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Boutin P, Froguel P. GAD2: a polygenic contribution to genetic susceptibility for common obesity? ACTA ACUST UNITED AC 2005; 53:305-7. [PMID: 16004939 DOI: 10.1016/j.patbio.2004.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2004] [Accepted: 09/21/2004] [Indexed: 02/01/2023]
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202
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Späth B, Kirchner S, Vogel A, Schubert S, Meinlschmidt P, Aymanns S, Nezzar J, Marchfelder A. Analysis of the functional modules of the tRNA 3' endonuclease (tRNase Z). J Biol Chem 2005; 280:35440-7. [PMID: 16118225 DOI: 10.1074/jbc.m506418200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
tRNA 3' processing is one of the essential steps during tRNA maturation. The tRNA 3'-processing endonuclease tRNase Z was only recently isolated, and its functional domains have not been identified so far. We performed an extensive mutational study to identify amino acids and regions involved in dimerization, tRNA binding, and catalytic activity. 29 deletion and point variants of the tRNase Z enzyme were generated. According to the results obtained, variants can be sorted into five different classes. The first class still had wild type activity in all three respects. Members of the second and third class still formed dimers and bound tRNAs but had reduced catalytic activity (class two) or no catalytic activity (class three). The fourth class still formed dimers but did not bind the tRNA and did not process precursors. Since this class still formed dimers, it seems that the amino acids mutated in these variants are important for RNA binding. The fifth class did not have any activity anymore. Several conserved amino acids could be mutated without or with little loss of activity.
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Affiliation(s)
- Bettina Späth
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany
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203
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Gopalakrishnan M, Shieh CC. Potassium channel subtypes as molecular targets for overactive bladder and other urological disorders. Expert Opin Ther Targets 2005; 8:437-58. [PMID: 15469394 DOI: 10.1517/14728222.8.5.437] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Potassium channels have re-emerged as attractive targets for overactive bladder and other urological diseases in recent years, in part due to an enhanced understanding of their molecular heterogeneity, tissue distribution, functional roles and regulation in physiological and pathological states. Cloning and heterologous expression analysis, coupled with the advancement of improved high-throughput screening techniques, have enabled expeditious identification of selective small-molecule openers and blockers for ATP-sensitive K+ channels, Ca2+-activated K+ channels and voltage-dependent K+ channel-KQT-like subfamily (KCNQ) members, and has paved the way in the assessment of efficacy and adverse effects in preclinical models. This review focuses on the rationale for molecular targeting of K+ channels, the current status of target validation, including preclinical proof-of-concept studies, and provides perspectives on the limitations and hurdles to be overcome in realising the potential of these targets for diverse urological indications such as overactive bladder, erectile dysfunction and prostate diseases.
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Affiliation(s)
- Murali Gopalakrishnan
- Abbott Laboratories, Neuroscience Research, Global Pharmaceutical Research and Development, Building AP9A, 3rd floor, 100 Abbott Park Road, Abbott Park, Illinois 60064, USA.
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204
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Varga D, Michel I, Patino-Garcia B, Paiss T, Vogel W, Maier C. Radiosensitivity detected by the micronucleus test is not generally increased in sporadic prostate cancer patients. Cytogenet Genome Res 2005; 111:41-5. [PMID: 16093719 DOI: 10.1159/000085668] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Accepted: 12/16/2004] [Indexed: 11/19/2022] Open
Abstract
The micronucleus test (MNT) has shown increased micronuclei (MN) frequencies in BRCA associated and sporadic breast cancer patients, Ataxia telangiectasia and Nijmegen Breakage Syndrome patients, demonstrating a common cellular phenotype of increased radiosensitivity. Some genes, causative of these diseases, have also recently been associated with prostate cancer. In order to investigate if prostate cancer exhibits the cellular phenotype of increased radiosensitivity, we performed MNT analysis on 22 sporadic prostate cancer patients and 43 male controls. We determined the baseline MN frequency, in order to see in vivo chromosomal damage without radiation, and induced (after irradiation with 2 Gy) frequency of MN, both in binucleated cells (BNC) obtained from cultured peripheral blood lymphocytes. An automated image analysis system was used to score the MN employing two different classifiers (Classifier A and B) for detection of BNC. The mean baseline frequencies were 48/43 MN/1000 BNC (A/B) for the controls and 42/50 (A/B) for prostate cancer patients. The induced MN frequencies amounted to 107/111 MN/1000 BNC (A/B) for controls and 111/114 MN/1000 BNC (A/B) for prostate cancer patients. The obtained MN frequencies did not result in a statistically significant difference between unselected cases and controls. However, restricting the analysis to young patients (50-60 years, N = 7) and age-matched controls (N = 7) revealed marginally significant higher MN frequencies in patients. We conclude that increased radiosensitivity is not a property of prostate cancer patients in general.
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Affiliation(s)
- D Varga
- Department of Human Genetics, University of Ulm, Ulm, Germany
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205
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Douglas JA, Zuhlke KA, Beebe-Dimmer J, Levin AM, Gruber SB, Wood DP, Cooney KA. Identifying Susceptibility Genes for Prostate Cancer--A Family-Based Association Study of Polymorphisms in CYP17, CYP19, CYP11A1, and LH-. Cancer Epidemiol Biomarkers Prev 2005; 14:2035-9. [PMID: 16103457 DOI: 10.1158/1055-9965.epi-05-0170] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Polymorphisms in genes that code for enzymes or hormones involved in the synthesis and metabolism of androgens are compelling biological candidates for prostate cancer. Four such genes, CYP17, CYP19, CYP11A1, and LH-beta, are involved in the synthesis and conversion of testosterone to dihydrotestosterone and estradiol. In a study of 715 men with and without prostate cancer from 266 familial and early-onset prostate cancer families, we examined the association between prostate cancer susceptibility and common single-nucleotide polymorphisms in each of these four candidate genes. Family-based association tests revealed a significant association between prostate cancer and a common single-nucleotide polymorphism in CYP17 (P=0.004), with preferential transmission of the minor allele to unaffected men. Conditional logistic regression analysis of 461 discordant sibling pairs from these same families reaffirmed the association between the presence of the minor allele in CYP17 and prostate cancer risk (odds ratio, 0.51; 95% confidence interval, 0.28-0.92). These findings suggest that variation in or around CYP17 predicts susceptibility to prostate cancer. Family-based association tests may be especially valuable in studies of genetic variation and prostate cancer risk because this approach minimizes confounding due to population substructure, which is of particular concern for prostate cancer given the tremendous variation in the worldwide incidence of this disease.
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Affiliation(s)
- Julie A Douglas
- Department of Human Genetics, University of Michigan, Room 5912, Buhl Building, Ann Arbor, MI 48109-0618, USA.
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206
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Xu J, Dimitrov L, Chang BL, Adams TS, Turner AR, Meyers DA, Eeles RA, Easton DF, Foulkes WD, Simard J, Giles GG, Hopper JL, Mahle L, Moller P, Bishop T, Evans C, Edwards S, Meitz J, Bullock S, Hope Q, Hsieh CL, Halpern J, Balise RN, Oakley-Girvan I, Whittemore AS, Ewing CM, Gielzak M, Isaacs SD, Walsh PC, Wiley KE, Isaacs WB, Thibodeau SN, McDonnell SK, Cunningham JM, Zarfas KE, Hebbring S, Schaid DJ, Friedrichsen DM, Deutsch K, Kolb S, Badzioch M, Jarvik GP, Janer M, Hood L, Ostrander EA, Stanford JL, Lange EM, Beebe-Dimmer JL, Mohai CE, Cooney KA, Ikonen T, Baffoe-Bonnie A, Fredriksson H, Matikainen MP, Tammela TLJ, Bailey-Wilson J, Schleutker J, Maier C, Herkommer K, Hoegel JJ, Vogel W, Paiss T, Wiklund F, Emanuelsson M, Stenman E, Jonsson BA, Grönberg H, Camp NJ, Farnham J, Cannon-Albright LA, Seminara D. A combined genomewide linkage scan of 1,233 families for prostate cancer-susceptibility genes conducted by the international consortium for prostate cancer genetics. Am J Hum Genet 2005; 77:219-29. [PMID: 15988677 PMCID: PMC1224525 DOI: 10.1086/432377] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Accepted: 05/27/2005] [Indexed: 11/03/2022] Open
Abstract
Evidence of the existence of major prostate cancer (PC)-susceptibility genes has been provided by multiple segregation analyses. Although genomewide screens have been performed in over a dozen independent studies, few chromosomal regions have been consistently identified as regions of interest. One of the major difficulties is genetic heterogeneity, possibly due to multiple, incompletely penetrant PC-susceptibility genes. In this study, we explored two approaches to overcome this difficulty, in an analysis of a large number of families with PC in the International Consortium for Prostate Cancer Genetics (ICPCG). One approach was to combine linkage data from a total of 1,233 families to increase the statistical power for detecting linkage. Using parametric (dominant and recessive) and nonparametric analyses, we identified five regions with "suggestive" linkage (LOD score >1.86): 5q12, 8p21, 15q11, 17q21, and 22q12. The second approach was to focus on subsets of families that are more likely to segregate highly penetrant mutations, including families with large numbers of affected individuals or early age at diagnosis. Stronger evidence of linkage in several regions was identified, including a "significant" linkage at 22q12, with a LOD score of 3.57, and five suggestive linkages (1q25, 8q13, 13q14, 16p13, and 17q21) in 269 families with at least five affected members. In addition, four additional suggestive linkages (3p24, 5q35, 11q22, and Xq12) were found in 606 families with mean age at diagnosis of < or = 65 years. Although it is difficult to determine the true statistical significance of these findings, a conservative interpretation of these results would be that if major PC-susceptibility genes do exist, they are most likely located in the regions generating suggestive or significant linkage signals in this large study.
