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Johnson EO, Hancock DB, Gaddis NC, Levy JL, Page G, Novak SP, Glasheen C, Saccone NL, Rice JP, Moreau MP, Doheny KF, Romm JM, Brooks AI, Aouizerat BE, Bierut LJ, Kral AH. Novel genetic locus implicated for HIV-1 acquisition with putative regulatory links to HIV replication and infectivity: a genome-wide association study. PLoS One 2015; 10:e0118149. [PMID: 25786224 PMCID: PMC4364715 DOI: 10.1371/journal.pone.0118149] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 01/05/2015] [Indexed: 11/18/2022] Open
Abstract
Fifty percent of variability in HIV-1 susceptibility is attributable to host genetics. Thus identifying genetic associations is essential to understanding pathogenesis of HIV-1 and important for targeting drug development. To date, however, CCR5 remains the only gene conclusively associated with HIV acquisition. To identify novel host genetic determinants of HIV-1 acquisition, we conducted a genome-wide association study among a high-risk sample of 3,136 injection drug users (IDUs) from the Urban Health Study (UHS). In addition to being IDUs, HIV- controls were frequency-matched to cases on environmental exposures to enhance detection of genetic effects. We tested independent replication in the Women’s Interagency HIV Study (N=2,533). We also examined publicly available gene expression data to link SNPs associated with HIV acquisition to known mechanisms affecting HIV replication/infectivity. Analysis of the UHS nominated eight genetic regions for replication testing. SNP rs4878712 in FRMPD1 met multiple testing correction for independent replication (P=1.38x10-4), although the UHS-WIHS meta-analysis p-value did not reach genome-wide significance (P=4.47x10-7 vs. P<5.0x10-8) Gene expression analyses provided promising biological support for the protective G allele at rs4878712 lowering risk of HIV: (1) the G allele was associated with reduced expression of FBXO10 (r=-0.49, P=6.9x10-5); (2) FBXO10 is a component of the Skp1-Cul1-F-box protein E3 ubiquitin ligase complex that targets Bcl-2 protein for degradation; (3) lower FBXO10 expression was associated with higher BCL2 expression (r=-0.49, P=8x10-5); (4) higher basal levels of Bcl-2 are known to reduce HIV replication and infectivity in human and animal in vitro studies. These results suggest new potential biological pathways by which host genetics affect susceptibility to HIV upon exposure for follow-up in subsequent studies.
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Affiliation(s)
- Eric O. Johnson
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
- * E-mail:
| | - Dana B. Hancock
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Nathan C. Gaddis
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Joshua L. Levy
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Grier Page
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Scott P. Novak
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Cristie Glasheen
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Nancy L. Saccone
- Washington University School of Medicine, St. Louis, MO, United States of America
| | - John P. Rice
- Washington University School of Medicine, St. Louis, MO, United States of America
| | - Michael P. Moreau
- Rutgers University Cell and DNA Repository (RUCDR), Piscataway, NJ, United States of America
| | - Kimberly F. Doheny
- Center for Inherited Disease Research (CIDR), Johns Hopkins University, Baltimore, MD, United States of America
| | - Jane M. Romm
- Center for Inherited Disease Research (CIDR), Johns Hopkins University, Baltimore, MD, United States of America
| | - Andrew I. Brooks
- Rutgers University Cell and DNA Repository (RUCDR), Piscataway, NJ, United States of America
| | - Bradley E. Aouizerat
- School of Nursing, University of California San Francisco, San Francisco, CA, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, United States of America
| | - Laura J. Bierut
- Washington University School of Medicine, St. Louis, MO, United States of America
| | - Alex H. Kral
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
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3
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Shenje LT, Andersen P, Halushka MK, Lui C, Fernandez L, Collin GB, Amat-Alarcon N, Meschino W, Cutz E, Chang K, Yonescu R, Batista DAS, Chen Y, Chelko S, Crosson JE, Scheel J, Vricella L, Craig BD, Marosy BA, Mohr DW, Hetrick KN, Romm JM, Scott AF, Valle D, Naggert JK, Kwon C, Doheny KF, Judge DP. Mutations in Alström protein impair terminal differentiation of cardiomyocytes. Nat Commun 2014; 5:3416. [PMID: 24595103 PMCID: PMC3992616 DOI: 10.1038/ncomms4416] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 02/10/2014] [Indexed: 02/08/2023] Open
Abstract
Cardiomyocyte cell division and replication in mammals proceed through embryonic development and abruptly decline soon after birth. The process governing cardiomyocyte cell cycle arrest is poorly understood. Here we carry out whole exome sequencing in an infant with evidence of persistent postnatal cardiomyocyte replication to determine the genetic risk factors. We identify compound heterozygous ALMS1 mutations in the proband, and confirm their presence in her affected sibling, one copy inherited from each heterozygous parent. Next, we recognise homozygous or compound heterozygous truncating mutations in ALMS1 in four other children with high levels of postnatal cardiomyocyte proliferation. Alms1 mRNA knockdown increases multiple markers of proliferation in cardiomyocytes, the percentage of cardiomyocytes in G2/M phases, and the number of cardiomyocytes by 10% in cultured cells. Homozygous Alms1-mutant mice have increased cardiomyocyte proliferation at two weeks postnatal compared to wild-type littermates. We conclude that deficiency of Alström protein impairs postnatal cardiomyocyte cell cycle arrest.
