification or by rearrangements, each ultimately leading to increased levels of myc protein. Amplification of the normal myc genes is seen frequently in SCLC and rarely in NSCLC.
The loss or inactivation of tumor suppressor genes may also be important steps in the pathway leading to invasive cancer. Tumor suppressor genes function normally to suppress cellular proliferation, and since they are recessive oncogenes, mutations or deletions must occur in both alleles of these genes before transformation occurs.
A phosphoprotein p53, which is encoded by a gene located on chromosome 17p, suppresses transformation in its wild-type state. While in its mutant state, p53 acts as a dominant oncogene. p53 functions in DNA binding and transcription activation. Mutations of p53 have been found in many human cancers including colon, breast, brain and lung cancer cells. (Birrer, et al., Cancer Res. (suppl) 1992, 52:2658s-2664s). In NSCLC cell lines, p53 mutations have been found at a rate of up to 74%. (Mitsudomi, et al., "p53 gene mutations in non-small-cell lung cancer cell lines and their correlation with the presence of ras mutations and clinical features," Oncogene 1992; 7:171-180).
Despite all of the advances made in the area of lung cancer, medical and surgical intervention has resulted in little change in the 5-year survival rate for lung cancer patients. Early detection holds the greatest hope for successful intervention. There remains a need for a practical method to diagnose lung cancer as close to its inception as possible. In order for early detection to be feasible, it is important that specific markers be found and their sequences elucidated.
A lung cancer marker antigen, specific for NSCLC, has now been found, sequenced, and cloned. The antigen is useful in methods for detection of non-small cell lung cancer and for potential production of antibodies and probes for treatment compositions.
SUMMARY OF THE INVENTION
The invention concerns a lung cancer antigen (HCAVIII) gene specific for non-small cell lung cancer.
In one embodiment, the invention relates to a substantially purified nucleic acid (SEQ ID NO:1) encoding the pre-protein sequence shown in SEQ ID NO:2.
In other embodiments, the invention relates to cDNAs which encode the mature form of the protein (SEQ ID NO:4), or a truncated form of the protein lacking the transmembrane domain (SEQ ID NO:13 and SEQ ID NO:15), or a protein in which one or more of the amino acids in the phosphorylation region have been altered to affect that function, an example of which is shown in SEQ ID NO:18.
In other embodiments, proteins encoded by the cDNA of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:12, SEQ ID NO:14, and SEQ ID NO:17 are provided.
In another aspect, the invention relates to a recombinant DNA clone for HCAVIII.
In further aspects of the invention, expression vectors for HCAVIII and modifications thereof are an object.
The invention further relates to methods of detecting lung cancer.
In one aspect an in situ hybridization technique is provided. In another aspect, a fluorescence in situ hybridization technique is provided. In a further aspect, an ELISA assay is provided. In another aspect, detection of carbonic anhydrase activity which correlates with lung cancer antigen is provided.
BRIEF DESCRIPTION OF THE DRAWING
FIG. 1 depicts the alignment of the amino acid sequence of HCAVIII with previously described carbonic anhydrases. Conserved amino acids are shown in bold.
DETAILED DESCRIPTION OF THE INVENTION
The nucleic acid sequence coding for a cell surface protein (said protein hereinafter designated HCAVIII) which is highly specific for non-small cell lung cancer cells has now been obtained. This gene sequence will facilitate detection and treatment of the disease, which to date has often proven difficult.
The HCAVIII cDNA in the vector pLC56 has been sequenced and characterized including the entire coding region and substantially all of the upstream and downstream non-translated regions. The cDNA in pLC56 was sequenced on both strands from exonuclease III-generated deletions and subsequent subcloning into M13 vectors or directly from the cloning vectors using the di-deoxy method and a SEQUENASE .RTM. Version 2.0 kit (U.S. Biochemicals, Cleveland, Ohio). Additional regions of DNA were subcloned as small restriction fragments into the same vectors for sequence analysis. Overlapping segments were ordered using MacVector Align software (Kodak/IBI Technologies, New Haven Conn.). SEQ ID NO:1represents the cDNA encoding HCAVIII and a presumed signal peptide. SEQ ID NO:2 represents the signal peptide (amino acid residues -29 to -1) followed by the mature protein (amino acid residues 1 to 325). As predicted from the cDNA sequence in pLC56, a protein of about 354 amino acids is encoded with the predictive size of 39448 daltons. A hydrophilicity plot (MacVector software, Kodak/IBI Technologies) of this protein provided strong evidence of a leader peptide at the N-terminus and a membrane-spanning segment near the C-terminus. The membrane-spanning segment provides evidence that this protein is membrane bound, as also predicted by its positive selection with panning methodology (See Watson, et al., Recombinant DNA, 2nd ed., pp. 115-116, 1992). The cleavage site of the signal as predicted by von Heijne (von Heijne, Gunnar, Nucleic Acids Res 1986; 14:4683-4690) is 29 amino acids down from the N-terminus methionine. SEQ ID NO:3 corresponds approximately to the coding region of the mature polypeptide. The subsequent "mature" protein is proposed to be 325 amino acids, initiating with serine, and of a calculated 36401 daltons and a pI of 6.42 (SEQ ID NO:4).
Homology searches against NCBI BlastN or BlastX version 1.3.12MP (National Center for Biotechnology Information, Bethesda, Md.) provided evidence the gene and protein are novel, not previously identified in either database. (Altschul, et al., "Basic local alignment search tool," J Mol Biol 1990; 215:403-410). Additional searches against another database (Entrez, version 9) gave similar results.
