1
|
Petersen MI, Carignano HA, Suarez Archilla G, Caffaro ME, Alvarez I, Miretti MM, Trono K. Expression-based analysis of genes related to single nucleotide polymorphism hits associated with bovine leukemia virus proviral load in Argentinean dairy cattle. J Dairy Sci 2020; 104:1993-2007. [PMID: 33246606 DOI: 10.3168/jds.2020-18924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/29/2020] [Indexed: 12/29/2022]
Abstract
In dairy cattle infected with bovine leukemia virus (BLV), the proviral load (PVL) level is directly related to the viral transmission from infected animals to their healthy herdmates. Two contrasting phenotypic groups can be identified when assessing PVL in peripheral blood of infected cows. A large number of reports point to bovine genetic variants (single nucleotide polymorphisms) as one of the key determinants underlying PVL level. However, biological mechanisms driving BLV PVL profiles and infection progression in cattle have not yet been elucidated. In this study, we evaluated whether a set of candidate genes affecting BLV PVL level according to whole genome association studies are differentially expressed in peripheral blood mononuclear cells derived from phenotypically contrasting groups of BLV-infected cows. During a 10-mo-long sampling scheme, 129 Holstein cows were phenotyped measuring anti-BLV antibody levels, PVL quantification, and white blood cell subpopulation counts. Finally, the expression of 8 genes (BOLA-DRB3, PRRC2A, ABT1, TNF, BAG6, BOLA-A, LY6G5B, and IER3) located within the bovine major histocompatibility complex region harboring whole genome association SNP hits was evaluated in 2 phenotypic groups: high PVL (n = 7) and low PVL (n = 8). The log2 initial fluorescence value (N0) transformed mean expression values for the ABT1 transcription factor were statistically different in high- and low-PVL groups, showing a higher expression of the ABT1 gene in low-PVL cows. The PRRC2A and IER3 genes had a significant positive (correlation coefficient = 0.61) and negative (correlation coefficient = -0.45) correlation with the lymphocyte counts, respectively. Additionally, the relationships between gene expression values and lymphocyte counts were modeled using linear regressions. Lymphocyte levels in infected cows were better explained (coefficient of determination = 0.56) when fitted a multiple linear regression model using both PRRC2A and IER3 expression values as independent variables. The present study showed evidence of differential gene expression between contrasting BLV infection phenotypes. These genes have not been previously related to BLV pathobiology. This valuable information represents a step forward in understanding the BLV biology and the immune response of naturally infected cows under a commercial milk production system. Efforts to elucidate biological mechanisms leading to BLV infection progression in cows are valuable for BLV control programs. Further studies integrating genotypic data, global transcriptome analysis, and BLV progression phenotypes are needed to better understand the BLV-host interaction.
Collapse
Affiliation(s)
- M I Petersen
- Instituto de Virología e Innovaciones Tecnológicas, Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas, B1686 Hurlingham, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina
| | - H A Carignano
- Instituto de Virología e Innovaciones Tecnológicas, Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas, B1686 Hurlingham, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Genética, Instituto Nacional de Tecnología Agropecuaria, B1686 Hurlingham, Argentina.
| | - G Suarez Archilla
- Estación Experimental Agropecuaria Rafaela, Instituto Nacional de Tecnología Agropecuaria, S2300 Rafaela, Argentina
| | - M E Caffaro
- Instituto de Genética, Instituto Nacional de Tecnología Agropecuaria, B1686 Hurlingham, Argentina
| | - I Alvarez
- Instituto de Virología e Innovaciones Tecnológicas, Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas, B1686 Hurlingham, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina
| | - M M Miretti
- Consejo Nacional de Investigaciones Científicas y Técnicas, C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina; Grupo de Investigación en Genética Aplicada, Instituto de Biología Subtropical, FCEQyN, Universidad Nacional de Misiones, N3300 Posadas, Argentina
| | - K Trono
- Instituto de Virología e Innovaciones Tecnológicas, Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas, B1686 Hurlingham, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
2
|
Huang Q, Chan KY, Tobey IG, Chan YA, Poterba T, Boutros CL, Balazs AB, Daneman R, Bloom JM, Seed C, Deverman BE. Delivering genes across the blood-brain barrier: LY6A, a novel cellular receptor for AAV-PHP.B capsids. PLoS One 2019; 14:e0225206. [PMID: 31725765 PMCID: PMC6855452 DOI: 10.1371/journal.pone.0225206] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/29/2019] [Indexed: 12/26/2022] Open
Abstract
The engineered AAV-PHP.B family of adeno-associated virus efficiently delivers genes throughout the mouse central nervous system. To guide their application across disease models, and to inspire the development of translational gene therapy vectors for targeting neurological diseases in humans, we sought to elucidate the host factors responsible for the CNS tropism of the AAV-PHP.B vectors. Leveraging CNS tropism differences across 13 mouse strains, we systematically determined a set of genetic variants that segregate with the permissivity phenotype, and rapidly identified LY6A as an essential receptor for the AAV-PHP.B vectors. Interfering with LY6A by CRISPR/Cas9-mediated Ly6a disruption or with blocking antibodies reduced transduction of mouse brain endothelial cells by AAV-PHP.eB, while ectopic expression of Ly6a increased AAV-PHP.eB transduction of HEK293T and CHO cells by 30-fold or more. Importantly, we demonstrate that this newly discovered mode of AAV binding and transduction can occur independently of other known AAV receptors. These findings illuminate the previously reported species- and strain-specific tropism characteristics of the AAV-PHP.B vectors and inform ongoing efforts to develop next-generation AAV vehicles for human CNS gene therapy.
Collapse
Affiliation(s)
- Qin Huang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Ken Y. Chan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Isabelle G. Tobey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Yujia Alina Chan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Tim Poterba
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Christine L. Boutros
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States of America
| | - Alejandro B. Balazs
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States of America
| | - Richard Daneman
- Departments of Neurosciences and Pharmacology, University of California, San Diego, La Jolla, CA, United States of America
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States of America
| | - Jonathan M. Bloom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Cotton Seed
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Benjamin E. Deverman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- * E-mail:
| |
Collapse
|
3
|
Yu J, Murthy V, Liu SL. Relating GPI-Anchored Ly6 Proteins uPAR and CD59 to Viral Infection. Viruses 2019; 11:E1060. [PMID: 31739586 PMCID: PMC6893729 DOI: 10.3390/v11111060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/10/2019] [Accepted: 11/12/2019] [Indexed: 12/30/2022] Open
Abstract
The Ly6 (lymphocyte antigen-6)/uPAR (urokinase-type plasminogen activator receptor) superfamily protein is a group of molecules that share limited sequence homology but conserved three-fingered structures. Despite diverse cellular functions, such as in regulating host immunity, cell adhesion, and migration, the physiological roles of these factors in vivo remain poorly characterized. Notably, increasing research has focused on the interplays between Ly6/uPAR proteins and viral pathogens, the results of which have provided new insight into viral entry and virus-host interactions. While LY6E (lymphocyte antigen 6 family member E), one key member of the Ly6E/uPAR-family proteins, has been extensively studied, other members have not been well characterized. Here, we summarize current knowledge of Ly6/uPAR proteins related to viral infection, with a focus on uPAR and CD59. Our goal is to provide an up-to-date view of the Ly6/uPAR-family proteins and associated virus-host interaction and viral pathogenesis.
Collapse
Affiliation(s)
- Jingyou Yu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (J.Y.); (V.M.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Vaibhav Murthy
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (J.Y.); (V.M.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (J.Y.); (V.M.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
4
|
Emerging Role of LY6E in Virus-Host Interactions. Viruses 2019; 11:v11111020. [PMID: 31684192 PMCID: PMC6893646 DOI: 10.3390/v11111020] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 12/19/2022] Open
Abstract
As a canonical lymphocyte antigen-6/urokinase-type plasminogen activator receptor Ly6/uPAR family protein, lymphocyte antigen 6 complex, locus E (LY6E), plays important roles in immunological regulation, T cell physiology, and oncogenesis. Emerging evidence indicates that LY6E is also involved in the modulation of viral infection. Consequently, viral infection and associated pathogenesis have been associated with altered LY6E gene expression. The interaction between viruses and the host immune system has offered insights into the biology of LY6E. In this review, we summarize the current knowledge of LY6E in the context of viral infection, particularly viral entry.
Collapse
|
5
|
Upadhyay G. Emerging Role of Lymphocyte Antigen-6 Family of Genes in Cancer and Immune Cells. Front Immunol 2019; 10:819. [PMID: 31068932 PMCID: PMC6491625 DOI: 10.3389/fimmu.2019.00819] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 03/27/2019] [Indexed: 12/14/2022] Open
Abstract
Stem Cell Antigen-1 (Sca-1/Ly6A) was the first identified member of the Lymphocyte antigen-6 (Ly6) gene family. Sca-1 serves as a marker of cancer stem cells and tissue resident stem cells in mice. The Sca-1 gene is located on mouse chromosome 15. While a direct homolog of Sca-1 in humans is missing, human chromosome 8—the syntenic region to mouse chromosome 15—harbors several genes containing the characteristic domain known as LU domain. The function of the LU domain in human LY6 gene family is not yet defined. The LY6 gene family proteins are present on human chromosome 6, 8, 11, and 19. The most interesting of these genes are located on chromosome 8q24.3, a frequently amplified locus in human cancer. Human LY6 genes represent novel biomarkers for poor cancer prognosis and are required for cancer progression in addition to playing an important role in immune escape. Although the mechanism associated with these phenotype is not yet clear, it is timely to review the current literature in order to address the critical need for future advancements in this field. This review will summarize recent findings which describe the role of human LY6 genes—LY6D, LY6E, LY6H, LY6K, PSCA, LYPD2, SLURP1, GML, GPIHBP1, and LYNX1; and their orthologs in mice at chromosome 15.
Collapse
Affiliation(s)
- Geeta Upadhyay
- Department of Pathology, John P. Murtha Cancer Center, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| |
Collapse
|
6
|
CD4-Dependent Modulation of HIV-1 Entry by LY6E. J Virol 2019; 93:JVI.01866-18. [PMID: 30674630 DOI: 10.1128/jvi.01866-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/16/2019] [Indexed: 01/06/2023] Open
Abstract
Lymphocyte antigen 6E (LY6E) is a GPI-anchored, interferon-inducible protein that has been shown to modulate viral infection in a cell type-dependent manner. Our recent work showed that LY6E promotes HIV-1 infection in some high-CD4-expressing cells, including human peripheral blood mononuclear cells (PBMCs) and the SupT1 cell line. In this work, we provide evidence that LY6E inhibits HIV-1 entry and spread in low-CD4-expressing Jurkat cells and human monocyte-derived macrophages (MDMs) through downregulation of the viral receptor CD4. We found that knockdown of LY6E in Jurkat cells and MDMs increases HIV-1 infection, yet overexpression of LY6E in Jurkat cells inhibits HIV-1 entry and replication. LY6E was found to be colocalized with CD4 on the plasma membrane of Jurkat cells and MDMs and enhances CD4 internalization. We artificially manipulated the CD4 level in Jurkat and SupT1 cells and found that overexpression of CD4 in Jurkat cells overcomes the inhibitory effect of LY6E; conversely, blocking the function of CD4 in SupT1 with a neutralizing antibody eliminates the enhancement of LY6E on HIV-1 entry. The CD4-dependent inhibitory phenotype of LY6E in low-CD4-expressing human MDMs can be recapitulated for a panel of transmitted founder viruses and laboratory-adapted HIV-1 strains. Given that HIV-1 can target low-CD4-expressing cells during acute infection yet replicates efficiently in high-CD4-expressing T cells at the late stage of disease, our observation that LY6E differentially modulates HIV-1 replication in a CD4-dependent manner has implications for understanding the complex roles of interferon (IFN)-induced proteins in AIDS pathogenesis.IMPORTANCE The role of IFN-induced genes (ISGs) in viral infection remains incompletely understood. While most ISGs are antiviral, some ISGs have been shown to promote viral infection, including HIV-1 infection. We previously showed that IFN-inducible LY6E protein promotes HIV-1 infection in human PMBCs and high-CD4-expressing SupT1 cells. Here we found that LY6E inhibits HIV-1 entry and replication in low-CD4-expressing MDMs and Jurkat cells. Mechanistically, we demonstrated that LY6E downregulates the cell surface receptor CD4, thus impairing the virus binding to target cells. This is in contrast to the situation of high-CD4-expressing cells, where LY6E predominantly promotes viral membrane fusion. The opposing role of IFN-inducible LY6E in modulating HIV-1 infection highlights the complex roles of ISGs in viral infection and viral pathogenesis.
