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Wang J, Tan L, Yu X, Cao X, Jia B, Chen R, Li J. lncRNA ZNRD1-AS1 promotes malignant lung cell proliferation, migration, and angiogenesis via the miR-942/TNS1 axis and is positively regulated by the m 6A reader YTHDC2. Mol Cancer 2022; 21:229. [PMID: 36581942 PMCID: PMC9801573 DOI: 10.1186/s12943-022-01705-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022] Open
Abstract
RATIONALE Lung cancer is the most prevalent form of cancer and has a high mortality rate, making it a global public health concern. The N6-methyladenosine (m6A) modification is a highly dynamic and reversible process that is involved in a variety of essential biological processes. Using in vitro, in vivo, and multi-omics bioinformatics, the present study aims to determine the function and regulatory mechanisms of the long non-coding (lnc)RNA zinc ribbon domain-containing 1-antisense 1 (ZNRD1-AS1). METHODS The RNAs that were bound to the m6A 'reader' were identified using YTH domain-containing 2 (YTHDC2) RNA immunoprecipitation (RIP)-sequencing. Utilizing methylated RIP PCR/quantitative PCR, pull-down, and RNA stability assays, m6A modification and ZNRD1-AS1 regulation were analyzed. Using bioinformatics, the expression levels and clinical significance of ZNRD1-AS1 in lung cancer were evaluated. Using fluorescent in situ hybridization and quantitative PCR assays, the subcellular location of ZNRD1-AS1 was determined. Using cell migration, proliferation, and angiogenesis assays, the biological function of ZNRD1-AS1 in lung cancer was determined. In addition, the tumor suppressor effect of ZNRD1-AS1 in vivo was validated using a xenograft animal model. Through bioinformatics analysis and in vitro assays, the downstream microRNAs (miRs) and competing endogenous RNAs were also predicted and validated. RESULTS This study provided evidence that m6A modification mediates YTHDC2-mediated downregulation of ZNRD1-AS1 in lung cancer and cigarette smoke-exposed cells. Low levels of ZNRD1-AS1 expression were linked to adverse clinicopathological characteristics, immune infiltration, and prognosis. ZNRD1-AS1 overexpression was shown to suppress lung cancer cell proliferation, migration, and angiogenesis in vitro and in vivo, and to reduce tumor growth in nude mice. ZNRD1-AS1 expression was shown to be controlled by treatment of cells with either the methylation inhibitor 3-Deazaadenosine or the demethylation inhibitor Meclofenamic. Furthermore, the miR-942/tensin 1 (TNS1) axis was demonstrated to be the downstream regulatory signaling pathway of ZNRD1-AS1. CONCLUSIONS ZNRD1-AS1 serves an important function and has clinical relevance in lung cancer. In addition, the findings suggested that m6A modification could mediate the regulation of the ZNRD1-AS1/miR-942/TNS1 axis via the m6A reader YTHDC2.
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Affiliation(s)
- Jin Wang
- grid.263761.70000 0001 0198 0694School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu China
| | - Lirong Tan
- grid.263761.70000 0001 0198 0694School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu China
| | - Xueting Yu
- grid.263761.70000 0001 0198 0694School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu China
| | - Xiyuan Cao
- grid.263761.70000 0001 0198 0694School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu China
| | - Beibei Jia
- grid.263761.70000 0001 0198 0694School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu China
| | - Rui Chen
- grid.452666.50000 0004 1762 8363Department of Respiratory Medicine, The Second Affiliated Hospital of Soochow University, Suzhou Jiangsu, 215004 China
| | - Jianxiang Li
- grid.263761.70000 0001 0198 0694School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu China
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Celerino da Silva R, Segat L, Kuhn L, Chies JAB, Crovella S. Association of SNPs in HLA-C and ZNRD1 Genes With HIV-1 Mother-to-Child Transmission in Zambia Population. J Acquir Immune Defic Syndr 2021; 86:509-515. [PMID: 33252547 DOI: 10.1097/qai.0000000000002584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/15/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND Human leukocyte antigen C (HLA-C) and Zinc ribbon domain containing 1 (ZNRD1) are considered HIV-1 restriction factors and are expressed in the placenta. Variations in HLA-C and ZNRD1 genes are known to influence HIV-1 infection, including viral replication and progression to AIDS. Little is known about the role of variants in these genes in HIV-1 mother-to-child transmission. METHODS We evaluated the distribution of HLA-C (rs10484554, rs9264942) and ZNRD1 (rs8321, rs3869068) variants in a Zambian population composed of 333 children born to HIV-1+ mothers (248 HIV-1 noninfected/85 HIV-1 infected) and 97 HIV-1+ mothers. RESULTS Genotypic distribution of HLA-C and ZNRD1 were in Hardy-Weinberg equilibrium, except for HLA-C rs10484554 in both groups. In mothers, no significant differences were observed in their allele and genotypic distributions for both genes. The T and TT variants (rs10484554-HLA-C) were significantly more frequent among HIV-1+ children, specifically those who acquired the infection in utero (IU) and intrapartum (IP). For ZNRD1, the T allele (rs3869068) was more frequent in HIV-1- children, showing significant differences in relation to those infected via IP and postpartum (PP). The CT and TT genotypes were significantly more frequent in HIV-1- children. CONCLUSIONS Variations in HLA-C (T and TT-rs10484554) and ZNRD1 (T and CT/TT-rs3869068) can increase and decrease the susceptibility to HIV-1 infection via mother-to-child transmission, respectively. Further studies are encouraged focusing on a greater number of variants and sample size, with functional validation and in other populations.
