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Ong DCT, Ho YM, Rudduck C, Chin K, Kuo WL, Lie DKH, Chua CLM, Tan PH, Eu KW, Seow-Choen F, Wong CY, Hong GS, Gray JW, Lee ASG. LARG at chromosome 11q23 has functional characteristics of a tumor suppressor in human breast and colorectal cancer. Oncogene 2009; 28:4189-200. [PMID: 19734946 PMCID: PMC2844776 DOI: 10.1038/onc.2009.266] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Deletion of 11q23-q24 is frequent in a diverse variety of malignancies, including breast and colorectal carcinoma, implicating the presence of a tumor suppressor gene at that chromosomal region. We examined a 6-Mb region on 11q23 by high-resolution deletion mapping, using both loss of heterozygosity analysis and customized microarray comparative genomic hybridization. LARG (leukemia-associated Rho guanine-nucleotide exchange factor) (also called ARHGEF12), identified from the analysed region, is frequently underexpressed in breast and colorectal carcinomas with a reduced expression observed in all breast cancer cell lines (n=11), in 12 of 38 (32%) primary breast cancers, 5 of 10 (50%) colorectal cell lines and in 20 of 37 (54%) primary colorectal cancers. Underexpression of the LARG transcript was significantly associated with genomic loss (P=0.00334). Hypermethylation of the LARG promoter was not detected in either breast or colorectal cancer, and treatment of four breast and four colorectal cancer cell lines with 5-aza-2'-deoxycytidine and/or trichostatin A did not result in a reactivation of LARG. Enforced expression of LARG in breast and colorectal cancer cells by stable transfection resulted in reduced cell proliferation and colony formation, as well as in a markedly slower cell migration rate in colorectal cancer cells, providing functional evidence for LARG as a candidate tumor suppressor gene.
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Affiliation(s)
- DCT Ong
- Division of Medical Sciences, National Cancer Centre, Singapore
| | - YM Ho
- Division of Medical Sciences, National Cancer Centre, Singapore
| | - C Rudduck
- Department of Pathology, Singapore General Hospital, Singapore
| | - K Chin
- UCSF Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - W-L Kuo
- UCSF Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - DKH Lie
- Division of Medical Sciences, National Cancer Centre, Singapore
| | - CLM Chua
- Division of Medical Sciences, National Cancer Centre, Singapore
| | - PH Tan
- Department of Pathology, Singapore General Hospital, Singapore
| | - KW Eu
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - F Seow-Choen
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - CY Wong
- Department of General Surgery, Singapore General Hospital, Singapore
| | - GS Hong
- Department of General Surgery, Singapore General Hospital, Singapore
| | - JW Gray
- UCSF Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - ASG Lee
- Division of Medical Sciences, National Cancer Centre, Singapore
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Chin K, Devries S, Fridlyand J, Spellman P, Kuo WL, Lapuk A, Neve R, Tokuyasu T, Kingsley C, Dairkee S, Chew K, Jain A, Ljung BM, Esserman L, Waldman F, Gray JW. Genomic and transcriptional events associated with poor clinical responses to conventional therapies. Breast Cancer Res 2005. [PMCID: PMC4233480 DOI: 10.1186/bcr1059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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3
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Hsu YH, Kuo WL, Su IJ. Clinicopathologic study of Kaposi's sarcoma and strain analysis of human herpesvirus 8 (HHV-8) DNA in the Hua-Lien area of eastern Taiwan. J Formos Med Assoc 2001; 100:449-54. [PMID: 11579609] [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: 02/21/2023] Open
Abstract
BACKGROUND AND PURPOSE Kaposi's sarcoma (KS) is a spindle cell malignancy of endothelial cell origin. The tumor has been demonstrated to be associated with human herpesvirus 8 (HHV-8) or Kaposi's sarcoma-associated herpesvirus-like virus (KSHV). Previous studies have revealed the distribution of unique viral strains in different ethnic populations. Eastern Taiwan has an ethnically mixed population with a relatively high incidence of KS. This study was designed to characterize the clinicopathologic features of KS and to evaluate the HHV-8 strain distribution in the Hua-Lien area of Eastern Taiwan. METHODS Clinical records and laboratory data were collected from 15 cases of KS diagnosed and treated between 1993 and 1999 in Tzu-Chi General Hospital. For nine cases, paraffin blocks were available for the molecular study of HHV-8. HHV-8 genomic variation was analyzed using polymerase chain reaction nucleotide sequencing of ORF26 and ORF75 of HHV-8 genomes derived from different subgroups of KS. RESULTS Among the 15 patients with KS, two had AIDS-associated disease, four had gouty arthritis and psoriasis and were receiving corticosteroid therapy (iatrogenic type), and nine had classical KS. Nine of the 15 cases occurred in aborigines, including one with AIDS-associated disease, four with iatrogenic disease, and four with classical disease. Among the nine cases for which tissue was available for DNA analysis, eight were positive for HHV-8 DNA. Sequence analysis revealed that the C strain occurred in three Han Chinese KS patients, whereas a hitherto rarely described strain (strain D) occurred in all four aborigines tested (including one with AIDS-associated KS) and one Han Chinese with AIDS from Burma. CONCLUSION This study found a high proportion of iatrogenic KS and the finding of a rarely described strain D virus in Eastern Taiwan aborigines. Our studies further confirm the distribution of different types of KS and virus strains in different ethnic populations.
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Affiliation(s)
- Y H Hsu
- Department of Pathology, Tzu-Chi General Hospital, Hua-Lien, Taiwan
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4
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Collins C, Volik S, Kowbel D, Ginzinger D, Ylstra B, Cloutier T, Hawkins T, Predki P, Martin C, Wernick M, Kuo WL, Alberts A, Gray JW. Comprehensive genome sequence analysis of a breast cancer amplicon. Genome Res 2001; 11:1034-42. [PMID: 11381030 PMCID: PMC311107 DOI: 10.1101/gr.gr1743r] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [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: 01/05/2023]
Abstract
Gene amplification occurs in most solid tumors and is associated with poor prognosis. Amplification of 20q13.2 is common to several tumor types including breast cancer. The 1 Mb of sequence spanning the 20q13.2 breast cancer amplicon is one of the most exhaustively studied segments of the human genome. These studies have included amplicon mapping by comparative genomic hybridization (CGH), fluorescent in-situ hybridization (FISH), array-CGH, quantitative microsatellite analysis (QUMA), and functional genomic studies. Together these studies revealed a complex amplicon structure suggesting the presence of at least two driver genes in some tumors. One of these, ZNF217, is capable of immortalizing human mammary epithelial cells (HMEC) when overexpressed. In addition, we now report the sequencing of this region in human and mouse, and on quantitative expression studies in tumors. Amplicon localization now is straightforward and the availability of human and mouse genomic sequence facilitates their functional analysis. However, comprehensive annotation of megabase-scale regions requires integration of vast amounts of information. We present a system for integrative analysis and demonstrate its utility on 1.2 Mb of sequence spanning the 20q13.2 breast cancer amplicon and 865 kb of syntenic murine sequence. We integrate tumor genome copy number measurements with exhaustive genome landscape mapping, showing that amplicon boundaries are associated with maxima in repetitive element density and a region of evolutionary instability. This integration of comprehensive sequence annotation, quantitative expression analysis, and tumor amplicon boundaries provide evidence for an additional driver gene prefoldin 4 (PFDN4), coregulated genes, conserved noncoding regions, and associate repetitive elements with regions of genomic instability at this locus.
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Affiliation(s)
- C Collins
- University of California San Francisco Cancer Center, San Francisco, California 94143-0808, USA.
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5
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Brown ML, Ramprasad MP, Umeda PK, Tanaka A, Kobayashi Y, Watanabe T, Shimoyamada H, Kuo WL, Li R, Song R, Bradley WA, Gianturco SH. A macrophage receptor for apolipoprotein B48: cloning, expression, and atherosclerosis. Proc Natl Acad Sci U S A 2000; 97:7488-93. [PMID: 10852956 PMCID: PMC16572 DOI: 10.1073/pnas.120184097] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [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: 11/18/2022] Open
Abstract
We have cloned a human macrophage receptor that binds to apolipoprotein (apo)B48 of dietary triglyceride (TG)-rich lipoproteins. TG-rich lipoprotein uptake by the apoB48R rapidly converts macrophages and apoB48R-transfected Chinese hamster ovary cells in vitro into lipid-filled foam cells, as seen in atherosclerotic lesions. The apoB48R cDNA (3,744 bp) encodes a protein with no known homologs. Its approximately 3.8-kb mRNA is expressed primarily by reticuloendothelial cells: monocytes, macrophages, and endothelial cells. Immunohistochemistry shows the apoB48R is in human atherosclerotic lesion foam cells. Normally, the apoB48R may provide essential lipids to reticuloendothelial cells. If overwhelmed, foam cell formation, endothelial dysfunction, and atherothrombogenesis may ensue, a mechanism for cardiovascular disease risk of elevated TG.
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Affiliation(s)
- M L Brown
- Department of Medicine, Division of Gerontology and Geriatrics, University of Alabama, Birmingham, AL 35294-0012, USA
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6
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Albertson DG, Ylstra B, Segraves R, Collins C, Dairkee SH, Kowbel D, Kuo WL, Gray JW, Pinkel D. Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat Genet 2000; 25:144-6. [PMID: 10835626 DOI: 10.1038/75985] [Citation(s) in RCA: 464] [Impact Index Per Article: 19.3] [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: 11/08/2022]
Abstract
We show here that quantitative measurement of DNA copy number across amplified regions using array comparative genomic hybridization (CGH) may facilitate oncogene identification by providing precise information on the locations of both amplicon boundaries and amplification maxima. Using this analytical capability, we resolved two regions of amplification within an approximately 2-Mb region of recurrent aberration at 20q13.2 in breast cancer. The putative oncogene ZNF217 (ref. 5) mapped to one peak, and CYP24 (encoding vitamin D 24 hydroxylase), whose overexpression is likely to lead to abrogation of growth control mediated by vitamin D, mapped to the other.