Collapse
|
7
|
Bibert S, Wójtowicz A, Taffé P, Tarr PE, Bernasconi E, Furrer H, Günthard HF, Hoffmann M, Kaiser L, Osthoff M, Fellay J, Cavassini M, Bochud PY. Interferon lambda 3/4 polymorphisms are associated with AIDS-related Kaposi's sarcoma. AIDS 2018; 32:2759-2765. [PMID: 30234607 DOI: 10.1097/qad.0000000000002004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Kaposi's sarcoma, the most common AIDS-related cancer, represents a major public concern in resource-limited countries. Single nucleotide polymorphisms within the Interferon lambda 3/4 region (IFNL3/4) determine the expression, function of IFNL4, and influence the clinical course of an increasing number of viral infections. OBJECTIVES To analyze whether IFNL3/4 variants are associated with susceptibility to AIDS-related Kaposi's sarcoma among MSM enrolled in the Swiss HIV Cohort Study (SHCS). METHODS The risk of developing Kaposi's sarcoma according to the carriage of IFNL3/4 SNPs rs8099917 and rs12980275 and their haplotypic combinations was assessed by using cumulative incidence curves and Cox regression models, accounting for relevant covariables. RESULTS Kaposi's sarcoma was diagnosed in 221 of 2558 MSM Caucasian SHCS participants. Both rs12980275 and rs8099917 were associated with an increased risk of Kaposi's sarcoma (cumulative incidence 15 versus 10%, P = 0.01 and 16 versus 10%, P = 0.009, respectively). Diplotypes predicted to produce the active P70 form (cumulative incidence 16 versus 10%, P = 0.01) but not the less active S70 (cumulative incidence 11 versus 10%, P = 0.7) form of IFNL4 were associated with an increased risk of Kaposi's sarcoma, compared with those predicted not to produce IFNL4. The associations remained significant in a multivariate Cox regression model after adjustment for age at infection, combination antiretroviral therapy, median CD4+ T-cell count nadir and CD4+ slopes (hazard ratio 1.42, 95% confidence interval 1.06-1.89, P = 0.02 for IFLN P70 versus no IFNL4). CONCLUSION This study reports for the first time an association between IFNL3/4 polymorphisms and susceptibility to AIDS-related Kaposi's sarcoma.
Collapse
Affiliation(s)
| | | | - Patrick Taffé
- Institute for Social and Preventive Medicine, University (IUMSP), Lausanne University Hospital, Lausanne
| | - Philip E Tarr
- Department of Medicine, Kantonspital Baselland, University of Basel, Bruderholz
| | - Enos Bernasconi
- Division of Infectious diseases, Regional hospital of Lugano, Lugano
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich
- Institute of Medical Virology, University of Zurich, Zurich
| | - Matthias Hoffmann
- Division of Infectious Diseases and Hospital Epidemiology, Department of Internal Medicine, Cantonal Hospital St. Gallen, St. Gallen
| | - Laurent Kaiser
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospital of Geneva and Medical School, University of Geneva, Geneva
| | - Michael Osthoff
- Division of Infectious Diseases and Hospital Epidemiology and Department of Internal Medicine, University Hospital Basel, Basel
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne
- Precision Medicine unit, Lausanne University Hospital, Lausanne, Switzerland
| | | | | |
Collapse
|
8
|
Mar KB, Rinkenberger NR, Boys IN, Eitson JL, McDougal MB, Richardson RB, Schoggins JW. LY6E mediates an evolutionarily conserved enhancement of virus infection by targeting a late entry step. Nat Commun 2018; 9:3603. [PMID: 30190477 PMCID: PMC6127192 DOI: 10.1038/s41467-018-06000-y] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 08/03/2018] [Indexed: 01/07/2023] Open
Abstract
Interferons (IFNs) contribute to cell-intrinsic antiviral immunity by inducing hundreds of interferon-stimulated genes (ISGs). In a screen to identify antiviral ISGs, we unexpectedly found that LY6E, a member of the LY6/uPAR family, enhanced viral infection. Here, we show that viral enhancement by ectopically expressed LY6E extends to several cellular backgrounds and affects multiple RNA viruses. LY6E does not impair IFN antiviral activity or signaling, but rather promotes viral entry. Using influenza A virus as a model, we narrow the enhancing effect of LY6E to uncoating after endosomal escape. Diverse mammalian orthologs of LY6E also enhance viral infectivity, indicating evolutionary conservation of function. By structure-function analyses, we identify a single amino acid in a predicted loop region that is essential for viral enhancement. Our study suggests that LY6E belongs to a class of IFN-inducible host factors that enhance viral infectivity without suppressing IFN antiviral activity. The interferon-induced gene LY6E increases virus infection, but the underlying mechanism is poorly understood. Here, Mar et al. show that LY6E enhances uncoating of influenza A virus after endosomal escape and that viral enhancement by LY6E is conserved across evolution.
Collapse
Affiliation(s)
- Katrina B Mar
- Department of Microbiology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, 75390, TX, USA
| | - Nicholas R Rinkenberger
- Department of Microbiology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, 75390, TX, USA
| | - Ian N Boys
- Department of Microbiology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, 75390, TX, USA
| | - Jennifer L Eitson
- Department of Microbiology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, 75390, TX, USA
| | - Matthew B McDougal
- Department of Microbiology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, 75390, TX, USA
| | - R Blake Richardson
- Department of Microbiology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, 75390, TX, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, 75390, TX, USA.
| |
Collapse
|
9
|
Carignano HA, Roldan DL, Beribe MJ, Raschia MA, Amadio A, Nani JP, Gutierrez G, Alvarez I, Trono K, Poli MA, Miretti MM. Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle. BMC Genomics 2018; 19:142. [PMID: 29439661 PMCID: PMC5812220 DOI: 10.1186/s12864-018-4523-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 02/01/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Bovine leukemia virus (BLV) infection is omnipresent in dairy herds causing direct economic losses due to trade restrictions and lymphosarcoma-related deaths. Milk production drops and increase in the culling rate are also relevant and usually neglected. The BLV provirus persists throughout a lifetime and an inter-individual variation is observed in the level of infection (LI) in vivo. High LI is strongly correlated with disease progression and BLV transmission among herd mates. In a context of high prevalence, classical control strategies are economically prohibitive. Alternatively, host genomics studies aiming to dissect loci associated with LI are potentially useful tools for genetic selection programs tending to abrogate the viral spreading. The LI was measured through the proviral load (PVL) set-point and white blood cells (WBC) counts. The goals of this work were to gain insight into the contribution of SNPs (bovine 50KSNP panel) on LI variability and to identify genomics regions underlying this trait. RESULTS We quantified anti-p24 response and total leukocytes count in peripheral blood from 1800 cows and used these to select 800 individuals with extreme phenotypes in WBCs and PVL. Two case-control genomic association studies using linear mixed models (LMMs) considering population stratification were performed. The proportion of the variance captured by all QC-passed SNPs represented 0.63 (SE ± 0.14) of the phenotypic variance for PVL and 0.56 (SE ± 0.15) for WBCs. Overall, significant associations (Bonferroni's corrected -log10p > 5.94) were shared for both phenotypes by 24 SNPs within the Bovine MHC. Founder haplotypes were used to measure the linkage disequilibrium (LD) extent (r2 = 0.22 ± 0.27 at inter-SNP distance of 25-50 kb). The SNPs and LD blocks indicated genes potentially associated with LI in infected cows: i.e. relevant immune response related genes (DQA1, DRB3, BOLA-A, LTA, LTB, TNF, IER3, GRP111, CRISP1), several genes involved in cell cytoskeletal reorganization (CD2AP, PKHD1, FLOT1, TUBB5) and modelling of the extracellular matrix (TRAM2, TNXB). Host transcription factors (TFs) were also highlighted (TFAP2D; ABT1, GCM1, PRRC2A). CONCLUSIONS Data obtained represent a step forward to understand the biology of BLV-bovine interaction, and provide genetic information potentially applicable to selective breeding programs.
Collapse
Affiliation(s)
- Hugo A. Carignano
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Genética, B1686 Hurlingham, Argentina
| | - Dana L. Roldan
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Genética, B1686 Hurlingham, Argentina
| | - María J. Beribe
- Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino, B2700 Pergamino, Argentina
| | - María A. Raschia
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Genética, B1686 Hurlingham, Argentina
| | - Ariel Amadio
- Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela, S2300, Rafaela, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina
| | - Juan P. Nani
- Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela, S2300, Rafaela, Argentina
| | - Gerónimo Gutierrez
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Virología, B686 Hurlingham, Argentina
| | - Irene Alvarez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Virología, B686 Hurlingham, Argentina
| | - Karina Trono
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Virología, B686 Hurlingham, Argentina
| | - Mario A. Poli
- Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA). Instituto de Genética, B1686 Hurlingham, Argentina
| | - Marcos M. Miretti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1033AAJ Ciudad Autónoma de Buenos Aires, Argentina
- Grupo de Investigación en Genética Aplicada, Instituto de Biología Subtropical (GIGA - IBS), Universidad Nacional de Misiones, N3300 Posadas, Argentina
| |
Collapse
|
10
|
Mackelprang RD, Bamshad MJ, Chong JX, Hou X, Buckingham KJ, Shively K, deBruyn G, Mugo NR, Mullins JI, McElrath MJ, Baeten JM, Celum C, Emond MJ, Lingappa JR. Whole genome sequencing of extreme phenotypes identifies variants in CD101 and UBE2V1 associated with increased risk of sexually acquired HIV-1. PLoS Pathog 2017; 13:e1006703. [PMID: 29108000 PMCID: PMC5690691 DOI: 10.1371/journal.ppat.1006703] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 11/16/2017] [Accepted: 10/19/2017] [Indexed: 12/27/2022] Open
Abstract
Host genetic variation modifying HIV-1 acquisition risk can inform development of HIV-1 prevention strategies. However, associations between rare or intermediate-frequency variants and HIV-1 acquisition are not well studied. We tested for the association between variation in genic regions and extreme HIV-1 acquisition phenotypes in 100 sub-Saharan Africans with whole genome sequencing data. Missense variants in immunoglobulin-like regions of CD101 and, among women, one missense/5' UTR variant in UBE2V1, were associated with increased HIV-1 acquisition risk (p = 1.9x10-4 and p = 3.7x10-3, respectively, for replication). Both of these genes are known to impact host inflammatory pathways. Effect sizes increased with exposure to HIV-1 after adjusting for the independent effect of increasing exposure on acquisition risk. TRIAL REGISTRATION ClinicalTrials.gov NCT00194519; NCT00557245.