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Affiliation(s)
- Ronaldo Celerino da Silva
- Department of Genetics, Federal University of Pernambuco (UFPE), Recife, Brazil
- Laboratory of Immunopathology Keizo Asami (LIKA), Federal University of Pernambuco (UFPE) Recife, Brazil
| | - Ludovica Segat
- Department of Surgical and Health Medical Sciences, Azienda Sanitaria Universitaria Integrata Giuliano Isontina (ASUGI), UCO Hygiene and Public Health, University of Trieste, Trieste, Italy
| | - Louise Kuhn
- Gertrude H. Sergievsky Center and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY; and
| | - José Artur Bogo Chies
- Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Sergio Crovella
- Department of Genetics, Federal University of Pernambuco (UFPE), Recife, Brazil
- Laboratory of Immunopathology Keizo Asami (LIKA), Federal University of Pernambuco (UFPE) Recife, Brazil
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Fernandes V, Brucato N, Ferreira JC, Pedro N, Cavadas B, Ricaut FX, Alshamali F, Pereira L. Genome-Wide Characterization of Arabian Peninsula Populations: Shedding Light on the History of a Fundamental Bridge between Continents. Mol Biol Evol 2019; 36:575-586. [PMID: 30649405 DOI: 10.1093/molbev/msz005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Arabian Peninsula (AP) was an important crossroad between Africa, Asia, and Europe, being the cradle of the structure defining these main human population groups, and a continuing path for their admixture. The screening of 741,000 variants in 420 Arabians and 80 Iranians allowed us to quantify the dominant sub-Saharan African admixture in the west of the peninsula, whereas South Asian and Levantine/European influence was stronger in the east, leading to a rift between western and eastern sides of the Peninsula. Dating of the admixture events indicated that Indian Ocean slave trade and Islamization periods were important moments in the genetic makeup of the region. The western-eastern axis was also observable in terms of positive selection of diversity conferring lactose tolerance, with the West AP developing local adaptation and the East AP acquiring the derived allele selected in European populations and existing in South Asia. African selected malaria resistance through the DARC gene was enriched in all Arabian genomes, especially in the western part. Clear European influences associated with skin and eye color were equally frequent across the Peninsula.
