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Sandrock R, Wheatley W, Drees E, Lualhati M, Kamb A, Caponigro G. A genetic selection method for expression products that induce apoptosis in adherent mammalian cell lines. Apoptosis 2003; 8:209-19. [PMID: 12766481 DOI: 10.1023/a:1022983012305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The process of apoptosis is carefully controlled in cells, and different cell types display different sensitivities to pro-apoptotic stimuli. The prospect of exploiting such differences for treatment of diseases such as cancer, via novel therapeutic agents, is extremely attractive. Therefore, genetic selections for novel expression products that kill cells may have considerable value. However, such selections are difficult to devise and perform because the selected cells do not grow. We developed a selection scheme designed to enrich for genetic agents that kill cells. The selection is based on detachment of apoptotic cultured mammalian cells from adherent monolayers. We characterized the properties of these detached cells (floating cells), and various aspects of the selection process. This selection method is potentially applicable to many mammalian cell lines.
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Affiliation(s)
- R Sandrock
- Deltagen Proteomics, Inc., 615 Arapeen Dr., Salt Lake City, UT 84108, USA
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2
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Sandrock TM, Risley B, Richards BT, Poritz MA, Austin HA, Yoo S, Kim MK, Roth B, Repetny K, Hsu F, Stump M, Teng DH, Kamb A. Exogenous peptide and protein expression levels using retroviral vectors in human cells. Mol Ther 2001; 4:398-406. [PMID: 11708876 DOI: 10.1006/mthe.2001.0476] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Pseudotyped retroviral vectors combine the advantages of broad host range, high expression, stable chromosomal integration, and ease of preparation. These vectors greatly facilitate delivery into mammalian cells of sequences encoding individual peptide inhibitors-including those with therapeutic utility-and inhibitor libraries. However, retroviral vectors vary in behavior, particularly with respect to expression levels in different cell lines. Expression level is especially important in transdominant experiments because the concentration of an inhibitor (for example, an expressed peptide) is one of the key determinants in the degree of complex formation between the inhibitor and its target. Thus, inhibitor concentration should have an impact on the expressivity and/or penetrance of an induced phenotype. Here, we compare several retroviral vectors and human cell lines for relative expression levels using a green fluorescent protein reporter. We show for a subset of these lines that cellular protein concentrations produced by single-copy vectors range up to about 2 microM. We also examine other variables that contribute to expression level, such as the nature of the expressed protein's carboxy terminus. Finally, we test the effect of increased concentration on phenotype with a nine-amino-acid peptide derived from the human papilloma virus protein E7 which overcomes E7-mediated cell growth.
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Affiliation(s)
- T M Sandrock
- Deltagen Proteomics, 615 Arapeen Dr., Suite 300, Salt Lake City, UT 84108, USA.
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3
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Sandrock R, Karpilow J, Richards B, Maxfield A, Wang C, Risley R, Rebentisch M, Drees B, Teng DH, Caponigro G, Kamb A. Enrichment during transdominant genetic experiments using a flow sorter. Cytometry 2001; 45:87-95. [PMID: 11590620 DOI: 10.1002/1097-0320(20011001)45:2<87::aid-cyto1150>3.0.co;2-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND Flow cytometry, in combination with retroviral expression libraries, is a powerful tool for genetic experimentation in mammalian cells. Expression libraries are transduced into cells engineered with a fluorescent reporter. Sorting for either bright or dim cells allows enrichment for specific inhibitors that alter reporter activity. This strategy has been used to isolate peptides and RNAs that either activate or suppress defined biochemical pathways. METHODS Several variables contribute to the enrichment process: (1) the background of the fluorescence bioassay; (2) the mean fluorescence ratio between the induced and noninduced reporter cell populations; (3) the genetic penetrance, or strength, of the inhibitor; and (4) the multiplicity of infection (MOI). An experimental and theoretical analysis, including computer modeling, of these issues in the context of a mammalian cell bioassay was undertaken. RESULTS MOI measurements were shown to be problematic. High MOI had little effect on enrichment early in the cycling process but a significant effect at later stages. Penetrance and background were critical throughout the process. Enrichments within about twofold of the theoretical maximum were observed. CONCLUSIONS Caution should be exercised in MOI determination because of the danger of significant underestimation. High MOI is potentially advantageous early in the selection process but hinders enrichment in the later rounds. Modeling shows that MOI, assay background and clone penetrance are the principal variables that determine the success of transdominant selections by FACS.
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4
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Poritz MA, Malmstrom S, Kim MK, Rossmeissl PJ, Kamb A. Graded mode of transcriptional induction in yeast pheromone signalling revealed by single-cell analysis. Yeast 2001; 18:1331-8. [PMID: 11571757 DOI: 10.1002/yea.777] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Signalling pathways typically convert a graded, analogue signal into a binary cellular output. In the several eukaryotic systems that have been investigated to date, including MAP kinase cascade activation in Xenopus oocytes, analogue-to-digital conversion occurs at points in the pathway between receptor activation and the effector mechanism. We used flow cytometry combined with an intracellular fluorescent reporter to examine the characteristics of the yeast pheromone-response pathway. Surprisingly, pheromone response in yeast, which relies on the MAP kinase cascade, behaved in a fundamentally graded manner. Expression of certain exogenous dominant inhibitors of the pathway converted the response to graded-or-none behaviour. These results have implications for the dissection of biological response mechanisms in cells and illustrate how signalling pathways, even homologous ones, may have strikingly different signal propagation/amplification characteristics.
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Affiliation(s)
- M A Poritz
- Arcaris Inc., 615 Arapeen Drive, Suite 300, Salt Lake City, UT 84108, USA.