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Affiliation(s)
- D G Albertson
- [1] Cancer Research Institute, University of California, San Francisco, Box 0808, San Francisco, California, USA.
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7
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Hernandez MC, Andres-Barquin PJ, Kuo WL, Israel MA. Assignment of the ectodermal-neural cortex 1 gene (ENC1) to human chromosome band 5q13 by in situ hybridization. Cytogenet Cell Genet 2000; 87:89-90. [PMID: 10640818 DOI: 10.1159/000015398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- M C Hernandez
- Preuss Laboratory for Molecular Neuro-Oncology, BTRC, Department of Neurological Surgery, School of Medicine, University of California San Francisco, 94143-0520, USA
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8
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Abstract
The protein SWAP-70 was isolated as part of a DNA recombination complex in B lymphocytes, where it is predominantly expressed. In resting B cells, SWAP-70 is found in the cytoplasm; upon B-cell activation, it is transported both into the nucleus and to the cell membrane, where it is associated with the B-cell receptor complex and may play a role in signal transduction. In the nucleus, its involvement in heavy-chain class switch recombination has been suggested. In this report, using restriction fragment length polymorphism, simple sequence length polymorphism, and fluorescence in situ hybridization, we map the chromosomal localization of the mouse and the human genes to syntenic regions of mouse mid Chromosome (Chr) 7 and human Chr 11p15.
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Affiliation(s)
- L Masat
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143-0670, USA.
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9
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Gray J, Chin K, Collins C, Yaswin P, Nonet G, Kowbel D, Kuo WL, Garcia E, Ortiz de Solorzano C, Knowles D, Lockett S, Bissell M, Weaver V, Pinkel D, Albertson D, Børresen-Dale AL, Waldnian F. Two molecular cytogenetic views of breast cancer. Breast Cancer Res 2000. [PMCID: PMC3300893 DOI: 10.1186/bcr195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- J Gray
- UCSF Cancer Center, University of California, San Francisco
| | - K Chin
- UCSF Cancer Center, University of California, San Francisco
| | - C Collins
- UCSF Cancer Center, University of California, San Francisco
| | - P Yaswin
- Biomedical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - G Nonet
- Biomedical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - D Kowbel
- UCSF Cancer Center, University of California, San Francisco
| | - W-L Kuo
- UCSF Cancer Center, University of California, San Francisco
| | - E Garcia
- Biomedical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - C Ortiz de Solorzano
- Biomedical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - D Knowles
- Biomedical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S Lockett
- Biomedical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - M Bissell
- Biomedical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - V Weaver
- Biomedical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - D Pinkel
- UCSF Cancer Center, University of California, San Francisco
| | - D Albertson
- UCSF Cancer Center, University of California, San Francisco
| | - A-L Børresen-Dale
- Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
| | - F Waldnian
- UCSF Cancer Center, University of California, San Francisco
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10
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Korn WM, Yasutake T, Kuo WL, Warren RS, Collins C, Tomita M, Gray J, Waldman FM. Chromosome arm 20q gains and other genomic alterations in colorectal cancer metastatic to liver, as analyzed by comparative genomic hybridization and fluorescence in situ hybridization. Genes Chromosomes Cancer 1999; 25:82-90. [PMID: 10337990 DOI: 10.1002/(sici)1098-2264(199906)25:2<82::aid-gcc2>3.0.co;2-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.8] [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: 11/09/2022] Open
Abstract
Comprehensive information about the molecular cytogenetic changes in metastases of colorectal cancer is not yet available. To define such changes in metastases, we measured relative DNA sequence copy numbers by comparative genomic hybridization (CGH). Samples from 27 liver metastases and 6 synchronous primary tumors were analyzed. An average of 9.9 aberrations per tumor was found in the metastases. Gains of chromosome arms 20q (85%), 13q (48%), 7p (44%), and 8q (44%) and losses of chromosome arms 18q (89%), 8p (59%), 1p (56%), and 18p (48%) were detected most frequently. Chromosomes 14 and 15 were lost in 26% and 30% of the metastases, respectively. No consistent differences were observed between primary tumors and synchronous metastases. Fluorescence in situ hybridization (FISH) was used for further characterization of gains of chromosome arm 20q. Touch preparations of 13 tumors that had demonstrated 20q gain with CGH were examined with FISH by use of a set of probes mapping to different parts of 20q. A probe for 20p was used as a reference. FISH showed relative gain of at least one 20q locus in 12 of the tumors. High-level gains were detected in 38% of the tumors, preferentially for probes mapping to band 20q13. Our CGH data indicate that colorectal metastases show chromosomal changes similar to those that have been reported for primary tumors. Chromosomal losses were seen at higher frequency, particularly for chromosomes 14 and 15. By FISH, we identified subregions on chromosome arm 20q that are frequently involved in DNA amplifications in colorectal cancer and that may harbor candidate proto-oncogenes.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Chromosome Aberrations/genetics
- Chromosome Disorders
- Chromosomes, Human/genetics
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 13/genetics
- Chromosomes, Human, Pair 14/genetics
- Chromosomes, Human, Pair 15/genetics
- Chromosomes, Human, Pair 18/genetics
- Chromosomes, Human, Pair 20/genetics
- Chromosomes, Human, Pair 7/genetics
- Chromosomes, Human, Pair 8/genetics
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/pathology
- Female
- Humans
- In Situ Hybridization, Fluorescence/methods
- Liver Neoplasms/genetics
- Liver Neoplasms/secondary
- Male
- Middle Aged
- Neoplasm Staging
- Nucleic Acid Hybridization/methods
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Affiliation(s)
- W M Korn
- Cancer Center, University of California-San Francisco, 94143, USA.
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11
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Abe MK, Kuo WL, Hershenson MB, Rosner MR. Extracellular signal-regulated kinase 7 (ERK7), a novel ERK with a C-terminal domain that regulates its activity, its cellular localization, and cell growth. Mol Cell Biol 1999; 19:1301-12. [PMID: 9891064 PMCID: PMC116059 DOI: 10.1128/mcb.19.2.1301] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.4] [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] [Received: 07/22/1998] [Accepted: 10/27/1998] [Indexed: 11/20/2022] Open
Abstract
Mitogen-activated protein (MAP) kinases play distinct roles in a variety of cellular signaling pathways and are regulated through multiple mechanisms. In this study, a novel 61-kDa member of the MAP kinase family, termed extracellular signal-regulated kinase 7 (ERK7), has been cloned and characterized. Although it has the signature TEY activation motif of ERK1 and ERK2, ERK7 is not activated by extracellular stimuli that typically activate ERK1 and ERK2 or by common activators of c-Jun N-terminal kinase (JNK) and p38 kinase. Instead, ERK7 has appreciable constitutive activity in serum-starved cells that is dependent on the presence of its C-terminal domain. Interestingly, the C-terminal tail, not the kinase domain, of ERK7 regulates its nuclear localization and inhibition of growth. Taken together, these results elucidate a novel type of MAP kinase whereby interactions via its C-terminal tail, rather than extracellular signal-mediated activation cascades, regulate its activity, localization, and function.
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Affiliation(s)
- M K Abe
- Department of Pediatrics, University of Chicago, Chicago, Illinois 60637, USA
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12
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Yu Y, Xu F, Peng H, Fang X, Zhao S, Li Y, Cuevas B, Kuo WL, Gray JW, Siciliano M, Mills GB, Bast RC. NOEY2 (ARHI), an imprinted putative tumor suppressor gene in ovarian and breast carcinomas. Proc Natl Acad Sci U S A 1999; 96:214-9. [PMID: 9874798 PMCID: PMC15119 DOI: 10.1073/pnas.96.1.214] [Citation(s) in RCA: 226] [Impact Index Per Article: 9.0] [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] [Received: 08/13/1998] [Indexed: 11/18/2022] Open
Abstract
Using differential display PCR, we have identified a gene [NOEY2, ARHI (designation by the Human Gene Nomenclature Committee)] with high homology to ras and rap that is expressed consistently in normal ovarian and breast epithelial cells but not in ovarian and breast cancers. Reexpression of NOEY2 through transfection suppresses clonogenic growth of breast and ovarian cancer cells. Growth suppression was associated with down-regulation of the cyclin D1 promoter activity and induction of p21(WAF1/CIP1). In an effort to identify mechanisms leading to NOEY2 silencing in cancer, we found that the gene is expressed monoallelically and is imprinted maternally. Loss of heterozygosity of the gene was detected in 41% of ovarian and breast cancers. In most of cancer samples with loss of heterozygosity, the nonimprinted functional allele was deleted. Thus, NOEY2 appears to be a putative imprinted tumor suppressor gene whose function is abrogated in ovarian and breast cancers.