The isolation of a second cDNA encoding HCAVIII permitted the identification of new sequences within the 5'-and 3'-prime untranslated regions of this gene. SEQ ID NO:5, a cDNA encoding HCAVIII and a portion of the 5' and 3' nontranslated regions, has substantial identity with SEQ ID NO:1 (positions 1-1104 of SEQ ID NO:1 are identical to positions 85-1188 of SEQ ID NO:5). The encoded protein is listed in SEQ ID NO:6 and is identical with SEQ ID NO:2. Homology searches of NCBI BlastN against SEQ ID NO:5 showed these gene sequences have not been previously identified. SEQ ID NO:7 represents additional cDNA sequences of the 3' nontranslated region of the HCAVIII gene located downstream from the sequences depicted in SEQ ID NO:5. Homology searches against the same data base identified two clones with homology to SEQ ID NO:7. Both sequences are expressed sequence tags (EST), the first EST04899 (345 bp) and the second HUMGS04024 (466 bp).
Alignment searches indicate this protein shares common features with the seven human carbonic anhydrase proteins previously identified. However, as described below, certain structural features distinct to HCAVIII exist that may confer unique properties to this protein and a role in the transformation pathway to tumorgenicity. This group of enzymes catalyze the hydration of carbon dioxide
and in reverse the dehydration of HCO.sub.3.sup.-. This protein is identified as a carbonic anhydrase (CA) based on the conservation of amino acids at positions critical for the binding of Zn.sup.+2, and the catalysis of CO.sub.2, as well as numerous other conserved amino acids (see FIG. 1). The protein is 34 to 64 amino acids longer (at the C-terminus) than any previously reported carbonic anhydrase by virtue of the membrane-spanning region also found in HCAIV and an additional approximate 30 amino acids contained in the cytoplasmic side of the cell and apparently missing in other human CA isoforms. In addition, this intracellular domain contains a phosphorylation site recognized by protein kinase C and other kinases, as defined by the motif "Arg-Arg-Lys-Ser" (SEQ ID NO:8 and SEQ ID NO:9) (amino acid residues 1-4 in SEQ ID NO:9 and amino acid residues 299-302 in SEQ ID NO:2, SEQ ID NO:4 and SEQ ID NO:6).
Interestingly, this motif is found only in HCAVIII, and at a functionally significant site, i.e., within the cytosol. A surface cleft essential for enzymatic function present on other carbonic anhydrases is conserved for this protein, suggesting that this protein will also confer enzymatic activity. Five possible N-glycosylation sites are predicted by the primary amino acid sequence and the motif "Asn-Xaa-Ser (Thr)", beginning at amino acid residues -2, 51, 133, 151, and 202 in SEQ ID NO:2, respectively.
HCAVIII is expressed at a much higher level in a non-small cell lung cancer cell line (A549) than in normal lung tissue, other normal tissues, and other tumor cell lines which makes it useful in distinguishing this disease. This is clearly demonstrated in Table 1. Data for this table was obtained as follows. Total cellular RNA was isolated from the indicated actively growing cell lines as described by Chirgwin, et al., "Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease," Biochemistry 1979; 18:5294-5299. RNA samples were fractionated over a 1% agarose-formaldehyde gel and transferred to a nylon membrane (Qiagen, Chatsworth, Calif.) by capillary action. The hybridization probe was generated from a 1 kilobase pair BstXI restriction fragment isolated from pLC56, a plasmid harboring the HCAVIII gene in its initial isolation. This fragment was radiolabeled with 32p using a PRIME-IT.RTM. Random Primer Labeling Kit obtained from Stratagene, La Jolla, Calif. A membrane containing RNA derived from healthy human tissue was purchased from Clonetech Laboratories, Inc., Palo Alto, Calif. RNA blots were hybridized in a standard cocktail containing .sup.32 P-labeled probe at 42.degree. C. overnight then exposed to X-ray film. The same blots were subsequently, upon removal of the probe, rehybridized with a second .sup.32 P-labeled DNA from .beta.-actin to serve as a positive control for integrity of the blotted RNA.
As shown in Table 1, normal lung tissue does not express the HCAVIII gene in detectable amounts. Other tumor cell lines fail to express, or express only in minor amounts, which will allow easy distinction of non-small cell carcinomas.
In one embodiment of the invention, probes are made corresponding to sequences of the cDNA shown in SEQ ID NO:3, which are complimentary to the mRNA for HCAVIII. These probes can be radioactively or non-radioactively labeled in a number of ways well known to the art. The probes can be made of various lengths. Such factors as stringency and GC content may influence the desired probe length for particular applications. The probes correspond to a length of 10-986 nucleotides from SEQ ID NO:3. The labeled probes can then be bound to detect the presence or absence of mRNA encoding the HCAVIII in biopsy material through in situ hybridization. The MRNA is expected to be associated with the presence of non-small cell tumors and to be a marker for the precancerous condition as well.