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Affiliation(s)
- Jianfeng Xu
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Latchezar Dimitrov
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Bao-Li Chang
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Tamara S. Adams
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Aubrey R. Turner
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Deborah A. Meyers
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Rosalind A. Eeles
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Douglas F. Easton
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - William D. Foulkes
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Jacques Simard
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Graham G. Giles
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - John L. Hopper
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Lovise Mahle
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Pal Moller
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Tim Bishop
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Chris Evans
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Steve Edwards
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Julia Meitz
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Sarah Bullock
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Questa Hope
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - ACTANE Consortium
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Chih-lin Hsieh
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Jerry Halpern
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Raymond N. Balise
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Ingrid Oakley-Girvan
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Alice S. Whittemore
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Charles M. Ewing
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Marta Gielzak
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Sarah D. Isaacs
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Patrick C. Walsh
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Kathleen E. Wiley
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - William B. Isaacs
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Stephen N. Thibodeau
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Shannon K. McDonnell
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Julie M. Cunningham
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Katherine E. Zarfas
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Scott Hebbring
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Daniel J. Schaid
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Danielle M. Friedrichsen
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Kerry Deutsch
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Suzanne Kolb
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Michael Badzioch
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Gail P. Jarvik
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Marta Janer
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Leroy Hood
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Elaine A. Ostrander
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Janet L. Stanford
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Ethan M. Lange
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Jennifer L. Beebe-Dimmer
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Caroline E. Mohai
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Kathleen A. Cooney
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Tarja Ikonen
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Agnes Baffoe-Bonnie
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Henna Fredriksson
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Mika P. Matikainen
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Teuvo LJ Tammela
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Joan Bailey-Wilson
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Johanna Schleutker
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Christiane Maier
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Kathleen Herkommer
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Josef J. Hoegel
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Walther Vogel
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Thomas Paiss
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Fredrik Wiklund
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Monica Emanuelsson
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Elisabeth Stenman
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Björn-Anders Jonsson
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Henrik Grönberg
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Nicola J. Camp
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - James Farnham
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Lisa A. Cannon-Albright
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
| | - Daniela Seminara
- Data Coordinating Center, ACTANE, BC/CA/HI, Johns Hopkins University, Mayo Clinic, PROGRESS, University of Michigan, University of Tampere and Tampere University Hospital, University of Ulm, University of Umeå, University of Utah, and National Cancer Institute
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207
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Zareen N, Yan H, Hopkinson A, Levinger L. Residues in the conserved His domain of fruit fly tRNase Z that function in catalysis are not involved in substrate recognition or binding. J Mol Biol 2005; 350:189-99. [PMID: 15935379 DOI: 10.1016/j.jmb.2005.04.073] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2005] [Revised: 04/26/2005] [Accepted: 04/27/2005] [Indexed: 11/28/2022]
Abstract
Transfer RNAs are transcribed as precursors with extensions at both the 5' and 3' ends. RNase P removes endonucleolytically the 5' end leader. tRNase Z can remove endonucleolytically the 3' end trailer as a necessary step in tRNA maturation. CCA is not transcriptionally encoded in the tRNAs of eukaryotes, archaebacteria and some bacteria and must be added by a CCA-adding enzyme after removal of the 3' end trailer. tRNase Z is a member of the beta-lactamase family of metal-dependent hydrolases, the signature sequence of which, the conserved histidine cluster (HxHxDH), is essential for activity. Starting with baculovirus-expressed fruit fly tRNase Z, we completed an 18 residue Ala scan of the His cluster to analyze the functional landscape of this critical region. Residues in and around the His cluster fall into three categories based on effects of the substitutions on processing efficiency: substitutions in eight residues have little effect, five substitutions reduce efficiency moderately (approximately 5-50-fold), while substitutions in five conserved residues, one serine, three histidine and one aspartate, severely reduce efficiency (approximately 500-5000-fold). Wild-type and mutant dissociation constants (Kd values), determined using gel shifts, displayed no substantial differences, and were of the same order as kM (2-20 nM). Lower processing efficiencies arising from substitutions in the His domain are almost entirely due to reduced kcat values; conserved, functionally important residues within the His cluster of tRNase Z are thus involved in catalysis, and substrate recognition and binding functions must reside elsewhere in the protein.
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Affiliation(s)
- Neela Zareen
- York College of The City University of New York, 94-20 Guy R. Brewer Blvd, Jamaica, NY 11451, USA
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208
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Maier C, Herkommer K, Hoegel J, Vogel W, Paiss T. A genomewide linkage analysis for prostate cancer susceptibility genes in families from Germany. Eur J Hum Genet 2005; 13:352-60. [PMID: 15536476 DOI: 10.1038/sj.ejhg.5201333] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer is a complex disease with a substantial genetic contribution involved in the disease risk. Several genomewide linkage studies conducted so far have demonstrated a strong heterogeneity of susceptibility. In order to assess candidate regions that are particularly relevant for the German population, we performed a genomewide linkage search on 139 prostate cancer families. A nonparametric method (Zlr scores), using GENEHUNTERPLUS, was applied at 500 markers (panel P1400, deCODE), with an average spacing of 7.25 cM. In the entire family collection, linkage was most evident at 8p22 (Zlr=2.47, P=0.0068), close to the previously identified susceptibility gene MSR1. Further local maxima with Zlr>2 (P<0.025) were observed at 1q, 5q and 15q. In a subgroup of 47 families, which matched the Johns Hopkins criteria of hereditary prostate cancer, suggestive linkage was found on 1p31 (Zlr=3.37, P=0.00038), a previously not described candidate region. The remaining 92 pedigrees, with no strong disease history, revealed a maximum Zlr=3.15 (P=0.00082) at 8q13, possibly indicating a gene with reduced penetrance or recessive inheritance. Our results suggest pronounced locus heterogeneity of prostate cancer susceptibility in Germany. In the present study population, the MSR1 gene could play a significant role. Other conspicuous loci, like 1p31 and 8q13, need further investigation in order to verify their relevance and to identify candidate genes.
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209
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Rennert H, Zeigler-Johnson CM, Addya K, Finley MJ, Walker AH, Spangler E, Leonard DGB, Wein A, Malkowicz SB, Rebbeck TR. Association of susceptibility alleles in ELAC2/HPC2, RNASEL/HPC1, and MSR1 with prostate cancer severity in European American and African American men. Cancer Epidemiol Biomarkers Prev 2005; 14:949-57. [PMID: 15824169 DOI: 10.1158/1055-9965.epi-04-0637] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Reported associations of ELAC2/HPC2, RNASEL/HPC1, and MSR1 with prostate cancer have been inconsistent and understudied in African Americans. We evaluated the role of 16 sequence variants in these genes with prostate cancer using 888 European American and 131 African American cases, and 473 European American and 163 African American, controls. We observed significant differences in ELAC2, RNASEL, and MSR1 allele frequencies by race. However, we did not observe significant associations between prostate cancer and any variants examined for both races combined. Associations were observed when stratified by race, family history, or disease severity. European American men homozygous for MSR1 IVS7delTTA had an elevated risk for localized stage [odds ratio, (OR), 3.5; 95% confidence interval (95% CI), 1.4-6.9], low-grade (OR, 3.2; 95% CI, 1.4-7.3) disease overall, and with low-grade (OR, 2.9; 95% CI, 1.2-7.2) or late-stage disease (OR, 5.2; 95% CI, 1.1-25.7) in family history-negative African Americans. MSR1 Arg293X was associated with family history-negative high-grade disease (OR, 4.0; 95% CI, 1.1-14.1) in European Americans. RNASEL Arg462Gln was associated with low-grade (OR, 1.5; 95% CI, 1.04-2.2) and early-stage (OR, 1.5; 95% CI, 1.02-2.1) disease in family history-negative European Americans. In family history-positive individuals, Arg462Gln was inversely associated with low-grade (OR, 0.43; 95% CI, 0.21-0.88) and low-stage (OR, 0.46; 95% CI, 0.22-0.95) disease. In African Americans, Arg462Gln was associated with positive family history high-stage disease (OR, 14.8; 95% CI, 1.6-135.7). Meta-analyses revealed significant associations of prostate cancer with MSR1 IVS7delTTA, -14,742 A>G, and Arg293X in European Americans; Asp174Tyr in African Americans; RNASEL Arg462Gln in European American's overall and in family history-negative disease; and Glu265X in family history-positive European Americans. Therefore, MSR1 and RNASEL may play a role in prostate cancer progression and severity.
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Affiliation(s)
- Hanna Rennert
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Health System, 7 Gates West, 3400 Spruce Street, Philadelphia, PA 19104, USA.
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210
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Schilling O, Vogel A, Kostelecky B, Natal da Luz H, Spemann D, Späth B, Marchfelder A, Tröger W, Meyer-Klaucke W. Zinc- and iron-dependent cytosolic metallo-beta-lactamase domain proteins exhibit similar zinc-binding affinities, independent of an atypical glutamate at the metal-binding site. Biochem J 2005; 385:145-53. [PMID: 15324305 PMCID: PMC1134682 DOI: 10.1042/bj20040773] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
ZiPD (zinc phosphodiesterase; synonyms are ElaC, ecoZ, RNaseZ and 3' tRNase) and the iron-dependent redox enzyme FlRd (flavorubredoxin) from Escherichia coli represent prototypical cases of proteins sharing the metallo-beta-lactamase fold that require strict metal selectivity for catalytic activity, yet their metal selectivity has only been partially understood. In contrast with hydrolytic metallo-beta-lactamase proteins, iron-dependent FlRd-like enzymes have an atypical glutamate ligand, which replaces one otherwise conserved histidine ligand. X-ray absorption spectroscopy revealed that the FlRd metallo-beta-lactamase domain is capable of incorporating two zinc ions into the binuclear metal-binding site. Zinc dissociation constants, determined by isothermal titration calorimetry are similar for zinc binding to E. coli ZiPD (K(d1)=2.2+/-0.2 microM and K(d2)=23.0+/-0.6 microM) and to the E. coli FlRd metallo-beta-lactamase domain (K(d1)=0.7+/-0.1 microM and K(d2)=26.0+/-0.1 microM). In good correspondence, apo-ZiPD requires incubation with 10 microM zinc for full reconstitution of the phosphodiesterase activity. Accordingly, metal selectivity of ZiPD and FlRd only partially relies on first shell metal ligands. Back mutation of the atypical glutamate in FlRd to a histidine unexpectedly resulted in an increased first zinc dissociation constant (K(d1)=30+/-4 microM and K(d2)=23+/-2 microM). In combination with a recent mutational study on ZiPD [Vogel, Schilling and Meyer-Klaucke (2004) Biochemistry 43, 10379-10386], we conclude that the atypical glutamate does not guide metal selectivity of the FlRd metallo-beta-lactamase domain but suppresses possible hydrolytic cross-activity.
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Affiliation(s)
- Oliver Schilling
- *EMBL Outstation Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Andreas Vogel
- *EMBL Outstation Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany
| | | | - Hugo Natal da Luz
- †Institute for Experimental Physics II, University of Leipzig, Linnéstr. 5, D-04103 Leipzig, Germany
| | - Daniel Spemann
- †Institute for Experimental Physics II, University of Leipzig, Linnéstr. 5, D-04103 Leipzig, Germany
| | - Bettina Späth
- ‡Molekulare Botanik, Universität Ulm, D-89069 Ulm, Germany
| | | | - Wolfgang Tröger
- †Institute for Experimental Physics II, University of Leipzig, Linnéstr. 5, D-04103 Leipzig, Germany
| | - Wolfram Meyer-Klaucke
- *EMBL Outstation Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany
- To whom correspondence should be addressed (email )
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211
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Bock CH, Peyser PA, Montie JE, Cooney KA. Decreasing age at prostate cancer diagnosis over successive generations in prostate cancer families. Prostate 2005; 64:60-6. [PMID: 15651090 DOI: 10.1002/pros.20220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The decline in age at prostate cancer diagnosis over the past decade is partially attributable to prostate specific antigen (PSA) screening. We examined age at diagnosis over successive generations within prostate cancer families. METHODS Families with at least two affected men were selected from the University of Michigan Prostate Cancer Genetics Project. The 1,345 individuals from 489 families were grouped into three generations. RESULTS Risk of prostate cancer diagnosis at a given age was estimated to increase 1.31 (95% CI: 1.13-1.51) times from one generation to the next. Among men diagnosed prior to the PSA era, inferences were similar (hazard ratio = 1.28, 95% CI: 0.97-1.68). No maternal versus paternal disease transmission effect was observed. CONCLUSIONS Age at prostate cancer diagnosis was observed to decrease over successive generations in families from an ongoing familial prostate cancer study. This finding, if confirmed, may have important implications for familial prostate cancer risk assessment.