Collapse
Affiliation(s)
- Romel D. Mackelprang
- Department of Global Health, University of Washington, Seattle, United States of America
| | - Michael J. Bamshad
- Department of Pediatrics, University of Washington, Seattle, United States of America
- Department of Genome Sciences, University of Washington, Seattle, United States of America
| | - Jessica X. Chong
- Department of Pediatrics, University of Washington, Seattle, United States of America
| | - Xuanlin Hou
- Department of Global Health, University of Washington, Seattle, United States of America
| | - Kati J. Buckingham
- Department of Pediatrics, University of Washington, Seattle, United States of America
| | - Kathryn Shively
- Department of Pediatrics, University of Washington, Seattle, United States of America
| | - Guy deBruyn
- Perinatal HIV Research Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Nelly R. Mugo
- Department of Global Health, University of Washington, Seattle, United States of America
- Partners in Health Research and Development, Kenya Medical Research Institute, Thika, Kenya
| | - James I. Mullins
- Department of Global Health, University of Washington, Seattle, United States of America
- Department of Microbiology, University of Washington, Seattle, United States of America
- Department of Medicine, University of Washington, Seattle, United States of America
| | - M. Juliana McElrath
- Department of Medicine, University of Washington, Seattle, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Jared M. Baeten
- Department of Global Health, University of Washington, Seattle, United States of America
- Department of Medicine, University of Washington, Seattle, United States of America
- Department of Epidemiology, University of Washington, Seattle, United States of America
| | - Connie Celum
- Department of Global Health, University of Washington, Seattle, United States of America
- Department of Medicine, University of Washington, Seattle, United States of America
- Department of Epidemiology, University of Washington, Seattle, United States of America
| | - Mary J. Emond
- Department of Biostatistics, University of Washington, Seattle, United States of America
| | - Jairam R. Lingappa
- Department of Global Health, University of Washington, Seattle, United States of America
- Department of Pediatrics, University of Washington, Seattle, United States of America
- Department of Epidemiology, University of Washington, Seattle, United States of America
- * E-mail:
| | | |
Collapse
|
11
|
Gaspar L, Howald C, Popadin K, Maier B, Mauvoisin D, Moriggi E, Gutierrez-Arcelus M, Falconnet E, Borel C, Kunz D, Kramer A, Gachon F, Dermitzakis ET, Antonarakis SE, Brown SA. The genomic landscape of human cellular circadian variation points to a novel role for the signalosome. eLife 2017; 6:e24994. [PMID: 28869038 PMCID: PMC5601996 DOI: 10.7554/elife.24994] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 09/01/2017] [Indexed: 11/18/2022] Open
Abstract
The importance of natural gene expression variation for human behavior is undisputed, but its impact on circadian physiology remains mostly unexplored. Using umbilical cord fibroblasts, we have determined by genome-wide association how common genetic variation impacts upon cellular circadian function. Gene set enrichment points to differences in protein catabolism as one major source of clock variation in humans. The two most significant alleles regulated expression of COPS7B, a subunit of the COP9 signalosome. We further show that the signalosome complex is imported into the nucleus in timed fashion to stabilize the essential circadian protein BMAL1, a novel mechanism to oppose its proteasome-mediated degradation. Thus, circadian clock properties depend in part upon a genetically-encoded competition between stabilizing and destabilizing forces, and genetic alterations in these mechanisms provide one explanation for human chronotype.
Collapse
Affiliation(s)
- Ludmila Gaspar
- Institute of Pharmacology and ToxicologyUniversity of ZurichZurichSwitzerland
| | - Cedric Howald
- Department of Genetic Medicine and DevelopmentUniversity of GenevaGenevaSwitzerland
- Institute of Genetics and Genomics in GenevaUniversity of GenevaGenevaSwitzerland
| | - Konstantin Popadin
- Department of Genetic Medicine and DevelopmentUniversity of GenevaGenevaSwitzerland
| | - Bert Maier
- Charité–UniversitätsmedizinLaboratory of ChronobiologyBerlinGermany
| | - Daniel Mauvoisin
- Department of Pharmacology and ToxicologyUniversity of LausanneLausanneSwitzerland
| | - Ermanno Moriggi
- Institute of Pharmacology and ToxicologyUniversity of ZurichZurichSwitzerland
| | - Maria Gutierrez-Arcelus
- Department of Genetic Medicine and DevelopmentUniversity of GenevaGenevaSwitzerland
- Institute of Genetics and Genomics in GenevaUniversity of GenevaGenevaSwitzerland
| | - Emilie Falconnet
- Department of Genetic Medicine and DevelopmentUniversity of GenevaGenevaSwitzerland
- Institute of Genetics and Genomics in GenevaUniversity of GenevaGenevaSwitzerland
| | - Christelle Borel
- Department of Genetic Medicine and DevelopmentUniversity of GenevaGenevaSwitzerland
- Institute of Genetics and Genomics in GenevaUniversity of GenevaGenevaSwitzerland
| | - Dieter Kunz
- Institute of Physiology, Charité-Universitätsmedizin Berlin, Working Group Sleep Research & Clinical ChronobiologyBerlinGermany
| | - Achim Kramer
- Charité–UniversitätsmedizinLaboratory of ChronobiologyBerlinGermany
| | - Frederic Gachon
- Department of Pharmacology and ToxicologyUniversity of LausanneLausanneSwitzerland
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and DevelopmentUniversity of GenevaGenevaSwitzerland
- Institute of Genetics and Genomics in GenevaUniversity of GenevaGenevaSwitzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and DevelopmentUniversity of GenevaGenevaSwitzerland
- Institute of Genetics and Genomics in GenevaUniversity of GenevaGenevaSwitzerland
| | - Steven A Brown
- Institute of Pharmacology and ToxicologyUniversity of ZurichZurichSwitzerland
| |
Collapse
|
12
|
Lang MA, Jenkins SA, Balzano P, Owoyele A, Patel A, Bamezai AK. Engaging Ly-6A/Sca-1 triggers lipid raft-dependent and -independent responses in CD4 + T-cell lines. IMMUNITY INFLAMMATION AND DISEASE 2017; 5:448-460. [PMID: 28660664 PMCID: PMC5691314 DOI: 10.1002/iid3.182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/22/2017] [Accepted: 05/26/2017] [Indexed: 12/31/2022]
Abstract
INTRODUCTION The lymphocyte antigen 6 (Ly-6) supergene family encodes proteins of 12-14 kda in molecular mass that are either secreted or anchored to the plasma membrane through a glycosyl-phosphatidylinisotol (GPI) lipid anchor at the carboxy-terminus. The lipidated GPI-anchor allows localization of Ly-6 proteins to the 10-100 nm cholesterol-rich nano-domains on the membrane, also known as lipid rafts. Ly-6A/Sca-1, a member of Ly-6 gene family is known to transduce signals despite the absence of transmembrane and cytoplasmic domains. It is hypothesized that the localization of Ly-6A/Sca-1 with in lipid rafts allows this protein to transduce signals to the cell interior. METHODS AND RESULTS In this study, we found that cross-linking mouse Ly-6A/Sca-1 protein with a monoclonal antibody results in functionally distinct responses that occur simultaneously. Ly-6A/Sca-1 triggered a cell stimulatory response as gauged by cytokine production with a concurrent inhibitory response as indicated by growth inhibition and apoptosis. While production of interleukin 2 (IL-2) cytokine by CD4+ T cell line in response to cross-linking Ly-6A/Sca-1 was dependent on the integrity of lipid rafts, the observed cell death occurred independently of it. Growth inhibited CD4+ T cells showed up-regulated expression of the inhibitory cell cycle protein p27kip but not of p53. In addition, Ly-6A/Sca-1 induced translocation of cytochrome C to the cytoplasm along with activated caspase 3 and caspase 9, thereby suggesting an intrinsic apoptotic cell death mechanism. CONCLUSIONS We conclude that opposing responses with differential dependence on the integrity of lipid rafts are triggered by engaging Ly-6A/Sca-1 protein on the membrane of transformed CD4+ T cells.
Collapse
Affiliation(s)
- Melissa A Lang
- Department of Biology, Villanova University, Villanova, Pennsylvania
| | - Sultan A Jenkins
- Department of Biology, Villanova University, Villanova, Pennsylvania
| | - Phillip Balzano
- Department of Biology, Villanova University, Villanova, Pennsylvania
| | - Adeyinka Owoyele
- Department of Biology, Villanova University, Villanova, Pennsylvania
| | - Akshay Patel
- Department of Biology, Villanova University, Villanova, Pennsylvania
| | - Anil K Bamezai
- Department of Biology, Villanova University, Villanova, Pennsylvania
| |
Collapse
|
13
|
Coexpression Analysis of Transcriptome on AIDS and Other Human Disease Pathways by Canonical Correlation Analysis. Int J Genomics 2017; 2017:9163719. [PMID: 28695125 PMCID: PMC5488239 DOI: 10.1155/2017/9163719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 02/24/2017] [Accepted: 03/08/2017] [Indexed: 11/17/2022] Open
Abstract
Acquired immune deficiency syndrome is a severe disease in humans caused by human immunodeficiency virus. Several human genes were characterized as host genetic factors that impact the processes of AIDS disease. Recent studies on AIDS patients revealed a series disease is complicating with AIDS. To resolve gene interaction between AIDS and complicating diseases, a canonical correlation analysis was used to identify the global correlation between AIDS and other disease pathway genes expression. The results showed that HLA-B, HLA-A, MH9, ZNED1, IRF1, TLR8, TSG101, NCOR2, and GML are the key AIDS-restricted genes highly correlated with other disease pathway genes. Furthermore, pathway genes in several diseases such as asthma, autoimmune thyroid disease, and malaria were globally correlated with ARGs. It suggests that these diseases are a high risk in AIDS patients as complicating diseases.
Collapse
|
14
|
Yu J, Liang C, Liu SL. Interferon-inducible LY6E Protein Promotes HIV-1 Infection. J Biol Chem 2017; 292:4674-4685. [PMID: 28130445 DOI: 10.1074/jbc.m116.755819] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/24/2017] [Indexed: 11/06/2022] Open
Abstract
LY6E is a glycosylphosphatidylinositol-anchored, IFN-inducible protein that regulates T lymphocytes proliferation, differentiation, and development. Single-nucleotide polymorphism rs2572886 in the LY6 family protein locus has been shown to associate with accelerated progression to AIDS. In this study, we show that LY6E promotes HIV, type 1 (HIV-1) infection by enhancing viral entry and gene expression. Knockdown of LY6E in human peripheral blood mononuclear, SupT1, and THP-1 cells diminishes HIV-1 replication. Virion-cell and cell-cell fusion experiments revealed that LY6E promotes membrane fusion of the viral entry step. Interestingly, we find that LTR-driven HIV-1 gene expression is also enhanced by LY6E, suggesting additional roles of LY6E in HIV-1 replication. HIV-1 infection induces LY6E expression in human peripheral blood mononuclear cells, concomitant with increased production of type I IFN and some classical IFN-stimulated genes. Altogether, our results demonstrate that IFN-inducible LY6E promotes HIV-1 entry and replication and highlight a positive regulatory role of IFN-induced proteins in HIV-1 infection. Our work emphasizes the complexity of IFN-mediated signaling in HIV-host interaction and AIDS pathogenesis.