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Affiliation(s)
- Y Yu
- Division of Medicine, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
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13
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Shayesteh L, Lu Y, Kuo WL, Baldocchi R, Godfrey T, Collins C, Pinkel D, Powell B, Mills GB, Gray JW. PIK3CA is implicated as an oncogene in ovarian cancer. Nat Genet 1999; 21:99-102. [PMID: 9916799 DOI: 10.1038/5042] [Citation(s) in RCA: 811] [Impact Index Per Article: 32.4] [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: 12/12/2022]
Abstract
Ovarian cancer is the leading cause of death from gynecological malignancy and the fourth leading cause of cancer death among American women, yet little is known about its molecular aetiology. Studies using comparative genomic hybridization (CGH) have revealed several regions of recurrent, abnormal, DNA sequence copy number that may encode genes involved in the genesis or progression of the disease. One region at 3q26 found to be increased in copy number in approximately 40% of ovarian and others cancers contains PIK3CA, which encodes the p110alpha catalytic subunit of phosphatidylinositol 3-kinase (PI3-kinase). The association between PIK3CA copy number and PI3-kinase activity makes PIK3CA a candidate oncogene because a broad range of cancer-related functions have been associated with PI3-kinase mediated signalling. These include proliferation, glucose transport and catabolism, cell adhesion, apoptosis, RAS signalling and oncogenic transformation. In addition, downstream effectors of PI3-kinase, AKT1 and AKT2, have been found to be amplified or activated in human tumours, including ovarian cancer. We show here that PIK3CA is frequently increased in copy number in ovarian cancers, that the increased copy number is associated with increased PIK3CA transcription, p110alpha protein expression and PI3-kinase activity and that treatment with the PI3-kinase inhibitor LY294002 decreases proliferation and increases apoptosis. Our observations suggest PIK3CA is an oncogene that has an important role in ovarian cancer.
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Affiliation(s)
- L Shayesteh
- UCSF Cancer Center, University of California, San Francisco 941430-0808, USA
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14
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Abstract
The Id proteins belong to a family of nuclear HLH proteins lacking a basic region and thought to function as dominant-negative regulators of bHLH proteins during cell growth and differentiation. In this paper, we report the genomic organization of the mouse Id2 and Id4 genes. These genes each span approximately 3 kb of the mouse genome and are each organized as three exons with recognizable splice donor and acceptor consensus sequences. Their genomic organization is very similar, consistent with their having evolved from a common, ancestral Id-like gene. Using FISH analysis, we have localized the mouse Id2 and Id4 genes to mouse chromosome 12 and 13, respectively.
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Affiliation(s)
- A Mantani
- The Preuss Laboratory for Molecular Neuro-Oncology, Brain Tumor Research Center, Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
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15
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Mears AJ, Jordan T, Mirzayans F, Dubois S, Kume T, Parlee M, Ritch R, Koop B, Kuo WL, Collins C, Marshall J, Gould DB, Pearce W, Carlsson P, Enerbäck S, Morissette J, Bhattacharya S, Hogan B, Raymond V, Walter MA. Mutations of the forkhead/winged-helix gene, FKHL7, in patients with Axenfeld-Rieger anomaly. Am J Hum Genet 1998; 63:1316-28. [PMID: 9792859 PMCID: PMC1377542 DOI: 10.1086/302109] [Citation(s) in RCA: 234] [Impact Index Per Article: 9.0] [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: 01/13/2023] Open
Abstract
Genetic linkage, genome mismatch scanning, and analysis of patients with alterations of chromosome 6 have indicated that a major locus for development of the anterior segment of the eye, IRID1, is located at 6p25. Abnormalities of this locus lead to glaucoma. FKHL7 (also called "FREAC3"), a member of the forkhead/winged-helix transcription-factor family, has also been mapped to 6p25. DNA sequencing of FKHL7 in five IRID1 families and 16 sporadic patients with anterior-segment defects revealed three mutations: a 10-bp deletion predicted to cause a frameshift and premature protein truncation prior to the FKHL7 forkhead DNA-binding domain, as well as two missense mutations of conserved amino acids within the FKHL7 forkhead domain. Mf1, the murine homologue of FKHL7, is expressed in the developing brain, skeletal system, and eye, consistent with FKHL7 having a role in ocular development. However, mutational screening and genetic-linkage analyses excluded FKHL7 from underlying the anterior-segment disorders in two IRID1 families with linkage to 6p25. Our findings demonstrate that, although mutations of FKHL7 result in anterior-segment defects and glaucoma in some patients, it is probable that at least one more locus involved in the regulation of eye development is also located at 6p25.
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Affiliation(s)
- A J Mears
- Departments of Ophthalmology and Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
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16
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Zhou H, Kuang J, Zhong L, Kuo WL, Gray JW, Sahin A, Brinkley BR, Sen S. Tumour amplified kinase STK15/BTAK induces centrosome amplification, aneuploidy and transformation. Nat Genet 1998; 20:189-93. [PMID: 9771714 DOI: 10.1038/2496] [Citation(s) in RCA: 959] [Impact Index Per Article: 36.9] [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: 01/05/2023]
Abstract
The centrosomes are thought to maintain genomic stability through the establishment of bipolar spindles during cell division, ensuring equal segregation of replicated chromosomes to two daughter cells. Deregulated duplication and distribution of centrosomes have been implicated in chromosome segregation abnormalities, leading to aneuploidy seen in many cancer cell types. Here, we report that STK15 (also known as BTAK and aurora2), encoding a centrosome-associated kinase, is amplified and overexpressed in multiple human tumour cell types, and is involved in the induction of centrosome duplication-distribution abnormalities and aneuploidy in mammalian cells. STK15 amplification has been previously detected in breast tumour cell lines and in colon tumours; here, we report its amplification in approximately 12% of primary breast tumours, as well as in breast, ovarian, colon, prostate, neuroblastoma and cervical cancer cell lines. Additionally, high expression of STK15 mRNA was detected in tumour cell lines without evidence of gene amplification. Ectopic expression of STK15 in mouse NIH 3T3 cells led to the appearance of abnormal centrosome number (amplification) and transformation in vitro. Finally, overexpression of STK15 in near diploid human breast epithelial cells revealed similar centrosome abnormality, as well as induction of aneuploidy. These findings suggest that STK15 is a critical kinase-encoding gene, whose overexpression leads to centrosome amplification, chromosomal instability and transformation in mammalian cells.
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Affiliation(s)
- H Zhou
- Division of Pathology & Laboratory Medicine, University of Texas M.D. Anderson Cancer Center, Houston 77030, USA
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17
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Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998; 20:207-11. [PMID: 9771718 DOI: 10.1038/2524] [Citation(s) in RCA: 1420] [Impact Index Per Article: 54.6] [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: 01/25/2023]
Abstract
Gene dosage variations occur in many diseases. In cancer, deletions and copy number increases contribute to alterations in the expression of tumour-suppressor genes and oncogenes, respectively. Developmental abnormalities, such as Down, Prader Willi, Angelman and Cri du Chat syndromes, result from gain or loss of one copy of a chromosome or chromosomal region. Thus, detection and mapping of copy number abnormalities provide an approach for associating aberrations with disease phenotype and for localizing critical genes. Comparative genomic hybridization (CGH) was developed for genome-wide analysis of DNA sequence copy number in a single experiment. In CGH, differentially labelled total genomic DNA from a 'test' and a 'reference' cell population are cohybridized to normal metaphase chromosomes, using blocking DNA to suppress signals from repetitive sequences. The resulting ratio of the fluorescence intensities at a location on the 'cytogenetic map', provided by the chromosomes, is approximately proportional to the ratio of the copy numbers of the corresponding DNA sequences in the test and reference genomes. CGH has been broadly applied to human and mouse malignancies. The use of metaphase chromosomes, however, limits detection of events involving small regions (of less than 20 Mb) of the genome, resolution of closely spaced aberrations and linking ratio changes to genomic/genetic markers. Therefore, more laborious locus-by-locus techniques have been required for higher resolution studies. Hybridization to an array of mapped sequences instead of metaphase chromosomes could overcome the limitations of conventional CGH (ref. 6) if adequate performance could be achieved. Copy number would be related to the test/reference fluorescence ratio on the array targets, and genomic resolution could be determined by the map distance between the targets, or by the length of the cloned DNA segments. We describe here our implementation of array CGH. We demonstrate its ability to measure copy number with high precision in the human genome, and to analyse clinical specimens by obtaining new information on chromosome 20 aberrations in breast cancer.
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Affiliation(s)
- D Pinkel
- Cancer Genetics Program, UCSF Cancer Center, University of California San Francisco, 94143-0808, USA.
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18
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Chen LC, Manjeshwar S, Lu Y, Moore D, Ljung BM, Kuo WL, Dairkee SH, Wernick M, Collins C, Smith HS. The human homologue for the Caenorhabditis elegans cul-4 gene is amplified and overexpressed in primary breast cancers. Cancer Res 1998; 58:3677-83. [PMID: 9721878] [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] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Amplification is a key mechanism whereby a cancer cell increases the message level of genes that confer a selective advantage when they are overexpressed. In breast cancer, there are many chromosome regions present in multiple copies relative to overall DNA copy number (amplicons), and their target genes are unknown. Using differential display, we have cloned and sequenced the full coding region of a candidate amplicon target gene located on chromosome 13. This candidate is the human homologue of the Caenorhabditis elegans cul-4 gene, cul-4A, a member of the novel cullin gene family, which is involved in cell cycle control of C. elegans. cul-4A was amplified and overexpressed in 3 of 14 breast cancer cell lines analyzed, and it was overexpressed in 8 additional cell lines in which it was not amplified. The latter observation, indicating that its overexpression can occur by mechanisms other than gene amplification, suggests that cul-4A plays a key role in carcinogenesis. Moreover, cul-4A was found to be amplified in 17 of 105 (16%) cases of untreated primary breast cancers, and 14 of 30 cases analyzed (47%) were shown by RNA in situ hybridization to overexpress cul-4A. These results suggest that up-regulation of cul-4A may play an important role in tumor progression.