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Affiliation(s)
- Cathryn H Bock
- Wayne State University School of Medicine, Karmanos Cancer Institute, Detroit, Michigan 48201, USA.
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212
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Yamashita S, Suzuki S, Nomoto T, Kondo Y, Wakazono K, Tsujino Y, Sugimura T, Shirai T, Homma Y, Ushijima T. Linkage and microarray analyses of susceptibility genes in ACI/Seg rats: a model for prostate cancers in the aged. Cancer Res 2005; 65:2610-6. [PMID: 15805257 DOI: 10.1158/0008-5472.can-04-2932] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
ACI/Seg (ACI) rats develop prostate cancers spontaneously with aging, similar to humans. Here, to identify genes involved in prostate cancer susceptibility, we did linkage analysis and oligonucleotide microarray analysis. Linkage analysis was done using 118 effective rats, and prostate cancer susceptibility 1 (Pcs1), whose ACI allele dominantly induced prostate cancers, was mapped on chromosome 19 [logarithm of odds (LOD) score of 5.0]. PC resistance 1 (Pcr1), whose ACI allele dominantly and paradoxically suppressed the size of prostate cancers, was mapped on chromosome 2 (LOD score of 5.0). When linkage analysis was done in 51 rats with single or no macroscopic testicular tumors, which had larger prostates and higher testosterone levels than those with bilateral testicular tumors, Pcs2 and Pcr2 were mapped on chromosomes 20 and 1, respectively. By oligonucleotide microarray analysis with 8,800 probe sets and confirmation by quantitative reverse transcription-PCR, only two genes within these four loci were found to be differentially expressed >1.8-fold. Membrane metalloendopeptidase (Mme), known to inhibit androgen-independent growth of prostate cancers, on Pcr1 was expressed 2.0- to 5.5-fold higher in the ACI prostate, in accordance with its paradoxical effect. Cdkn1a on Pcs2 was expressed 1.5- to 4.5-fold lower in the ACI prostate. Additionally, genes responsible for testicular tumors and unilateral renal agenesis were mapped on chromosomes 11 and 14, respectively. These results showed that prostate cancer susceptibility of ACI rats involves at least four loci, and suggested Mme and Cdkn1a as candidates for Pcr1 and Pcs2.
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Affiliation(s)
- Satoshi Yamashita
- Carcinogenesis Division, National Cancer Center Research Institute, 1-1 Tsukiji 5-chome, Chuo-ku, Tokyo, Japan
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213
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Baffoe-Bonnie AB, Smith JR, Stephan DA, Schleutker J, Carpten JD, Kainu T, Gillanders EM, Matikainen M, Teslovich TM, Tammela T, Sood R, Balshem AM, Scarborough SD, Xu J, Isaacs WB, Trent JM, Kallioniemi OP, Bailey-Wilson JE. A major locus for hereditary prostate cancer in Finland: localization by linkage disequilibrium of a haplotype in the HPCX region. Hum Genet 2005; 117:307-16. [PMID: 15906096 DOI: 10.1007/s00439-005-1306-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Accepted: 03/10/2005] [Indexed: 12/21/2022]
Abstract
BACKGROUND Prostate cancer (PRCA) is the most common cancer in males in the western world. In Finland PRCA has an age-adjusted incidence of 81.5 per 100,000. We previously reported that in Finland, the late-onset cases in families with "no-male-to-male" (NMM) transmission of PRCA accounted for most of the linkage to the HPCX region (Xq27-28). The aim of the present study was to test for linkage disequilibrium (LD) and haplotype-sharing around marker DXS1205 between cases from hereditary prostate cancer (HPC) families and population controls. The initial allelic association was performed between 108 PRCA cases and 257 population controls genotyped for 23 markers in the Xq26-28 region. This resulted in a highly significant nominal one-sided Fisher's exact P-value of 0.0003 for allele ''180'' of marker DXS1205. Subsequently, a similar level of significance was observed for the same allele for marker DXS1205 (P=0.0002) when comparing 60 NMM cases and 257 controls. These results were still significant after Bonferroni correction for multiple testing. Fine mapping efforts included the genotyping of four additional markers D3S2390, bG82i1.9, bG82i1.1, bG82i1.0 and four single nucleotide polymorphisms (SNPs) to augment the original markers around DXS1205. RESULTS Our major finding is that markers extending from ''D3S2390'' to ''bG82i1.0'' flank the critical locus, about 150 kb. Levin and Bertell's LD measure (delta), a guide to localization of a possible variant, was 0.42 and 0.41 for alleles of markers bG82i1.9 and DXS1205, respectively. CONCLUSIONS In this study, the most significant haplotype comprised the three tightly linked, contiguous markers: ''cen-bG82i1.9-SNP-Hap B-bG82i1.1-tel'' [''197-2-234''] among several possible haplotypes (nominal Fisher's one-sided P=0.003). The two transcription units mapping within this interval are the LDOC1 and SPANXC genes. Positional cloning of the HPCX gene(s) is being facilitated by this exploration of the Xq26-28 region. This study represents the first report identifying a haplotype in the Xq27-28 region for an association between HPCX and X-linked prostate cancer with no-male-to-male transmission in the Finnish population.
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Affiliation(s)
- Agnes B Baffoe-Bonnie
- Division of Population Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
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214
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Schaid DJ, Chang BL. Description of the International Consortium For Prostate Cancer Genetics, and failure to replicate linkage of hereditary prostate cancer to 20q13. Prostate 2005; 63:276-90. [PMID: 15599943 DOI: 10.1002/pros.20198] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The International Consortium for Prostate Cancer Genetics (ICPCG) is an international collaborative effort to pool pedigrees with hereditary prostate cancer (PC) in order to replicate linkage findings for PC. A strength of the ICPCG is the large number of well-characterized pedigrees, allowing linkage analyses within large subsets. Given the heterogeneity and complexity of PC, the historical difficulties of synthesizing different studies reporting positive and negative linkage replication, and the use of different statistical analysis methods and different stratification criteria, the ICPCG provides a valuable resource to evaluate linkage for hereditary PC. To date, linkage of chromosome 20 (HPC20) to hereditary PC has been one of the strongest linkage signals, yet the efforts to replicate this linkage have been limited. This paper reports a linkage analysis of chromosome 20 markers for 1,234 pedigrees with multiple cases of PC ascertained through the ICPCG, and represents the most thorough attempt to confirm or refute linkage to chromosome 20. From the original 158 Mayo pedigrees in which linkage was detected, the maximum heterogeneity LOD (HLOD) score, under a recessive model, was 2.78. In contrast, for the 1,076 pedigrees not included in the original study, the maximum HLOD score (recessive model) was 0.06. Although, a few small linkage signals for chromosome 20 were found in various strata of this pooled analysis, this large study failed to replicate linkage to HPC20. This study illustrates the value of the ICPCG family collection to evaluate reported linkage signals and suggests that the HPC20 region does not make a major contribution to PC susceptibility.
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Affiliation(s)
- Daniel J Schaid
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
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215
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Chen Y, Beck A, Davenport C, Chen Y, Shattuck D, Tavtigian SV. Characterization of TRZ1, a yeast homolog of the human candidate prostate cancer susceptibility gene ELAC2 encoding tRNase Z. BMC Mol Biol 2005; 6:12. [PMID: 15892892 PMCID: PMC1156898 DOI: 10.1186/1471-2199-6-12] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Accepted: 05/13/2005] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND In humans, mutation of ELAC2 is associated with an increased risk of prostate cancer. ELAC2 has been shown to have tRNase Z activity and is associated with the gamma-tubulin complex. RESULTS In this work, we show that the yeast homolog of ELAC2, encoded by TRZ1 (tRNase Z 1), is involved genetically in RNA processing. The temperature sensitivity of a trz1 mutant can be rescued by multiple copies of REX2, which encodes a protein with RNA 3' processing activity, suggesting a role of Trz1p in RNA processing in vivo. Trz1p has two putative nucleotide triphosphate-binding motifs (P-loop) and a conserved histidine motif. The histidine motif and the putative nucleotide binding motif at the C-domain are important for Trz1p function because mutant proteins bearing changes to the critical residues in these motifs are unable to rescue deletion of TRZ1. The growth defect exhibited by trz1 yeast is not complemented by the heterologous ELAC2, suggesting that Trz1p may have additional functions in yeast. CONCLUSION Our results provide genetic evidence that prostate cancer susceptibility gene ELAC2 may be involved in RNA processing, especially rRNA processing and mitochondrial function.
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Affiliation(s)
- Yang Chen
- Myriad Genetics, Inc. 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Audrey Beck
- Myriad Genetics, Inc. 320 Wakara Way, Salt Lake City, UT 84108, USA
| | | | - Yuan Chen
- Myriad Genetics, Inc. 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Donna Shattuck
- Myriad Genetics, Inc. 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Sean V Tavtigian
- Myriad Genetics, Inc. 320 Wakara Way, Salt Lake City, UT 84108, USA
- International Agency for Research on Cancer, World Health Organization, 150 Cours Albert-Thomas, 69372 Lyon Cedex 08, France
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216
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Schilling O, Späth B, Kostelecky B, Marchfelder A, Meyer-Klaucke W, Vogel A. Exosite Modules Guide Substrate Recognition in the ZiPD/ElaC Protein Family. J Biol Chem 2005; 280:17857-62. [PMID: 15699034 DOI: 10.1074/jbc.m500591200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli ZiPD is the best characterized protein encoded by the elaC gene family and is a model for the 3'-pre-tRNA processing endoribonucleases (tRNase Z). A metal ligand-based sequence alignment of ZiPD with metallo-beta-lactamase domain proteins of known crystallographic structure identifies a ZiPD-specific sequence insertion of approximately 50 residues, which we will refer to as the ZiPD exosite. Functionally characterized ZiPD homologs from Bacillus subtilis, Methanococcus janaschii, and human share the presence of the ZiPD exosite, which is also present in the amino-terminal, but not in the carboxyl-terminal, domain of ElaC2 proteins. Another class of functionally characterized tRNase Z enzymes from Thermotoga maritima and Arabidopsis thaliana lack characteristic motifs in the exosite but possess a sequence segment with clustered basic amino acid residues. As an experimental attempt to investigate the function of the exosite we constructed a ZiPD variant that lacks this module (ZiPDDelta). ZiPDDelta has almost wild-type-like catalytic properties for hydrolysis of the small, chromogenic substrate bis(p-nitrophenyl) phosphate. Removal of the ZiPD exosite only affects k(cat), which is reduced by less than 40%, whereas both K' andthe Hill coefficient (measures of the substrate affinity and cooperativity, respectively) remain unchanged. Hence, the exosite is not required for the intrinsic phosphodiesterase activity of ZiPD. Removal of the exosite also does not affect the dimerization properties of ZiPD. In contrast to the wild-type enzyme, ZiPDDelta does not process pre-tRNA, and gel shift assays demonstrate that only the wild-type enzyme, but not ZiPDDelta, binds mature tRNA. These findings show that the exosite is essential for pre-tRNA recognition. In conclusion, we identify a ZiPD exosite that guides physiological substrate recognition in the ZiPD/ElaC protein family.