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5
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Teng DH, Hsu F, Peterson I, Cardon KE, Caponigro G, Kamb A. Template selection during manipulation of complex mixtures by PCR. Biotechniques 2001; 30:868-72, 874, 876-7. [PMID: 11314269 DOI: 10.2144/01304rr04] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
PCR is ubiquitous in molecular biology. It is used to amplify single sequences from large genomes, or populations of sequences from complex mixtures such as cDNA libraries in mammalian cells. These cDNA libraries are often employed in subsequent labor-intensive experiments such as genetic screens, the outcome of which depends on library quality. The use of PCR to amplify diverse sequence populations raises important technical issues. One question is whether or not PCR is capable of maintaining population diversity, specifically with respect to template selection in the first rounds of the amplification process (i.e., the possibility that rare sequences in a complex mixture are lost because of amplification failure at the outset of the PCR). Here, we analyze the properties of PCR in the context of template selection in complex mixtures and show that it is an excellent method for preserving diversity.
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6
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Abstract
Peptide inhibitors isolated from libraries either through genetic screens or binding assays have gained visibility in the past year - especially with the publication of four studies in model systems (two in yeast, two in Escherichia coli). These and other studies demonstrate that forward and reverse genetic experiments with peptides can be extremely efficient in validating candidate drug targets and in defining elements of biochemical pathways.
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Affiliation(s)
- A Kamb
- Arcaris Inc., 615 Arapeen Drive, Suite 300, Salt Lake City, UT 84108, USA.
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7
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Kamb A, Teng DH. Transdominant genetics, peptide inhibitors and drug targets. Curr Opin Mol Ther 2000; 2:662-9. [PMID: 11249744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
The future of medical therapy is tied to the discovery of high-quality drug targets and drugs. Transdominant genetics provides a function-based route to peptide inhibitors that can be used as probes to identify protein targets or as reagents for drug development. Both forward-genetic and reverse-genetic applications have been implemented. The move is now underway to expand upon advances made in model systems and exploit screens of real therapeutic value.
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Affiliation(s)
- A Kamb
- Arcaris Inc, 615 Arapeen Dr, Suite 300, Salt Lake City, UT 84108, USA.
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8
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Feldhaus MJ, Lualhati M, Cardon K, Roth B, Kamb A. Oligonucleotide-conjugated beads for transdominant genetic experiments. Nucleic Acids Res 2000; 28:534-43. [PMID: 10606653 PMCID: PMC102503 DOI: 10.1093/nar/28.2.534] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/1999] [Revised: 11/09/1999] [Accepted: 11/09/1999] [Indexed: 11/13/2022] Open
Abstract
Transdominant genetics using expression libraries can identify proteins and peptides that affect cell division. In conjunction with these libraries, oligo-nucleotide-conjugated beads and flow cytometry were used to test a strategy that potentially expands the range of such genetic studies. The experimental approach involved creation of tagged expression libraries, introduction of these libraries into cells, growth of the cultured cells for several generations and recovery on oligonucleotide-conjugated beads of sequences that encode growth-modulatory proteins or peptides. Experiments in Saccharomyces cerevisiae demonstrating the feasibility of the strategy are presented.
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Affiliation(s)
- M J Feldhaus
- Arcaris Inc., 615 Arapeen Drive, Salt Lake City, UT 84108, USA.
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9
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Richards B, Karpilow J, Dunn C, Zharkikh L, Maxfield A, Kamb A, Teng DH. Creation of a stable human reporter cell line suitable for FACS-based, transdominant genetic selection. Somat Cell Mol Genet 1999; 25:191-205. [PMID: 11586787 DOI: 10.1023/a:1019206625658] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Quality bioassays are central to all approaches directed at understanding or perturbing the function of proteins. One type of cell-based bioassay involves an engineered reporter whose transcriptional activity serves as a readout for upstream signals of a biochemical pathway(s) that feeds into the reporter. We describe a general strategy for creating a mammalian reporter line with attributes suitable for a high complexity, en masse transdominant genetic screen. The basic criteria required of the mammalian cells engineered with the reporter include ease of maintenance, ease of sorting by FACS, ability to be transduced by retroviruses, and high expression of transduced peptides or cDNAs. For maximal enrichment during selection, the reporter line should have a relatively homogeneous response and a high signal-to-background ratio. We use a melanoma cell line transduced with a retinoic-acid-responsive promoter coupled to a GFP reporter as a case study to demonstrate the strategy. We characterize an optimized retinoic-acid-responsive reporter clone to determine the kinetics of reporter induction and decay in the presence and absence of retinoids. Dose-response studies reveal that the reporter responds to all-trans retinoic acid with an EC50 of approximately 1 nM. The strategy described is general and may be applied to create other reporter lines that respond to a specific stimulus.
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Affiliation(s)
- B Richards
- Arcaris, Inc, 615 Arapeen Drive, Suite 300, Salt Lake City, Utah 84108, USA
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10
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Abstract
Genetic selections that use proteinaceous transdominant inhibitors encoded by DNA libraries to cause mutant phenocopies may facilitate genetic analysis in traditionally nongenetic organisms. We performed a selection for random short peptides and larger protein fragments (collectively termed "perturbagens") that inhibit the yeast pheromone response pathway. Peptide and protein fragment perturbagens that permit cell division in the presence of pheromone were recovered. Two perturbagens were derived from proteins required for pheromone response, and an additional two were derived from proteins that may negatively influence the pheromone response pathway. Furthermore, three known components of the pathway were identified as probable perturbagen targets based on physical interaction assays. Thus, by selection for transdominant inhibitors of pheromone response, multiple pathway components were identified either directly as gene fragments or indirectly as the likely targets of specific perturbagens. These results, combined with the results of previous work [Holzmayer, T. A., Pestov, D. G. & Roninson, I. B. (1992) Nucl. Acids. Res. 20, 711-717; Whiteway, M., Dignard, D. & Thomas, D. Y. (1992) Proc. Natl. Acad. Sci. USA 89, 9410-9414; and Gudkov, A. V., Kazarov, A. R., Thimmapaya, R., Axenovich, S. A., Mazo, I. A. & Roninson, I. B. (1994) Proc. Natl. Acad. Sci. USA 91, 3744-3748], suggest that transdominant genetic analysis of the type described here will be broadly applicable.