In situ hybridization provides a specificity to the target tissue that is not obtainable in Northern, PCR or other probe-driven technologies. In situ hybridization permits localization of signal in mixed-tissue specimens commonly found in most tumors and is compatible with many histologic staining procedures. This technique is comprised of three basic components: first is the preparation of the tissue sample provided by the pathologist to permit successful hybridization to the probe. Second is the preparation of the hybridization probe, typically a RNA complementary to the mRNA of the gene of interest (i.e., antisense RNA). RNA probes are preferred over DNA probes for in situ hybridizations mainly because background hybridization of the probe to irrelevant nucleic acids or nonspecific attachment to cell debris or subcellular organelles can be eliminated with RNAse treatment post-hybridization. Third is the hybridization and post-hybridization detection. Typically the RNA transcript probe has been radiolabeled by the incorporation of .sup.32 P or .sup.35 S nucleotides to permit subsequent detection of the probed specimen by autoradiography or quantitation of silver grains following treatment with autoradiographic emulsion. Nonradioactive detection systems have also been developed. In one example, biotinylated nucleotides can be substituted for the radioactive nucleotide in the RNA probe preparation, permitting visualization of the probed sample by immunocytochemistry-derived techniques. Example 1 describes in situ hybridization procedures using RNA probes derived from the HCAVIII gene. Example 2 provides exemplary fluorescent in situ (FISH) hybridization procedures.
The cDNA for HCAVIII (SEQ ID NO:3) is currently in an expression vector which is be used to generate the protein in E. coli. This expression system described in Example 3 produces HCAVIII to be used as an antigen for the generation of antibodies (Example 4) for use in an ELISA assay to detect shed HCAVIII in body fluids as described in Example 5. The methods for production of antibodies and ELISA type assays are well known in the art. Exemplary methods and components of these procedures have been chosen and developed and are described in Examples 4 and 5.
The expression and purification of foreign proteins in E. coli is often problematic. On occasion, the protein is expressed at high levels but is deposited within the cell as an insoluble, denatured form termed an inclusion body. These bodies are often observed when the foreign protein contains a hydrophobic domain, such as found in the membrane spanning segment of HCAVIII. Through recombinant DNA technology, the DNA sequences encoding the membrane spanning segment of HCAVIII are deleted. The protein expressed in E. coli from this engineered plasmid is now in a soluble and native form within the cell, permitting a rapid and less harsh purification. In addition, the ELISA test to measure HCAVIII shed into body fluids as described in Example 5 relies on the recombinant protein produced from E. coli. Typically, the shed antigen is a membrane-bound receptor that was released from the membrane spanning segment anchoring it to the cell. Consequently, the recombinant HCAVIII engineered to remove the membrane spanning segment is a more accurate representation of the putative HCAVIII shed antigen found in specimens and may prove to be the preferred antigen for polyclonal antisera and monoclonal antibody production as described for the development of an ELISA test.
To produce the engineered plasmid, a first plasmid is constructed by cleaving pLC56 with the restriction enzyme Tth111 I, followed by treatment with T.sub.4 -DNA polymerase and dGTP, DATP, dTTP and dCTP, and finally with alkaline phosphatase to remove 5'-terminal phosphates. The DNA sample is then purified by phenol/chloroform extraction and ethanol precipitation. The sample is digested with the restriction endonuclease BspE1, then the fragments are resolved by agarose gel electrophoresis to permit the isolation of a 267 base pair fragment. A second plasmid described previously for expression of the HCAVIII mature protein (SEQ ID NO:4), is cleaved with EcoRI and BspE1 followed by alkaline phosphatase treatment and purification by phenol/chloroform extraction and ethanol precipitation. Two oligonucleotides are synthesized, being 5'-TGAGTCGACG (SEQ ID NO:10) and 5'-AATTCGTCGACTCA (SEQ ID NO:11), that complement each other and upon annealing, provide a termination codon (TGA) and sequence complementary to EcoRI cleaved DNA. Finally, the two oligonucleotides, the 267 base pair fragment, and the BspEI/EcoRI cleaved plasmid will be combined in a ligation reaction, and the resultant plasmid which contains the truncated DNA sequence (SEQ ID NO:12) is used to transform competent E. coli. Upon expression in E. coli, the resulting truncated protein (SEQ ID NO:13) is 271 amino acids as determined by SDS polyacrylamide electrophoresis and of a size consistent with other HCA's but lacking the membrane spanning segment and the intracellular domain. A second plasmid encoding a HCAVIII truncated protein (SEQ ID NO:14) lacking the membrane spanning segment and intracellular domain was created as described above, except that restriction enzyme Ple I was substituted for Tth111 I, resulting in a gel purified DNA fragment of 276 base pairs. Upon expression in E. coli, the resulting protein is now 274 amino acids (SEQ ID NO:15).