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Affiliation(s)
- Lincoln T Shenje
- 1] Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA [2]
| | - Peter Andersen
- 1] Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA [2]
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Cecillia Lui
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Laviel Fernandez
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | | | - Nuria Amat-Alarcon
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Wendy Meschino
- North York General Hospital, Toronto, Ontario, Canada M2K 1E1
| | - Ernest Cutz
- Division of Pathology, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | - Kenneth Chang
- 1] Division of Pathology, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8 [2] KK Women's and Children's Hospital and Duke-NUS Graduate Medical School, Singapore 229899, Singapore
| | - Raluca Yonescu
- 1] Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA [2] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Denise A S Batista
- 1] Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA [2] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Yan Chen
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Stephen Chelko
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Jane E Crosson
- Division of Cardiology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Janet Scheel
- Division of Cardiology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Luca Vricella
- Division of Cardiothoracic Surgery, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Brian D Craig
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Beth A Marosy
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - David W Mohr
- 1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA [2] High Throughput Sequencing Facility, Genetic Resources Core Facility, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Kurt N Hetrick
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Jane M Romm
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Alan F Scott
- 1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA [2] High Throughput Sequencing Facility, Genetic Resources Core Facility, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | | | - Chulan Kwon
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Kimberly F Doheny
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Daniel P Judge
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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5
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Iacobuzio-Donahue CA, van der Heijden MS, Baumgartner MR, Troup WJ, Romm JM, Doheny K, Pugh E, Yeo CJ, Goggins MG, Hruban RH, Kern SE. Large-scale allelotype of pancreaticobiliary carcinoma provides quantitative estimates of genome-wide allelic loss. Cancer Res 2004; 64:871-5. [PMID: 14871814 DOI: 10.1158/0008-5472.can-03-2756] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Studies of the allelotype of human cancers have provided valuable insights into those chromosomes targeted for genetic inactivation during tumorigenesis. We present the comprehensive allelotype of 82 xenografted pancreatic or biliary cancers using 386 microsatellite markers and spanning the entire genome at an average coverage of 10 cM. Allelic losses were nonrandomly distributed across the genome and most prevalent for chromosome arms 9p, 17p, and 18q (>60%), sites of the known tumor suppressor genes CDKN2A, TP53, and MADH4. Moderate rates of loss (at any one locus) were noted for chromosome arms 3p, 6q, 8p, 17q, 18p, 21q, and 22q (40-60%). A mapping of individual loci of allelic loss revealed 11 "hot spots" of loss of heterozygosity (>30%) in addition to loci near known tumor suppressor genes, corresponding to 3p, 4q, 5q, 6q, 8p, 12q, 14q, 21q, 22q, and the X chromosome. The average genomic fractional allelic loss was 15.3% of all tested markers for the 82 xenografted cancers, with allelic loss affecting as little as 1.5% to as much as 32.1% of tested loci, a remarkable 20-fold range. We determined the chromosome location (in cM) of each of the 386 markers used based on mapping data available from the National Center for Biotechnology Information, and we provide the first distance-based estimates of chromosome material lost in a human epithelial cancer. Specifically, we found that the cumulative size of allelic losses ranged from 58 to 1160 cM, with an average loss of 561.32 cM/tumor. We compared the genomic fractional allelic loss of each xenografted cancer with known clinicopathological features for each patient and found a significant correlation with smoking status (P < 0.01). These findings offer new loci for investigation of the genetic alterations common to pancreaticobiliary cancers and aid the understanding of mechanisms of allelic loss in human carcinogenesis.
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