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Affiliation(s)
- Veronica Fernandes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Nicolas Brucato
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Joana C Ferreira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Nicole Pedro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Bruno Cavadas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - François-Xavier Ricaut
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Farida Alshamali
- Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
| | - Luisa Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,Faculdade de Medicina da Universidade do Porto, Porto, Portugal
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Tsiara CG, Nikolopoulos GK, Dimou NL, Pantavou KG, Bagos PG, Mensah B, Talias M, Braliou GG, Paraskeva D, Bonovas S, Hatzakis A. Interleukin gene polymorphisms and susceptibility to HIV-1 infection: a meta-analysis. J Genet 2018; 97:235-251. [PMID: 29666343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Some subjects are repeatedly exposed to human immunodeficiency virus (HIV), yet they remain uninfected. This suggests the existence of host-resistance mechanisms. The current study synthesizes the evidence regarding the association between interleukin (IL) gene polymorphisms and HIV susceptibility. Medline, Scopus and the Web of Science databases were systematically searched, and a meta-analysis of case-control studies was conducted. Univariate and bivariate methods were used. The literature search identified 42 eligible studies involving 15,727 subjects. Evidence was obtained on eight single-nucleotide polymorphisms (SNPs): IL1A -889 C>T (rs1800587), IL1B +3953/4 C>T (rs1143634), IL4 -589/90 C>T (rs2243250), IL6 -174 G>C (rs1800795), IL10 -592 C>A (rs1800872), IL10-1082 A>G (rs1800896), IL12B -1188 A>C (rs3212227) and IL28B C>T (rs12979860). The IL1B +3953/4 C>T variant appears to increase the risk of HIV acquisition, under the assumption of a recessive genetic model (odds ratio (OR): 4.47, 95% CI: 2.35-8.52). The AA homozygotes of the IL10 -592 C>A SNP had an increased, marginally nonsignificant, risk (OR: 1.39, 95% CI: 0.97-2.01). It reached, however, significance in sub analyses (OR: 1.49, 95% CI: 1.04-2.12). Finally, the well-studied hepatitis C virus (HCV) infection IL28B (rs12979860) CT/TT genotypes were associated with a 27% decrease in HIV infection risk, especially in populations infected with HCV (OR: 0.73, 95% CI: 0.57-0.95). Interleukin signalling is perhaps important in HIV infection and some interleukin genetic variants may affect the risk of HIV acquisition. Approaches targeting specific genes and genome wide association studies should be conducted to decipher the effect of these polymorphisms.
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Affiliation(s)
- Chrissa G Tsiara
- Hellenic Centre for Disease Control and Prevention, 15123 Athens, Greece. ,
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Liu Z, Song C, Wen J, Xu L, Liu Y, Zhu J, Zhu L, Hu Z, Ma H, Liu L. Hepatitis B virus genotypes, expression quantitative trait loci for ZNRD1-AS1 and their interactions in hepatocellular carcinoma. Oncotarget 2018; 7:44076-44083. [PMID: 27286450 PMCID: PMC5190080 DOI: 10.18632/oncotarget.9854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/01/2016] [Indexed: 12/13/2022] Open
Abstract
Genetic variants in zinc ribbon domain-containing 1 antisense RNA 1 (ZNRD1-AS1) have been reported to be associated with development of hepatocellular carcinoma (HCC). We sought to determine the influences of ZNRD1-AS1 polymorphisms and their interactions with Hepatitis B virus (HBV) genotypes on the risk of HCC. In this study, we conducted a large population case-control study with 1,507 HBV-related HCC cases and 1,560 HBV persistent carriers. Three single-nucleotide polymorphisms (SNPs) in ZNRD1-AS1 (rs3757328, rs6940552 and rs9261204) were genotyped using a TaqMan allelic discrimination assay, and the HBV genotypes were identified by multiplex PCR. We found consistently significant associations between the ZNRD1-AS1 rs6940552 and rs9261204 SNPs with an increased risk of HCC (additive genetic model: adjusted OR = 1.16, 95% CI = 1.03-1.32 for rs6940552; adjusted OR =1.20, 95% CI = 1.06-1.35 for rs9261204) and found a borderline association between rs3757328 and HCC risk. Besides, we observed a dose-dependent relationship between increasing numbers of variant alleles of the SNPs and HCC risk (P for trend <0.001). Moreover, we observed a stronger combined effect of the three SNPs on HCC risk among the subjects infected with non-B genotype HBV (adjusted OR = 1.26, 95% CI = 1.05-1.50) compared with HBV B-related genotypes (adjusted OR = 0.89, 95% CI = 0.69-1.15; P= 0.029 for heterogeneity test). We also found that a multiplicative interaction between the variant alleles and the HBV genotype significantly affected HCC susceptibility (P = 0.030). Together, these results indicate that ZNRD1-AS1 may influence HCC risk accompanied by HBV genotypes.