An understanding of protein phosphorylation and its role in the mechanism of cell transformation has been actively pursued, most notably with tyrosine phosphorylation and oncogene activation. The role of serine/threonine protein phosphorylation by a variety of protein kinases including protein kinase C has been studied extensively with respect to signal transduction, but its role in oncogenesis is less clear. To provide a valuable tool to be used in the study of the role of HCAVIII serine phosphorylation in oncogenesis, an altered cDNA can be prepared to code for an altered protein. Changes to amino acids other than "Gly" may be realized by alterations to the oligonucleotide sequence (SEQ ID NO:16) used to encode the selected residue. Other modifications to alter the serine phosphorylation site would utilize the described technology to modify either both "Arg" residues located within SEQ ID NO:9 or amino acid residues 299 and 300 of SEQ ID NO:2, SEQ ID NO:4 and SEQ ID NO:6. Since "Arg" residues contain a net positive charge, the substituted amino acids would preferably be "Lys" or "His," also positively charged amino acids. An exemplary plasmid is produced in which the "Ser" codon (amino acid residue 4 of SEQ ID NO:9; amino acid residue 302 in SEQ ID NO:2, SEQ ID NO:4 and SEQ ID NO:6), is converted to a "Gly" codon using an in vitro mutagenesis technique described in Example 3 and previously recited in Kunkel, Thomas, "Rapid and efficient site-specific mutagenesis without phenotypic selection," Proc Natl Acad Sci USA 1985; 82:488-492, and the oligonucleotide 5'-CTTTTTTGATACCCTTCCTTCTGAA (SEQ ID NO:16) (located in SEQ ID NO:1 at the base pairs 1010-1034 with 1022 as the mutagenized base pair). The DNA sequences containing the HCAVIII gene engineered for production of the mature protein and mutagenized codon is released from the mutagenesis vector by BamHI and EcoRI restriction endonucleases and ligated into pGEX4T1 cleaved with the same enzymes, and the resultant plasmid is used to transform competent E. coli. The codon mutagenesis is confirmed by DNA sequence analysis, and the protein is expressed and purified from E. coli as described in Example 3. The DNA sequence of the altered plasmid as shown in SEQ ID NO:17 differs from the gene encoding the mature protein (SEQ ID NO:3) in that the nucleotide 1022 is changed from "A" to "G", and the protein sequence (SEQ ID NO:18) expressed by the altered plasmid is identical to the mature protein (SEQ ID NO:4) except that amino acid residue 302 is changed from "Ser" to "Gly."
Another way to detect the presence of increased HCAVIII could be to assay for levels of carbonic anhydrase activity in biopsy materials as described in Example 6. This should be a useful test as HCAVIII, although it is an immunologically unique molecule, contains small but distinct regions which are conserved between previously reported carbonic anhydrase proteins.
In another embodiment of the invention, primers are made complimentary to the HCAVIII cDNA (SEQ ID NO:3) for detecting expression of the gene. PCR amplification of cDNA from lung biopsy cells would indicate the presence of the same non-small cell lung carcinoma.
Due to the non-small cell lung cancer specificity of HCAVIII and the gene encoding the protein, antibodies specific for HCAVIII would also exhibit non-small cell lung cancer specificity which can be employed for diagnostic detection of HCAVIII in body fluids such as serum or urine or HCAVIII containing cells. Targeting of cancer therapeutic drugs to HCAVIII containing cells can also be developed using HCAVIII specific antibodies. The genetic expression of the gene encoding HCAVIII could be modulated by drugs or anti-sense technology resulting in an alteration of the cancer state of the HCAVIII containing cells.
EXAMPLE 1
In Situ Hybridization using RNA Probes Derived from the HCAVIII Gene
Tissue samples are treated with 4% paraformaldehyde (or equivalent fixative), dehydrated in sequential ethanol solutions of increasing concentrations (e.g., 70%, 95% and 100%) with a final xylene incubation (see Current Protocols in Molecular Biology, pp. 14.01-14.3 and Immunocytochemistry II:IBRO Handbook Series: Methods in the Neurosciences Vol 14; pp 281-300, incorporated herein by reference). The tissue is embedded in molten paraffin, molded in a casting block and can be stored at room temperature. Tissue slices, typically 8 .mu.m thick, are prepared with a microtome, dried onto gelatin-treated glass slides and stored at -20.degree. C.
DNA sequences from the HCAVIII gene (SEQ ID NO:3) are subcloned into a plasmid engineered for production of RNA probes. In this example, a 776 bp DNA fragment is released from a pLC56 plasmid following BamHI/AccI digestion, where the BamHI site has been created by in vitro mutagenesis (see E. coli expression below). This fragment is ligated into pGEM-2 (Promega Biotec, Madison, Wis.) that was cleaved with BamHI and AccI and transformed into competent E. coli. This constructed plasmid contains the T7 RNA polymerase promoter downstream of the AccI restriction site and hence can drive transcription of the antisense HCAVIII sequences defined by the BamHI/AccI fragment. Following linearization of the subsequent plasmid with BamHI, an in vitro transcription reaction composed of transcription buffer (40 mM Tris-HCl, pH 7.5, 6 mM MgCl.sub.2, 2 mM spermidine, 10 mM NaCl, 10 mM dithiothreitol, 1 U/ul ribonuclease inhibitor), linearized plasmid, 10 mM GTP, 10 mM ATP, 10 mM CTP, 100 .mu.Ci of (.sup.35 S)UTP, and T7 RNA polymerase is incubated at 37.degree. C. Multiple RNA copies of the gene are produced that then are used as a hybridization probe. The reaction is terminated by the addition of DNAase, and the synthesized RNA is recovered from unincorporated nucleotides by phenol/chloroform extraction and sequential ethanol precipitations in the presence of 2.5M ammonium acetate.
The slides containing fixed, sectioned tissues are rehydrated in decreasing concentration of ethanol (100%, 70% and 50%), followed by sequential treatments with 0.2N HCl, 2.times. SSC (where 20.times. SSC is 3M NaCl and 0.3M sodium citrate) at 70.degree. C. to deparaffinate the sample, phosphate buffered saline (PBS), fixation in 4% paraformaldehyde and PBS wash. The slides are blocked to prevent nonspecific binding by the sequential additions of PBS/10 mM dithiothreitol (45.degree. C.), 10 mM dithiothreitol/0.19% iodoacetamide/0.12% N-ethylmaleimide and PBS wash. The slides are equilibrated in 0.1M triethylamine, pH 8.0, followed by treatment in 0.1M triethylamine/0.25% acetic anhydride and 0.1M triethylamine/0.5% acetic anhydride and washed in 2.times. SSC. The slides are then dehydrated in increasing concentrations of ethanol (50%, 70% and 100%) and stored at -80.degree. C.