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Affiliation(s)
- G Caponigro
- Ventana Genetics, Inc., 421 Wakara Way, Salt Lake City, UT 84108, USA
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11
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Affiliation(s)
- A Kamb
- Myriad Genetics, Inc., Salt Lake City, UT 84108, USA
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12
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Abstract
Peptide aptamers provide probes for biological processes and adjuncts for development of novel pharmaceutical molecules. Such aptamers are analogous to compounds derived from combinatorial chemical libraries which have specific binding or inhibitory activities. Much as it is generally difficult to determine the composition of combinatorial chemical libraries in a quantitative manner, determining the quality and characteristics of peptide libraries displayed in vivo is problematical. To help address these issues we have adapted green fluorescent protein (GFP) as a scaffold for display of conformationally constrained peptides. The GFP-peptide libraries permit analysis of library diversity and expression levels in cells and allow enrichment of the libraries for sequences with predetermined characteristics, such as high expression of correctly folded protein, by selection for high fluorescence.
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Affiliation(s)
- M R Abedi
- Ventana Genetics Inc., 421 Wakara Way, Salt Lake City, UT 84108, USA
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13
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Cannon-Albright LA, Kamb A, Skolnick M. A review of inherited predisposition to melanoma. Semin Oncol 1996; 23:667-72. [PMID: 8970585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In this review, we discuss the progress of the last few years in the genetic analysis of the susceptibility to melanoma. The inclusion of dysplastic nevi in the analysis of susceptibility, although appropriate conceptually, has not greatly clarified the picture of genetic susceptibility to melanoma. One predisposing gene has clearly been linked to chromosome 9 while a second linkage to chromosome 1 is still uncertain. A gene, CDKN2, is an appealing candidate for melanoma susceptibility.
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Affiliation(s)
- L A Cannon-Albright
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, USA
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14
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Stone S, Dayananth P, Kamb A. Reversible, p16-mediated cell cycle arrest as protection from chemotherapy. Cancer Res 1996; 56:3199-202. [PMID: 8764106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A model system has been developed to explore the relationship between cell cycle arrest and chemotherapeutic toxicity. An isopropyl-1-thio-beta-D-galactopyranoside-inducible P16 construct was introduced stably into a melanoma cell line and used to promote G0-G1 arrest in the recipient cells. The state of arrest was reversible and did not compromise cell viability over a period of at least 7 days. Isopropyl-1-thio-beta-D-galactopyranoside-treated, arrested cells were significantly more resistant to the chemotherapeutic agents methotrexate (approximately 50 times), vinblastine (>100 times), and cisplatin (approximately 10 times) compared to controls. This strategy of protection from chemotherapy exploits one of the basic genotypic differences between normal cells and tumor cells: the integrity of genetic pathways that regulate growth.
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Affiliation(s)
- S Stone
- Myriad Genetics, Inc., Salt Lake City, Utah 84108, USA
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15
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Teng DH, Bogden R, Mitchell J, Baumgard M, Bell R, Berry S, Davis T, Ha PC, Kehrer R, Jammulapati S, Chen Q, Offit K, Skolnick MH, Tavtigian SV, Jhanwar S, Swedlund B, Wong AK, Kamb A. Low incidence of BRCA2 mutations in breast carcinoma and other cancers. Nat Genet 1996; 13:241-4. [PMID: 8640236 DOI: 10.1038/ng0696-241] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Inherited mutant alleles of familial tumour suppressor genes predispose individuals to particular types of cancer. In addition to an involvement in inherited susceptibility to cancer, these tumour suppressor genes are targets for somatic mutations in sporadic cancers of the same type found in the familial forms. An exception is BRCA1, which contributes to a significant fraction of familial breast and ovarian cancer, but undergoes mutation at very low rates in sporadic breast and ovarian cancers. This finding suggests that other genes may be the principal targets for somatic mutation in breast carcinoma. A second, recently identified familial breast cancer gene, BRCA2 (refs 5-8), accounts for a proportion of breast cancer roughly equal to BRCA1. Like BRCA1, BRCA2 behaves as a dominantly inherited tumour suppressor gene. Individuals who inherit one mutant allele are at increased risk for breast cancer, and the tumours they develop lose the wild-type allele by heterozygous deletion. The BRCA2 coding sequence is huge, composed of 26 exons that span 10,443 bp. Here we investigate the rate of BRCA2 mutation in sporadic breast cancers and in a set of cell lines that represent twelve other tumour types. Surprisingly, mutations in BRCA2 are infrequent in cancers including breast carcinoma. However, a probable germline mutation in a pancreatic tumour cell line suggests a role for BRCA2 in susceptibility to pancreatic cancer.
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Affiliation(s)
- D H Teng
- Myriad Genetics, Inc., Salt Lake City, Utah 84108, USA
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16
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Kamb A, Neuhausen S. The cancers of man and woman. Trends Genet 1996; 12:198. [PMID: 8984736 DOI: 10.1016/0168-9525(96)30020-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- A Kamb
- Myriad Genetics Incorporation, Salt Lake City, UT 84108, USA.