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Affiliation(s)
- Zhenzhen Liu
- Digestive Endoscopy Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ci Song
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Juan Wen
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Nanjing, China
| | - Lu Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yao Liu
- Pathology Center and Department of Pathology, Soochow University, Suzhou, China
| | - Jian Zhu
- Qidong Liver Cancer Institute, The First People's Hospital of Qidong, Qidong, China
| | - Liguo Zhu
- Department of Infection Diseases, Jiangsu Province Center for Disease Prevention and Control, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Li Liu
- Digestive Endoscopy Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Wang F, Wang H, Wang L, Zhou S, Chang M, Zhou J, Dou Y, Wang Y, Shi X. Association Between Single Nucleotide Polymorphisms in NFATC1 Signaling Pathway Genes and Susceptibility to Congenital Heart Disease in the Chinese Population. Pediatr Cardiol 2016; 37:1548-1561. [PMID: 27567908 DOI: 10.1007/s00246-016-1469-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/16/2016] [Indexed: 01/29/2023]
Abstract
The nuclear factor of activated T lymphocytes (NFATC1) signaling has been demonstrated to play important roles in cardiac valve and septal development. Genetic variants in genes involved in NFATC1 signaling may affect their expression and promote the formation of congenital heart disease (CHD). The goal of this study was to investigate the associations of single nucleotide polymorphism (SNP) in seven genes (NFATC1, VEGFR, VEGF, RANKL, FGFR1, BCL-6 and ZNRD1) with the risk of CHD. Twenty-nine polymorphisms were genotyped by using MassARRAY RS1000 platform in 277 CHD child patients and 293 controls from the Henan Province in China. Fours SNPs were excluded for the association analysis because of deviation from the Hardy-Weinberg equilibrium. Of the 25 SNPs, only two were found to be significantly associated with increased CHD risk after Bonferroni correction (RANKL, rs4531631: homozygous, AA vs. GG; OR 2.38, 95 % CI 1.40-4.07, p = 0.001; recessive, AA vs. AG + GG; OR 2.54, 95 % CI 1.53-4.22, p = 0.0003; FGFR1, rs13317: recessive, CC vs. CT + TT; OR 2.06, 95 % CI 1.30-3.25, p = 0.00196). Our findings suggest rs4531631 and rs13317 may be potential biomarkers for genetic diagnosis and treatment of CHD.
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Affiliation(s)
- Fengyu Wang
- Henan Research Institute of Population and Family Planning, National Health and Family Planning Commission Key Laboratory of Birth Defects Prevention, No. 26, Jingwu Road, Jinshui, Zhengzhou, 450002, China
| | - Haili Wang
- Henan Research Institute of Population and Family Planning, National Health and Family Planning Commission Key Laboratory of Birth Defects Prevention, No. 26, Jingwu Road, Jinshui, Zhengzhou, 450002, China
| | - Lina Wang
- Henan Research Institute of Population and Family Planning, National Health and Family Planning Commission Key Laboratory of Birth Defects Prevention, No. 26, Jingwu Road, Jinshui, Zhengzhou, 450002, China
| | - Shiyuan Zhou
- Henan Research Institute of Population and Family Planning, National Health and Family Planning Commission Key Laboratory of Birth Defects Prevention, No. 26, Jingwu Road, Jinshui, Zhengzhou, 450002, China.
| | - Mingxiu Chang
- Henan Research Institute of Population and Family Planning, National Health and Family Planning Commission Key Laboratory of Birth Defects Prevention, No. 26, Jingwu Road, Jinshui, Zhengzhou, 450002, China
| | - Jiping Zhou
- Henan Research Institute of Population and Family Planning, National Health and Family Planning Commission Key Laboratory of Birth Defects Prevention, No. 26, Jingwu Road, Jinshui, Zhengzhou, 450002, China
| | - Yongheng Dou
- Henan Research Institute of Population and Family Planning, National Health and Family Planning Commission Key Laboratory of Birth Defects Prevention, No. 26, Jingwu Road, Jinshui, Zhengzhou, 450002, China
| | - Yanli Wang
- Henan Research Institute of Population and Family Planning, National Health and Family Planning Commission Key Laboratory of Birth Defects Prevention, No. 26, Jingwu Road, Jinshui, Zhengzhou, 450002, China
| | - Xiangdong Shi
- Henan Research Institute of Population and Family Planning, National Health and Family Planning Commission Key Laboratory of Birth Defects Prevention, No. 26, Jingwu Road, Jinshui, Zhengzhou, 450002, China
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Thørner LW, Erikstrup C, Harritshøj LH, Larsen MH, Kronborg G, Pedersen C, Larsen CS, Pedersen G, Gerstoft J, Obel N, Ullum H. Impact of polymorphisms in the HCP5 and HLA-C, and ZNRD1 genes on HIV viral load. INFECTION GENETICS AND EVOLUTION 2016; 41:185-190. [PMID: 27083073 DOI: 10.1016/j.meegid.2016.03.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/11/2016] [Accepted: 03/30/2016] [Indexed: 01/16/2023]