A hybridization mix is prepared by combining 50% deionized formamide, 0.3M NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1.times. Denhardt's solution (0.02% Ficoll 400, 0.02% polyvinylpyrrolidone, 0.02% bovine serum albumin (BSA)), 500 .mu.g/ml yeast tRNA, 500 .mu.g/ml poly(A), 50 mM dithiothreitol, 10% polyethyleneglycol 6000 and the .sup.35 S-labeled RNA probe. This solution is placed on the fixed, blocked tissue slides which are then incubated at 45.degree. C. in a moist chamber for 0.5 to 3 hours. The slides are washed to remove unbound probe in 50% formamide, 2.times. SSC, 20 mM 2-mercaptoethanol (55.degree. C.), followed by 50% formamide, 2.times. SSC, 20 mM 2-mercaptoethanol and 0.5% Triton-X 100 (50.degree. C.) and finally in 2.times. SSC/20 mM 2-mercaptoethanol (room temperature). The slides are treated with 10 mM Tris-HCl, pH 8.0/0.3M NaCl/40 .mu.g/ml RNase A/2 .mu.g/ml RNAse T1 (37.degree. C.) to reduce levels of unbound RNA probe. Following RNAse treatment, the slides are washed in formamide/SSC buffers at 50.degree. C., room temperature and then dehydrated in increasing ethanol concentrations containing 0.3M ammonium acetate, and one final 100% ethanol wash. The slides are then exposed to X-ray film followed by emulsion autoradiography to detect silver grains.
Test tissue samples are compared to matched controls derived from normal lung tissue. Evidence of elevated transcription of the HCAVIII gene in test tissue compared to normal tissue, as determined by autoradiography (X-ray film) or alternatively by the quantitation of silver grains following emulsion autoradiography would provide evidence of a positive diagnosis for lung cancer.
EXAMPLE 2
Fluorescent In Situ Hybridization (FISH) Using DNA Probes Derived from the HCAVIII Gene
A genomic clone to the HCAVIII gene (SEQ ID NO:1) is isolated using a PCR primer pair which have been identified from the pLC56 cDNA sequence. This primer pair is located in putative exon 6 of the pLC56 gene, and they are identified as Probe Exon 6A (5'-ACATTGAAGAGCTGCTTCCGG-3'; SEQ ID NO:19) and Probe Exon 6B (5'-AATTTGCACGGGGTTTCGG-3'; SEQ ID NO:20). The genomic clone of HCAVIII is then identified as a PCR product of about 119 bp using this primer pair from the designated genomic clone. This result is confirmed by Southern blotting and DNA sequence analysis. A sequence of 1363 bp derived from the HCAVIII genomic clone is reported in SEQ ID NO:21. This sequence is located directly before the HCAVIII cDNA and constitutes the putative promoter of this gene and likely contains transcription regulatory elements directly implicated in HCAVIII expression.
The DNA probe comprising the genomic clone of HCAVIII plus flanking sequences is labeled in a random primer reaction with digoxigenin-11-dUTP (Boehringer Mannheim Biochemicals, Indianapolis, Ind.) by combining the DNA with dNTP(-TTP, final 0.05 mM), digoxigenin-11-dUTP/dTTP (0.0125 mM and 0.0375 mM, final), 10 mM 2-mercaptoethanol, 50 mM Tris-HCl, pH 7.5, 10 MM MgCl.sub.2, 20 U of DNA polymerase I and 1 ng/ml DNAase. The reaction is incubated at 15.degree. C. for two hours, and then terminated by adding EDTA to a final concentration of 10 mM. The labeled DNA probe is further purified by gel filtration chromatography. It is apparent to those skilled in the art that other suitable substrates such as biotin-11-dUTP can be substituted for digoxigenin-11-dUTP in the procedure above.
A hybridization mix is prepared by combining 50% deionized formamide, 0.3 M NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1.times. Denhardt's solution (0.02% Ficoll 400, 0.02% polyvinylpyrrolidone, and 0.02% bovine serum albumin), 500 .mu.g/ml yeast tRNA, 500 .mu.g/ml poly(A), 50 mM dithiothreitol, 10% polyethyleneglycol 6000, and the labeled DNA probe.
Single cell suspensions of tissue biopsy material or normal tissue are fixed in methanol/glacial acetic acid (3:1 vol/vol) and dropped onto microscope slides. (Aanastasi, et al., "Detection of Trisomy 12 in chronic lymphocytic leukemia by fluorescence in situ hybridization to interphase cells: a simple and sensitive method," Blood 1992; 77:2456-2462). After the slides are heated for 1-2 hours at 60.degree. C., the hybridization mix is applied to the slides which are then incubated at 45.degree. C. in a moist chamber for 0.5-3 hours. After incubation, the slides are washed three times with a solution comprising 50% formamide and 2.times. SSC at 42.degree. C., washed twice in 2.times. SSC at 42.degree. C., and finally washed in 4.times. SSC at room temperature. The slide is blocked with a solution of 4.times. SSC and 1% BSA, and then washed with a solution of 4.times. SSC and 1% Triton X-100.