Collapse
Affiliation(s)
- Jingyou Yu
- From the Center for Retrovirus Research.,Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210
| | - Chen Liang
- the McGill AIDS Centre, Lady Davis Institute, Montreal, Quebec H3T 1E2, Canada, and.,the Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Shan-Lu Liu
- From the Center for Retrovirus Research, .,Center for Microbial Interface Biology, and
| |
Collapse
|
15
|
Miller SI, Chaudhary A. A Cellular GWAS Approach to Define Human Variation in Cellular Pathways Important to Inflammation. Pathogens 2016; 5:pathogens5020039. [PMID: 27128945 PMCID: PMC4931390 DOI: 10.3390/pathogens5020039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 04/07/2016] [Accepted: 04/21/2016] [Indexed: 12/17/2022] Open
Abstract
An understanding of common human diversity in innate immune pathways should be beneficial in understanding autoimmune diseases, susceptibility to infection, and choices of anti-inflammatory treatment. Such understanding could also result in definition of currently unknown components of human inflammation pathways. A cellular genome-wide association studies (GWAS) platform, termed Hi-HOST (High-throughput human in vitro susceptibility testing), was developed to assay in vitro cellular phenotypes of infection in genotyped lymphoblastoid cells from genetically diverse human populations. Hi-HOST allows for measurement of multiple host and pathogen parameters of infection/inflammation including: bacterial invasion and intracellular replication, host cell death, and cytokine production. Hi-HOST has been used to successfully define a significant portion of the heritable human diversity in inflammatory cell death in response to Salmonella typhimurium. It also led to the discovery of genetic variants important to protection against systemic inflammatory response syndrome (SIRS) and protection against death and bacteremia in individuals with SIRS. Our laboratory is currently using this platform to define human diversity in autophagy and the NLPR3 inflammasome pathways, and to define new components that can impact the expression of phenotypes related to these pathways.
Collapse
Affiliation(s)
- Samuel I Miller
- Department of Microbiology, Department of Immunology, Department of Medicine, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - Anu Chaudhary
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
16
|
Differences in T cell distribution and CCR5 expression in HIV-positive and HIV-exposed seronegative persons who inject drugs. Med Microbiol Immunol 2015; 205:231-9. [PMID: 26696529 DOI: 10.1007/s00430-015-0444-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/09/2015] [Indexed: 01/30/2023]
Abstract
Some individuals remain uninfected despite repeated exposure to HIV. This protection against HIV has been partly associated with altered T cell subset distributions and CCR5 expression levels. However, the majority of studies have been conducted in sexually exposed subjects. We aimed to assess whether HIV infection and intravenous drug use were associated with differences in CCR5 expression, immune activation on the CD4+ and CD8+ T cells and T cell distribution among Caucasian persons who inject drugs (PWIDs). Analyses of the data from 41 HIV-positive PWIDs, 47 HIV-exposed seronegative PWIDs (ESNs) and 47 age- and gender-matched HIV-negative non-drug users are presented. Of all of the study subjects, 111 (82 %) were male, and the median age was 29 years. T cell phenotyping was performed in peripheral blood mononuclear cells with multicolour flow cytometry using anti-CD3, CD4, CD8, CD45RA, CD45RO, HLA-DR and CCR5 antibodies. The ESNs exhibited greater levels of immune activation and higher percentages of CD4+ CD45RA+RO+ and CD8+ CD45RA+RO+ cells compared to the controls but not the HIV-positive people. The CCR5 expression on the CD4+ T cell subsets in the ESNs was lower than that in the controls but similar to that the HIV positives. The percentages of CCR5+ T cells were similar in all study groups and in most of the studied cell populations. Intravenous drug use was similarly associated with differences in T cell subset distributions and CCR5 expression among both the HIV-positive and HIV-negative PWIDs compared with the controls.
Collapse
|
17
|
Hancock DB, Gaddis NC, Levy JL, Bierut LJ, Kral AH, Johnson EO. Associations of common variants in the BST2 region with HIV-1 acquisition in African American and European American people who inject drugs. AIDS 2015; 29:767-77. [PMID: 25985399 PMCID: PMC4439198 DOI: 10.1097/qad.0000000000000604] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
OBJECTIVE The bone marrow stromal cell antigen 2 (BST2) gene encodes a host restriction factor that acts as an innate immune sensor of HIV-1 exposure and suppresses release of HIV-1 particles. We aimed to identify associations of variants in the BST2 gene region with HIV-1 acquisition and disease progression. DESIGN/METHODS Using HIV+ cases and HIV- controls from the Urban Health Study (n=3136 African Americans and European Americans who inject drugs), we tested 470 variants in BST2 and its flanking regions for association with HIV-1 acquisition and log-transformed viral load. RESULTS We found that the single nucleotide polymorphism (SNP) rs113189798 surpassed the P value threshold corrected for multiple testing. The rs113189798-G allele (frequency=16% in African Americans, 4% in European Americans) was associated with increased HIV-1 acquisition risk (meta-analysis P=1.43 × 10): odds ratio (95% confidence interval) of 1.22 (1.01-1.49) in African Americans and 2.17 (1.43-3.33) in European Americans. We also found that the previously reported rs12609479-A allele (frequency=35% in African Americans, 81% in European Americans) was nominally associated with decreased risk of acquiring HIV-1 in our study (meta-analysis P=0.036). Rs12609479-A is predicted to increase BST2 expression and thereby decrease risk of acquiring HIV-1. Rs113189798 and rs12609479 were only weakly correlated [square of the correlation coefficient (r)=0.2-0.4] and represented distinct association signals. None of our tested variants were significantly associated with log-transformed viral load among the HIV-infected cases. CONCLUSION Our findings support BST2 as a genetic susceptibility factor for HIV-1 acquisition: identifying a novel SNP association for rs13189798 and linking the previously reported regulatory SNP rs12609479 to HIV-1 acquisition.
Collapse
Affiliation(s)
- Dana B Hancock
- aBehavioral Health Epidemiology Program, Behavioral Health and Criminal Justice Division bResearch Computing Division, Research Triangle Institute (RTI) International, Research Triangle Park, North Carolina cDepartment of Psychiatry, Washington University School of Medicine, St. Louis, Missouri dUrban Health Program, Behavioral Health and Criminal Justice Division, RTI International, San Francisco, California eFellow Program and Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, North Carolina, USA
| | | | | | | | | | | |
Collapse
|
18
|
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] [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.
Collapse
Affiliation(s)
- Eric O. Johnson
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - 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
| |
Collapse
|
19
|
Xu X, Qiu C, Zhu L, Huang J, Li L, Fu W, Zhang L, Wei J, Wang Y, Geng Y, Zhang X, Qiao W, Xu J. IFN-stimulated gene LY6E in monocytes regulates the CD14/TLR4 pathway but inadequately restrains the hyperactivation of monocytes during chronic HIV-1 infection. THE JOURNAL OF IMMUNOLOGY 2014; 193:4125-36. [PMID: 25225669 DOI: 10.4049/jimmunol.1401249] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Owing to ongoing recognition of pathogen-associated molecular patterns, immune activation and upregulation of IFN-stimulated genes (ISGs) are sustained in the chronically infected host. Albeit most ISGs are important effectors for containing viral replication, some might exert compensatory immune suppression to limit pathological dysfunctions, although the mechanisms are not fully understood. In this study, we report that the ISG lymphocyte Ag 6 complex, locus E (LY6E) is a negative immune regulator of monocytes. LY6E in monocytes negatively modulated CD14 expression and subsequently dampened the responsiveness to LPS stimulation in vitro. In the setting of chronic HIV infection, the upregulation of LY6E was correlated with reduced CD14 level on monocytes; however, the immunosuppressive effect of LY6E was not adequate to remedy the hyperresponsiveness of activated monocytes. Taken together, the regulatory LY6E pathway in monocytes represents one of negative feedback mechanisms that counterbalance monocyte activation, which might be caused by LPS translocation through the compromised gastrointestinal tract during persistent HIV-1 infection and may serve as a potential target for immune intervention.
Collapse
Affiliation(s)
- Xuan Xu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai 201508, China; Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Chao Qiu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai 201508, China;
| | - Lingyan Zhu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai 201508, China
| | - Jun Huang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai 201508, China
| | - Lishuang Li
- Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Weihui Fu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai 201508, China
| | - Linxia Zhang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai 201508, China
| | - Jun Wei
- Yuncheng Center for Disease Control and Prevention, Shanxi 044400, China
| | - Ying Wang
- Shanghai Center for Disease Control and Prevention, Shanghai 200336, China; and
| | - Yunqi Geng
- Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai 201508, China; State Key Laboratory for Infectious Disease Prevention and Control, China Centers for Disease Control and Prevention, Beijing 102206, China
| | - Wentao Qiao
- Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin 300071, China;
| | - Jianqing Xu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai 201508, China; State Key Laboratory for Infectious Disease Prevention and Control, China Centers for Disease Control and Prevention, Beijing 102206, China
| |
Collapse
|
20
|
Abstract
OBJECTIVE To evaluate the impact of mitochondrial DNA (mtDNA) haplogroups on virologic and immunological outcomes of HIV infection. DESIGN HAART-naive African American adolescent participants to the Reaching for Excellence in Adolescent Care and Health study. METHODS The mtDNA haplogroups were inferred from sequenced mtDNA hypervariable regions HV1 and HV2 and their predictive value on HIV outcomes were evaluated in linear mixed models, controlled for human leukocyte antigen (HLA)-B27, HLA-B57 and HLA-B35-Px alleles and other covariates. RESULTS We report data showing that the mtDNA L2 lineage, a group composed of L2a, L2b and L2e mtDNA haplogroups in the studied population, is significantly associated (beta = -0.08; Bonferroni-adjusted P = 0.004) with decline of CD4 T cells (median loss of 8 ± 1 cells per month) in HAART-naive HIV-infected individuals of African American descent (n = 133). No significant association (P < 0.05) with set-point viral load was observed with any of the tested mtDNA haplogroups. The present data concur with previous findings in the AIDS Clinical Trials Group study 384, implicating the L2 lineage with slower CD4 T-cell recovery after antiretroviral therapy in African Americans. CONCLUSIONS Whereas the L2 lineage showed an association with unfavorable immunological outcomes of HIV infection, its phylogenetic divergence from J and U5a, two lineages associated with accelerated HIV progression in European Americans, raises the possibility that interactions with common nucleus-encoded variants drive HIV progression. Disentangling the effects of mitochondrial and nuclear gene variants on the outcomes of HIV infection is an important step to be taken toward a better understanding of HIV/AIDS pathogenesis and pharmacogenomics.