Abstract
AIMS Single nucleotide polymorphisms (SNPs) in the human leucocyte antigen (HLA) complex P5 (HCP5), HLA-C, and near the zinc ribbon domain containing 1 (ZNRD1) have been shown to influence viral load (VL) set point in HIV-infected individuals with a known seroconversion onset. We aimed to determine the influence of HCP5 rs2395029, HLA-C rs9264942, and ZNRD1 rs3869068 on VL in antiretroviral-naïve individuals and on time to the first VL<51 copies/ml and on CD4(+) T-cell recovery after initiation of combination antiretroviral therapy (cART). MATERIAL AND METHODS We genotyped the rs2395029 (A>C), rs9264942 (T>C), and rs3869068 (C>T) SNPs in 1897 Caucasians from The Danish HIV Cohort Study - a prospective, nationwide, population-based study of HIV-infected individuals in Denmark. General linear models evaluated the effect of SNPs on VL in antiretroviral-naïve individuals 0-18months after diagnosis and on CD4(+) T-cell recovery during cART. Cox proportional hazard regression analysis assessed the association with time to first VL<51 copies/ml. All models were assuming additive genetic effects. RESULTS The rs2395029, rs9264942, and rs3869068 minor alleles were associated with lower VL in antiretroviral-naïve individuals (rs2395029: [mean VL (copies/ml)], A/A: 70,795 [61,660-79,433], A/C: 33,884 [19,498-58,884], P=0.002; rs9264942: TT: 81,283 [67,608-97,724], T/C: 63,096 [54,954-75,858], CC: 38,905 [25,119-58,884], P<0.0001; rs3869068, CC: 72,444 [63,096-83,176], C/T: 45,709 [33,113-64,565], TT: 58,884 [20,417-169,824], P=0.01). Moreover, the C-alleles of rs2395029 and rs9264942 were associated with shorter time to VL<51 copies/ml: (HR [95% confidence interval], 1.67 [1.09-1.72], P=0.008; 1.16 [1.06-1.28], P=0.002; 1.30 [1.08-1.53], P=0.005, respectively, adjusted for last VL before cART). None of the SNPs predicted CD4(+) T-cell recovery during cART. CONCLUSIONS The minor alleles of rs2395029, rs9264942, and rs3689068 associate with lower VL among antiretroviral-naïve individuals and with shorter time to first VL<51copies/ml during cART even after adjustment for VL before cART.
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Affiliation(s)
- Lise Wegner Thørner
- Dept. of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark.
| | - Christian Erikstrup
- Dept. of Clinical Immunology, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Lene Holm Harritshøj
- Dept. of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Margit Hørup Larsen
- Dept. of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Gitte Kronborg
- Dept. of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Court Pedersen
- Dept. of Infectious Diseases, Odense University Hospital, Odense, Denmark
| | | | - Gitte Pedersen
- Dept. of Infectious Diseases, Aarhus University Hospital, Aalborg, Denmark
| | - Jan Gerstoft
- Dept. of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Niels Obel
- Dept. of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Henrik Ullum
- Dept. of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
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An P, Penugonda S, Thorball CW, Bartha I, Goedert JJ, Donfield S, Buchbinder S, Binns-Roemer E, Kirk GD, Zhang W, Fellay J, Yu XF, Winkler CA. Role of APOBEC3F Gene Variation in HIV-1 Disease Progression and Pneumocystis Pneumonia. PLoS Genet 2016; 12:e1005921. [PMID: 26942578 PMCID: PMC4778847 DOI: 10.1371/journal.pgen.1005921] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 02/16/2016] [Indexed: 12/26/2022] Open
Abstract
Human APOBEC3 cytidine deaminases are intrinsic resistance factors to HIV-1. However, HIV-1 encodes a viral infectivity factor (Vif) that degrades APOBEC3 proteins. In vitro APOBEC3F (A3F) anti-HIV-1 activity is weaker than A3G but is partially resistant to Vif degradation unlike A3G. It is unknown whether A3F protein affects HIV-1 disease in vivo. To assess the effect of A3F gene on host susceptibility to HIV- acquisition and disease progression, we performed a genetic association study in six well-characterized HIV-1 natural cohorts. A common six-Single Nucleotide Polymorphism (SNP) haplotype of A3F tagged by a codon-changing variant (p. I231V, with allele (V) frequency of 48% in European Americans) was associated with significantly lower set-point viral load and slower rate of progression to AIDS (Relative Hazards (RH) = 0.71, 95% CI: 0.56, 0.91) and delayed development of pneumocystis pneumonia (PCP) (RH = 0.53, 95% CI: 0.37-0.76). A validation study in the International Collaboration for the Genomics of HIV (ICGH) showed a consistent association with lower set-point viral load. An in vitro assay revealed that the A3F I231V variant may influence Vif mediated A3F degradation. Our results provide genetic epidemiological evidence that A3F modulates HIV-1/AIDS disease progression.