The hybridized digoxigenin-labeled probe is detected by adding a mixture of sheep anti-digoxigenin antibody (Boehringer Mannheim) diluted in 0.1M sodium phosphate, pH 8.0, 5% nonfat dry milk, and 0.02% sodium azide, followed by the addition of fluorescein-conjugated rabbit anti-sheep IG for detection. The slides are then washed in PBS, mounted in Vectashield (Vector Laboratories, Inc., Burlingame, Calif.), and viewed by fluorescent microscopy.
Hybridization signals are enumerated in tumor derived tissue and then compared to normal tissue. Normal tissue displays two distinct hybridization signal characteristics of a diploid state. Enumeration over the rate of two hybridization signals/cell is considered significant.
EXAMPLE 3
Expression of HCAVIII
Expression of foreign proteins is often performed in E. coli when an immunogen or large amounts of protein are desired, as in the development of a diagnostic kit. A preferred system for E. coli expression has been described (Smith, et al., "Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione-s-transferase," Gene 1988; 67:31-40) whereby glutathione transferase is expressed with amino acids representing the cloned protein of interest attached to the carboxyl-terminus. The fusion protein can then be purified via affinity chromatography and the protein of interest fused to glutathione transferase released by digestion with the protease thrombin or alternatively the fusion protein is released intact from the affinity column by competing levels of free glutathione.
To express the HCAVIII protein (SEQ ID NO:4) of this invention in E. coli using the above described technology, an expression plasmid was produced fused to the glutathione transferase gene in frame with the HCAVIII gene (SEQ ID NO:1) to produce a fusion protein. The is fusion gene/expression plasmid was assembled from nucleic acids derived from the following sources. First, the expression plasmid pGEX4T1 (Pharmacia, Piscataway, N.J.) was cleaved in the polycloning region with the restriction endonucleases BamHI and EcoRI to permit insertion of the HCAVIII gene. Second, an oligonucleotide was synthesized, being 5'-GTCCACTTGGATCCGTTCACTGG-3' (SEQ ID NO:22). Using the in vitro mutagenesis procedure described by Kunkel (Proc Natl Acad Sci USA 1985; 82:488-492) and the above oligonucleotide, a BamHI restriction site was created without altering the amino acid codons of the original protein. In addition the created BamHI site was situated in correct reading frame and proximity to the predicted cleavage site separating the signal peptide from the mature protein. The DNA sequences encoding the mature protein were released from the mutagenesis vector as a BamHI/EcoRI fragment, where the EcoRI site originates from a polycloning region of the DNA sequencing vector pUC19 found downstream of the HCAVIII gene. The DNA fragments described above comprised of pGEX4T-1 cleaved at BamHI and EcoRI and the HCAVIII gene released as a BamHI/EcoRI fragment was combined in a mixture composed of 1.times. T.sub.4 ligase buffer (50 mM Tris-HCl, 10 mM MgCl.sub.2, 20 mM dithiothreitol, 1 mM ATP, 50 .mu.g/ml BSA, final pH 7.5) and T.sub.4 DNA ligase (New England Biolabs, Beverly, Mass.). The ligated DNA was used to transform a suitable strain of E. coli such as XL-1 Blue (Stratagene). The recovered plasmid is sequenced to confirm the expected DNA sequence. Protein expression is induced in E. Coli with the chemical isopropyl .beta.-thiogalactoside, and the fusion protein is released by cell lysis, followed by denaturation and resolubilization of the fusion protein with 8M urea/ 20 mM Tris.Cl (pH 8.5)/10 mM dithiothreitol, dialysis and protein renaturation, and finally binding to an affinity column composed of glutathione-agarose (Sigma, St. Louis, Mo.) and cleavage with thrombin to release the HCAVIII protein. The resulting protein is suitable as an immunogen for polyclonal or monoclonal antibody production and for usage in an ELISA kit as a internal standard and positive control. Carbonic anhydrase enzyme activity (as described in Example 6) was measured for E.coli-derived HCAVIII and HCAVIII-truncated form (SEQ ID NO:15) and compared to commercially obtained human carbonic anhydrase II (Sigma, St. Louis, Mo.). The activity, as reported in Enzyme Unit (U)/mg, for human carbonic anhydrase II was 3571 U/mg, for HCAVIII was 274 U/mg and HCAVIII truncated form was 2632 U/mg. These results indicated an enzymatically active and renaturable HCAVIII derived from E.coli of comparable enzymatic activity to human carbonic anhydrase II was obtained.
The length of the resulting protein can be varied by altering the length of SEQ ID NO:1 prior to insertion into the expression plasmid, or by cleavage of amino acids from the protein resulting in the above example. Structure/function studies of other HCA's suggest modifications (as defined by deletions at the N-terminal and C-terminal) more extensive than disclosed in SEQ ID NO:12 would still permit the production and use of a protein as an immunogen or standard, these deletions being a protein defined by about amino acid residue 3 to amino acid residue 259 in SEQ ID NO:12. Using existing technology one could synthesize a peptide of approximately 10 to 40 amino acids in length that comprises a structural domain of HCAVIII. This synthesized peptide, coupled to a carrier protein, could be used for generating polyclonal antisera specific for native HCAVIII.