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Affiliation(s)
- Oliver Schilling
- European Molecular Biology Laboratory Outstation Hamburg, Notkestrasse 85, 22603 Hamburg and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
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217
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Minagawa A, Takaku H, Takagi M, Nashimoto M. The missense mutations in the candidate prostate cancer gene ELAC2 do not alter enzymatic properties of its product. Cancer Lett 2005; 222:211-5. [PMID: 15863270 DOI: 10.1016/j.canlet.2004.09.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2004] [Accepted: 09/07/2004] [Indexed: 10/26/2022]
Abstract
The candidate prostate cancer gene ELAC2 encodes tRNA 3' processing endoribonuclease (tRNase ZL). We produced recombinant human tRNase ZL's, which contain one to three amino-acid substitutions from three missense mutations (Ser217Leu, Ala541Thr, and Arg781His) that are associated with the occurrence of prostate cancer. These enzymes were examined for the pre-tRNA cleavage and the RNase 65 activity. We did not observe any differences in enzymatic properties such as Km and k(cat) values between the wild-type tRNase ZL and its variants. We conclude that there is no causality between the enzymatic properties of tRNase ZL and the prostate cancer.
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Affiliation(s)
- Asako Minagawa
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niitsu, Niigata 956-8603, Japan
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218
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Maier C, Haeusler J, Herkommer K, Vesovic Z, Hoegel J, Vogel W, Paiss T. Mutation screening and association study of RNASEL as a prostate cancer susceptibility gene. Br J Cancer 2005; 92:1159-64. [PMID: 15714208 PMCID: PMC2361943 DOI: 10.1038/sj.bjc.6602401] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
To date, germline mutations have been found in three candidate genes for hereditary prostate cancer: ELAC2 at 17p11, RNASEL at 1q25 and MSR1 at 8p22. RNASEL, encoding the 2',5'-oligoadenylate-dependant RNase L, seems to have rare mutations in different ethnicities, such as M1I in Afro-Americans, E265X in men of European descent and 471delAAAG in Ashkenazi Jews. In order to evaluate the relevance of RNASEL in the German population, we sequenced its open reading frame to determine the spectrum and frequency of germline mutations. The screen included 303 affected men from 136 Caucasian families, of which 45 met the criteria for hereditary prostate cancer. Variants were analysed using a family-based association test, and genotyped in an additional 227 sporadic prostate cancer patients and 207 controls. We identified only two sib pairs (1.4% of our families) cosegregating conspicuous RNASEL variants with prostate cancer: the nonsense mutation E265X, and a new amino-acid substitution (R400P) of unknown functional relevance. Both alleles were also found at low frequencies (1.4 and 0.5%, respectively) in controls. No significant association of polymorphisms (I97L, R462Q and D541E) was observed, neither in case-control analyses nor by family-based association tests. In contrast to previous reports, our study does not suggest that common variants (i.e. R462Q) modify disease risk. Our results are not consistent with a high penetrance of deleterious RNASEL mutations. Due to the low frequency of germline mutations present in our sample, RNASEL does not have a significant impact on prostate cancer susceptibility in the German population.
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Affiliation(s)
- C Maier
- Abteilung Humangenetik, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - J Haeusler
- Abteilung Humangenetik, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - K Herkommer
- Urologische Universitätsklinik und Poliklinik, Abteilung für Urologie und Kinderurologie, Universitätsklinikum Ulm, Prittwitzstrasse 43, 89075 Ulm, Germany
| | - Z Vesovic
- Abteilung Humangenetik, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - J Hoegel
- Abteilung Humangenetik, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - W Vogel
- Abteilung Humangenetik, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - T Paiss
- Urologische Universitätsklinik und Poliklinik, Abteilung für Urologie und Kinderurologie, Universitätsklinikum Ulm, Prittwitzstrasse 43, 89075 Ulm, Germany
- Urologische Universitätsklinik und Poliklinik, Abteilung für Urologie und Kinderurologie, Universitätsklinikum Ulm, Prittwitzstrasse 43, 89075 Ulm, Germany. E-mail:
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219
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Shibata HS, Takaku H, Takagi M, Nashimoto M. The T loop structure is dispensable for substrate recognition by tRNase ZL. J Biol Chem 2005; 280:22326-34. [PMID: 15824113 DOI: 10.1074/jbc.m502048200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
tRNA 3'-processing endoribonucleases (tRNase Z, or 3'-tRNase; EC 3.1.26.11) are enzymes that remove 3'-trailers from pre-tRNAs. An about 12-base-pair stem, a T loop-like structure, and a 3'-trailer were considered to be the minimum requirements for recognition by the long form (tRNase ZL) of tRNase Z; tRNase ZL can recognize and cleave a micro-pre-tRNA or a hooker/target RNA complex that resembles a micro-pre-tRNA. We examined four hook RNAs containing systematically weakened T stems for directing target RNA cleavage by tRNase ZL. As expected, the cleavage efficiency decreased with the decrease in T stem stability, and to our surprise, even the hook RNA that forms no T stem-loop-directed slight cleavage of the target RNA, suggesting that the T stem-loop structure is important but dispensable for substrate recognition by tRNase ZL. To analyze the effect of the T loop on substrate recognition, we compared the cleavage reaction for a micro-pre-tRNA with that for a 12-base-pair double-stranded RNA, which is the same as the micro-pre-tRNA except for the lack of the T loop structure. The observed rate constant value for the double-stranded RNA was comparable with that for the micro-pre-tRNA, whereas the K(d) value for the complex with the double-stranded RNA was much higher than that for the complex with the micro-pre-tRNA. These results suggest that the T loop structure is not indispensable for the recognition, although the interaction between the T loop and the enzyme exists. Cleavage assays for such double-stranded RNA substrates of various lengths suggested that tRNase ZL can recognize and cleave double-stranded RNA substrates that are longer than 5 base pairs and shorter than 20 base pairs. We also showed that double-stranded RNA is not a substrate for the short form of tRNase Z.
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Affiliation(s)
- Hirotaka S Shibata
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niitsu, Niigata 956-8603, Japan
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220
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Perez-Iratxeta C, Palidwor G, Porter CJ, Sanche NA, Huska MR, Suomela BP, Muro EM, Krzyzanowski PM, Hughes E, Campbell PA, Rudnicki MA, Andrade MA. Study of stem cell function using microarray experiments. FEBS Lett 2005; 579:1795-801. [PMID: 15763554 DOI: 10.1016/j.febslet.2005.02.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Revised: 02/10/2005] [Accepted: 02/10/2005] [Indexed: 11/17/2022]
Abstract
DNA Microarrays are used to simultaneously measure the levels of thousands of mRNAs in a sample. We illustrate here that a collection of such measurements in different cell types and states is a sound source of functional predictions, provided the microarray experiments are analogous and the cell samples are appropriately diverse. We have used this approach to study stem cells, whose identity and mechanisms of control are not well understood, generating Affymetrix microarray data from more than 200 samples, including stem cells and their derivatives, from human and mouse. The data can be accessed online (StemBase; http://www.scgp.ca:8080/StemBase/).
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Affiliation(s)
- Carolina Perez-Iratxeta
- Ontario Genomics Innovation Centre, Ottawa Health Research Institute, Molecular Medicine Program, 501 Smyth Road, Ottawa, Canada K1H 8L6
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221
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Narla G, Difeo A, Reeves HL, Schaid DJ, Hirshfeld J, Hod E, Katz A, Isaacs WB, Hebbring S, Komiya A, McDonnell SK, Wiley KE, Jacobsen SJ, Isaacs SD, Walsh PC, Zheng SL, Chang BL, Friedrichsen DM, Stanford JL, Ostrander EA, Chinnaiyan AM, Rubin MA, Xu J, Thibodeau SN, Friedman SL, Martignetti JA. A germline DNA polymorphism enhances alternative splicing of the KLF6 tumor suppressor gene and is associated with increased prostate cancer risk. Cancer Res 2005; 65:1213-22. [PMID: 15735005 DOI: 10.1158/0008-5472.can-04-4249] [Citation(s) in RCA: 174] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Prostate cancer is a leading and increasingly prevalent cause of cancer death in men. Whereas family history of disease is one of the strongest prostate cancer risk factors and suggests a hereditary component, the predisposing genetic factors remain unknown. We first showed that KLF6 is a tumor suppressor somatically inactivated in prostate cancer and since then, its functional loss has been further established in prostate cancer cell lines and other human cancers. Wild-type KLF6, but not patient-derived mutants, suppresses cell growth through p53-independent transactivation of p21. Here we show that a germline KLF6 single nucleotide polymorphism, confirmed in a tri-institutional study of 3,411 men, is significantly associated with an increased relative risk of prostate cancer in men, regardless of family history of disease. This prostate cancer-associated allele generates a novel functional SRp40 DNA binding site and increases transcription of three alternatively spliced KLF6 isoforms. The KLF6 variant proteins KLF6-SV1 and KLF6-SV2 are mislocalized to the cytoplasm, antagonize wtKLF6 function, leading to decreased p21 expression and increased cell growth, and are up-regulated in tumor versus normal prostatic tissue. Thus, these results are the first to identify a novel mechanism of self-encoded tumor suppressor gene inactivation and link a relatively common single nucleotide polymorphism to both regulation of alternative splicing and an increased risk in a major human cancer.
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Affiliation(s)
- Goutham Narla
- Department of Medicine, Mount Sinai School of Medicine, New York, New York, USA
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222
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Gimba ERP, Barcinski MA. Molecular aspects of prostate cancer: implications for future directions. Int Braz J Urol 2005; 29:401-10; discussion 411. [PMID: 15745584 DOI: 10.1590/s1677-55382003000500003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2003] [Accepted: 08/28/2003] [Indexed: 11/21/2022] Open
Abstract
Many studies have been developed trying to understand the complex molecular mechanisms involved in oncogenesis and progression of prostate cancer (PCa). Current biotechnological methodologies, especially genomic studies, are adding important aspects to this area. The construction of extensive DNA sequence data and gene expression profiles have been intensively explored to search for candidate biomarkers to evaluate PCa. The use of DNA micro-array robotic systems constitutes a powerful approach to simultaneously monitor the expression of a great number of genes. The resulting gene expressing profiles can be used to specifically describe tumor staging and response to cancer therapies. Also, it is possible to follow PCa pathological properties and to identify genes that anticipate the behavior of clinical disease. The molecular pathogenesis of PCa involves many contributing factors, such as alterations in signal transduction pathways, angiogenesis, adhesion molecules expression and cell cycle control. Also, molecular studies are making clear that many genes, scattered through several different chromosomal regions probably cause predisposition to PCa. The discovery of new molecular markers for PCa is another relevant advance resulting from molecular biology studies of prostate tumors. Interesting tissue and serum markers have been reported, resulting in many cases in useful novelties to diagnostic and prognostic approaches to follow-up PCa. Finally, gene therapy comes as an important approach for therapeutic intervention in PCa. Clinical trials for PCa have been demonstrating that gene therapy is relatively safe and well tolerated, although some improvements are yet to be developed.
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Affiliation(s)
- Etel R P Gimba
- Department of Research, Division of Experimental Medicine, National Institute of Cancer, Rio de Janeiro, Brazil.