Collapse
|
21
|
Ballana E, Esté JA. Insights from host genomics into HIV infection and disease: Identification of host targets for drug development. Antiviral Res 2013; 100:473-86. [PMID: 24084487 DOI: 10.1016/j.antiviral.2013.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/17/2013] [Accepted: 09/20/2013] [Indexed: 01/11/2023]
Abstract
HIV susceptibility and disease progression show a substantial degree of individual heterogeneity, ranging from fast progressors to long-term non progressors or elite controllers, that is, subjects that control infection in the absence of therapy. Recent years have seen a significant increase in understanding of the host genetic determinants of susceptibility to HIV infection and disease progression, driven in large part by candidate gene studies, genome-wide association studies, genome-wide transcriptome analyses, and large-scale functional screens. These studies have identified common variants in host loci that clearly influence disease progression, characterized the scale and dynamics of gene and protein expression changes in response to infection, and provided the first comprehensive catalogue of genes and pathways involved in viral replication. This review highlights the potential of host genomic influences in antiviral therapy by pointing to promising novel drug targets but also providing the basis of the identification and validation of host mechanisms that might be susceptible targets for novel antiviral therapies.
Collapse
Affiliation(s)
- Ester Ballana
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.
| | | |
Collapse
|
22
|
Ko DC, Urban TJ. Understanding human variation in infectious disease susceptibility through clinical and cellular GWAS. PLoS Pathog 2013; 9:e1003424. [PMID: 23935492 PMCID: PMC3731241 DOI: 10.1371/journal.ppat.1003424] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of
| | | |
Collapse
|
23
|
Andrews T, Sjollema G, Goodnow C. Understanding the immunological impact of the human mutation explosion. Trends Immunol 2013; 34:99-106. [DOI: 10.1016/j.it.2012.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/17/2012] [Accepted: 12/17/2012] [Indexed: 02/02/2023]
|
24
|
Abstract
Since the discovery of HIV as the cause of AIDS, numerous insights have been gained from studies of its natural history and epidemiology. It has become clear that there are substantial interindividual differences in the risk of HIV acquisition and course of disease. Meanwhile, the field of human genetics has undergone a series of rapid transitions that have fundamentally altered the approach to studying HIV host genetics. We aim to describe the field as it has transitioned from the era of candidate-gene studies and the era of genome-wide association studies (GWAS) to its current state in the infancy of comprehensive sequencing. In some ways the field has come full circle, having evolved from being driven almost exclusively by our knowledge of immunology, to a bias-free GWAS approach, to a point where our ability to catalogue human variation far outstrips our ability to biologically interpret it.
Collapse
Affiliation(s)
- Patrick R Shea
- Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina 27708, USA.
| | | | | | | |
Collapse
|
25
|
Functional genetic screen of human diversity reveals that a methionine salvage enzyme regulates inflammatory cell death. Proc Natl Acad Sci U S A 2012; 109:E2343-52. [PMID: 22837397 DOI: 10.1073/pnas.1206701109] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies can identify common differences that contribute to human phenotypic diversity and disease. When genome-wide association studies are combined with approaches that test how variants alter physiology, biological insights can emerge. Here, we used such an approach to reveal regulation of cell death by the methionine salvage pathway. A common SNP associated with reduced expression of a putative methionine salvage pathway dehydratase, apoptotic protease activating factor 1 (APAF1)-interacting protein (APIP), was associated with increased caspase-1-mediated cell death in response to Salmonella. The role of APIP in methionine salvage was confirmed by growth assays with methionine-deficient media and quantitation of the methionine salvage substrate, 5'-methylthioadenosine. Reducing expression of APIP or exogenous addition of 5'-methylthioadenosine increased Salmonellae-induced cell death. Consistent with APIP originally being identified as an inhibitor of caspase-9-dependent apoptosis, the same allele was also associated with increased sensitivity to the chemotherapeutic agent carboplatin. Our results show that common human variation affecting expression of a single gene can alter susceptibility to two distinct cell death programs. Furthermore, the same allele that promotes cell death is associated with improved survival of individuals with systemic inflammatory response syndrome, suggesting a possible evolutionary pressure that may explain the geographic pattern observed for the frequency of this SNP. Our study shows that in vitro association screens of disease-related traits can not only reveal human genetic differences that contribute to disease but also provide unexpected insights into cell biology.
Collapse
|
26
|
Sharma G, Kaur G, Mehra N. Genetic correlates influencing immunopathogenesis of HIV infection. Indian J Med Res 2012; 134:749-68. [PMID: 22310811 PMCID: PMC3284087 DOI: 10.4103/0971-5916.92623] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Variability to HIV infection, its progression as well as responsiveness to antiretroviral therapy (ART) is observed among individuals including viraemia controllers or exposed uninfected, rapid versus slow progressors and ART responders compared to non responders. This differential responsiveness/vulnerability to HIV-1 is governed by multiple host genetic factors that include HLA, cytokines, chemokines, their receptors and others. This review highlights the influence of these genetic factors on HIV/AIDS outcome; however, in India, the information in this area is very limited and most of these genetic studies have been conducted in Caucasian and South African populations. Considering, the population specific differences in the frequencies of protective or susceptibility favouring alleles and their influence on the disease outcome, it is of utmost importance to strengthen ongoing efforts towards defining largely unknown genetic propensity in Indian population, particularly by recruitment of large cohorts of well categorized exposed uninfected individuals, rapid, long term non progressors and elite viraemic controllers. Multi-parametric analysis of these potentially interactive immunogenetic variables in these cohorts may help to define potential targets for diagnostics and therapy in a population specific manner.
Collapse
Affiliation(s)
- Gaurav Sharma
- Department of Transplant Immunology & Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | | | | |
Collapse
|
27
|
Contribution of a single host genetic locus to mouse adenovirus type 1 infection and encephalitis. mBio 2012; 3:mBio.00131-12. [PMID: 22647790 PMCID: PMC3372963 DOI: 10.1128/mbio.00131-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Susceptibility to mouse adenovirus type 1 (MAV-1) is mouse strain dependent; susceptible mice die from hemorrhagic encephalomyelitis. The MAV-1 susceptibility quantitative trait locus Msq1 accounts for ~40% of the phenotypic (brain viral load) variance that occurs between resistant BALB/c and susceptible SJL mice after MAV-1 infection. Using an interval-specific congenic mouse strain (C.SJL-Msq1SJL), in which the SJL-derived allele Msq1SJL is present in a BALB/c background, we demonstrate that Msq1SJL controls the development of high brain viral titers in response to MAV-1 infection, yet does not account for the total extent of brain pathology or mortality in SJL mice. C.SJL-Msq1SJL mice had disruption of the blood-brain barrier and increased brain water content after MAV-1 infection, but these effects occurred later and were not as severe, respectively, as those noted in infected SJL mice. As expected, BALB/c mice showed minimal pathology in these assays. Infection of SJL- and C.SJL-Msq1SJL-derived primary mouse brain endothelial cells resulted in loss of barrier properties, whereas BALB/c-derived cells retained their barrier properties despite being equally capable of supporting MAV-1 infection. Finally, we provide evidence that organ pathology and inflammatory cell recruitment to the brain following MAV-1 infection were both influenced by Msq1. These results validate Msq1 as an important host factor in MAV-1 infection and refine the major role of the locus in development of MAV-1 encephalitis. They further suggest that additional host factors or gene interactions are involved in the mechanism of pathogenesis in MAV-1-infected SJL mice. A successful viral infection requires both host and viral factors; identification of host components involved in viral replication and pathogenesis is important for development of therapeutic interventions. A genetic locus (Msq1) controlling mouse adenovirus type 1 (MAV-1) brain infection was previously identified. Genes in Msq1 belong to the same family of genes associated with susceptibility to other encephalitic viruses, HIV-1 and West Nile virus. We constructed an interval-specific congenic mouse strain to examine the contribution of Msq1 to MAV-1 susceptibility and brain morbidity. We compared infected resistant, susceptible, and congenic mice regarding known MAV-1 disease manifestations in the brain (survival, viral loads, blood-brain barrier disruption, edema, mouse brain endothelial cell barrier properties, pathology, and inflammatory cell recruitment) to determine the extent to which Msq1 influences MAV-1 infection outcome. Our results showed that Msq1 is a critical host genetic factor that controls many aspects of MAV-1 infection.
Collapse
|
28
|
Abstract
Recent years have seen a significant increase in understanding of the host genetic and genomic determinants of susceptibility to HIV-1 infection and disease progression, driven in large part by candidate gene studies, genome-wide association studies, genome-wide transcriptome analyses, and large-scale in vitro genome screens. These studies have identified common variants in some host loci that clearly influence disease progression, characterized the scale and dynamics of gene and protein expression changes in response to infection, and provided the first comprehensive catalogs of genes and pathways involved in viral replication. Experimental models of AIDS and studies in natural hosts of primate lentiviruses have complemented and in some cases extended these findings. As the relevant technology continues to progress, the expectation is that such studies will increase in depth (e.g., to include host whole exome and whole genome sequencing) and in breadth (in particular, by integrating multiple data types).
Collapse
Affiliation(s)
- Amalio Telenti
- Institute of Microbiology, University Hospital and University of Lausanne, 1011 Lausanne, Switzerland.
| | | |
Collapse
|
29
|
Mohindra V, Singh A, Barman AS, Tripathi R, Sood N, Lal KK. Development of EST derived SSRs and SNPs as a genomic resource in Indian catfish, Clarias batrachus. Mol Biol Rep 2011; 39:5921-31. [PMID: 22207175 DOI: 10.1007/s11033-011-1404-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 12/17/2011] [Indexed: 01/19/2023]
Abstract
Clarias batrachus, an Indian catfish species, is endemic to the Indian subcontinent and potential cultivable species. The genomic resources in C. batrachus in the form of ESTs containing microsatellite repeats (EST-SSR) and single nucleotide polymorphisms (SNPs) that are associated with the expressed genes from spleen were mined. From a total of 1,937 ESTs generated, 1,698 unique sequences were obtained, out of which 221 EST-SSRs were identified and 54% could be functionally annotated by similarity searches. A total of 23 contigs containing 3 or more ESTs were found to contain 31 SNP loci, out of which 8 ESTs showed similarity to genes of known function and 1 for hypothetical protein. Nine ESTs with SSRs and/or SNPs identified in this study were reported to be associated with diseases in human and animals. These identified loci can be developed into markers in C. batrachus, which can be useful in linkage mapping, comparative genomics studies and for its genetic improvement programmes.
Collapse
Affiliation(s)
- Vindhya Mohindra
- National Bureau of Fish Genetic Resources, Canal Ring Road, PO Dilkusha, Lucknow, 226 002, UP, India.
| | | | | | | | | | | |
Collapse
|
30
|
Polymorphisms in Ly6 genes in Msq1 encoding susceptibility to mouse adenovirus type 1. Mamm Genome 2011; 23:250-8. [PMID: 22101863 DOI: 10.1007/s00335-011-9368-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 10/20/2011] [Indexed: 12/17/2022]
Abstract
Strain-specific differences in susceptibility to mouse adenovirus type 1 (MAV-1) are linked to the quantitative trait locus Msq1 on mouse chromosome 15. This region contains 14 Ly6 or Ly6-related genes, many of which are known to be expressed on the surface of immune cells, suggesting a possible role in host defense. We analyzed these genes for polymorphisms between MAV-1-susceptible and MAV-1-resistant inbred mouse strains. Sequencing of cDNAs identified 12 coding-region polymorphisms in 2010109I03Rik, Ly6e, Ly6a, Ly6c1, and Ly6c2, six of which were nonsynonymous and five of which were previously unlisted in dbSNP Build 132. We also clarified sequence discrepancies in GenBank for the coding regions of I830127L07Rik and Ly6g. Additionally, Southern blotting revealed size polymorphisms within the DNA regions of Ly6e, Ly6a, and Ly6g. Collectively, these genetic variations have implications for the structure, function, and/or expression of Ly6 and Ly6-related genes that may contribute to the observed strain-specific differences in susceptibility to MAV-1.