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Affiliation(s)
- L C Chen
- Geraldine Brush Cancer Research Institute, California Pacific Medical Center, San Francisco 94115, USA
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19
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Collins C, Rommens JM, Kowbel D, Godfrey T, Tanner M, Hwang SI, Polikoff D, Nonet G, Cochran J, Myambo K, Jay KE, Froula J, Cloutier T, Kuo WL, Yaswen P, Dairkee S, Giovanola J, Hutchinson GB, Isola J, Kallioniemi OP, Palazzolo M, Martin C, Ericsson C, Pinkel D, Albertson D, Li WB, Gray JW. Positional cloning of ZNF217 and NABC1: genes amplified at 20q13.2 and overexpressed in breast carcinoma. Proc Natl Acad Sci U S A 1998; 95:8703-8. [PMID: 9671742 PMCID: PMC21140 DOI: 10.1073/pnas.95.15.8703] [Citation(s) in RCA: 233] [Impact Index Per Article: 9.0] [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] [Received: 01/13/1998] [Indexed: 02/08/2023] Open
Abstract
We report here the molecular cloning of an approximately 1-Mb region of recurrent amplification at 20q13.2 in breast cancer and other tumors and the delineation of a 260-kb common region of amplification. Analysis of the 1-Mb region produced evidence for five genes, ZNF217, ZNF218, and NABC1, PIC1L (PIC1-like), CYP24, and a pseudogene CRP (Cyclophillin Related Pseudogene). ZNF217 and NABC1 emerged as strong candidate oncogenes and were characterized in detail. NABC1 is predicted to encode a 585-aa protein of unknown function and is overexpressed in most but not all breast cancer cell lines in which it was amplified. ZNF217 is centrally located in the 260-kb common region of amplification, transcribed in multiple normal tissues, and overexpressed in all cell lines and tumors in which it is amplified and in two in which it is not. ZNF217 is predicted to encode alternately spliced, Kruppel-like transcription factors of 1,062 and 1,108 aa, each having a DNA-binding domain (eight C2H2 zinc fingers) and a proline-rich transcription activation domain.
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Affiliation(s)
- C Collins
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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20
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Polikoff D, Kuo WL, Cochran JF, Wernick M, Kowbel D, Myambo K, Collins CC. Assignment of protease, serine-like 1 (PRSSL1) to human chromosome 19q13 by in situ hybridization and radiation hybrid mapping. Cytogenet Cell Genet 1998; 79:147-8. [PMID: 9533035 DOI: 10.1159/000134705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- D Polikoff
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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21
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Abe MK, Kartha S, Karpova AY, Li J, Liu PT, Kuo WL, Hershenson MB. Hydrogen peroxide activates extracellular signal-regulated kinase via protein kinase C, Raf-1, and MEK1. Am J Respir Cell Mol Biol 1998; 18:562-9. [PMID: 9533945 DOI: 10.1165/ajrcmb.18.4.2958] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.8] [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: 11/24/2022] Open
Abstract
We have previously demonstrated that hydrogen peroxide (H2O2) treatment of bovine tracheal myocytes increases the activity of extracellular signal-regulated kinases (ERK), serine/threonine kinases of the mitogen-activated protein (MAP) kinase superfamily thought to play a key role in the transduction of mitogenic signals to the cell nucleus. Moreover, H2O2-induced ERK activation was partially reduced by pretreatment with phorbol 12,13-dibutyrate, which depletes protein kinase C (PKC). In this study, we further examined the signaling intermediates responsible for ERK activation by H2O2 in airway smooth muscle, focusing on MAP kinase/ERK kinase (MEK), a dual-function kinase which is required and sufficient for ERK activation in bovine tracheal myocytes; Raf-1, a serine/threonine kinase known to activate MEK; and PKC. Pretreatment of cells with inhibitors of MEK (PD98059), Raf-1 (forskolin), and PKC (chelerythrine) each reduced H2O2-induced ERK activity. In addition, H2O2 treatment significantly increased both MEK1 and Raf-1 activity. No activation of MEK2 was detected. Together these data suggest that H2O2 may stimulate ERK via successive activation of PKC, Raf-1, and MEK1.
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Affiliation(s)
- M K Abe
- Department of Pediatrics, University of Chicago, Chicago, Illinois 60637, USA
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22
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Trask BJ, Friedman C, Martin-Gallardo A, Rowen L, Akinbami C, Blankenship J, Collins C, Giorgi D, Iadonato S, Johnson F, Kuo WL, Massa H, Morrish T, Naylor S, Nguyen OT, Rouquier S, Smith T, Wong DJ, Youngblom J, van den Engh G. Members of the olfactory receptor gene family are contained in large blocks of DNA duplicated polymorphically near the ends of human chromosomes. Hum Mol Genet 1998; 7:13-26. [PMID: 9384599 DOI: 10.1093/hmg/7.1.13] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.3] [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: 02/05/2023] Open
Abstract
We have identified three new members of the olfactory receptor (OR) gene family within a large segment of DNA that is duplicated with high similarity near many human telomeres. This segment is present at 3q, 15q, and 19p in each of 45 unrelated humans sampled from various populations. Additional copies are present polymorphically at 11 other subtelomeric locations. The frequency with which the block is present at some locations varies among populations. While humans carry seven to 11 copies of the OR-containing block, it is located in chimpanzee and gorilla predominantly at a single site, which is not orthologous to any of the locations in the human genome. The observation that sequences flanking the OR-containing segment are duplicated on larger and different sets of chromosomes than the OR block itself demonstrates that the segment is part of a much larger, complex patchwork of subtelomeric duplications. The population analyses and structural results suggest the types of processes that have shaped these regions during evolution. From its sequence, one of the OR genes in this duplicated block appears to be potentially functional. Our findings raise the possibility that functional diversity in the OR family is generated in part through duplications and inter-chromosomal rearrangements of the DNA near human telomeres.
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Affiliation(s)
- B J Trask
- Department of Molecular Biotechnology, Box 357730, University of Washington, Seattle, WA 98195, USA.
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23
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Morton SM, Veile RA, Helms C, Lee M, Kuo WL, Gray J, Donis-Keller H. Subregional localization of 21 chromosome 7-specific expressed sequence tags (ESTs) by FISH using newly identified YACs and P1s. Genomics 1997; 46:491-4. [PMID: 9441757 DOI: 10.1006/geno.1997.5051] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Twenty-one putative chromosome 7-derived expressed sequence tags (ESTs) identified 33 yeast artificial chromosomes (YACs) or P1 clones, which were then used as reagents for physical mapping. FISH mapping established that the ESTs contained within these clones were distributed throughout chromosome 7, with all major cytogenetic bands represented, except 7p13-p15, 7p11, 7q31.2, and 7q35. Each EST sequence identified at least one other sequence in publicly available databases (using search tools such as BLASTN, basic local alignment search tool), and many of the ESTs identified cDNAs and several genomic DNA sequences. However, 7 ESTs did not identify highly significant matches (P < 1 x 10(-5)). Only one (EST01924-D7S2281E) failed to identify any other EST from the dbEST homology searches. BLAST analysis identified at least five genes from EST sequence comparisons: protein tyrosine phosphatase zeta (PTPRZ, also known as RPTPZ) (EST02092), which we had mapped to 7q31.3, in agreement with previous studies; cAMP-dependent protein kinase regulatory subunit bI (EST01644); rat integral membrane glycoprotein (EST00085); human IFNAR gene for interferon alpha/beta receptor (EST00817); and rat 14-3.3 protein gamma subtype (putative protein kinase C regulatory protein) (EST00762). These ESTs will help to develop the map of chromosome 7, which integrates physical, transcriptional, and cytogenetic data, as well as to provide candidate disease genes for chromosome 7-specific disorders.
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Affiliation(s)
- S M Morton
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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24
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Xia H, Winokur ST, Kuo WL, Altherr MR, Bredt DS. Actinin-associated LIM protein: identification of a domain interaction between PDZ and spectrin-like repeat motifs. J Cell Biol 1997; 139:507-15. [PMID: 9334352 PMCID: PMC2139795 DOI: 10.1083/jcb.139.2.507] [Citation(s) in RCA: 171] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
PDZ motifs are protein-protein interaction domains that often bind to COOH-terminal peptide sequences. The two PDZ proteins characterized in skeletal muscle, syntrophin and neuronal nitric oxide synthase, occur in the dystrophin complex, suggesting a role for PDZ proteins in muscular dystrophy. Here, we identify actinin-associated LIM protein (ALP), a novel protein in skeletal muscle that contains an NH2-terminal PDZ domain and a COOH-terminal LIM motif. ALP is expressed at high levels only in differentiated skeletal muscle, while an alternatively spliced form occurs at low levels in the heart. ALP is not a component of the dystrophin complex, but occurs in association with alpha-actinin-2 at the Z lines of myofibers. Biochemical and yeast two-hybrid analyses demonstrate that the PDZ domain of ALP binds to the spectrin-like motifs of alpha-actinin-2, defining a new mode for PDZ domain interactions. Fine genetic mapping studies demonstrate that ALP occurs on chromosome 4q35, near the heterochromatic locus that is mutated in fascioscapulohumeral muscular dystrophy.