EXAMPLE 4
Production of Antibodies to HCAVIII
The production of polyclonal antisera is described in great detail in Harlow, et al., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratories, New York, 1988 incorporated herein by reference. The HCAVIII protein (SEQ ID NO:4) in the presence of an adjuvant is injected into rabbits with a series of booster shots as a prescribed schedule optimal for high titers of antibody in serum. A total of seven biweekly bleeds were obtained from two rabbits immunized with HCAVIII truncated protein (SEQ ID NO:15). The resulting anti-HCAVIII serum titer was compared to preimmune sera of the same rabbits and determined to be 1000 to 2000-fold greater, hence suitable as a reagent for indirect ELISA (Example 5). Rabbit antibody was partially purified by precipitation with ammonium sulfate (50%, final) followed by dialysis and fractionation by preparative DEAE-HPLC.
An extensive description for producing monoclonal antibodies derived from the spleen B cells of an immunized mouse and a immortalized myeloma cell is found in the above reference for polyclonal antisera production. Mice are immunized with either the purified HCAVIII protein or a glutathione/HCAVIII fusion protein. Following cell fusion, selection for hybrid cells and subcloning, hybridomas are screened for a positive antibody against whole A549 cells or purified HCAVIII protein using an indirect ELISA assay as described for the ELISA kit (see Example 5).
EXAMPLE 5
ELISA Assay of Shed HCAVIII
An indirect ELISA screening assay for HCAVIII protein (SEQ ID NO:4) has been designed to detect and monitor the HCAVIII protein in body fluids including but not limited to serum and other biological fluids such as sputum or bronchial effluxion at effective levels necessary for sensitive but accurate determinations. It is intended to aid in the early diagnosis of non-small cell lung cancer, for which there currently is no effective treatment. An early-detection, accurate, non-invasive assay for non-small cell lung cancer would be of great benefit in the management of this disease.
The immunochemicals used in this procedure were rabbit anti-human HCAVIII antibody (purified IgG, IgM) produced according to the procedure given in Example 4, mouse anti-human HCAVIII (monoclonal) also produced according to the procedure given in Example 4, and goat anti-Rabbit IgG/peroxidase conjugate. The HCAVIII protein standard and internal positive control were produced as described in Example 3 for expression in E. coli.
Substrate components include 1M H.sub.2 SO.sub.4 stored at room temperature and 3',5,5'-tetramethylbenzidine (TMB) (Sigma Chemical Co.) used as a peroxidase substrate and stored at room temperature in the dark to prevent exposure to light.
Several buffers, diluents, and blocking agents were used in the procedure. Note that no sodium azide preservative was used in any of the buffers. This was done to avoid any possible interference from the azide with the peroxidase conjugate.
Phosphate buffered saline (PBS) was prepared by adding 32.0 g sodium chloride, 0.8 g potassium phosphate, monobasic, 0.8 g potassium chloride, and 4.6 g sodium phosphate, dibasic, anhydrous, to 3.2 L deionized water and mixing to dissolve. After bringing the solution to 4 L with deionized water and mixing, the pH was about 7.2. The buffer can be stored at 4.degree. C. for a maximum of 3 weeks.
Two bovine serum albumin solutions (BSA) were utilized as diluents. A 1% BSA solution in PBS, utilized as the second antibody/conjugate diluent, was prepared by adding 1 g BSA (bovine albumin, Fraction V, Sigma Chemical Co.) to 80 ml of PBS, allowing it to stand as it slowly goes into solution, adding PBS to a final volume of 100 ml, and then mixing. This diluent can be stored at 4.degree. C. for a maximum of 2 weeks; however if the solution becomes turbid, it should be discarded. As a diluent for the standards and samples, a 0.025% BSA solution in PBS was prepared fresh for each assay by diluting the 1% BSA diluent with PBS 1:40 (vol/vol).
A borate blocking buffer (0.17M H.sub.3 BO.sub.3, 0.12M NaCl, 0.05% Tween 20, 1 mM EDTA and 0.25% BSA was also used.
The substrate buffer was phosphate-citrate/sodium per borate (Sigma, St. Louis, Mo.).
All assays were performed in Immulon IV plates (Dynatech, Chantilly, Va. #011-010-6301). The assay plates were coated with a monoclonal antibody against HCAVIII by adding 50 ul of a 10 ug/ml solution of antibody in PBS to each well of Immulon IV plates. The plates were covered and incubated overnight at room temperature. The antibody solution was removed and the wells rinsed three times with deionized water. Three-hundred microliters (300 ul) of the borate blocking buffer was added to each well and incubated at room temperature for thirty minutes. The buffer was removed, the wells rinsed three times with deionized water, and the plates air dried. The plates were then wrapped and stored at 4.degree. C.
The standard E.coli-derived HCAVIII truncated protein (SEQ ID NO:15), was diluted to 32 ng/ml in PBS/0.025% BSA and two-fold serial dilutions were made in same. The samples were also diluted in PBS/0.025% BSA and 50 ul of standard or sample was applied to each well. The plates were incubated overnight, covered, at room temperature.
The standard and sample solutions were removed from the wells and the wells were rinsed three times with deionized water. Three-hundred microliters (300 ul) borate blocking buffer was added to each well and incubated at room temperature for thirty minutes. The plates were rinsed again with deionized water and tapped (inverted) on paper towels to remove excess water. The second antibody rabbit antisera to HCAVIII truncated protein (SEQ ID NO:15), was diluted to 1 ug/ml in PBS/1% BSA and 50 ul was added to each well. The plates were covered and incubated at room temperature two hours.