Collapse
|
31
|
van Manen D, Delaneau O, Kootstra NA, Boeser-Nunnink BD, Limou S, Bol SM, Burger JA, Zwinderman AH, Moerland PD, van 't Slot R, Zagury JF, van 't Wout AB, Schuitemaker H. Genome-wide association scan in HIV-1-infected individuals identifying variants influencing disease course. PLoS One 2011; 6:e22208. [PMID: 21811574 PMCID: PMC3141012 DOI: 10.1371/journal.pone.0022208] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 06/17/2011] [Indexed: 01/20/2023] Open
Abstract
Background AIDS develops typically after 7–11 years of untreated HIV-1 infection, with extremes of very rapid disease progression (<2 years) and long-term non-progression (>15 years). To reveal additional host genetic factors that may impact on the clinical course of HIV-1 infection, we designed a genome-wide association study (GWAS) in 404 participants of the Amsterdam Cohort Studies on HIV-1 infection and AIDS. Methods The association of SNP genotypes with the clinical course of HIV-1 infection was tested in Cox regression survival analyses using AIDS-diagnosis and AIDS-related death as endpoints. Results Multiple, not previously identified SNPs, were identified to be strongly associated with disease progression after HIV-1 infection, albeit not genome-wide significant. However, three independent SNPs in the top ten associations between SNP genotypes and time between seroconversion and AIDS-diagnosis, and one from the top ten associations between SNP genotypes and time between seroconversion and AIDS-related death, had P-values smaller than 0.05 in the French Genomics of Resistance to Immunodeficiency Virus cohort on disease progression. Conclusions Our study emphasizes that the use of different phenotypes in GWAS may be useful to unravel the full spectrum of host genetic factors that may be associated with the clinical course of HIV-1 infection.
Collapse
Affiliation(s)
- Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Olivier Delaneau
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers and ANRS Genomic Group, Paris, France
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Brigitte D. Boeser-Nunnink
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Sophie Limou
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers and ANRS Genomic Group, Paris, France
| | - Sebastiaan M. Bol
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Judith A. Burger
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Aeilko H. Zwinderman
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Perry D. Moerland
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Bioinformatics Center (NBIC), Nijmegen, The Netherlands
| | - Ruben van 't Slot
- Complex Genetics Section, Department of Biomedical Genetics at the University Medical Center, Utrecht, The Netherlands
| | - Jean-François Zagury
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers and ANRS Genomic Group, Paris, France
| | - Angélique B. van 't Wout
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
| |
Collapse
|
32
|
Host Genomic Profiling in Human Immunodeficiency Virus Infection. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
33
|
Robyr D, Friedli M, Gehrig C, Arcangeli M, Marin M, Guipponi M, Farinelli L, Barde I, Verp S, Trono D, Antonarakis SE. Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. PLoS One 2011; 6:e17634. [PMID: 21408183 PMCID: PMC3049788 DOI: 10.1371/journal.pone.0017634] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 02/04/2011] [Indexed: 02/02/2023] Open
Abstract
Comparative analyses of various mammalian genomes have identified numerous conserved non-coding (CNC) DNA elements that display striking conservation among species, suggesting that they have maintained specific functions throughout evolution. CNC function remains poorly understood, although recent studies have identified a role in gene regulation. We hypothesized that the identification of genomic loci that interact physically with CNCs would provide information on their functions. We have used circular chromosome conformation capture (4C) to characterize interactions of 10 CNCs from human chromosome 21 in K562 cells. The data provide evidence that CNCs are capable of interacting with loci that are enriched for CNCs. The number of trans interactions varies among CNCs; some show interactions with many loci, while others interact with few. Some of the tested CNCs are capable of driving the expression of a reporter gene in the mouse embryo, and associate with the oligodendrocyte genes OLIG1 and OLIG2. Our results underscore the power of chromosome conformation capture for the identification of targets of functional DNA elements and raise the possibility that CNCs exert their functions by physical association with defined genomic regions enriched in CNCs. These CNC-CNC interactions may in part explain their stringent conservation as a group of regulatory sequences.
Collapse
Affiliation(s)
- Daniel Robyr
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
- * E-mail: (SEA); (DR)
| | - Marc Friedli
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | - Corinne Gehrig
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | - Mélanie Arcangeli
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | - Marilyn Marin
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | | | - Isabelle Barde
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sonia Verp
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
- * E-mail: (SEA); (DR)
| |
Collapse
|
34
|
Aouizerat BE, Pearce CL, Miaskowski C. The search for host genetic factors of HIV/AIDS pathogenesis in the post-genome era: progress to date and new avenues for discovery. Curr HIV/AIDS Rep 2011; 8:38-44. [PMID: 21221856 PMCID: PMC3035795 DOI: 10.1007/s11904-010-0065-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Though pursuit of host genetic factors that influence the pathogenesis of HIV began over two decades ago, progress has been slow. Initial genome-level searches for variations associated with HIV-related traits have yielded interesting candidates, but less in the way of novel pathways to be exploited for therapeutic targets. More recent genome-wide association studies (GWAS) that include different phenotypes, novel designs, and that have examined different population characteristics suggest novel targets and affirm the utility of additional searches. Recent findings from these GWAS are reviewed, new directions for research are identified, and the promise of systems biology to yield novel insights is discussed.
Collapse
Affiliation(s)
- Bradley E. Aouizerat
- Department of Physiological Nursing and Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143-0610 USA
| | - C. Leigh Pearce
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Christine Miaskowski
- Department of Physiological Nursing, University of California San Francisco, San Francisco, CA 94143-0610 USA
| |
Collapse
|
35
|
Abstract
Macrophages and CD4+ T cells are natural target cells for HIV-1, and both cell types contribute to the establishment of the viral reservoir that is responsible for continuous residual virus replication during antiretroviral therapy and viral load rebound upon treatment interruption. Scientific findings that support a critical role for the infected monocyte/macrophage in HIV-1-associated diseases, such as neurological disorders and cardiovascular disease, are accumulating. To prevent or treat these HIV-1-related diseases, we need to halt HIV-1 replication in the macrophage reservoir. This article describes our current knowledge of how monocytes and certain macrophage subsets are able to restrict HIV-1 infection, in addition to what makes macrophages respond less well to current antiretroviral drugs as compared with CD4+ T cells. These insights will help to find novel approaches that can be used to meet this challenge.
Collapse
Affiliation(s)
- Sebastiaan M Bol
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Viviana Cobos-Jiménez
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | | |
Collapse
|
36
|
Hunt PW, Landay AL, Sinclair E, Martinson JA, Hatano H, Emu B, Norris PJ, Busch MP, Martin JN, Brooks C, McCune JM, Deeks SG. A low T regulatory cell response may contribute to both viral control and generalized immune activation in HIV controllers. PLoS One 2011; 6:e15924. [PMID: 21305005 PMCID: PMC3031543 DOI: 10.1371/journal.pone.0015924] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 11/30/2010] [Indexed: 11/18/2022] Open
Abstract
HIV-infected individuals maintaining undetectable viremia in the absence of therapy (HIV controllers) often maintain high HIV-specific T cell responses, which has spurred the development of vaccines eliciting HIV-specific T cell responses. However, controllers also often have abnormally high T cell activation levels, potentially contributing to T cell dysfunction, CD4+ T cell depletion, and non-AIDS morbidity. We hypothesized that a weak T regulatory cell (Treg) response might contribute to the control of viral replication in HIV controllers, but might also contribute to generalized immune activation, contributing to CD4+ T cell loss. To address these hypotheses, we measured frequencies of activated (CD38+ HLA-DR+), regulatory (CD4+CD25+CD127dim), HIV-specific, and CMV-specific T cells among HIV controllers and 3 control populations: HIV-infected individuals with treatment-mediated viral suppression (ART-suppressed), untreated HIV-infected “non-controllers” with high levels of viremia, and HIV-uninfected individuals. Despite abnormally high T cell activation levels, controllers had lower Treg frequencies than HIV-uninfected controls (P = 0.014). Supporting the propensity for an unusually low Treg response to viral infection in HIV controllers, we observed unusually high CMV-specific CD4+ T cell frequencies and a strong correlation between HIV-specific CD4+ T cell responses and generalized CD8+ T cell activation levels in HIV controllers (P≤0.001). These data support a model in which low frequencies of Tregs in HIV controllers may contribute to an effective adaptive immune response, but may also contribute to generalized immune activation, potentially contributing to CD4 depletion.
Collapse
Affiliation(s)
- Peter W Hunt
- Departments of Medicine and Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
A systematic enhancer screen using lentivector transgenesis identifies conserved and non-conserved functional elements at the Olig1 and Olig2 locus. PLoS One 2010; 5:e15741. [PMID: 21206754 PMCID: PMC3012086 DOI: 10.1371/journal.pone.0015741] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Accepted: 11/23/2010] [Indexed: 01/22/2023] Open
Abstract
Finding sequences that control expression of genes is central to understanding genome function. Previous studies have used evolutionary conservation as an indicator of regulatory potential. Here, we present a method for the unbiased in vivo screen of putative enhancers in large DNA regions, using the mouse as a model. We cloned a library of 142 overlapping fragments from a 200 kb-long murine BAC in a lentiviral vector expressing LacZ from a minimal promoter, and used the resulting vectors to infect fertilized murine oocytes. LacZ staining of E11 embryos obtained by first using the vectors in pools and then testing individual candidates led to the identification of 3 enhancers, only one of which shows significant evolutionary conservation. In situ hybridization and 3C/4C experiments suggest that this enhancer, which is active in the neural tube and posterior diencephalon, influences the expression of the Olig1 and/or Olig2 genes. This work provides a new approach for the large-scale in vivo screening of transcriptional regulatory sequences, and further demonstrates that evolutionary conservation alone seems too limiting a criterion for the identification of enhancers.
Collapse
|
38
|
Li J, Liu Y, Kim T, Min R, Zhang Z. Gene expression variability within and between human populations and implications toward disease susceptibility. PLoS Comput Biol 2010; 6. [PMID: 20865155 PMCID: PMC2928754 DOI: 10.1371/journal.pcbi.1000910] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Accepted: 07/28/2010] [Indexed: 01/15/2023] Open
Abstract
Variations in gene expression level might lead to phenotypic diversity across individuals or populations. Although many human genes are found to have differential mRNA levels between populations, the extent of gene expression that could vary within and between populations largely remains elusive. To investigate the dynamic range of gene expression, we analyzed the expression variability of ∼18, 000 human genes across individuals within HapMap populations. Although ∼20% of human genes show differentiated mRNA levels between populations, our results show that expression variability of most human genes in one population is not significantly deviant from another population, except for a small fraction that do show substantially higher expression variability in a particular population. By associating expression variability with sequence polymorphism, intriguingly, we found SNPs in the untranslated regions (5′ and 3′UTRs) of these variable genes show consistently elevated population heterozygosity. We performed differential expression analysis on a genome-wide scale, and found substantially reduced expression variability for a large number of genes, prohibiting them from being differentially expressed between populations. Functional analysis revealed that genes with the greatest within-population expression variability are significantly enriched for chemokine signaling in HIV-1 infection, and for HIV-interacting proteins that control viral entry, replication, and propagation. This observation combined with the finding that known human HIV host factors show substantially elevated expression variability, collectively suggest that gene expression variability might explain differential HIV susceptibility across individuals. Many human genes have population-specific expression levels, which are linked to population-specific polymorphisms and copy-number variations. However, it is unclear whether human genes show similar dynamic range of expression between populations. In this work we analyzed HapMap gene expression compendium, and quantified the between-population and within-population expression variability for ∼18,000 human transcripts. We first concluded that the majority of the human genes have similar levels of within-population variability. However, a small fraction (∼4%) does show much higher expression variability in one population, and the deviation is consistently associated with increased SNP heterozygosity in their UTR regulatory regions. We further showed that genes with the greatest within-population expression variability are significantly enriched for chemokine signaling associated with HIV-1 infection. Combined with the finding that human HIV-1 host factors tend to have increased expression variability within populations, our analysis may explain, at least in part, different susceptibility to HIV infection within the human population. This work provides a fresh angle for analyzing gene expression variations in populations.