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Affiliation(s)
- H Xia
- Department of Physiology, University of California at San Francisco, San Francisco, California 94143, USA
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25
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Kuo WL, Chung KC, Rosner MR. Differentiation of central nervous system neuronal cells by fibroblast-derived growth factor requires at least two signaling pathways: roles for Ras and Src. Mol Cell Biol 1997; 17:4633-43. [PMID: 9234720 PMCID: PMC232316 DOI: 10.1128/mcb.17.8.4633] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.5] [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: 02/04/2023] Open
Abstract
To evaluate the role of mitogen-activated protein (MAP) kinase and other signaling pathways in neuronal cell differentiation by basic fibroblast-derived growth factor (bFGF), we used a conditionally immortalized cell line from rat hippocampal neurons (H19-7). Previous studies have shown that activation of MAP kinase kinase (MEK) is insufficient to induce neuronal differentiation of H19-7 cells. To test the requirement for MEK and MAP kinase (ERK1 and ERK2), H19-7 cells were treated with the MEK inhibitor PD098059. Although the MEK inhibitor blocked the induction of differentiation by constitutively activated Raf, the H19-7 cells still underwent differentiation by bFGF. These results suggest that an alternative pathway is utilized by bFGF for differentiation of the hippocampal neuronal cells. Expression in the H19-7 cells of a dominant-negative Ras (N17-Ras) or Raf (C4-Raf) blocked differentiation by bFGF, suggesting that Ras and probably Raf are required. Expression of dominant-negative Src (pcSrc295Arg) or microinjection of an anti-Src antibody blocked differentiation by bFGF in H19-7 cells, indicating that bFGF also signals through a Src kinase-mediated pathway. Although neither constitutively activated MEK (MEK-2E) nor v-Src was sufficient individually to differentiate the H19-7 cells, coexpression of constitutively activated MEK and v-Src induced neurite outgrowth. These results suggest that (i) activation of MAP kinase (ERK1 and ERK2) is neither necessary nor sufficient for differentiation by bFGF; (ii) activation of Src kinases is necessary but not sufficient for differentiation by bFGF; and (iii) differentiation of H19-7 neuronal cells by bFGF requires at least two signaling pathways activated by Ras and Src.
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Affiliation(s)
- W L Kuo
- Ben May Institute for Cancer Research and Department of Pharmacological and Physiological Sciences, University of Chicago, Illinois 60637, USA
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26
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Li L, Krantz ID, Deng Y, Genin A, Banta AB, Collins CC, Qi M, Trask BJ, Kuo WL, Cochran J, Costa T, Pierpont ME, Rand EB, Piccoli DA, Hood L, Spinner NB. Alagille syndrome is caused by mutations in human Jagged1, which encodes a ligand for Notch1. Nat Genet 1997; 16:243-51. [PMID: 9207788 DOI: 10.1038/ng0797-243] [Citation(s) in RCA: 846] [Impact Index Per Article: 31.3] [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: 02/04/2023]
Abstract
Alagille syndrome is an autosomal dominant disorder characterized by abnormal development of liver, heart, skeleton, eye, face and, less frequently, kidney. Analyses of many patients with cytogenetic deletions or rearrangements have mapped the gene to chromosome 20p12, although deletions are found in a relatively small proportion of patients (< 7%). We have mapped the human Jagged1 gene (JAG1), encoding a ligand for the developmentally important Notch transmembrane receptor, to the Alagille syndrome critical region within 20p12. The Notch intercellular signalling pathway has been shown to mediate cell fate decisions during development in invertebrates and vertebrates. We demonstrate four distinct coding mutations in JAG1 from four Alagille syndrome families, providing evidence that it is the causal gene for Alagille syndrome. All four mutations lie within conserved regions of the gene and cause translational frameshifts, resulting in gross alterations of the protein product Patients with cytogenetically detectable deletions including JAG1 have Alagille syndrome, supporting the hypothesis that haploinsufficiency for this gene is one of the mechanisms causing the Alagille syndrome phenotype.
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Affiliation(s)
- L Li
- Stowers Institute for Medical Research, Department of Molecular Biotechnology, University of Washington, Seattle 98195 USA
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27
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Hwang S, Kuo WL, Cochran JF, Guzman RC, Tsukamoto T, Bandyopadhyay G, Myambo K, Collins CC. Assignment of HMAT1, the human homolog of the murine mammary transforming gene (MAT1) associated with tumorigenesis, to 1q21.1, a region frequently gained in human breast cancers. Genomics 1997; 42:540-2. [PMID: 9205133 DOI: 10.1006/geno.1997.4768] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- S Hwang
- MS74-157 Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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28
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Chang CH, Scott GK, Kuo WL, Xiong X, Suzdaltseva Y, Park JW, Sayre P, Erny K, Collins C, Gray JW, Benz CC. ESX: a structurally unique Ets overexpressed early during human breast tumorigenesis. Oncogene 1997; 14:1617-22. [PMID: 9129154 DOI: 10.1038/sj.onc.1200978] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.9] [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: 02/04/2023]
Abstract
The >30 known members of the Ets multigene family of transcriptional regulators are increasingly being recognized for their involvement in early embryonic development and late tissue maturation, directing stage-specific and tissue-restricted programs of target gene expression. Identifiable primarily by their 85 amino acid ETS DNA-binding domain and dispersed across all metazoan lineages into distinct subfamilies, Ets genes also produce malignancies in humans and other vertebrates when overexpressed or rearranged into chimeras retaining the ETS domain, suggesting that their oncogenic potential is determined by the program of target genes they regulate. Searching for Ets factors that regulate expression of the HER2/neu (c-erbB2) oncogene in human breast cancer, we identified a new epithelium-restricted Ets encoding an ETS domain homologous to the Drosophila E74/human Elf-1 subfamily, an amino-terminal region (A-region or Pointed domain) homologous to the distantly related Ets-1 subfamily, and a serine-rich box homologous to the transactivating domain of the lymphocyte-restricted High Mobility Group (HMG) protein, SOX4. Recombinant protein encoded by ESX (for epithelial-restricted with serine box) exhibits Ets-like DNA binding specificity in electrophoretic mobility shift assays and, in transient transfection assays, transactivates Ets-responsive promoter elements including that found in the HER2/neu oncogene. ESX is located at chromosome 1q32 in a region known to be amplified in 50% of early breast cancers, is heregulin-inducible and overexpressed in HER2/neu activated breast cancer cells. Tissue hybridization suggests that ESX becomes overexpressed at an early stage of human breast cancer development known as ductal carcinoma in situ (DCIS).
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Affiliation(s)
- C H Chang
- Cancer Research Institute and Division of Oncology-Hematology, University of California at San Francisco, 94143, USA
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29
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Karpova AY, Abe MK, Li J, Liu PT, Rhee JM, Kuo WL, Hershenson MB. MEK1 is required for PDGF-induced ERK activation and DNA synthesis in tracheal myocytes. Am J Physiol 1997; 272:L558-65. [PMID: 9124614 DOI: 10.1152/ajplung.1997.272.3.l558] [Citation(s) in RCA: 38] [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] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We tested whether activation of mitogen-activated protein kinase/ extracellular signal-regulated kinase kinase-1 (MEK1) is required and sufficient for extracellular signal-regulated kinase (ERK) activation in airway smooth muscle cells. First, we transiently cotransfected bovine tracheal myocytes with an epitope-tagged ERK2 and a dominant-negative or a constitutively active form of the gene encoding MEK1 and assessed ERK2 activation by in vitro phosphorylation assay. Expression of the dominant-negative MEK1 inhibited platelet-derived growth factor (PDGF)-induced ERK2 activation, whereas expression of the constitutively active MEK1 induced ERK2 activation, suggesting that MEK1 is required and sufficient for ERK activation in these cells. Next, we assessed the effect of PD-98059, a synthetic MEK inhibitor, on PDGF-induced MEK1 and ERK activation. PD-98059 (10 microM) inhibited MEK1 and ERK activation, confirming that MEK1 is required for ERK activation in bovine tracheal myocytes. PD-98059 had no effect on Src or Raf-1 activity, evidence that PD-98059 is a specific inhibitor of MEK in this system. Finally, PD-98059 reduced PDGF-induced [(3)H]thymidine incorporation in a concentration-dependent manner, suggesting that catalytic activation of MEK1 and ERKs is required for DNA synthesis. We conclude that MEK1 is required for PDGF-induced ERK activation in bovine tracheal myocytes and that MEK1 and ERKs are required for PDGF-induced DNA synthesis in these cells.
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Affiliation(s)
- A Y Karpova
- Department of Pediatrics, University of Chicago, Illinois 60637, USA
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30
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Nehlin JO, Hara E, Kuo WL, Collins C, Campisi J. Genomic organization, sequence, and chromosomal localization of the human helix-loop-helix Id1 gene. Biochem Biophys Res Commun 1997; 231:628-34. [PMID: 9070860 DOI: 10.1006/bbrc.1997.6152] [Citation(s) in RCA: 30] [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: 02/04/2023]
Abstract
The helix-loop-helix protein Id-1 regulates growth and differentiation in many mammalian cells. In human fibroblasts, Id1 and Id1', a putative splicing variant, are cell cycle regulated, essential for proliferation, repressed by senescence, and overexpressed by some tumor cells. To better understand Id1, we determined the complete sequence, transcriptional start, and localization of the human Id1 gene. Human Id1 has two exons (426 bp and 42 bp), separated by an intron (239 bp). Id1' results from failure to splice the intron, which encodes 7 amino acids prior to a stop codon. Thus, Id1 and Id1' proteins differ only at the extreme C-terminus. Id1 transcription initiated 96 bp upstream of the initiation AUG; 2 kb of upstream sequence stimulated transcription of a reporter gene. Human Id1 maps to chromosome 20 at q11, very close to the centromere but outside the amplicons frequently found in human cancers.