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17
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Kamb A. Human melanoma genetics. J Investig Dermatol Symp Proc 1996; 1:177-82. [PMID: 9627713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Melanoma is an important human cancer, the etiology of which has been the subject of much study. Recently a gene for familial melanoma, MLM, has been mapped and isolated. This gene encodes the cell-cycle regulator p16 and is mutated in a variety of sporadic human cancers in addition to melanoma. The isolation of MLM answers some questions in the area of melanoma biology, but raises others. Identification of p16 and other genes that contribute to melanoma development may be viewed as one step in the attempt to understand, diagnose, and treat this malignant disease.
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Affiliation(s)
- A Kamb
- Myriad Genetics, Inc., Salt Lake City, UT 84108, USA
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18
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Tavtigian SV, Simard J, Rommens J, Couch F, Shattuck-Eidens D, Neuhausen S, Merajver S, Thorlacius S, Offit K, Stoppa-Lyonnet D, Belanger C, Bell R, Berry S, Bogden R, Chen Q, Davis T, Dumont M, Frye C, Hattier T, Jammulapati S, Janecki T, Jiang P, Kehrer R, Leblanc JF, Mitchell JT, McArthur-Morrison J, Nguyen K, Peng Y, Samson C, Schroeder M, Snyder SC, Steele L, Stringfellow M, Stroup C, Swedlund B, Swense J, Teng D, Thomas A, Tran T, Tranchant M, Weaver-Feldhaus J, Wong AK, Shizuya H, Eyfjord JE, Cannon-Albright L, Tranchant M, Labrie F, Skolnick MH, Weber B, Kamb A, Goldgar DE. The complete BRCA2 gene and mutations in chromosome 13q-linked kindreds. Nat Genet 1996; 12:333-7. [PMID: 8589730 DOI: 10.1038/ng0396-333] [Citation(s) in RCA: 546] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Breast carcinoma is the most common malignancy among women in developed countries. Because family history remains the strongest single predictor of breast cancer risk, attention has focused on the role of highly penetrant, dominantly inherited genes in cancer-prone kindreds (1). BRCA1 was localized to chromosome 17 through analysis of a set of high-risk kindreds (2), and then identified four years later by a positional cloning strategy (3). BRCA2 was mapped to chromosomal 13q at about the same time (4). Just fifteen months later, Wooster et al. (5) reported a partial BRCA2 sequence and six mutations predicted to cause truncation of the BRCA2 protein. While these findings provide strong evidence that the identified gene corresponds to BRCA2, only two thirds of the coding sequence and 8 out of 27 exons were isolated and screened; consequently, several questions remained unanswered regarding the nature of BRCA2 and the frequency of mutations in 13q-linked families. We have now determined the complete coding sequence and exonic structure of BRCA2 (GenBank accession #U43746), and examined its pattern of expression. Here, we provide sequences for a set of PCR primers sufficient to screen the entire coding sequence of BRCA2 using genomic DNA. We also report a mutational analysis of BRCA2 in families selected on the basis of linkage analysis and/or the presence of one or more cases of male breast cancer. Together with the specific mutations described previously, our data provide preliminary insight into the BRCA2 mutation profile.
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19
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Hattier T, Bell R, Shaffer D, Stone S, Phelps RS, Tavtigian SV, Skolnick MH, Shattuck-Eidens D, Kamb A. Monitoring the efficacy of hybrid selection during positional cloning: the search for BRCA1. Mamm Genome 1995; 6:873-9. [PMID: 8747927 DOI: 10.1007/bf00292438] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Positional cloning often requires isolation of candidate genes from a large, genetically defined region. Hybrid selection (direct cDNA selection, solution hybrid capture) is a rapid, simple procedure that has been used to identify expressed sequence tags (ESTs) from cloned genomic DNA. We used hybrid selection to screen a 600-kb region that includes the BRCA1 gene. From a set of 931 sequenced clones, we obtained 118 nonoverlapping candidate ESTs from ovary and lymphocyte cDNA. We analyzed the results of our hybrid selection experiments with particular attention to the overall completeness, efficiency, and background noise of the experiment. We introduce simple parameters that serve as measures of important aspects of the hybrid selection process in the context of positional cloning.
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Affiliation(s)
- T Hattier
- Myriad Genetics, Inc., Salt Lake City, Utah 84108, USA
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20
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Jiang P, Stone S, Wagner R, Wang S, Dayananth P, Kozak CA, Wold B, Kamb A. Comparative analysis of Homo sapiens and Mus musculus cyclin-dependent kinase (CDK) inhibitor genes p16 (MTS1) and p15 (MTS2). J Mol Evol 1995; 41:795-802. [PMID: 8587124 DOI: 10.1007/bf00173159] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Cyclin-dependent kinase inhibitors are a growing family of molecules that regulate important transitions in the cell cycle. At least one of these molecules, p16, has been implicated in human tumorigenesis while its close homolog, p15, is induced by cell contact and transforming growth factor-beta (TGF-beta). To investigate the evolutionary and functional features of p15 and p16, we have isolated mouse (Mus musculus) homologs of each gene. Comparative analysis of these sequences provides evidence that the genes have similar functions in mouse and human. In addition, the comparison suggests that a gene conversion event is part of the evolution of the human p15 and p16 genes.
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Affiliation(s)
- P Jiang
- Myriad Genetics, Inc., Salt Lake City, UT 84108, USA
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21
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Phelps RS, Chadwick RB, Conrad MP, Kronick MN, Kamb A. Efficient, automatic detection of heterozygous bases during large-scale DNA sequence screening. Biotechniques 1995; 19:984-9. [PMID: 8747666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A crucial factor in the success of positional cloning efforts is the ability to screen rapidly many different candidate genes for mutations. By modifying standard software, we have improved the detection of heterozygous base positions in PCR products sequenced by cycle sequencing. A key element of the method is the incorporation of a modified heterozygote detection algorithm that permits the use of DNA sequence data derived from PCR and sequencing reactions that have not been fully optimized. This allows sequencing runs of average quality to be used. We demonstrate that the sensitivity and specificity of the method are well suited to mutation detection applications such as positional cloning.