Collapse
Affiliation(s)
- Jingjing Li
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Yu Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - TaeHyung Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
| | - Renqiang Min
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
- * E-mail:
| |
Collapse
|
39
|
An P, Winkler CA. Host genes associated with HIV/AIDS: advances in gene discovery. Trends Genet 2010; 26:119-31. [PMID: 20149939 PMCID: PMC3792714 DOI: 10.1016/j.tig.2010.01.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 12/31/2009] [Accepted: 01/03/2010] [Indexed: 02/06/2023]
Abstract
Twenty-five years after the discovery of HIV as the cause of AIDS there is still no effective vaccine and no cure for this disease. HIV susceptibility shows a substantial degree of individual heterogeneity, much of which can be conferred by host genetic variation. In an effort to discover host factors required for HIV replication, identify crucial pathogenic pathways, and reveal the full armament of host defenses, there has been a shift from candidate-gene studies to unbiased genome-wide genetic and functional studies. However, the number of securely identified host factors involved in HIV disease remains small, explaining only approximately 15-20% of the observed heterogeneity - most of which is attributable to human lymphocyte antigen (HLA) variants. Multidisciplinary approaches integrating genetic epidemiology to systems biology will be required to fully understand virus-host interactions to effectively combat HIV/AIDS.
Collapse
Affiliation(s)
| | - Cheryl A. Winkler
- Laboratory of Genomic Diversity, SAIC-Frederick, Inc., National Cancer Institute- Frederick, Frederick, MD
| |
Collapse
|
40
|
Rotger M, Dang KK, Fellay J, Heinzen EL, Feng S, Descombes P, Shianna KV, Ge D, Günthard HF, Goldstein DB, Telenti A. Genome-wide mRNA expression correlates of viral control in CD4+ T-cells from HIV-1-infected individuals. PLoS Pathog 2010; 6:e1000781. [PMID: 20195503 PMCID: PMC2829051 DOI: 10.1371/journal.ppat.1000781] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 01/20/2010] [Indexed: 12/17/2022] Open
Abstract
There is great interindividual variability in HIV-1 viral setpoint after seroconversion, some of which is known to be due to genetic differences among infected individuals. Here, our focus is on determining, genome-wide, the contribution of variable gene expression to viral control, and to relate it to genomic DNA polymorphism. RNA was extracted from purified CD4+ T-cells from 137 HIV-1 seroconverters, 16 elite controllers, and 3 healthy blood donors. Expression levels of more than 48,000 mRNA transcripts were assessed by the Human-6 v3 Expression BeadChips (Illumina). Genome-wide SNP data was generated from genomic DNA using the HumanHap550 Genotyping BeadChip (Illumina). We observed two distinct profiles with 260 genes differentially expressed depending on HIV-1 viral load. There was significant upregulation of expression of interferon stimulated genes with increasing viral load, including genes of the intrinsic antiretroviral defense. Upon successful antiretroviral treatment, the transcriptome profile of previously viremic individuals reverted to a pattern comparable to that of elite controllers and of uninfected individuals. Genome-wide evaluation of cis-acting SNPs identified genetic variants modulating expression of 190 genes. Those were compared to the genes whose expression was found associated with viral load: expression of one interferon stimulated gene, OAS1, was found to be regulated by a SNP (rs3177979, p = 4.9E-12); however, we could not detect an independent association of the SNP with viral setpoint. Thus, this study represents an attempt to integrate genome-wide SNP signals with genome-wide expression profiles in the search for biological correlates of HIV-1 control. It underscores the paradox of the association between increasing levels of viral load and greater expression of antiviral defense pathways. It also shows that elite controllers do not have a fully distinctive mRNA expression pattern in CD4+ T cells. Overall, changes in global RNA expression reflect responses to viral replication rather than a mechanism that might explain viral control.
Collapse
Affiliation(s)
- Margalida Rotger
- Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Kristen K. Dang
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Jacques Fellay
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Erin L. Heinzen
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Sheng Feng
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | | | - Kevin V. Shianna
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Dongliang Ge
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Huldrych F. Günthard
- Division of Infectious Diseases, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - David B. Goldstein
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Amalio Telenti
- Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | | |
Collapse
|
41
|
Spindler KR, Welton AR, Lim ES, Duvvuru S, Althaus IW, Imperiale JE, Daoud AI, Chesler EJ. The major locus for mouse adenovirus susceptibility maps to genes of the hematopoietic cell surface-expressed LY6 family. THE JOURNAL OF IMMUNOLOGY 2010; 184:3055-62. [PMID: 20164425 DOI: 10.4049/jimmunol.0903363] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Susceptibility to mouse adenovirus type 1 is associated with the major quantitative trait locus Msq1. Msq1 was originally mapped to a 13-Mb region of mouse chromosome (Chr) 15 in crosses between SJL/J and BALB/cJ inbred mice. We have now narrowed Msq1 to a 0.75-Mb interval from 74.68 to 75.43 Mb, defined by two anonymous markers, rs8259436 and D15Spn14, using data from 1396 backcross mice. The critical interval includes 14 Ly6 or Ly6-related genes, including Ly6a (encoding Sca-1/TAP), Ly6e (Sca-2/Tsa1), Ly6g (Gr-1), and gpihbp1 (GPI-anchored high-density lipoprotein-binding protein 1), as well as the gene encoding an aldosterone synthase (Cyp11b2). The Ly6 family members are attractive candidates for virus susceptibility genes because their products are GPI-anchored membrane proteins expressed on lymphoid and myeloid cells, with proposed functions in cell adhesion and cell signaling. To determine interstrain variation in susceptibility and produce additional resources for cloning Msq1, we assayed the susceptibility phenotype of four previously untested inbred mouse strains. Susceptibility of strain 129S6/SvEvTac was subsequently localized to the Ly6 complex region, using polymorphic genetic markers on Chr 15 in a population of 271 (129S6/SvEvTac x BALB/cJ)F(1) x BALB/cJ backcross mice. We identified a major 129S6/SvEvTac susceptibility allele, Msq1(129S6), on Chr 15 in the same region as Msq1(SJL). The results indicate that a major host factor in mouse adenovirus type 1 susceptibility is likely to be a member of the Ly6 gene family.
Collapse
Affiliation(s)
- Katherine R Spindler
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Kaur G, Mehra N. Genetic determinants of HIV-1 infection and progression to AIDS: immune response genes. ACTA ACUST UNITED AC 2009; 74:373-85. [PMID: 19765261 DOI: 10.1111/j.1399-0039.2009.01337.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genomic studies involving well-defined multicenter cohorts of HIV-1/AIDS covering multiple populations have led to a greater understanding of the role of host determinants in viral acquisition, disease progression, transmission, and response to anti-retroviral therapy. Similarly, recent knowledge on the virus genetic diversity has helped in elucidating mechanisms leading to the evolution of viral escape mutants and the role played by host immune determinants, in particular the major histocompatibility complex (MHC) associated genes. At least two alleles, HLA-B*27 and B*57, have been identified as 'protective' against HIV-1 while B*35 and B*53 act as susceptibility favoring factors. How human leukocyte antigen (HLA)-mediated selection drives the evolution of HIV-1 and which circulating variants are more likely to evade immune surveillance of the population are now beginning to become clear. Importantly, the rare HLA alleles in a population bear a selective advantage to the host because these can induce immune responses against pre-adapted viruses. It is conceivable that previously established protective HLA associations are shifting with the evolving cytotoxic T lymphocyte (CTL) epitopes and may not remain protective in future. At the same time, this process is unraveling novel sub-dominant epitopes of the virus which could now be incorporated as the dominant target CTL epitopes. An insight into the population-specific correlates of protection is hence necessary for designing future anti-HIV therapeutic and/or prophylactic vaccine formulation(s).
Collapse
Affiliation(s)
- G Kaur
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India.
| | | |
Collapse
|
43
|
Ortiz M, Guex N, Patin E, Martin O, Xenarios I, Ciuffi A, Quintana-Murci L, Telenti A. Evolutionary trajectories of primate genes involved in HIV pathogenesis. Mol Biol Evol 2009; 26:2865-75. [PMID: 19726537 DOI: 10.1093/molbev/msp197] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The current availability of five complete genomes of different primate species allows the analysis of genetic divergence over the last 40 million years of evolution. We hypothesized that the interspecies differences observed in susceptibility to HIV-1 would be influenced by the long-range selective pressures on host genes associated with HIV-1 pathogenesis. We established a list of human genes (n = 140) proposed to be involved in HIV-1 biology and pathogenesis and a control set of 100 random genes. We retrieved the orthologous genes from the genome of humans and of four nonhuman primates (Pan troglodytes, Pongo pygmaeus abeli, Macaca mulatta, and Callithrix jacchus) and analyzed the nucleotide substitution patterns of this data set using codon-based maximum likelihood procedures. In addition, we evaluated whether the candidate genes have been targets of recent positive selection in humans by analyzing HapMap Phase 2 single-nucleotide polymorphisms genotyped in a region centered on each candidate gene. A total of 1,064 sequences were used for the analyses. Similar median K(A)/K(S) values were estimated for the set of genes involved in HIV-1 pathogenesis and for control genes, 0.19 and 0.15, respectively. However, genes of the innate immunity had median values of 0.37 (P value = 0.0001, compared with control genes), and genes of intrinsic cellular defense had K(A)/K(S) values around or greater than 1.0 (P value = 0.0002). Detailed assessment allowed the identification of residues under positive selection in 13 proteins: AKT1, APOBEC3G, APOBEC3H, CD4, DEFB1, GML, IL4, IL8RA, L-SIGN/CLEC4M, PTPRC/CD45, Tetherin/BST2, TLR7, and TRIM5alpha. A number of those residues are relevant for HIV-1 biology. The set of 140 genes involved in HIV-1 pathogenesis did not show a significant enrichment in signals of recent positive selection in humans (intraspecies selection). However, we identified within or near these genes 24 polymorphisms showing strong signatures of recent positive selection. Interestingly, the DEFB1 gene presented signatures of both interspecies positive selection in primates and intraspecies recent positive selection in humans. The systematic assessment of long-acting selective pressures on primate genomes is a useful tool to extend our understanding of genetic variation influencing contemporary susceptibility to HIV-1.