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223
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Dominski Z, Yang XC, Purdy M, Wagner EJ, Marzluff WF. A CPSF-73 homologue is required for cell cycle progression but not cell growth and interacts with a protein having features of CPSF-100. Mol Cell Biol 2005; 25:1489-500. [PMID: 15684398 PMCID: PMC548002 DOI: 10.1128/mcb.25.4.1489-1500.2005] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Formation of the mature 3' ends of the vast majority of cellular mRNAs occurs through cleavage and polyadenylation and requires a cleavage and polyadenylation specificity factor (CPSF) containing, among other proteins, CPSF-73 and CPSF-100. These two proteins belong to a superfamily of zinc-dependent beta-lactamase fold proteins with catalytic specificity for a wide range of substrates including nucleic acids. CPSF-73 contains a zinc-binding histidine motif involved in catalysis in other members of the beta-lactamase superfamily, whereas CPSF-100 has substitutions within the histidine motif and thus is unlikely to be catalytically active. Here we describe two previously unknown human proteins, designated RC-68 and RC-74, which are related to CPSF-73 and CPSF-100 and which form a complex in HeLa and mouse cells. RC-68 contains the intact histidine motif, and hence it might be a functional counterpart of CPSF-73, whereas RC-74 lacks this motif, thus resembling CPSF-100. In HeLa cells RC-68 is present in both the cytoplasm and the nucleus whereas RC-74 is exclusively nuclear. RC-74 does not interact with CPSF-73, and neither RC-68 nor RC-74 is found in a complex with CPSF-160, indicating that these two proteins form a separate entity independent of the CPSF complex and are likely involved in a pre-mRNA processing event other than cleavage and polyadenylation of the vast majority of cellular pre-mRNAs. RNA interference-mediated depletion of RC-68 arrests HeLa cells early in G(1) phase, but surprisingly the arrested cells continue growing and reach the size typical of G(2) cells. RC-68 is highly conserved from plants to humans and may function in conjunction with RC-74 in the 3' end processing of a distinct subset of cellular pre-mRNAs encoding proteins required for G(1) progression and entry into S phase.
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Affiliation(s)
- Zbigniew Dominski
- Program in Molecular Biology and Biotechnology, CB #3280, University of North Carolina, Chapel Hill, NC 27599.
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224
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Abstract
Haplotypes have played a major role in the study of highly-penetrant single-gene disorders, and recent evidence that the human genome has hot-spots and cold-spots for recombination have suggested that haplotype-based methods may play a key role in the study of common complex traits. This report reviews the motivation of using haplotypes for the study of the genetic basis of human traits, ranging from biologic function, to statistical power advantages of haplotypes, to linkage disequilibrium fine-mapping. Recent developments of regression models for haplotype analyses are reviewed, offering a synthesis of current methods, as well as their limitations and areas that require further research. Regression models provide significant advantages, such as the ability to control for non-genetic covariates, the effects of the haplotypes can be modeled, step-wise selection can be used to screen for a subset of markers that explain most of the association, haplotype x environment interactions can be evaluated, and regression diagnostics are well developed. Despite these strengths, the current regression methods tend to lack the sophisticated population genetic perspectives offered by coalescent and other similar approaches. Future work that links regression methods with population genetic models may prove beneficial.
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Affiliation(s)
- Daniel J Schaid
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA.
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225
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Abstract
This quantitative study determines the values, beliefs, and attitudes influencing the intention of men to undergo or defer genetic testing for prostate cancer risk using a model based on components of the Theory of Reasoned Action and Health Belief Model. Telephone interviews of a community sample of 400 men in a large, East Coast metropolitan area of diverse educational, ethnic, and age backgrounds were conducted to rank key values and beliefs about genetic testing for prostate cancer risk in anticipation of its future availability. Descriptive statistics, univariate analyses, and logistic regression were used in data analysis. The factors of values attached to consequences, motivation from self, beliefs in benefits, and a motivation to comply with others (borderline) were statistically significant for testing intention. Of all demographics, only increased education was associated with diminished interest in testing. Desire to be tested varied widely across groups of men. Based on these identified values, health professionals can better understand men's values and beliefs on the risks and benefits of testing. The relationship of men to others, family and society, require further investigation in this and other aspects of genetic testing.
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Affiliation(s)
- David J Doukas
- Department of Family and Geriatric Medicine, Institute of Bioethics, Public Policy and Law, University of Louisville, KY 40202, USA.
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226
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Bonatto D, Revers LF, Brendel M, Henriques JAP. The eukaryotic Pso2/Snm1/Artemis proteins and their function as genomic and cellular caretakers. Braz J Med Biol Res 2005; 38:321-34. [PMID: 15761611 DOI: 10.1590/s0100-879x2005000300002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA double-strand breaks (DSBs) represent a major threat to the genomic stability of eukaryotic cells. DNA repair mechanisms such as non-homologous end joining (NHEJ) are responsible for the maintenance of eukaryotic genomes. Dysfunction of one or more of the many protein complexes that function in NHEJ can lead to sensitivity to DNA damaging agents, apoptosis, genomic instability, and severe combined immunodeficiency. One protein, Pso2p, was shown to participate in the repair of DSBs induced by DNA inter-strand cross-linking (ICL) agents such as cisplatin, nitrogen mustard or photo-activated bi-functional psoralens. The molecular function of Pso2p in DNA repair is unknown, but yeast and mammalian cell line mutants for PSO2 show the same cellular responses as strains with defects in NHEJ, e.g., sensitivity to ICLs and apoptosis. The Pso2p human homologue Artemis participates in V(D)J recombination. Mutations in Artemis induce a variety of immunological deficiencies, a predisposition to lymphomas, and an increase in chromosomal aberrations. In order to better understand the role of Pso2p in the repair of DSBs generated as repair intermediates of ICLs, an in silico approach was used to characterize the catalytic domain of Pso2p, which led to identification of novel Pso2p homologues in other organisms. Moreover, we found the catalytic core of Pso2p fused to different domains. In plants, a specific ATP-dependent DNA ligase I contains the catalytic core of Pso2p, constituting a new DNA ligase family, which was named LIG6. The possible functions of Pso2p/Artemis/Lig6p in NHEJ and V(D)J recombination and in other cellular metabolic reactions are discussed.
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Affiliation(s)
- D Bonatto
- Departamento de Biofísica, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
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227
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Trepanier A, Ahrens M, McKinnon W, Peters J, Stopfer J, Grumet SC, Manley S, Culver JO, Acton R, Larsen-Haidle J, Correia LA, Bennett R, Pettersen B, Ferlita TD, Costalas JW, Hunt K, Donlon S, Skrzynia C, Farrell C, Callif-Daley F, Vockley CW. Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. J Genet Couns 2005; 13:83-114. [PMID: 15604628 DOI: 10.1023/b:jogc.0000018821.48330.77] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
These cancer genetic counseling recommendations describe the medical, psychosocial, and ethical ramifications of identifying at-risk individuals through cancer risk assessment with or without genetic testing. They were developed by members of the Practice Issues Subcommittee of the National Society of Genetic Counselors Cancer Genetic Counseling Special Interest Group. The information contained in this document is derived from extensive review of the current literature on cancer genetic risk assessment and counseling as well as the personal expertise of genetic counselors specializing in cancer genetics. The recommendations are intended to provide information about the process of genetic counseling and risk assessment for hereditary cancer disorders rather than specific information about individual syndromes. Key components include the intake (medical and family histories), psychosocial assessment (assessment of risk perception), cancer risk assessment (determination and communication of risk), molecular testing for hereditary cancer syndromes (regulations, informed consent, and counseling process), and follow-up considerations. These recommendations should not be construed as dictating an exclusive course of management, nor does use of such recommendations guarantee a particular outcome. These recommendations do not displace a health care provider's professional judgment based on the clinical circumstances of a client.
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Affiliation(s)
- Angela Trepanier
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
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228
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Larson GP, Ding Y, Cheng LSC, Lundberg C, Gagalang V, Rivas G, Geller L, Weitzel J, MacDonald D, Archambeau J, Slater J, Neuberg D, Daly MB, Angel I, Benson AB, Smith K, Kirkwood JM, O'Dwyer PJ, Raskay B, Sutphen R, Drew R, Stewart JA, Werndli J, Johnson D, Ruckdeschel JC, Elston RC, Krontiris TG. Genetic Linkage of Prostate Cancer Risk to the Chromosome 3 Region Bearing FHIT. Cancer Res 2005. [DOI: 10.1158/0008-5472.805.65.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
We conducted linkage analysis of 80 candidate genes in 201 brother pairs affected with prostatic adenocarcinoma. Markers representing two adjacent candidate genes on chromosome 3p, CDC25A and FHIT, showed suggestive evidence for linkage with single-point identity-by-descent allele-sharing statistics. Fine-structure multipoint linkage analysis yielded a maximum LOD score of 3.17 (P = 0.00007) at D3S1234 within FHIT intron 5. For a subgroup of 38 families in which three or more affected brothers were reported, the LOD score was 3.83 (P = 0.00001). Further analysis reported herein suggested a recessive mode of inheritance. Association testing of 16 single nucleotide polymorphisms (SNP) spanning a 381-kb interval surrounding D3S1234 in 202 cases of European descent with 143 matched, unrelated controls revealed significant evidence for association between case status and the A allele of single nucleotide polymorphism rs760317, located within intron 5 of FHIT (Pearson's χ2 = 8.54, df = 1, P = 0.0035). Our results strongly suggest involvement of germline variations of FHIT in prostate cancer risk.
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Affiliation(s)
| | - Yan Ding
- 1Divisions of Molecular Medicine and
| | - Li S-C. Cheng
- 2Information Sciences, Beckman Research Institute and
| | | | | | | | | | - Jeffrey Weitzel
- 1Divisions of Molecular Medicine and
- 3Department of Cancer Genetics, City of Hope National Medical Center, Duarte, California
| | - Deborah MacDonald
- 3Department of Cancer Genetics, City of Hope National Medical Center, Duarte, California
| | - John Archambeau
- 4Department of Radiation Medicine, Loma Linda University Medical Center, Loma Linda, California
| | - Jerry Slater
- 4Department of Radiation Medicine, Loma Linda University Medical Center, Loma Linda, California
| | - Donna Neuberg
- 5Division of Biostatistics, Dana-Farber Cancer Institute, Harvard Medical School and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Mary B. Daly
- 6Department of Population Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Irene Angel
- 6Department of Population Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Al B. Benson
- 7Department of Medicine, Division of Hematology/Oncology and
| | - Kimberly Smith
- 8Clinical Research Office, Robert J. Lurie Comprehensive Cancer Center, Northwestern University School of Medicine, Chicago, Illinois
| | - John M. Kirkwood
- 9Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Peter J. O'Dwyer
- 10Department of Medicine, Hematology-Oncology Division, University of Pennsylvania Cancer Center, Philadelphia, Pennsylvania
| | - Barbara Raskay
- 10Department of Medicine, Hematology-Oncology Division, University of Pennsylvania Cancer Center, Philadelphia, Pennsylvania
| | - Rebecca Sutphen
- 11Interdisciplinary Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, Florida
| | - Rosalind Drew
- 11Interdisciplinary Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, Florida
| | - James A. Stewart
- 12University of Wisconsin Comprehensive Cancer Center and University of Wisconsin School of Medicine, Madison, Wisconsin
| | - Jae Werndli
- 12University of Wisconsin Comprehensive Cancer Center and University of Wisconsin School of Medicine, Madison, Wisconsin
| | - David Johnson
- 13Division of Hematology & Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | - Robert C. Elston
- 15Department of Epidemiology and Biostatistics, Case Western Reserve University, Metro Health Medical Center, Cleveland, Ohio
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229
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Ishii R, Minagawa A, Takaku H, Takagi M, Nashimoto M, Yokoyama S. Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima. J Biol Chem 2005; 280:14138-44. [PMID: 15701599 DOI: 10.1074/jbc.m500355200] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The maturation of the tRNA 3' end is catalyzed by a tRNA 3' processing endoribonuclease named tRNase Z (RNase Z or 3'-tRNase) in eukaryotes, Archaea, and some bacteria. The tRNase Z generally cuts the 3' extra sequence from the precursor tRNA after the discriminator nucleotide. In contrast, Thermotoga maritima tRNase Z cleaves the precursor tRNA precisely after the CCA sequence. In this study, we determined the crystal structure of T. maritima tRNase Z at 2.6-A resolution. The tRNase Z has a four-layer alphabeta/betaalpha sandwich fold, which is classified as a metallo-beta-lactamase fold, and forms a dimer. The active site is located at one edge of the beta-sandwich and is composed of conserved motifs. Based on the structure, we constructed a docking model with the tRNAs that suggests how tRNase Z may recognize the substrate tRNAs.