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Affiliation(s)
- J O Nehlin
- Department of Cancer Biology and Molecular Cytogenetics Resource, Berkeley National Laboratory, University of California 94720, USA
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31
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Collins C, Nehlin JO, Stubbs JD, Kowbel D, Kuo WL, Parry G. Mapping of a newly discovered human gene homologous to the apoptosis associated-murine mammary protein, MFG-E8, to chromosome 15q25. Genomics 1997; 39:117-8. [PMID: 9027496 DOI: 10.1006/geno.1996.4425] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [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)
- C Collins
- Berkeley National Laboratory, California 94720, USA.
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32
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Brzoska PM, Chen H, Levin NA, Kuo WL, Collins C, Fu KK, Gray JW, Christman MF. Cloning, mapping, and in vivo localization of a human member of the PKCI-1 protein family (PRKCNH1). Genomics 1996; 36:151-6. [PMID: 8812426 DOI: 10.1006/geno.1996.0435] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [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
We report here the complete cDNA sequence, genomic mapping, and immunolocalization of the first human member of the protein kinase C inhibitor (PKCI-1) gene family. The predicted human protein (hPKCI-1) is 96% identical to bovine and 53% identical to maize members, indicating the great evolutionary conservation of this protein family. The hPKCI-1 gene (HGMV-approved symbol PRKCNH1) maps to human chromosome 5q31.2 by fluorescence in situ hybridization. Indirect immunofluorescence shows that hPKCI-1 localizes to cytoskeletal structures in the cytoplasm of a human fibroblast cell line and is largely excluded from the nucleus. The cytoplasmic localization of hPKCI-1 is consistent with a postulated role in mediating a membrane-derived signal in response to ionizing radiation.
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Affiliation(s)
- P M Brzoska
- Department of Radiation Oncology, University of California, San Francisco, California, 94143, USA
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33
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Ma T, Yang B, Kuo WL, Verkman AS. cDNA cloning and gene structure of a novel water channel expressed exclusively in human kidney: evidence for a gene cluster of aquaporins at chromosome locus 12q13. Genomics 1996; 35:543-50. [PMID: 8812490 DOI: 10.1006/geno.1996.0396] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.0] [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: 02/02/2023]
Abstract
A 1.8-kb cDNA clone (designed hKID, gene symbol AQP2L) with homology to the aquaporins was isolated from a human kidney cDNA library. The longest open reading frame of 846 bp encoded a 282-amino-acid hydrophobic protein that contained the conserved NPA motifs of MIP family members. Cell-free translation produced a nonglycosylated protein migrating at 29 kDa. Amino acid alignment showed the greatest homology of hKID to human MIP (48% identity) and AQP-2 (52%), with lesser homology to human MIWC (AQP-4, 34%), CHIP28 (AQP-1, 38%), and GLIP (AQP-3, 22%). Northern blot analysis revealed a 2.2-kb transcript expressed only in human kidney. PCR/Southern blot analysis of human kidney cDNA using primers flanking the hKID coding sequence revealed expression of a full-length mRNA and short transcripts with partial exon 1 and partial exon 4 deletions. Expression of hKID cRNA in Xenopus oocytes did not increase glycerol or urea permeability, but increased osmotic water permeability from (2.8 +/- 0.5) x 10(-4) to (7.4 +/- 0.7) x 10(-4) cm/s (10 degrees C) in a mercurial-sensitive manner. Sequence comparison of hKID cDNA with a cloned 21-kb genomic DNA indicated three introns (lengths 0.7, 0.25, and 0.4 kb) separating four exons with boundaries at amino acids 121, 174, and 201. The hKID promoter was identified and contained TATA, SP1, E-box, and AP1 and AP2 elements; primer extension revealed hKID transcription initiation 654 bp upstream from the translational initiation site. Genomic Southern blot indicated a single-copy hKID gene. PCR analysis of a human/rodent somatic hybrid panel localized the hKID gene to chromosome 12. Chromosomal fluorescence in situ hybridization mapped the hKID (AQP2L) gene to chromosome locus 12q13, the same location as the AQP. 2 and MIP genes. The high sequence homology, similar genomic structure, and identical chromosomal loci of hKID, MIP, and AQP-2 suggest a MIP family gene cluster at chromosome locus 12q13. Further work is needed to establish the physiological significance of hKID.
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Affiliation(s)
- T Ma
- Department of Medicine, University of California, San Francisco 94143-0521, USA
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34
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Kahn M, Ishii K, Kuo WL, Piper M, Connolly A, Shi YP, Wu R, Lin CC, Coughlin SR. Conserved structure and adjacent location of the thrombin receptor and protease-activated receptor 2 genes define a protease-activated receptor gene cluster. Mol Med 1996; 2:349-57. [PMID: 8784787 PMCID: PMC2230143] [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] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Thrombin is a serine protease that elicits a variety of cellular responses. Molecular cloning of a thrombin receptor revealed a G protein-coupled receptor that is activated by a novel proteolytic mechanism. Recently, a second protease-activated receptor was discovered and dubbed PAR2. PAR2 is highly related to the thrombin receptor by sequence and, like the thrombin receptor, is activated by cleavage of its amino terminal exodomain. Also like the thrombin receptor, PAR2 can be activated by the hexapeptide corresponding to its tethered ligand sequence independent of receptor cleavage. Thus, functionally, the thrombin receptor and PAR2 constitute a fledgling receptor family that shares a novel proteolytic activation mechanism. To further explore the relatedness of the two known protease-activated receptors and to examine the possibility that a protease-activated gene cluster might exist, we have compared the structure and chromosomal locations of the thrombin receptor and PAR2 genes. MATERIALS AND METHODS The genomic structures of the two protease-activated receptor genes were determined by analysis of lambda phage, P1 bacteriophage, and bacterial artificial chromosome (BAC) genomic clones. Chromosomal location was determined with fluorescent in situ hybridization (FISH) on metaphase chromosomes, and the relative distance separating the two genes was evaluated both by means of two-color FISH and analysis of YACs and BACs containing both genes. RESULTS Analysis of genomic clones revealed that the two protease-activated receptor genes share a two-exon genomic structure in which the first exon encodes 5'-untranslated sequence and signal peptide, and the second exon encodes the mature receptor protein and 3'-untranslated sequence. The two receptor genes also share a common locus with the two human genes located at 5q13 and the two mouse genes at 13D2, a syntenic region of the mouse genome. These techniques also suggest that the physical distance separating these two genes is less than 100 kb. CONCLUSIONS The fact that the thrombin receptor and PAR2 genes share an identical structure and are located within approximately 100 kb of each other in the genome demonstrates that these genes arose from a gene duplication event. These results define a new protease-activated receptor gene cluster in which new family members may be found.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Chromosome Mapping
- Chromosomes, Artificial, Yeast
- Chromosomes, Human, Pair 5
- Conserved Sequence
- Exons
- Female
- Genomic Library
- Humans
- Introns
- Mice
- Molecular Sequence Data
- Multigene Family
- Placenta/metabolism
- Polymerase Chain Reaction
- Pregnancy
- Receptor, PAR-2
- Receptors, Cell Surface/chemistry
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Receptors, Thrombin/chemistry
- Receptors, Thrombin/genetics
- Receptors, Thrombin/metabolism
- Restriction Mapping
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Affiliation(s)
- M Kahn
- Department of Medicine, University of California, San Francisco 94143-0524, USA
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35
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Kuo WL, Abe M, Rhee J, Eves EM, McCarthy SA, Yan M, Templeton DJ, McMahon M, Rosner MR. Raf, but not MEK or ERK, is sufficient for differentiation of hippocampal neuronal cells. Mol Cell Biol 1996; 16:1458-70. [PMID: 8657119 PMCID: PMC231130 DOI: 10.1128/mcb.16.4.1458] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.5] [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: 02/01/2023] Open
Abstract
To elucidate signal transduction pathways leading to neuronal differentiation, we have investigated a conditionally immortalized cell line from rat hippocampal neurons (H19-7) that express a temperature sensitive simian virus 40 large T antigen. Treatment of H19-7 cells with the differentiating agent basic fibroblast growth factor at 39 degrees C, the nonpermissive temperature for T function, resulted in the activation of c-Raf-1, MEK, and mitogen-activated protein (MAP) kinases (ERK1 and -2). To evaluate the role of Raf-1 in neuronal cell differentiation, we stably transfected H19-7 cells with v-raf or an oncogenic human Raf-1-estrogen receptor fusion gene (deltaRaf-1:ER). deltaRaf-1:ER transfectants in the presence of estradiol for 1 to 2 days expressed a differentiation phenotype only at the nonpermissive temperature. However, extended exposure of the deltaRaf-1:ER transfectants to estradiol or stable expression of the v-raf construct yielded cells that extended processes at the permissive as well as the nonpermissive temperature, suggesting that cells expressing the large T antigen are capable of responding to the Raf differentiation signal. deltaRaf-1:ER, MEK, and MAP kinase activities in the deltaRaf-1:ER cells were elevated constitutively for up to 36 h of estradiol treatment at the permissive temperature. At the nonpermissive temperature, MEK and ERKs were activated to a significantly lesser extent, suggesting that prolonged MAP kinase activation may not be sufficient for differentiation. To test this possibility, H19-7 cells were transfected or microinjected with constitutively activated MEK. The results indicate that prolonged activation of MEK or MAP kinases (ERK1 and -2) is not sufficient for differentiation of H19-7 neuronal cells and raise the possibility that an alternative signaling pathway is required for differentiation of H19-7 cells by Raf.