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Affiliation(s)
- R S Phelps
- Myriad Genetics, Inc., Salt Lake City, UT, USA
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22
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Stone S, Dayananth P, Jiang P, Weaver-Feldhaus JM, Tavtigian SV, Cannon-Albright L, Kamb A. Genomic structure, expression and mutational analysis of the P15 (MTS2) gene. Oncogene 1995; 11:987-91. [PMID: 7675459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The P15 gene (MTS2) encodes a cyclin-dependent kinase (CDK) inhibitor with considerable sequence identity and biochemical similarity to the CDK inhibitor p16. It is closely linked to the P16 gene (MTS1) and is homozygously deleted in many tumor cell lines. These features suggest that p15 may be a tumor suppressor. We have determined the genomic structure of P15 and examined its pattern of mRNA expression. In addition, we have shown that ectopic expression of p15 inhibits growth of tumor-derived cell lines. We have also searched for P15 mutations in tumor cell lines and in 9p21-linked melanoma kindreds. Other than the previously described homozygous deletions, no mutations of P15 were found. Collectively, these observations suggest a role for p15 in growth regulation, but a limited role for p15 in tumor progression.
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Affiliation(s)
- S Stone
- Myriad Genetics, Inc., Salt Lake City, Utah 84018, USA
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23
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Stone S, Jiang P, Dayananth P, Tavtigian SV, Katcher H, Parry D, Peters G, Kamb A. Complex structure and regulation of the P16 (MTS1) locus. Cancer Res 1995; 55:2988-94. [PMID: 7606716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The p16 gene (P16, MTS1, CDKN2) encodes a negative regulator of the cell cycle. Molecular genetic techniques have been used to explore the role of p16 in normal development and cancer. Two transcripts derived from the p16 gene with distinct protein coding potentials are described. The previously undescribed transcript form has the same exons 2 and 3 as the p16-encoding mRNA but contains a different exon 1. The human p16 transcripts are detected in various tissues, and the ratio of the transcripts is regulated in both a tissue-specific and cell cycle-specific manner. The P16-derived mRNAs are probably generated from separate promoters, and transcription from one of the promoters appears to be regulated, at least in part, by the retinoblastoma gene product.
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Affiliation(s)
- S Stone
- Myriad Genetics, Inc., Salt Lake City, Utah 84018, USA
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Gruis NA, van der Velden PA, Sandkuijl LA, Prins DE, Weaver-Feldhaus J, Kamb A, Bergman W, Frants RR. Homozygotes for CDKN2 (p16) germline mutation in Dutch familial melanoma kindreds. Nat Genet 1995; 10:351-3. [PMID: 7670475 DOI: 10.1038/ng0795-351] [Citation(s) in RCA: 205] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The p16 gene (CDKN2) which is localized on chromosome 9p21, is deleted in a significant number of sporadic cancers. Moreover, germline mutations identified in some melanoma-prone kindreds last year suggested that CDKN2 is identical to the 9p21-linked melanoma susceptibility gene (MLM); however, failure to identify p16 mutations in all melanoma kindreds putatively linked to 9p21 left some doubts. We have analysed CDKN2 coding sequences in 15 Dutch familial atypical multiple mole-melanoma (FAMMM) syndrome pedigrees, and identified a 19 basepair (bp) germline deletion in 13 of them. All 13 families originate from an endogamous population. The deletion causes a reading frame shift, predicted to result in a severely truncated p16 protein. Interestingly, two family members are homozygous for the deletion, one of whom shows no obvious signs of disease. This surprising finding demonstrates that homozygotes for this CDKN2 mutation are viable, and suggests the presence of a genetic mechanism that can compensate for the functional loss of p16. Our results also greatly strengthen the notion that p16 is indeed MLM.
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Affiliation(s)
- N A Gruis
- Department of Human Genetics, Leiden University, the Netherlands
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Kelley MJ, Nakagawa K, Steinberg SM, Mulshine JL, Kamb A, Johnson BE. Differential inactivation of CDKN2 and Rb protein in non-small-cell and small-cell lung cancer cell lines. J Natl Cancer Inst 1995; 87:756-61. [PMID: 7563154 DOI: 10.1093/jnci/87.10.756] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The CDKN2 gene encodes the human cyclin-dependent kinase 4 inhibitor. This inhibitor protein is believed to be a tumor suppressor that plays an essential role in cell cycle regulation. One half of all cancer cell lines and one fourth of lung cancer cell lines examined to date contain homozygous deletions (i.e., both alleles lost) of CDKN2. However, the relative frequency of homozygous CDKN2 deletions in non-small-cell lung cancers (NSCLC) and in small-cell lung cancers (SCLC) has not been determined. Inactivation or loss of another tumor suppressor encoded by the retinoblastoma gene (the Rb protein) is more common in SCLC than in NSCLC. PURPOSE We measured the frequency of homozygous CDKN2 deletions in 77 NSCLC and in 93 SCLC tumor cell lines. In addition, possible associations were explored between CDKN2 gene loss, the presence or absence of Rb protein, and the clinical status of lung cancer patients. METHODS DNA was isolated from each tumor cell line and from the primary tumor and normal tissue of one NSCLC patient. Sequences corresponding to exons 1 and 2 of the CDKN2 gene were amplified by use of the polymerase chain reaction, and the resulting amplification products were analyzed by agarose gel electrophoresis and DNA blotting. Genomic DNA blotting was also used to evaluate CDKN2 gene deletions. The frequency of homozygous CDKN2 loss and the presence or absence of functional Rb protein (reported previously) in the cell lines were compared. RESULTS Homozygous deletion of CDKN2 was detected in 18 (23%) of 77 cell lines established from patients with NSCLC, compared with one (1%) of 93 cell lines established from patients with SCLC (P < .001). No CDKN2 gene loss was observed in the normal tissue of an NSCLC patient whose tumor cell line showed homozygous deletion of the gene; however, the primary tumor from this patient had evidence of CDKN2 loss. Homozygous CDKN2 deletion was detected in 13 (28%) of 46 tumor cell lines from patients with stage III or stage IV NSCLC, compared with zero of 10 tumor cell lines from patients with stage I or stage II NSCLC. Coincident loss of CDKN2 genes and functional Rb protein was rarely observed (in two of 135 cell lines). CONCLUSION The frequency of homozygous CDKN2 gene deletion in NSCLC cell lines is greater than that observed for any other known, or candidate, tumor suppressor gene. IMPLICATION Further study of the role of CDKN2 gene alteration in the pathogenesis of NSCLC is needed.