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Affiliation(s)
- Ryohei Ishii
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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230
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Li de la Sierra-Gallay I, Pellegrini O, Condon C. Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z. Nature 2005; 433:657-61. [PMID: 15654328 DOI: 10.1038/nature03284] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Accepted: 12/16/2004] [Indexed: 11/08/2022]
Abstract
Transfer RNAs (tRNAs) are synthesized as part of longer primary transcripts that require processing of both their 3' and 5' extremities in every living organism known. The 5' side is processed (matured) by the ubiquitously conserved endonucleolytic ribozyme, RNase P, whereas removal of the 3' tails can be either exonucleolytic or endonucleolytic. The endonucleolytic pathway is catalysed by an enzyme known as RNase Z, or 3' tRNase. RNase Z cleaves precursor tRNAs immediately after the discriminator base (the unpaired nucleotide 3' to the last base pair of the acceptor stem, used as an identity determinant by many aminoacyl-tRNA synthetases) in most cases, yielding a tRNA primed for addition of the CCA motif by nucleotidyl transferase. Here we report the crystal structure of Bacillus subtilis RNase Z at 2.1 A resolution, and propose a mechanism for tRNA recognition and cleavage. The structure explains the allosteric properties of the enzyme, and also sheds light on the mechanisms of inhibition by the CCA motif and long 5' extensions. Finally, it highlights the extraordinary adaptability of the metallo-hydrolase domain of the beta-lactamase family for the hydrolysis of covalent bonds.
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231
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Habu Y, Miyano-Kurosaki N, Kitano M, Endo Y, Yukita M, Ohira S, Takaku H, Nashimoto M, Takaku H. Inhibition of HIV-1 gene expression by retroviral vector-mediated small-guide RNAs that direct specific RNA cleavage by tRNase ZL. Nucleic Acids Res 2005; 33:235-43. [PMID: 15647506 PMCID: PMC546152 DOI: 10.1093/nar/gki164] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Revised: 12/15/2004] [Accepted: 12/15/2004] [Indexed: 11/13/2022] Open
Abstract
The tRNA 3'-processing endoribonuclease (tRNase Z or 3' tRNase; EC 3.1.26.11) is an essential enzyme that removes the 3' trailer from pre-tRNA. The long form (tRNase ZL) can cleave a target RNA in vitro at the site directed by an appropriate small-guide RNA (sgRNA). Here, we investigated whether this sgRNA/tRNase ZL strategy could be applied to gene therapy for AIDS. We tested the ability of four sgRNA-expression plasmids to inhibit HIV-1 gene expression in COS cells, using a transient-expression assay. The three sgRNAs guide inhibition of HIV-1 gene expression in cultured COS cells. Analysis of the HIV-1 mRNA levels suggested that sgRNA directed the tRNase ZL to mediate the degradation of target RNA. The observation that sgRNA was localized primarily in nuclei suggests that tRNase ZL cleaves the HIV-1 mRNA when complexed with sgRNA in this location. We also examined the ability of two retroviral vectors expressing sgRNA to suppress HIV-1 expression in HIV-1-infected Jurkat T cells. sgRNA-SL4 suppressed HIV-1 expression almost completely in infected cells for up to 18 days. These results suggest that the sgRNA/tRNase ZL approach is effective in downregulating HIV-1 gene expression.
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Affiliation(s)
- Yuichiro Habu
- High Technology Research Center, Chiba Institute of Technology2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Naoko Miyano-Kurosaki
- Department of Life and Environmental Sciences, Chiba Institute of Technology2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
- High Technology Research Center, Chiba Institute of Technology2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Michiko Kitano
- Department of Life and Environmental Sciences, Chiba Institute of Technology2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Yumihiko Endo
- Department of Life and Environmental Sciences, Chiba Institute of Technology2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Masakazu Yukita
- Department of Life and Environmental Sciences, Chiba Institute of Technology2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Shigeru Ohira
- Department of Life and Environmental Sciences, Chiba Institute of Technology2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Hiroaki Takaku
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences265-1 Higashito, Niitsu, Niigata 956-8603, Japan
| | - Masayuki Nashimoto
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences265-1 Higashito, Niitsu, Niigata 956-8603, Japan
| | - Hiroshi Takaku
- Department of Life and Environmental Sciences, Chiba Institute of Technology2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
- High Technology Research Center, Chiba Institute of Technology2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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232
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Akhter S, Richie CT, Deng JM, Brey E, Zhang X, Patrick C, Behringer RR, Legerski RJ. Deficiency in SNM1 abolishes an early mitotic checkpoint induced by spindle stress. Mol Cell Biol 2005; 24:10448-55. [PMID: 15542852 PMCID: PMC529044 DOI: 10.1128/mcb.24.23.10448-10455.2004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spindle poisons represent an important class of anticancer drugs that act by interfering with microtubule polymerization and dynamics and thereby induce mitotic checkpoints and apoptosis. Here we show that mammalian SNM1 functions in an early mitotic stress checkpoint that is distinct from the well-characterized spindle checkpoint that regulates the metaphase-to-anaphase transition. Specifically, we found that compared to wild-type cells, Snm1-deficient mouse embryonic fibroblasts exposed to spindle poisons exhibited elevated levels of micronucleus formation, decreased mitotic delay, a failure to arrest in mitosis prior to chromosome condensation, supernumerary centrosomes, and decreased viability. In addition, we show that both Snm1 and 53BP1, previously shown to interact, coimmunoprecipitate with components of the anaphase-promoting complex (APC)/cyclosome. These findings suggest that Snm1 is a component of a mitotic stress checkpoint that negatively targets the APC prior to chromosome condensation.
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Affiliation(s)
- Shamima Akhter
- University of Texas M. D. Anderson Cancer Center, Department of Molecular Genetics, 1515 Holcombe Blvd., Houston, TX 77030, USA
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233
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Camp NJ, Swensen J, Horne BD, Farnham JM, Thomas A, Cannon-Albright LA, Tavtigian SV. Characterization of linkage disequilibrium structure, mutation history, and tagging SNPs, and their use in association analyses:ELAC2 and familial early-onset prostate cancer. Genet Epidemiol 2005; 28:232-43. [PMID: 15593091 DOI: 10.1002/gepi.20054] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In association analyses, it is critical that informative single-nucleotide polymorphisms (SNPs) be selected for study and utilized appropriately. We sequenced 38 kb, including exons of ELAC2, promoter region and conserved upstream intergenic sequences. A comprehensive characterization of linkage disequilibrium (LD) structure and mutation history was performed using our principal components analysis (PCA) method and a phylogenetic analysis. We identified a complex pattern of LD structure consistent with the occurrence of both recombination and mutation events within ELAC2. Four overlapping and noncontiguous LD groups were defined. Eight tagging SNPs (tSNPs) were identified, accounting for over 90% of the genetic variation of the 19 total variants. We tested associations between familial early-onset prostate cancer (PRCA) and each variant independently and in haplotypes. We performed these tests using all 19 variants and the 8 tSNPs; the results using tSNP haplotypes accurately represent the association evidence for the full haplotypes. We observed increased evidence for association when SNPs were analyzed in haplotypes. The phylogenetic analysis indicated three haplotypes, clustered farthest from the root-node, all of which were found more often in cases than controls. These three haplotypes together showed the best evidence of association with familial, early-onset PRCA (P=0.0024; odds ratio=2.23; 95% CI, 1.33-3.74), indicating possible allelic heterogeneity. Our results suggest that 8 tSNPs are required to comprehensively assess associations in ELAC2, and that haplotypes should be considered for analysis, and that a knowledge of mutation history may be helpful in parsing allelic heterogeneity and suggesting combinations of haplotypes to be tested.
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Affiliation(s)
- Nicola J Camp
- Genetic Epidemiology Division, Department of Medical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, USA.
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234
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Hassan MO, Albarwani S, Al Yahyaee S, Al Haddabi S, Rizwi S, Jaffer A, Al-Lawati J, Cai G, Comuzzie AG, Bayoumi RA. A Family Study in Oman: Large, Consanguineous, Polygamous Omani Arab Pedigrees. ACTA ACUST UNITED AC 2005; 8:56-60. [PMID: 15767758 DOI: 10.1159/000083341] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
OBJECTIVE To establish a suitable human model for the study of the genetics of complex diseases. METHODS We have selected an Omani Arab population to provide the statistical power required to study the genetics of complex diseases with confidence. This model consists of five multigenerational highly inbred pedigrees, descending from a small number of founders just a few generations ago with environmental homogeneity, restricted geographical distribution, detailed records and well-ascertained and -validated pedigrees. Stringent criteria were adopted for defining the phenotypes of hypertension, diabetes mellitus, dyslipidemias and obesity. The SOLAR genetic software package was used to draw the pedigree structure. RESULTS Outstanding statistical power to detect susceptibility loci was obtained. CONCLUSIONS This model represents a large homogeneous human family-based population for the study of genetic and environmental factors contributing to complex diseases.
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Affiliation(s)
- M O Hassan
- College of Medicine, Sultan Qaboos University, Muscat, Sultanate of Oman.