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Affiliation(s)
- W L Kuo
- Ben May Institute, University of Chicago, Ilinois 60637, USA
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36
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Kuo WL, Hirschhorn R, Huie ML, Hirschhorn K. Localization and ordering of acid alpha-glucosidase (GAA) and thymidine kinase (TK1) by fluorescence in situ hybridization. Hum Genet 1996; 97:404-6. [PMID: 8786092 DOI: 10.1007/bf02185782] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [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: 02/02/2023]
Abstract
Genomic DNA clones of human acid alpha glucosidase (GAA) and thymidine kinase (TK1) were used to map the exact location and order of these genes on human chromosome 17. Both genes were localized to the 17q25-qter band (17q25.2-q25.3), with GAA distal to TK1. They were also shown to be, respectively, distal and proximal to an anonymous cosmid (cK17.71) previously mapped to this region.
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Affiliation(s)
- W L Kuo
- Division of Molecular Cytometry, Department of Laboratory Medicine, University of California, San Francisco, 94143, USA
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37
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Zhu W, Dahmen J, Bulfone A, Rigolet M, Hernandez MC, Kuo WL, Puelles L, Rubenstein JL, Israel MA. Id gene expression during development and molecular cloning of the human Id-1 gene. Brain Res Mol Brain Res 1995; 30:312-26. [PMID: 7637581 DOI: 10.1016/0169-328x(95)00017-m] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Id genes encode helix-loop-helix proteins that inhibit transcription by forming inactive heterodimers with basic helix-loop-helix (bHLH) proteins. bHLH proteins normally form either homodimers or heterodimers with other bHLH proteins and bind to a DNA sequence element activating transcription. Id-containing heterodimers are inactive because Id proteins lack the basic amino acid region necessary to form a DNA-binding domain. We have examined the relative levels of Id-1 and Id-2 mRNA during normal development and in malignant tissues. In the course of these experiments we cloned and sequenced the human Id-1 cDNA. Two related cDNA molecules encoding human Id-1 mRNAs were identified. Id-1a is a cDNA of 958 nucleotides and can encode a protein of 135 amino acids. Id-1b cDNA is 1145 nucleotides, can encode a protein of 149 amino acids, and appears to be a splice variant of Id-1a. The amino acid sequence of human Id-1 is greater than 90% homologous to that of mouse Id-1. The patterns of Id-1 and Id-2 expression during mouse development vary widely, and we detected Id-1 expression in human fetal and adult tissues from lung, liver, and brain. High Id-1 mRNA expression was found in many human tumor cell lines, including those isolated from nervous system tumors. We mapped Id-2 to human chromosome 2p25.
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Affiliation(s)
- W Zhu
- Preuss Laboratory, Department of Neurological Surgery, San Francisco, CA 94143, USA
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38
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Stokke T, Collins C, Kuo WL, Kowbel D, Shadravan F, Tanner M, Kallioniemi A, Kallioniemi OP, Pinkel D, Deaven L. A physical map of chromosome 20 established using fluorescence in situ hybridization and digital image analysis. Genomics 1995; 26:134-7. [PMID: 7782072 DOI: 10.1016/0888-7543(95)80092-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [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 physical locations of 46 cosmid clones and 21 P1 clones were determined along the chromosome 20 axis relative to the p terminus (FLpter) using fluorescence in situ hybridization (FISH) and digital image microscopy. The cosmid clones were selected from the chromosomally enriched library LA20NC01. Nine P1 clones were selected from a pooled DuPont genomic library using PCR with primer pairs selected to amplify genetically mapped sequence-tagged sites. This information was used to relate the physical map to the genetic map. Twelve P1 clones were selected from the same library using PCR primer pairs that amplified known genes. Two of these, E2F and BCLX, had not been mapped previously.
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Affiliation(s)
- T Stokke
- University of California, San Francisco, USA
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39
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Abstract
We have used two complementary approaches to analyze the chromosomal location of the gamma-glutamyl carboxylase gene. The amplification of a carboxylase-specific genomic fragment by polymerase chain reaction (PCR) in a human-rodent hybrid cell mapping panel localized the gene to chromosome 2. Mapping by fluorescence in situ hybridization assigned the gene to p12 of chromosome 2. Our results indicate that the gamma-glutamyl carboxylase gene has a single locus in the human genome.
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Affiliation(s)
- W L Kuo
- Division of Molecular Cytometry, University of California at San Francisco 94103, USA
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40
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Sakamoto M, Pinkel D, Mascio L, Sudar D, Peters D, Kuo WL, Yamakawa K, Nakamura Y, Drabkin H, Jericevic Z. Semiautomated DNA probe mapping using digital imaging microscopy: II. System performance. Cytometry 1995; 19:60-9. [PMID: 7705186 DOI: 10.1002/cyto.990190108] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
This paper describes an evaluation of a semiautomated, multicolor image-analysis system to map cloned probes along metaphase chromosomes. Mapping with this system consists of fluorescence in situ hybridization (FISH) for probe localization, automatic acquisition of multicolor images showing total chromosomal DNA and probe location(s), and automatic determination of the fractional locations of the probes along the chromosomes relative to the short arm telomere (FLpter). The system was evaluated by mapping ten phage and ten cosmid probes previously mapped to chromosome 3 with other procedures. The standard deviations of FLpter measurements averaged 3.4 Mb and 2.6 Mb for phage and cosmid probes, respectively. With this variation, the order of two probes mapped in separate hybridizations could be determined with 95% confidence when their separation was greater than 2.5 Mb. In all cases, the probe locations and order were consistent with previous mapping data. FLpter values were converted to band locations using measurements of the band locations made using digital imaging microscopy. This proved superior to conversions made using ISCN ideograms.
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Affiliation(s)
- M Sakamoto
- Division of Molecular Cytometry, University of California, San Francisco 94143-0808, USA
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41
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Mascio LN, Verbeek PW, Sudar D, Kuo WL, Gray JW. Semiautomated DNA probe mapping using digital imaging microscopy: I. System development. Cytometry 1995; 19:51-9. [PMID: 7705185 DOI: 10.1002/cyto.990190107] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Algorithms have been developed to help automate the mapping of DNA sequences along metaphase chromosomes using fluorescence in situ hybridization (FISH). Custom algorithms computationally define chromosome boundaries and compute chromosomal medial axes. A dynamic regional thresholding (DRT) algorithm is described that allows reliable detection of hybridization domains, even when they differ substantially in size and intensity. Chromosomal locations are calculated by determining the fractional location of each hybridization probe along the medial axis of a metaphase chromosome relative to the short arm (FLpter). These algorithms were tested on simulated data and by analysis of the location of probes that had been previously mapped by other techniques. These algorithms allow probes to be mapped rapidly along human chromosomes with a precision of 2-3 Mb.
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Affiliation(s)
- L N Mascio
- Engineering Research Division/Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California, USA
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42
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Hsiao GH, Chang CC, Chen JC, Kuo WL, Huang SF. Trichosporon beigelii fungemia with cutaneous dissemination. A case report and literature review. Acta Derm Venereol 1994; 74:481-2. [PMID: 7701893 DOI: 10.2340/0001555574481482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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43
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Kuo WL, Gehm BD, Rosner MR, Li W, Keller G. Inducible expression and cellular localization of insulin-degrading enzyme in a stably transfected cell line. J Biol Chem 1994; 269:22599-606. [PMID: 8077210] [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: 01/28/2023] Open
Abstract
Insulin degrading enzyme (IDE) is an evolutionarily conserved, nonlysosomal metalloprotease that has been implicated in the cellular degradation and processing of insulin. However, the site and the mode of the action of this enzyme are unclear. We have addressed these questions by establishing several Ltk- cell lines that can overexpress human insulin-degrading enzyme (hIDE) upon glucocorticoid induction. The level of overexpression of hIDE protein and transcripts in these lines correlates well with an increase in insulin degradation in both cell lysates and intact cells. Comparison of the deduced amino acid sequences of mammalian and Drosophila IDEs reveals a conserved carboxyl-terminal peroxisomal targeting sequence (A/S-K-L), suggesting that IDE may be localized in peroxisomes. To test this possibility, we determined the cellular location of the stably transfected hIDE by both immunofluorescence and immunocryoelectron microscopy. The overexpressed hIDE predominantly colocalized with catalase in peroxisomes, although IDE was also found in the cytosol at a much lower concentration. These results demonstrate that stably transfected IDE catalyzes a rate-limiting step in cellular insulin degradation and is localized predominantly in peroxisomes.
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Affiliation(s)
- W L Kuo
- Ben May Institute, University of Chicago, Illinois 60637
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44
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Tanner MM, Tirkkonen M, Kallioniemi A, Collins C, Stokke T, Karhu R, Kowbel D, Shadravan F, Hintz M, Kuo WL. Increased copy number at 20q13 in breast cancer: defining the critical region and exclusion of candidate genes. Cancer Res 1994; 54:4257-60. [PMID: 8044767] [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] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Studies by comparative genomic hybridization have indicated that a major new locus for DNA amplification in breast cancer is 20q13 and suggested that this genetic event is associated with aggressive clinical behavior. We used interphase fluorescence in situ hybridization with anonymous cosmid probes and gene-specific P1 clones to determine the minimal common region of increased copy number and to study involvement of known genes at 20q13. Based on high-level copy number increases (3 to 10-fold) found with one or more probes in 5 of 14 (35%) breast cancer cell lines and in 3 of 36 (8%) primary tumors, the critical region was narrowed to approximately 1.5 megabases at 20q13.2 defined by fractional length pter values 0.81-0.84. Previously known genes were excluded as candidates, implying that this chromosomal region harbors a novel oncogene that contributes to the malignant progression of breast cancer.