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Affiliation(s)
- M J Kelley
- NCI-Navy Medical Oncology Branch, National Naval Medical Center, Bethesda, MD 20889-5105, USA
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Abstract
Cancer is a disease characterized by loss of cellular growth control. As such, it is not surprising that the molecular machinery of the cell cycle is involved in tumorigenesis. Recent discoveries have brought several cell-cycle regulators into sharp focus as factors in human cancer. Among the most conspicuous types of molecule to emerge from ongoing studies in this field are the cyclin-dependent kinase inhibitors such as p16. These molecules have several hallmarks of tumor suppressors and are perfectly positioned to regulate critical decisions in cell growth. The P16 gene appears to be a particularly significant target for mutation in sporadic tumors and in at least one form of hereditary cancer.
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Affiliation(s)
- A Kamb
- Myriad Genetics, Inc., Salt Lake City, UT 84108, USA
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Kamb A, Wang C, Thomas A, DeHoff BS, Norris FH, Richardson K, Rine J, Skolnick MH, Rosteck PR. Software trapping: a strategy for finding genes in large genomic regions. Comput Biomed Res 1995; 28:140-53. [PMID: 7656550 DOI: 10.1006/cbmr.1995.1010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We present an approach to the gene identification phase of positional cloning that combines sparse sampling of DNA sequences from large genomic regions with computational analysis. We call the method "software trapping." The goal is to find coding exons while avoiding massive DNA sequence determination and contig assembly. Instead, rapid sequence sampling is combined with exon screening software such as a newly developed package called XPOUND to identify coding sequences. We have tested the approach using a set of model genomic sequences with known intron/exon structures as well as with bona fide P1 genomic clones. The results suggest that the strategy is a useful complement to other methods for finding genes in poorly characterized regions of genomes.
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Affiliation(s)
- A Kamb
- Myriad Genetics, Inc., Salt Lake City, Utah 84108, USA
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Kamb A. Response
: Sunlight and Melanoma: an Answer from MTS1 (p16). Science 1995; 267:16. [PMID: 17840043 DOI: 10.1126/science.267.5194.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Neuhausen SL, Swensen J, Miki Y, Liu Q, Tavtigian S, Shattuck-Eidens D, Kamb A, Hobbs MR, Gingrich J, Shizuya H. A P1-based physical map of the region from D17S776 to D17S78 containing the breast cancer susceptibility gene BRCA1. Hum Mol Genet 1994; 3:1919-26. [PMID: 7874107 DOI: 10.1093/hmg/3.11.1919] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
BRCA1, a breast and ovarian cancer susceptibility locus, has been isolated and maps to 17q21. A physical map of the BRCA1 region which extended from the proximal boundary at D17S776 to the distal boundary at D17S78 was constructed and consists of 51 sequence tagged sites (STSs) from P1 and YAC ends, nine new short-tandem repeat (STR) polymorphic markers, and eight identified genes. The contig, which spans the estimated 2.3 Mb region, contains 29 P1s, 11 YACs, two BACs, and one cosmid. Based on key recombinants in two linked families, BRCA1 was further localized to a region bounded by D17S1321 on the proximal side and D17S1325 on the distal side. Within this estimated 600 kb region, the contig was composed completely of P1s and BACs ordered by STS-content mapping and confirmed by DNA restriction fragment fingerprinting.
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Affiliation(s)
- S L Neuhausen
- Department of Medical Informatics, University of Utah Medical Center, Salt Lake City 84132
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Cannon-Albright LA, Goldgar DE, Neuhausen S, Gruis NA, Anderson DE, Lewis CM, Jost M, Tran TD, Nyguen K, Kamb A. Localization of the 9p melanoma susceptibility locus (MLM) to a 2-cM region between D9S736 and D9S171. Genomics 1994; 23:265-8. [PMID: 7829086 DOI: 10.1006/geno.1994.1491] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A familial melanoma susceptibility locus (MLM) was identified on the short arm of chromosome 9 in a set of Utah and Texas kindreds. Subsequent confirmation was reported for a set of 26 Australian kindreds, a set of 7 Dutch kindreds, and a set of 13 NIH melanoma kindreds. The original localization report placed the locus near the IFNA-D9S126 interval on chromosome 9p. We report further localization using D9S171 and a newly developed marker, D9S736, both of which lie in the IFNA-D9S126 interval. Analysis of this set of kindreds places the melanoma susceptibility locus in a 2-cM region that is proximal to D9S736 and distal to D9S171.