The antibody solution was removed from the wells which were then rinsed with deionized water three times. They were then blocked for ten minutes at room temperature with borate blocking buffer, rinsed again with deionied water three times, and tapped on paper towels. The antibody conjugate, goat F(ab')2.times.rabbit IgG & IgL-HPRO (Tago, Camarillo, Calif.) was diluted 1:16,000 in PBS/1%BSA and 50 ul was added to each well. The plates were covered and incubated at room temperature two hours.
The antibody conjugate solution was removed from the wells and they were rinsed with deionized water three times, blocked with three-hundred ul borate buffer at room temperature then minutes, rinsed three times with deionized water, and tapped on paper towels. The substrate was prepared no more than fifteen minues before use by dissolving one capsule of phosphate-citrate/sodium perborate (Signma, St. Louis, Mo.) in 100 ml water. For each plate, one tablet of TMB was added to 10 ml of the phosphate-citrate/sodium perborate buffer and syringe filtered. One-hundred ul was added to each well and the plates were covered and incubated at room temperature in the dark for one hour. The reaction was stopped by adding 50 ul of 1M H.sub.2 SO.sub.4 to each well. The plates were read on a Molecular Devices microplate reader at 450nm. Under these conditions, a linear response was obtained from 0.5 to 32 ng/ml using HCAVIII truncated protein as a standard, with the assay sensitivity at 0.5 ng/ml. No cross-reaction was observed against HCAII, an abundant carbonic anhydrase in human serum.
EXAMPLE 6
Carbonic Anhydrase (CA) Activity of Biopsy Tissue
Ice cold solutions of ITB (20 mM imidazole, 5 mM Tris, and 0.4 mM para-nitrophenol, pH 9.4-9.9) and Buffer A (25 mM triethanolamine, 59 mM H.sub.2 SO.sub.4, and 1 mM benzamidine HCl) are prepared.
A homogenate is prepared by scraping with a cell scraper into 1-2 ml of Buffer A a monolayer of tissue cells cultured from a tissue sample taken from a biopsy. A portion of the sample is then boiled to inactivate CA.
A tube is placed in an ice water bath. For the macroassay, a 10.times.75 mm glass tubes and rubber stopper with 16 gauge and 18 gauge needle ports is used; for the microassay, a 6.times.50 mm glass tubes and rubber stopper with 18 gauge needle port and 20 gauge needle with attached PE90 tubing. The sample is added and along with ice cold water to a final volume of 500 .mu.l for macroassay or 50 .mu.l for microassay. 500 .mu.l (macro) or 50 .mu.l (micro) ice cold water is used for a water control. 10 .mu.l antifoam (A. H. Thomas, Philadelphia, Pa.) is added to the tube which is then incubated in ice water for 0.5 to 3 minutes.
The tube is capped with a stopper and CO.sub.2 at 150 ml/min (macro) or 100 ml/min (micro) is bubbled through the smaller needle port for 30 sec.
50 .mu.l (macro) or 50 .mu.l (micro) of the ITB solution is rapidly added through the larger needle port with a cold Hamilton syringe. The sample becomes yellow.
Using a timer or stopwatch, the time at which the solution in the tube becomes colorless is measured and recorded. The tube may be momentarily removed from the bath and held in front of a white background to determine the color change. Comparison to a previously acidified sample may be used.
The procedure is repeated with the boiled sample. The volume of sample that corresponds to approximately one enzyme unit is determined using the formula below.
The assay is repeated 1-3 times with the sample and boiled sample, using the adjusted volume of sample.
Claims
Certificate of Correction present
The claims shown below may not include correction changes. Use the corrected PDF for authoritative text.
We claim:
1. An isolated protein comprising a membrane ion and a phosphorylation site comprising the amino acids Arg-Arg-Lys-Ser, said protein further characterized by carbonic anhydrase activity and specificity for expression in non-small cell lung cancer.
2. An isolated protein comprising an amino acid sequence encoded by the coding region of the nucleic acid sequence depicted in SEQ ID NO:1.
3. An isolated protein comprising the amino acid sequence depicted in SEQ ID NO:2.
4. The isolated protein of claim 2 wherein the amino acid sequence is encoded by the coding region from position 19 to position 1093 of SEQ ID NO:1, which is SEQ ID NO:3.
5. An isolated protein comprising the amino acid sequence depicted in SEQ ID NO:4.
6. An isolated protein comprising the amino acid sequence encoded by the coding region of the nucleic acid sequence depicted in SEQ ID NO:12.
7. An isolated protein comprising the amino acid sequence depicted in SEQ ID NO:13.
8. An isolated protein comprising the amino acid sequence encoded by the coding region of the nucleic acid sequence depicted in SEQ ID NO:14.
9. An isolated protein comprising the amino acid sequence depicted in SEQ ID NO:15.
10. An isolated protein possessing specificity for expression in non-small cell lung cancer and a phosphorylation site, said phosphorylation site comprising a sequence selected from the group consisting of: R-Arg-Lys-Ser, Arg-R-Lys-Ser, Arg-Arg-R-Ser, R-R-Lys-Ser, R-R-Lys-R, and Arg-Arg-Lys-R, where R represents an alternate amino acid.
11. The isolated protein of claim 10 wherein the amino acid sequence is encoded by the nucleic acid sequence depicted in SEQ ID NO:17.
12. The isolated protein of claim 10 wherein the amino acid sequence comprises the sequence depicted in SEQ ID NO:18.
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