Collapse
Affiliation(s)
- Millán Ortiz
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Ko DC, Shukla KP, Fong C, Wasnick M, Brittnacher MJ, Wurfel MM, Holden TD, O'Keefe GE, Van Yserloo B, Akey JM, Miller SI. A genome-wide in vitro bacterial-infection screen reveals human variation in the host response associated with inflammatory disease. Am J Hum Genet 2009; 85:214-27. [PMID: 19664744 DOI: 10.1016/j.ajhg.2009.07.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 07/14/2009] [Accepted: 07/20/2009] [Indexed: 12/13/2022] Open
Abstract
Recent progress in cataloguing common genetic variation has made possible genome-wide studies that are beginning to elucidate the causes and consequences of our genetic differences. Approaches that provide a mechanistic understanding of how genetic variants function to alter disease susceptibility and why they were substrates of natural selection would complement other approaches to human-genome analysis. Here we use a novel cell-based screen of bacterial infection to identify human variation in Salmonella-induced cell death. A loss-of-function allele of CARD8, a reported inhibitor of the proinflammatory protease caspase-1, was associated with increased cell death in vitro (p = 0.013). The validity of this association was demonstrated through overexpression of alternative alleles and RNA interference in cells of varying genotype. Comparison of mammalian CARD8 orthologs and examination of variation among different human populations suggest that the increase in infectious-disease burden associated with larger animal groups (i.e., herds and colonies), and possibly human population expansion, may have naturally selected for loss of CARD8. We also find that the loss-of-function CARD8 allele shows a modest association with an increased risk of systemic inflammatory response syndrome in a small study (p = 0.05). Therefore, a by-product of the selected benefit of loss of CARD8 could be increased inflammatory diseases. These results demonstrate the utility of genome-wide cell-based association screens with microbes in the identification of naturally selected variants that can impact human health.
Collapse
|
45
|
Bol SM, van Remmerden Y, Sietzema JG, Kootstra NA, Schuitemaker H, van't Wout AB. Donor variation in in vitro HIV-1 susceptibility of monocyte-derived macrophages. Virology 2009; 390:205-11. [PMID: 19535121 DOI: 10.1016/j.virol.2009.05.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 03/15/2009] [Accepted: 05/24/2009] [Indexed: 11/17/2022]
Abstract
Primary human cells from different donors vary in their susceptibility to in vitro infection with HIV-1. In order to perform genetic analysis to identify host factors that affect HIV-1 susceptibility, it is important that a clear phenotype is defined. Here, we report a standardized method to study variation for in vitro HIV-1 infection in monocyte-derived macrophages (MDM) from large numbers of individuals. With this assay, HIV-1 susceptibility of MDM from 489 different donors shows more than 3 log variation and a good correlation with the 32 base pair deletion in the CCR5 co-receptor (ccr5 Delta 32 genotype) of the donors. However, in 7 of 12 donors completely resistant to infection with CCR5-using HIV-1, this was not explained by the ccr5 Delta 32 genotype, showing evidence that other host factors are likely to influence HIV-1 replication in MDM. Infections with VSV-G pseudotyped HIV-1 indeed confirmed the existence of post-entry level restrictions in MDM.
Collapse
Affiliation(s)
- Sebastiaan M Bol
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center of The University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | | | | |
Collapse
|
46
|
Kaur G, Mehra N. Genetic determinants of HIV-1 infection and progression to AIDS: susceptibility to HIV infection. TISSUE ANTIGENS 2009; 73:289-301. [PMID: 19317737 PMCID: PMC7169862 DOI: 10.1111/j.1399-0039.2009.01220.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2009] [Accepted: 01/11/2009] [Indexed: 01/14/2023]
Abstract
Interindividual variability in susceptibility to HIV-1 infection, its transmission, disease progression, and response to antiviral therapy has been attributed to host determinants and variability in multiple genes. Although most people exposed to the virus go on to develop full-blown disease at variable intervals, a proportion of them, labeled as long-term nonprogressors or exposed uninfected, possess 'natural resistance' to infection. A better understanding of genetic and immunologic basis of such a natural resistance to infection would bear important implications in designing therapeutic vaccine designs. The genetic variants that could influence susceptibility to HIV-1 and limit AIDS vary in different populations and among individuals. Meta-analyses of large cohort studies have identified numerous 'AIDS restriction genes' that regulate HIV cell entry (particularly chemokine coreceptors and their ligands), acquired and innate immunity (major histocompatibility complex, killer cell immunoglobulin-like receptor, and cytokines), and others [tripartite interaction motif 5 alpha (TRIM5alpha) and apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G] that influence outcome of HIV infection. Studies carried out in the Indian population with regard to genetic polymorphisms in chemokine receptors have shown that (i) the protective CCR5 Delta32 variant is rare, (ii) CCR5HHE carrying *59402A is associated with increased likelihood of infection and development of AIDS, and (iii) the Indian population generally has low CCL3L1 copy numbers (approximately 2.3). These data have implications in developing screening tests that could identify people at higher or lower risk of infection and rate of disease progression, predict vaccine responsiveness in clinical trials and understand the pathogenic mechanisms.
Collapse
Affiliation(s)
- G Kaur
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India.
| | | |
Collapse
|
47
|
Oleksyk TK, Shrestha S, Truelove AL, Goedert JJ, Donfield SM, Phair J, Mehta S, O'Brien SJ, Smith MW. Extended IL10 haplotypes and their association with HIV progression to AIDS. Genes Immun 2009; 10:309-22. [PMID: 19295541 DOI: 10.1038/gene.2009.9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Interleukin-10 (IL-10) is a pleiotropic cytokine with both immunosuppressive and immunostimulatory functions. Its roles in infections and autoimmunity may have resulted in selective pressures on polymorphisms within the gene, leading to genomic coexistence of several semi-conserved haplotypes involved with diverse pathogen interactions during genomic evolution. Previous studies focused either exclusively on promoter haplotypes or on individual SNPs. We genotyped 21 single nucleotide polymorphisms in the human IL10 gene and examined this variation compared to other mammalian species sequences. Haplotype heterogeneity in human populations is centered around 'classic' 'proximal' promoter polymorphisms: -592, -819 and -1082. High-producing GCC haplotypes are by far the most numerous and diverse group, the intermediate IL-10 producing ACC-inclusive haplotypes seem to be related most closely to the ancestral haplotype, and the ATA-inclusive haplotypes cluster a separate branch with strong bootstrap support. We looked at associations of corresponding haplotypes with HIV progression. A haplotype trend regression confirmed that individuals carrying the low-producing ATA-inclusive haplotypes in European Americans progress to AIDS faster, and most likely explain the role of IL10. Our findings are consistent with the hypothesis that existing polymorphisms in this gene may reflect a balance of historic adaptive responses to autoimmune, infectious and other disease agents.
Collapse
Affiliation(s)
- T K Oleksyk
- Laboratory of Genomic Diversity, and Basic Research Program, Science Applications International Corporation-Frederick, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Piacentini L, Biasin M, Fenizia C, Clerici M. Genetic correlates of protection against HIV infection: the ally within. J Intern Med 2009; 265:110-24. [PMID: 19093964 DOI: 10.1111/j.1365-2796.2008.02041.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Repeated exposure to HIV does not necessarily result in infection and HIV infection does not inevitably lead to the development of the AIDS. Multiple immunological and genetic features can confer resistance to HIV acquisition and progression at different steps in viral infection; a full understanding of these mechanisms could result in the development of novel therapeutic and vaccine approaches for HIV infection. In this review, we focus on the genetic mechanisms associated with resistance to HIV infection and to the progression to AIDS.
Collapse
Affiliation(s)
- L Piacentini
- Department of Preclinical Sciences, University of Milan, Segrate, Milan, Italy
| | | | | | | |
Collapse
|
49
|
Kazadi K, Loeuillet C, Deutsch S, Ciuffi A, Muñoz M, Beckmann JS, Moradpour D, Antonarakis SE, Telenti A. Genomic determinants of the efficiency of internal ribosomal entry sites of viral and cellular origin. Nucleic Acids Res 2008; 36:6918-25. [PMID: 18978018 PMCID: PMC2588522 DOI: 10.1093/nar/gkn812] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Variation in cellular gene expression levels has been shown to be inherited. Expression is controlled at transcriptional and post-transcriptional levels. Internal ribosome entry sites (IRES) are used by viruses to bypass inhibition of cap-dependent translation, and by eukaryotic cells to control translation under conditions when protein synthesis is inhibited. We aimed at identifying genomic determinants of variability in IRES-mediated translation of viral [Encephalomyocarditis virus (EMCV)] and cellular IRES [X-linked inhibitor-of-apoptosis (XIAP) and c-myc]. Bicistronic lentiviral constructs expressing two fluorescent reporters were used to transduce laboratory and B lymphoblastoid cell lines [15 CEPH pedigrees (n = 205) and 50 unrelated individuals]. IRES efficiency varied according to cell type and among individuals. Control of IRES activity has a significant genetic component (h2 of 0.47 and 0.36 for EMCV and XIAP, respectively). Quantitative linkage analysis identified a suggestive locus (LOD 2.35) on chromosome 18q21.2, and genome-wide association analysis revealed of a cluster of SNPs on chromosome 3, intronic to the FHIT gene, marginally associated (P = 5.9E-7) with XIAP IRES function. This study illustrates the in vitro generation of intermediate phenotypes by using cell lines for the evaluation of genetic determinants of control of elements such as IRES.
Collapse
Affiliation(s)
- Kayole Kazadi
- Institute of Microbiology, University Hospital Center, University of Lausanne, Switzerland
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Rio Frio T, Civic N, Ransijn A, Beckmann JS, Rivolta C. Two trans-acting eQTLs modulate the penetrance of PRPF31 mutations. Hum Mol Genet 2008; 17:3154-65. [PMID: 18640990 DOI: 10.1093/hmg/ddn212] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Dominant mutations in the gene encoding the ubiquitously-expressed splicing factor PRPF31 cause retinitis pigmentosa, a form of hereditary retinal degeneration, with reduced penetrance. We and others have previously shown that penetrance is tightly correlated with PRPF31 expression, as lymphoblastoid cell lines (LCLs) from affected patients produce less abundant PRPF31 transcripts than LCLs from their unaffected relatives carrying the same mutation. We have investigated the genetic elements determining the variable expression of PRPF31, and therefore possibly influencing the penetrance of its mutations, by quantifying PRPF31 mRNA levels in LCLs derived from 15 CEPH families (200 individuals), representative of the general population. We found that PRPF31 transcript abundance was a highly variable and highly heritable character. Moreover, by linkage analysis we showed that PRPF31 expression was significantly associated with at least one expression quantitative trait locus (eQTL), spanning a 8.2-Mb region on chromosome 14q21-23. We also investigated a previously mapped penetrance factor located near PRPF31 itself in LCLs from individuals belonging to selected families segregating PRPF31 mutations that displayed reduced penetrance. Our results indicate that, despite its constant association with the non-mutant allele, this factor was able to modulate the expression of both PRPF31 alleles. Furthermore, we showed that LCLs from affected patients have less PRPF31 RNA than those of asymptomatic patients, even at the pre-splicing stage. Altogether, these data demonstrate that PRPF31 mRNA expression and consequently the penetrance of PRPF31 mutations is managed by diffusible compounds encoded by at least two modifiers, acting in a co-regulatory system on both PRPF31 alleles during transcription.
Collapse
Affiliation(s)
- Thomas Rio Frio
- Department of Medical Genetics, University of Lausanne, Rue du Bugnon 27, Lausanne 1005, Switzerland
| | | | | | | | | |
Collapse
|