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Affiliation(s)
- Ping An
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- * E-mail: (PA); (CAW)
| | - Sudhir Penugonda
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Christian W. Thorball
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Istvan Bartha
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - James J. Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Sharyne Donfield
- Rho, Inc., Chapel Hill, North Carolina, United States of America
| | - Susan Buchbinder
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Elizabeth Binns-Roemer
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Gregory D. Kirk
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, China
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Xiao-Fang Yu
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, China
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Cheryl A. Winkler
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- * E-mail: (PA); (CAW)
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Assone T, Paiva A, Fonseca LAM, Casseb J. Genetic Markers of the Host in Persons Living with HTLV-1, HIV and HCV Infections. Viruses 2016; 8:v8020038. [PMID: 26848682 PMCID: PMC4776193 DOI: 10.3390/v8020038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 12/21/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1), hepatitis C virus (HCV) and human immunodeficiency virus type 1 (HIV-1) are prevalent worldwide, and share similar means of transmission. These infections may influence each other in evolution and outcome, including cancer or immunodeficiency. Many studies have reported the influence of genetic markers on the host immune response against different persistent viral infections, such as HTLV-1 infection, pointing to the importance of the individual genetic background on their outcomes. However, despite recent advances on the knowledge of the pathogenesis of HTLV-1 infection, gaps in the understanding of the role of the individual genetic background on the progress to disease clinically manifested still remain. In this scenario, much less is known regarding the influence of genetic factors in the context of dual or triple infections or their influence on the underlying mechanisms that lead to outcomes that differ from those observed in monoinfection. This review describes the main factors involved in the virus–host balance, especially for some particular human leukocyte antigen (HLA) haplotypes, and other important genetic markers in the development of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and other persistent viruses, such as HIV and HCV.
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Affiliation(s)
- Tatiane Assone
- Laboratory of Dermatology and Immune deficiencies, Department of Dermatology, University of São Paulo Medical School, LIM56, Av. Dr. Eneas de Carvalho Aguiar 500, 3rd Floor, Building II, São Paulo, SP, Brazil.
- Institute of Tropical Medicine of São Paulo, São Paulo, Brazil.
| | - Arthur Paiva
- Institute of Tropical Medicine of São Paulo, São Paulo, Brazil.
| | - Luiz Augusto M Fonseca
- Department of Preventive Medicine, University of São Paulo Medical School, São Paulo, Brazil.
| | - Jorge Casseb
- Laboratory of Dermatology and Immune deficiencies, Department of Dermatology, University of São Paulo Medical School, LIM56, Av. Dr. Eneas de Carvalho Aguiar 500, 3rd Floor, Building II, São Paulo, SP, Brazil.
- Institute of Tropical Medicine of São Paulo, São Paulo, Brazil.
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Abstract
PURPOSE OF REVIEW Rapid expansion of genomic technologies has resulted in an unprecedented ability to interrogate the impact of human genetic variation on disease. HIV-1 infection is a unique model for studying this impact because host genetic variation influences both clinical outcome and the genetic sequence and evolution of the pathogen itself. RECENT FINDINGS Several candidate gene studies have proposed novel associations with HIV acquisition and/or disease progression; however, many of these are not supported by larger genome-wide association studies. Thus, controversy remains as to which host and viral genetic factors truly impact HIV infection. Novel methods for assessing the genetic (viral and host) component of disease progression are becoming important areas of investigation. SUMMARY To fully understand the impact of human genetic variation in HIV disease, the field will need to come together to set a standard for discovery of new genes. Additionally, novel avenues of investigation such as sequencing studies (to define the role of rare variants), studies of epistasis and host/viral genome interaction will be of great value.
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