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235
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Berger EM, Dubrovsky EB. Juvenile hormone molecular actions and interactions during development of Drosophila melanogaster. VITAMINS AND HORMONES 2005; 73:175-215. [PMID: 16399411 DOI: 10.1016/s0083-6729(05)73006-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Edward M Berger
- Department Of Biology, Dartmouth College, Hanover, New Hampshire 03755, USA
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236
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Zhang X, Succi J, Feng Z, Prithivirajsingh S, Story MD, Legerski RJ. Artemis is a phosphorylation target of ATM and ATR and is involved in the G2/M DNA damage checkpoint response. Mol Cell Biol 2004; 24:9207-20. [PMID: 15456891 PMCID: PMC517881 DOI: 10.1128/mcb.24.20.9207-9220.2004] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Mutations in Artemis in both humans and mice result in severe combined immunodeficiency due to a defect in V(D)J recombination. In addition, Artemis mutants are radiosensitive and chromosomally unstable, which has been attributed to a defect in nonhomologous end joining (NHEJ). We show here, however, that Artemis-depleted cell extracts are not defective in NHEJ and that Artemis-deficient cells have normal repair kinetics of double-strand breaks after exposure to ionizing radiation (IR). Artemis is shown, however, to interact with known cell cycle checkpoint proteins and to be a phosphorylation target of the checkpoint kinase ATM or ATR after exposure of cells to IR or UV irradiation, respectively. Consistent with these findings, our results also show that Artemis is required for the maintenance of a normal DNA damage-induced G2/M cell cycle arrest. Artemis does not appear, however, to act either upstream or downstream of checkpoint kinase Chk1 or Chk2. These results define Artemis as having a checkpoint function and suggest that the radiosensitivity and chromosomal instability of Artemis-deficient cells may be due to defects in cell cycle responses after DNA damage.
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Affiliation(s)
- Xiaoshan Zhang
- Department of Molecular Genetics, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
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237
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Affiliation(s)
- Marvin Wickens
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
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238
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Farnham JM, Camp NJ, Swensen J, Tavtigian SV, Albright LAC. Confirmation of the HPCX prostate cancer predisposition locus in large Utah prostate cancer pedigrees. Hum Genet 2004; 116:179-85. [PMID: 15592687 DOI: 10.1007/s00439-004-1220-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2004] [Accepted: 11/03/2004] [Indexed: 11/28/2022]
Abstract
Several genetic predisposition loci for prostate cancer have been identified through linkage analysis, and it is now generally recognized that no single gene is responsible for more than a small proportion of prostate cancers. However, published confirmations of these loci have been few, and failures to confirm have been frequent. The genetic etiology of prostate cancer is clearly complex and includes significant genetic heterogeneity, phenocopies, and reduced penetrance. Powerful analyses that involve robust statistics and methods to reduce genetic heterogeneity are therefore necessary. We have performed linkage analysis on 143 Utah pedigrees for the previously published Xq27-28 (HPCX) prostate cancer susceptibility locus. We employed a robust multipoint statistic (TLOD) and a novel splitting algorithm to reduce intra-familial heterogeneity by iteratively removing the top generation from the large Utah pedigrees. In a dataset containing pedigrees having no more than five generations, we observed a multipoint TLOD of 2.74 (P=0.0002), which is statistically significant after correction for multiple testing. For both the full-structure pedigrees (up to seven generations) and the smaller sub-pedigrees, the linkage evidence was much reduced. This study thus represents the first significant confirmation of HPCX (Xq27-28) and argues for the continued utility of large pedigrees in linkage analyses for complex diseases.
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Affiliation(s)
- James M Farnham
- Genetic Epidemiology, Department of Medical Informatics, University of Utah, Salt Lake City, UT 84108, USA
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239
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Schaid DJ, Guenther JC, Christensen GB, Hebbring S, Rosenow C, Hilker CA, McDonnell SK, Cunningham JM, Slager SL, Blute ML, Thibodeau SN. Comparison of microsatellites versus single-nucleotide polymorphisms in a genome linkage screen for prostate cancer-susceptibility Loci. Am J Hum Genet 2004; 75:948-65. [PMID: 15514889 PMCID: PMC1182157 DOI: 10.1086/425870] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Accepted: 09/08/2004] [Indexed: 12/19/2022] Open
Abstract
Prostate cancer is one of the most common cancers among men and has long been recognized to occur in familial clusters. Brothers and sons of affected men have a 2-3-fold increased risk of developing prostate cancer. However, identification of genetic susceptibility loci for prostate cancer has been extremely difficult. Although the suggestion of linkage has been reported for many chromosomes, the most promising regions have been difficult to replicate. In this study, we compare genome linkage scans using microsatellites with those using single-nucleotide polymorphisms (SNPs), performed in 467 men with prostate cancer from 167 families. For the microsatellites, the ABI Prism Linkage Mapping Set version 2, with 402 microsatellite markers, was used, and, for the SNPs, the Early Access Affymetrix Mapping 10K array was used. Our results show that the presence of linkage disequilibrium (LD) among SNPs can lead to inflated LOD scores, and this seems to be an artifact due to the assumption of linkage equilibrium that is required by the current genetic-linkage software. After excluding SNPs with high LD, we found a number of new LOD-score peaks with values of at least 2.0 that were not found by the microsatellite markers: chromosome 8, with a maximum model-free LOD score of 2.2; chromosome 2, with a LOD score of 2.1; chromosome 6, with a LOD score of 4.2; and chromosome 12, with a LOD score of 3.9. The LOD scores for chromosomes 6 and 12 are difficult to interpret, because they occurred only at the extreme ends of the chromosomes. The greatest gain provided by the SNP markers was a large increase in the linkage information content, with an average information content of 61% for the SNPs, versus an average of 41% for the microsatellite markers. The strengths and weaknesses of microsatellite versus SNP markers are illustrated by the results of our genome linkage scans.
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Affiliation(s)
- Daniel J Schaid
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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240
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Loukola A, Chadha M, Penn SG, Rank D, Conti DV, Thompson D, Cicek M, Love B, Bivolarevic V, Yang Q, Jiang Y, Hanzel DK, Dains K, Paris PL, Casey G, Witte JS. Comprehensive evaluation of the association between prostate cancer and genotypes/haplotypes in CYP17A1, CYP3A4, and SRD5A2. Eur J Hum Genet 2004; 12:321-32. [PMID: 14560315 DOI: 10.1038/sj.ejhg.5201101] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Genes involved in the testosterone biosynthetic pathway - such as CYP17A1, CYP3A4, and SRD5A2 - represent strong candidates for affecting prostate cancer. Previous work has detected associations between individual variants in these three genes and prostate cancer risk and aggressiveness. To more comprehensively evaluate CYP17A1, CYP3A4, and SRD5A2, we undertook a two-phase study of the relationship between their genotypes/haplotypes and prostate cancer. Phase I of the study first searched for single-nucleotide polymorphisms (SNPs) in these genes by resequencing 24 individuals from the Coriell Polymorphism Discovery Resource, 92-110 men from prostate cancer case-control sibships, and by leveraging public databases. In all, 87 SNPs were discovered and genotyped in 276 men from case-control sibships. Those SNPs exhibiting preliminary case-control allele frequency differences, or distinguishing (ie, 'tagging') common haplotypes across the genes, were identified for further study (24 SNPs in total). In Phase II of the study, the 24 SNPs were genotyped in an additional 841 men from case-control sibships. Finally, associations between genotypes/haplotypes in CYP17A1, CYP3A4, and SRD5A2 and prostate cancer were evaluated in the total case-control sample of 1117 brothers from 506 sibships. Family-based analyses detected associations between prostate cancer risk or aggressiveness and a number of CYP3A4 SNPs (P-values between 0.006 and 0.05), a CYP3A4 haplotype (P-values 0.05 and 0.009 in nonstratified and stratified analysis, respectively), and two SRD5A2 SNPs in strong linkage disequilibrium (P=0.02). Undertaking a two-phase study comprising SNP discovery, haplotype tagging, and association analyses allowed us to more fully decipher the relation between CYP17A1, CYP3A4, and SRD5A2 and prostate cancer.
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Affiliation(s)
- Anu Loukola
- Amersham Biosciences, Sunnyvale, CA 94085, USA
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241
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Burmester JK, Suarez BK, Lin JH, Jin CH, Miller RD, Zhang KQ, Salzman SA, Reding DJ, Catalona WJ. Analysis of Candidate Genes for Prostate Cancer. Hum Hered 2004; 57:172-8. [PMID: 15583422 DOI: 10.1159/000081443] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Accepted: 04/29/2004] [Indexed: 12/28/2022] Open
Abstract
Considerable evidence demonstrates that genetic factors are important in the development and aggressiveness of prostate cancer. To identify genetic variants that predispose to prostate cancer we tested candidate SNPs from genomic regions that show linkage to prostate cancer susceptibility and/or aggressiveness, as well as genes that show a significant difference in mRNA expression level between tumor and normal tissue. Cases had histologically verified prostate cancer. Controls were at least 65 years old, never registered a PSA above 2.5 ng/ml, always had digital rectal examinations that were not suspicious for cancer, and have no known family history of prostate cancer. Thirty-nine coding SNPs and nine non-coding SNPs were tested in up to 590 cases and 556 controls resulting in over 40,000 SNP genotypes. Significant differences in allele frequencies between cases and controls were observed for ID3 (inhibitor of DNA binding), p = 0.05, HPN (hepsin), p = 0.009, BCAS1 (breast carcinoma amplified sequence 1), p = 0.007, CAV2 (caveolin 2), p = 0.007, EMP3 (epithelial membrane protein 3), p < 0.0001, and MLH1 (mutL homolog 1), p < 0.0001. SNPs in three of these genes (BCAS1, EMP3 and MLH1) remained significant in an age-matched subsample.
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Affiliation(s)
- James K Burmester
- Department of Cancer Genetics, Marshfield Clinic Research Foundation, Wisc 54449, USA.
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242
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Abstract
Prostate cancer is a heterogeneous disease with multiple loci contributing to susceptibility. Traditionally, genome-wide scans using high-risk families have utilized stratification by number of affected individuals, family history of other cancers, or family age at diagnosis to improve genetic homogeneity. In addition to locus heterogeneity, for later onset diseases such as prostate cancer, a major limitation to mapping efforts is that key parental DNA samples are rarely available. The lack of available samples from upper generations reduces inheritance information, and as a result, the standard 10-cM genome scan does not provide full power to detect linkage. To increase the ability to find disease-associated loci, much denser genome-wide scans must be undertaken in multiple ethnic groups. In addition, new ways of defining homogenous subsets of families need to be developed.
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Affiliation(s)
- Elaine A Ostrander
- Division of Clinical Research1, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA.
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243
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Rökman A, Baffoe-Bonnie AB, Gillanders E, Fredriksson H, Autio V, Ikonen T, Gibbs KD, Jones M, Gildea D, Freas-Lutz D, Markey C, Matikainen MP, Koivisto PA, Tammela TLJ, Kallioniemi OP, Trent J, Bailey-Wilson JE, Schleutker J. Hereditary prostate cancer in Finland: fine-mapping validates 3p26 as a major predisposition locus. Hum Genet 2004; 116:43-50. [PMID: 15549392 DOI: 10.1007/s00439-004-1214-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Accepted: 10/04/2004] [Indexed: 10/26/2022]
Abstract
In a recent genome-wide linkage (GWL) analysis of Finnish families at high risk for prostate cancer, we found two novel putative susceptibility loci at 3p25-p26 and 11q14. Here, we report the fine-mapping of these two critical regions at high resolution with 39 microsatellite markers in 16 families, including multiplex families that were not used in the GWL scan. The maximum multipoint HLOD was 3.39 at 3p26 and 1.42 at 11q14. The highest LOD scores were seen around markers D3S1270 and D3S4559 (alpha=0.89), covering approximately two megabases. The two known genes in this region CHL1 (cell adhesion molecule with homology to L1CAM) and CNTN6 (contactin 6) were screened for exonic mutations in the families showing the strongest linkage, but no disease-segregating sequence variants were observed. The recombination map pointed to a region proximal to the area of best linkage, suggesting that more genes may need to be investigated as candidates. These results provide strong evidence for the existence of a prostate cancer susceptibility gene at 3p26 in Finnish prostate cancer families. This locus has not been strongly linked with hereditary prostate cancer in other populations. However, the mildly positive 3p LOD scores in a recent GWL analysis of patients from the United States suggest that the locus may also be important in other populations.