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Affiliation(s)
- L A Cannon-Albright
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City 84108
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Kamb A, Futreal PA, Rosenthal J, Cochran C, Harshman KD, Liu Q, Phelps RS, Tavtigian SV, Tran T, Hussey C. Localization of the VHR phosphatase gene and its analysis as a candidate for BRCA1. Genomics 1994; 23:163-7. [PMID: 7829067 DOI: 10.1006/geno.1994.1473] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The VH1-related human protein (VHR) gene was localized to human chromosome 17q21 in a region thought to contain the BRCA1 locus, a locus that confers susceptibility to breast and ovarian cancer. VHR encodes a phosphatase with dual specificity for tyrosine and serine residues. Thus it is a plausible candidate for a tumor suppressor gene such as BRCA1. To test this possibility, the VHR coding sequence was screened in individuals with familial breast cancer and in sporadic breast tumor and breast cancer cell lines. No mutations were detected, suggesting that the VHR gene is not BRCA1.
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MESH Headings
- BRCA1 Protein
- Base Sequence
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Chromosomes, Human, Pair 17
- DNA Mutational Analysis
- DNA, Complementary/genetics
- DNA, Neoplasm/genetics
- Dual Specificity Phosphatase 3
- Female
- Genes
- Genes, Tumor Suppressor
- Genetic Predisposition to Disease
- Humans
- Molecular Sequence Data
- Neoplasm Proteins/genetics
- Neoplasm Proteins/physiology
- Polymerase Chain Reaction
- Polymorphism, Genetic
- Polymorphism, Single-Stranded Conformational
- Protein Tyrosine Phosphatases/genetics
- RNA, Messenger/genetics
- RNA, Neoplasm/genetics
- Transcription Factors
- Tumor Cells, Cultured
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Affiliation(s)
- A Kamb
- Myriad Genetics, Inc., Salt Lake City, Utah 84108
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Kamb A, Shattuck-Eidens D, Eeles R, Liu Q, Gruis NA, Ding W, Hussey C, Tran T, Miki Y, Weaver-Feldhaus J. Analysis of the p16 gene (CDKN2) as a candidate for the chromosome 9p melanoma susceptibility locus. Nat Genet 1994; 8:23-6. [PMID: 7987388 DOI: 10.1038/ng0994-22] [Citation(s) in RCA: 546] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A locus for familial melanoma, MLM, has been mapped within the same interval on chromosome 9p21 as the gene for a putative cell cycle regulator, p16INK4 (CDKN2) MTS1. This gene is homozygously deleted from many tumour cell lines including melanomas, suggesting that CDKN2 is a good candidate for MLM. We have analysed CDKN2 coding sequences in pedigrees segregating 9p melanoma susceptibility and 38 other melanoma-prone families. In only two families were potential predisposing mutations identified. No evidence was found for heterozygous deletions of CDKN2 in the germline of melanoma-prone individuals. The low frequency of potential predisposing mutations detected suggests that either the majority of mutations fall outside the CDKN2 coding sequence or that CDKN2 is not MLM.
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Affiliation(s)
- A Kamb
- Myriad Genetics, Inc., Salt Lake City, Utah 84108
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Weaver-Feldhaus J, Gruis NA, Neuhausen S, Le Paslier D, Stockert E, Skolnick MH, Kamb A. Localization of a putative tumor suppressor gene by using homozygous deletions in melanomas. Proc Natl Acad Sci U S A 1994; 91:7563-7. [PMID: 8052620 PMCID: PMC44442 DOI: 10.1073/pnas.91.16.7563] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The p21 region of human chromosome 9 is thought to contain a gene (MLM) involved in genetic susceptibility to melanoma and a gene or genes that influence progression of certain other tumors. Genomic clones that span a large region in 9p21 surrounding the presumptive tumor suppressor gene(s) have been isolated. A set of sequence-tagged sites in this region has been developed. By using these markers and others previously reported, the 9p21 region has been studied by physical mapping in 84 melanoma cell lines. A putative tumor suppressor gene, perhaps MLM itself, has been localized to a region of less than 40 kb that lies proximal (centromeric) to the alpha-interferon gene cluster.
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Kamb A, Gruis NA, Weaver-Feldhaus J, Liu Q, Harshman K, Tavtigian SV, Stockert E, Day RS, Johnson BE, Skolnick MH. A cell cycle regulator potentially involved in genesis of many tumor types. Science 1994; 264:436-40. [PMID: 8153634 DOI: 10.1126/science.8153634] [Citation(s) in RCA: 2063] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A putative tumor suppressor locus on the short arm of human chromosome 9 has been localized to a region of less than 40 kilobases by means of homozygous deletions in melanoma cell lines. This region contained a gene, Multiple Tumor Suppressor 1 (MTS1), that encodes a previously identified inhibitor (p16) of cyclin-dependent kinase 4. MTS1 was homozygously deleted at high frequency in cell lines derived from tumors of lung, breast, brain, bone, skin, bladder, kidney, ovary, and lymphocyte. Melanoma cell lines that carried at least one copy of MTS1 frequently carried nonsense, missense, or frameshift mutations in the gene. These findings suggest that MTS1 mutations are involved in tumor formation in a wide range of tissues.
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Affiliation(s)
- A Kamb
- Myriad Genetics, Inc., Salt Lake City, UT 84108
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Affiliation(s)
- M H Skolnick
- Department of Medical Informatics, University of Utah School of Medicine, Salt Lake City 84132, USA
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Affiliation(s)
- A Kamb
- Myriad Genetics, Inc., Salt Lake City, Utah 84108, USA
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Kamb A, Finer-Moore JS, Stroud RM. Cofactor triggers the conformational change in thymidylate synthase: implications for an ordered binding mechanism. Biochemistry 1992; 31:12876-84. [PMID: 1281428 DOI: 10.1021/bi00166a024] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have solved crystal structures of two complexes with Escherichia coli thymidylate synthase (TS) bound either to the cofactor analog N10-propargyl-5,8-dideazafolate (CB3717) or to a tighter binding polygutamyl derivative of CB3717. These structures suggest that cofactor binding alone is sufficient to induce the conformational change in TS; dUMP binding is not required. Because polyglutamyl folates are the primary cofactor form in vivo, and because they can bind more tightly than dUMP to TS, these structures may represent a key intermediate along the TS reaction pathway. These structures further suggest that the dUMP binding site is accessible in the TS-cofactor analog binary complexes. Conformational flexibility of the binary complex may permit dUMP to enter the active site of TS while the cofactor is bound. Alternatively, dUMP may enter the active site from the opposite side that the cofactor appears to enter; that is, through a portal flanked by arginines that also coordinate the phosphate group in the active site. Entry of dUMP through this portal may allow dUMP to bind to a TS-cofactor binary complex in which the complex has completed its conformational transition to the catalytically competent structure.