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Affiliation(s)
- M M Tanner
- Department of Laboratory Medicine, Tampere University Hospital, Finland
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45
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Chan AC, Kadlecek TA, Elder ME, Filipovich AH, Kuo WL, Iwashima M, Parslow TG, Weiss A. ZAP-70 deficiency in an autosomal recessive form of severe combined immunodeficiency. Science 1994; 264:1599-601. [PMID: 8202713 DOI: 10.1126/science.8202713] [Citation(s) in RCA: 374] [Impact Index Per Article: 12.5] [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: 01/29/2023]
Abstract
Protein tyrosine kinases (PTKs) play an integral role in T cell activation and differentiation. Defects in the Src-family PTKs in mice and in T cell lines have resulted in variable defects in thymic development and in T cell antigen receptor (TCR) signal transduction. Here, three siblings are described with an autosomal recessive form of severe combined immunodeficiency disease (SCID) in which ZAP-70, a non-Src PTK, is absent as a result of mutations in the ZAP-70 gene. This absence is associated with defects in TCR signal transduction, suggesting an important functional role for ZAP-70.
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Affiliation(s)
- A C Chan
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Francisco 94143
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46
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Schott DR, Chang JN, Deng G, Kurisu W, Kuo WL, Gray J, Smith HS. A candidate tumor suppressor gene in human breast cancers. Cancer Res 1994; 54:1393-6. [PMID: 8137235] [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] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have isolated a candidate gene (designated Brush-1) located at 13q12-q13, proximal to the retinoblastoma gene (RB1). Brush-1 codes for a 4.7-kilobase mRNA expressed at high levels in normal breast epithelium but drastically reduced in 6 of 13 breast cancer cell lines. RB1 mRNA expression is at normal levels for 5 of these 6 lines suggesting a greater importance of Brush-1 for breast cancer. Four primary breast tumors which showed no loss of heterozygosity in the 13q13-q14 region demonstrated normal levels of mRNA for both Brush-1 and RB1. However, four additional primary tumors which displayed loss of heterozygosity for this region had markedly decreased levels of Brush-1 mRNA while maintaining the normal levels for RB1. This differential loss of Brush-1 mRNA expression for both primary tumors and breast cancer cell lines is the expected pattern for a breast tumor suppressor gene.
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Affiliation(s)
- D R Schott
- Geraldine Brush Cancer Research Institute, California Pacific Medical Center, San Francisco 94115-1932
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47
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Perlman RK, Gehm BD, Kuo WL, Rosner MR. Functional analysis of conserved residues in the active site of insulin-degrading enzyme. J Biol Chem 1993; 268:21538-44. [PMID: 8104941] [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] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Insulin-degrading enzyme (IDE), a nonlysosomal metalloprotease involved in metabolizing internalized insulin, has catalytic properties that have been strongly conserved through evolution. Two major properties distinguish IDE from the prototypic metalloprotease thermolysin. 1) It is inhibited by cysteine protease inhibitors as well as metalloprotease inhibitors; 2) it contains an inversion of the HEXXH active site motif of thermolysin, where the histidines coordinate zinc and the glutamate participates in catalysis. Furthermore, cysteine is adjacent to the glutamate residue (HXCEH) in human, rat, and Drosophila IDE, although it is not conserved in their close homologue, Escherichia coli protease III. This cysteine has been postulated to mediate the differential sensitivity of IDE and protease III to cysteine protease inhibitors and chelators. The role of the cysteine in IDE catalysis and inhibitor sensitivity was examined by mutating Cys110 to glycine or serine. To determine whether glutamate in this unusual motif participates in catalysis, we mutated Glu111 to aspartate, valine, or glutamine. Vectors containing wild type or mutant enzymes were transfected into COS cells, and expression was confirmed by Western blotting. Although the glutamate mutants were devoid of insulin degrading activity, the cysteine mutants were indistinguishable from wild type enzyme in both catalytic activity and sensitivity to inhibitors. The loss of activity in the glutamate mutants was not due to gross alterations in tertiary structure, as shown by retention of the ability to bind substrate and by conservative and nonconservative mutation of a neighboring residue with no apparent effect on catalysis. These results demonstrate that the conserved glutamate in the zinc-binding site of human insulin-degrading enzyme is a major catalytic residue, while a conserved cysteine in this region is not essential for catalysis or inhibitor sensitivity.
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Affiliation(s)
- R K Perlman
- Ben May Institute, University of Chicago, Illinois 60637
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48
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Kunzelmann K, Schwiebert EM, Zeitlin PL, Kuo WL, Stanton BA, Gruenert DC. An immortalized cystic fibrosis tracheal epithelial cell line homozygous for the delta F508 CFTR mutation. Am J Respir Cell Mol Biol 1993; 8:522-9. [PMID: 7683197 DOI: 10.1165/ajrcmb/8.5.522] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.4] [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: 01/26/2023] Open
Abstract
The development of transformed human airway epithelial cell lines has been important in advancing the understanding of the biochemical and genetic mechanisms underlying the cystic fibrosis (CF) defect. Since the most common mutation associated with CF is a phenylalanine deletion at position 508 (delta F508) in the CF transmembrane conductance regulator (CFTR) gene, a transformed airway epithelial cell line homozygous for this mutation will be important for determining the biologic significance of this mutation in the airways. We report the genotypic and phenotypic characterization of a delta F508 homozygote cell line derived from luminal epithelium in the trachea. The cells were transformed with a plasmid containing an origin of replication defective SV40 genome and have progressed through crisis. Immunocytochemical characterization of the cells shows that they express keratin, indicating epithelial cell origin, and that a calcium-dependent cell adhesion molecule, cellCAM 120/80, is present at plasma membrane junctions between cells. Electrophysiologically, the cells show no cAMP-dependent Cl transport. However, after treatment with the calcium ionophore, ionomycin, cells secrete Cl, albeit at a lower level than that observed in normal cells. Genetically, the cells express CFTR mRNA as determined by polymerase chain reaction amplification and CFTR protein as determined by Western hybridization analysis. Karyotypic analysis shows that 70% of the cells contain two copies of chromosome 7.
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Affiliation(s)
- K Kunzelmann
- Department of Laboratory Medicine, University of California, San Francisco 94143-0911
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49
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Gehm BD, Kuo WL, Perlman RK, Rosner MR. Mutations in a zinc-binding domain of human insulin-degrading enzyme eliminate catalytic activity but not insulin binding. J Biol Chem 1993; 268:7943-8. [PMID: 8463315] [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: 01/30/2023] Open
Abstract
Insulin-degrading enzyme is a nonlysosomal metalloprotease that initiates degradation of internalized insulin in some cells. We previously identified a potential catalytic site containing an inversion of the Zn(2+)-binding domain of the thermolysin family (Kuo, W.-L., Gehm, B. D., and Rosner, M. R. (1991) Mol. Endocrinol. 4, 1580-1591). The role of this site in catalysis was examined by mutating one of the presumptive Zn(2+)-coordinating histidines (His108) in human insulin-degrading enzyme to leucine or glutamine, which were predicted to reduce or eliminate Zn2+ binding without substantially altering secondary structure. cDNAs for the mutant and wild-type enzymes were incorporated into an expression vector and transfected into COS cells. Expression of the transfected genes was confirmed by Northern and Western blots. In contrast to the wild-type gene, which increased insulin degradation by cell extracts and intact cells several-fold, the mutated genes had no effect on insulin degradation, indicating a loss of catalytic activity. However, the mutants' ability to bind substrate was unimpaired, as affinity labeling with 125I-insulin was increased compared to the wild type. These results suggest that an intact Zn(2+)-binding domain in human insulin-degrading enzyme is required for catalytic activity and can affect, but is not required for, substrate binding.
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Affiliation(s)
- B D Gehm
- Ben May Institute, University of Chicago, Illinois 60637
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50
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Toribara NW, Roberton AM, Ho SB, Kuo WL, Gum E, Hicks JW, Gum JR, Byrd JC, Siddiki B, Kim YS. Human gastric mucin. Identification of a unique species by expression cloning. J Biol Chem 1993; 268:5879-85. [PMID: 7680650] [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] Open
Abstract
Gastric mucin is a large glycoprotein which is thought to play a major role in the protection of the gastrointestinal tract from acid, proteases, pathogenic microorganisms, and mechanical trauma. In this paper we describe the isolation by expression cloning and characterization of cDNAs which code for human gastric mucin. The cDNA sequence is characterized by a tandem repeat region whose individual repeat unit is 507 base pairs (169 amino acids) long. The translated sequence is rich in threonine, serine, and proline (31, 18, and 15%, respectively) and contains a relatively large amount of histidine (7.1%) and alanine (5.6%). RNA blot analysis shows a polydisperse pattern which is characteristic of mucins. Expression of this gene is highest in the stomach and gall bladder, with weaker expression in the terminal ileum and right colon. This expression pattern is different from other human mucins and indicates that this gene codes for a unique mucin. Fluorescence in situ hybridization techniques have localized this gene to chromosome 11p15.4-11p15.5. This is the third mucin to be localized to the 11p15 region and suggests a clustering of secretory mucin genes. We propose that this gene for human gastric mucin be called MUC6.
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Affiliation(s)
- N W Toribara
- Gastrointestinal Research Laboratory, Department of Veterans Affairs Medical Center, San Francisco, California 94121
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