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Affiliation(s)
- Annika Rökman
- Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere 33014, Finland.
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244
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Horne BD, Camp NJ, Muhlestein JB, Cannon-Albright LA. Evidence for a Heritable Component in Death Resulting From Aortic and Mitral Valve Diseases. Circulation 2004; 110:3143-8. [PMID: 15520309 DOI: 10.1161/01.cir.0000147189.85636.c3] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background—
Cardiac valvular diseases contribute to >42 000 deaths yearly in the United States, but the role of genetics in these deaths is unknown. This study evaluated the familiality of death resulting from aortic, mitral, and all valvular diseases using a population-based genealogy linked to death records.
Methods and Results—
The Utah Population Database contains >2 million individual records with genealogy data and 250 000 linked death certificates. Nonrheumatic aortic (n=932), mitral (n=1165), and all valvular (n=2504) disease deaths and rheumatic heart disease deaths (n=4713) were studied. Familial relative risks (FRRs) were assessed for first- and second-degree relatives. Familiality was also evaluated with the genealogical index of familiality, which considers all relationships in the Utah Population Database. FRRs were increased only for mitral valve death in both first-degree (FRR, 2.55;
P
<0.0001) and second-degree (FRR, 1.67;
P
<0.0001) relatives. Genealogical index of familiality analysis showed significant excess relatedness for all groups (
P
<0.001). Genealogical index of familiality results (
P
<0.001) for early age at death cases showed higher mean relatedness, a common characteristic of heritable disorders. Excess familiality extended to distant relatives for mitral (second-degree relatives) and aortic (beyond second-degree relatives) valve death.
Conclusions—
Deaths resulting from nonrheumatic mitral and aortic diseases clustered among both close and distant relatives, especially among early age at death cases, suggesting a significant genetic component in death resulting from valvular diseases. Future studies should focus on gene discovery.
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Affiliation(s)
- Benjamin D Horne
- Genetic Epidemiology Division, Department of Medical Informatics, University of Utah, 391 Chipeta Way, Suite D, Salt Lake City, UT 84108-1266, USA.
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245
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Yokomizo A, Koga H, Kinukawa N, Tsukamoto T, Hirao Y, Akaza H, Mori M, Naito S. HPC2/ELAC2 polymorphism associated with Japanese sporadic prostate cancer. Prostate 2004; 61:248-52. [PMID: 15368467 DOI: 10.1002/pros.20107] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND HPC2/ELAC2 gene was identified by linkage analysis from familial prostate cancer (Pca) patients in USA. To determine the association of HPC2/ELAC2 gene with Japanese sporadic Pca, we performed a case-control study focused on two missense polymorphisms. METHODS We genotyped the two polymorphic sites of Ser217Leu and Ala541Thr in sporadic Japanese Pca patients (n = 285) and matched controls (n = 233). Controls were unrelated Japanese outpatients who had no history of any cancer and normal PSA level (less than 4.0 ng/ml). Statistical analyses were performed by Mann-Whitney's U-test, Fisher's exact test, and logistic regression analysis. RESULTS We observed a significantly higher frequency of the Thr allele at 541 polymorphic site in Pca patients (8.4%) compared to the control group (2.1%) (P = 0.0030, Odds Ratio (OR) = 4.02, 95% CI = 1.50-10.8). However, this SNP does not correlate with clinical stage, PSA level, Gleason score of biopsies or age at diagnosis. No association was identified at Ser217Leu polymorphic site. CONCLUSIONS Our results indicate that Thr allele at 541 in HPC2/ELAC2 has strong significance in the predisposition of sporadic Pca in Japan. This polymorphism can be useful to predict the personal Pca risk, which lead the effective screening of Pca.
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Affiliation(s)
- Akira Yokomizo
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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246
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GeneLink: a database to facilitate genetic studies of complex traits. BMC Genomics 2004; 5:81. [PMID: 15491493 PMCID: PMC526767 DOI: 10.1186/1471-2164-5-81] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2004] [Accepted: 10/18/2004] [Indexed: 11/10/2022] Open
Abstract
Background In contrast to gene-mapping studies of simple Mendelian disorders, genetic analyses of complex traits are far more challenging, and high quality data management systems are often critical to the success of these projects. To minimize the difficulties inherent in complex trait studies, we have developed GeneLink, a Web-accessible, password-protected Sybase database. Results GeneLink is a powerful tool for complex trait mapping, enabling genotypic data to be easily merged with pedigree and extensive phenotypic data. Specifically designed to facilitate large-scale (multi-center) genetic linkage or association studies, GeneLink securely and efficiently handles large amounts of data and provides additional features to facilitate data analysis by existing software packages and quality control. These include the ability to download chromosome-specific data files containing marker data in map order in various formats appropriate for downstream analyses (e.g., GAS and LINKAGE). Furthermore, an unlimited number of phenotypes (either qualitative or quantitative) can be stored and analyzed. Finally, GeneLink generates several quality assurance reports, including genotyping success rates of specified DNA samples or success and heterozygosity rates for specified markers. Conclusions GeneLink has already proven an invaluable tool for complex trait mapping studies and is discussed primarily in the context of our large, multi-center study of hereditary prostate cancer (HPC). GeneLink is freely available at .
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247
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Levinger L, Mörl M, Florentz C. Mitochondrial tRNA 3' end metabolism and human disease. Nucleic Acids Res 2004; 32:5430-41. [PMID: 15477393 PMCID: PMC524294 DOI: 10.1093/nar/gkh884] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Over 150 mutations in the mitochondrial genome have been shown to be associated with human disease. Remarkably, two-thirds of them are found in tRNA genes, which constitute only one-tenth of the mitochondrial genome. A total of 22 tRNAs punctuate the genome and are produced together with 11 mRNAs and 2 rRNAs from long polycistronic primary transcripts with almost no spacers. Pre-tRNAs thus require precise endonucleolytic excision. Furthermore, the CCA triplet which forms the 3' end of all tRNAs is not encoded, but must be synthesized by the CCA-adding enzyme after 3' end cleavage. Amino acid attachment to the CCA of mature tRNA is performed by aminoacyl-tRNA synthetases, which, like the preceding processing enzymes, are nuclear-encoded and imported into mitochondria. Here, we critically review the effectiveness and reliability of evidence obtained from reactions with in vitro transcripts that pathogenesis-associated mutant mitochondrial tRNAs can lead to deficiencies in tRNA 3' end metabolism (3' end cleavage, CCA addition and aminoacylation) toward an understanding of molecular mechanisms underlying human tRNA disorders. These defects probably contribute, individually and cumulatively, to the progression of human mitochondrial diseases.
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Affiliation(s)
- Louis Levinger
- York College/CUNY, 94-20 Guy R. Brewer Boulevard, Jamaica, NY 11451, USA.
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248
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Demuth I, Digweed M, Concannon P. Human SNM1B is required for normal cellular response to both DNA interstrand crosslink-inducing agents and ionizing radiation. Oncogene 2004; 23:8611-8. [PMID: 15467758 DOI: 10.1038/sj.onc.1207895] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
DNA interstrand crosslinks (ICLs) are critical lesions for the mammalian cell since they affect both DNA strands and block transcription and replication. The repair of ICLs in the mammalian cell involves components of different repair pathways such as nucleotide-excision repair and the double-strand break/homologous recombination repair pathways. However, the mechanistic details of mammalian ICL repair have not been fully delineated. We describe here the complete coding sequence and the genomic organization of hSNM1B, one of at least three human homologs of the Saccharomyces cerevisiae PSO2 gene. Depletion of hSNM1B by RNA interference rendered cells hypersensitive to ICL-inducing agents. This requirement for hSNM1B in the cellular response to ICL has been hypothesized before but never experimentally verified. In addition, siRNA knockdown of hSNM1B rendered cells sensitive to ionizing radiation, suggesting the possibility of hSNM1B involvement in homologous recombination repair of double-strand breaks arising as intermediates of ICL repair. Monoubiquitination of FANCD2, a key step in the FANC/BRCA pathway, is not affected in hSNM1B-depleted HeLa cells, indicating that hSNM1B is probably not a part of the Fanconi anemia core complex. Nonetheless, similarities in the phenotype of hSNM1B-depleted cells and cultured cells from patients suffering from Fanconi anemia make hSNM1B a candidate for one of the as yet unidentified Fanconi anemia genes not involved in monoubiquitination of FANCD2.
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Affiliation(s)
- Ilja Demuth
- Molecular Genetics Program, Benaroya Research Institute, Seattle, WA 98101-2795, USA
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249
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Edwards SM, Eeles RA. Unravelling the genetics of prostate cancer. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2004; 129C:65-73. [PMID: 15264274 DOI: 10.1002/ajmg.c.30027] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This review describes what is currently known about the genetics of prostate cancer. Traditionally, the genetics of a suspected inherited cancer predisposition have generally been thought of in terms of a single, high-risk gene with a dominant mode of inheritance. Such a gene might be observed in families, as has been documented in familial breast cancer (BRCA1/2), familial colorectal cancer (HNPCC), retinoblastoma (RB1), and Wilms tumor (WT1). This review investigates the evidence for the existence, first of familial prostate cancer, and second, for the presence of such a high-risk gene in those families by epidemiological and experimental approaches. Another current area of interest in prostate cancer is the investigation of the contribution of common lower penetrance genes to the disease. This alternative approach has become popular, as it raises the issue of frequently seen genetic variations such as single nucleotide polymorphisms (SNPs) having relevance to the risk of developing the disease. Finally, this article will explore the way forward, with emphasis on worldwide collaboration from teams attempting to find the genes responsible for the disease and investment in new technologies that will aid in their discovery.
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Affiliation(s)
- Stephen M Edwards
- Translational Cancer Genetics Team, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
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Watson RWG, Schalken JA. Future opportunities for the diagnosis and treatment of prostate cancer. Prostate Cancer Prostatic Dis 2004; 7 Suppl 1:S8-S13. [PMID: 15365576 DOI: 10.1038/sj.pcan.4500742] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Despite recent advances, current diagnostic tests and treatment of prostate cancer have limitations. In the last few years, numerous biomolecules have been investigated with the aim of improving diagnosis, including kallikrein-like proteases, growth factors and neuroendocrine markers. Analysis of susceptibility genes has also been a focus of attention. Extensive research into new therapeutic approaches is also underway, including targeting angiogenesis, immune regulation and stromal-epithelial interactions. Gene therapy, gene chip technology and proteomics have emerged as promising innovations. The host of novel diagnostic markers and therapies require appropriate validation, both phenotypical and functional. A further consideration is the need to re-evaluate clinical trial design and end points to facilitate progression of promising targets through the clinical trial process. Overall, the outlook for the treatment of prostate cancer looks promising, with any advances likely to require both a multimodal and multidisciplinary approach.
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Affiliation(s)
- R W G Watson
- Department of Surgery, Mater Misericordiae Hospital, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
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