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Affiliation(s)
- A Kamb
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143
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Abstract
Thymidylate synthase (TS) catalyzes the final step in the de novo synthesis of thymidine. In vivo TS binds a polyglutamyl cofactor, polyglutamyl methylenetetrahydrofolate (CH2-H4folate), which serves as a carbon donor. Glutamate residues on the cofactor contribute as much as 3.7 kcal to the interaction between the cofactor, substrate, and enzyme. Because many ligand/receptor interactions appear to be driven largely by hydrophobic forces, it is surprising that the addition of hydrophilic, soluble groups such as glutamates increases the affinity of the cofactor for TS. The structure of a polyglutamyl cofactor analog bound in ternary complex with deoxyuridine monophosphate (dUMP) and Escherichia coli TS reveals how the polyglutamyl moiety is positioned in TS and accounts in a qualitative way for the binding contributions of the different individual glutamate residues. The polyglutamyl moiety is not rigidly fixed by its interaction with the protein except for the first glutamate residue nearest the p-aminobenzoic acid ring of folate. Each additional glutamate is progressively more disordered than the previous one in the chain. The position of the second and third glutamate residues on the protein surface suggests that the polyglutamyl binding site could be utilized by a new family of inhibitors that might fill the binding area more effectively than polyglutamate.
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Affiliation(s)
- A Kamb
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143
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Abstract
The utility of baculovirus as a vehicle for protein expression for both soluble and integral membrane proteins has been proved repeatedly. Our results suggest that baculovirus also holds promise as a means for expressing ion channel proteins. Because Sf9 cells are especially well suited to electrophysiology and because the construction of recombinant viruses that carry cloned genes is easy, baculovirus may also prove valuable for detailed functional studies of ion channels.
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Affiliation(s)
- C Kenyon
- Department of Biochemistry and Biophysics University of California, San Francisco 94143
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Kamb A, Weir M, Rudy B, Varmus H, Kenyon C. Identification of genes from pattern formation, tyrosine kinase, and potassium channel families by DNA amplification. Proc Natl Acad Sci U S A 1989; 86:4372-6. [PMID: 2734290 PMCID: PMC287271 DOI: 10.1073/pnas.86.12.4372] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The study of gene family members has been aided by the isolation of related genes on the basis of DNA homology. We have adapted the polymerase chain reaction to screen animal genomes very rapidly and reliably for likely gene family members. Using conserved amino acid sequences to design degenerate oligonucleotide primers, we have shown that the genome of the nematode Caenorhabditis elegans contains sequences homologous to many Drosophila genes involved in pattern formation, including the segment polarity gene wingless (vertebrate int-1), and homeobox sequences characteristic of the Antennapedia, engrailed, and paired families. In addition, we have used this method to show that C. elegans contains at least five different sequences homologous to genes in the tyrosine kinase family. Lastly, we have isolated six potassium channel sequences from humans, a result that validates the utility of the method with large genomes and suggests that human potassium channel gene diversity may be extensive.
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Affiliation(s)
- A Kamb
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143
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Abstract
K+ channels are known through electrophysiology and pharmacology to be an exceptionally diverse group of channels. Molecular studies of the Shaker (Sh) locus in Drosophila have provided the first glimpse of K+ channel structure. The sequences of several Sh cDNA clones have been reported; none are identical. We have isolated and examined 18 additional Sh cDNAs in an attempt to understand the origin, extent, and significance of the variability. The diversity is extensive: we have already identified cDNAs representing at least nine distinct types, and Sh could potentially encode 24 or more products. This diversity, however, fits a simple pattern in which variable 3' and 5' ends are spliced onto a central constant region to yield different cDNA types. These different Sh cDNAs encode proteins with distinct structural features.
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Affiliation(s)
- A Kamb
- Division of Biology, California Institute of Technology, Pasadena 91125
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Abstract
The Drosophila Shaker (Sh) gene appears to encode a type of voltage-sensitive potassium (K+) channel called the A channel. We have isolated Sh as part of a 350 kb chromosomal walk. The region around Sh contains four identified transcription units. We find that Sh corresponds to a very large transcription unit encompassing a total of about 95 kb of genomic DNA and split by a major 85 kb intron. Sh has multiple hydrophobic domains that have a high probability of being membrane-spanning, consistent with the proposal that it encodes an ion channel.
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Schamboeck A, Korman AJ, Kamb A, Strominger JL. Organization of the transcriptional unit of a human class II histocompatibility antigen: HLA-DR heavy chain. Nucleic Acids Res 1983; 11:8663-75. [PMID: 6324094 PMCID: PMC326615 DOI: 10.1093/nar/11.24.8663] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A total of 5724 base pairs of a recombinant phage DNA containing a human HLA-DR heavy chain gene including flanking regions has been analyzed. The regions corresponding to all the exons have been identified. The sites of initiation of transcription and polyadenylation have been determined. A large intron of 2399 base pairs separates the first exon containing the 5' untranslated region and the signal peptide from the second exon containing the N-terminal peptide domain.
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