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Wu J, Xu L, Liu B, Sun W, Hu Y, Yang Y, Guo K, Jia X, Sun H, Wu J, Huang Y, Ji W, Fu S, Qiao Y, Zhang X. Biomedical association analysis between G2/M checkpoint genes and susceptibility to HIV-1 infection and AIDS progression from a northern chinese MSM population. AIDS Res Ther 2023; 20:51. [PMID: 37468905 PMCID: PMC10357704 DOI: 10.1186/s12981-023-00536-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/12/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND MSM are at high risk of HIV infection. Previous studies have shown that the cell cycle regulation plays an important role in HIV-1 infection, especially at the G2/M checkpoint. ATR, Chk1, Cdc25C and CDK1 are key genes of G2/M checkpoint. However, the association between SNPs of these genes and susceptibility to HIV-1 infection and AIDS progression remains unknown. METHODS In this study, 42 tSNPs from the above four G2/M checkpoint genes were genotyped in 529 MSM and 529 control subjects from northern China to analyze this association. RESULTS The results showed that rs34660854 A and rs75368165 A in ATR gene and rs3756766 A in Cdc25C gene could increase the risk of HIV-1 infection (P = 0.049, OR = 1.234, 95% CI 1.001-1.521; P = 0.020, OR = 1.296, 95% CI 1.042-1.611; P = 0.011, OR = 1.392, 95% CI 1.080-1.794, respectively), while Chk1 rs10893405 (P = 0.029, OR = 1.629, 95% CI 1.051-2.523) were significantly associated with AIDS progression. Besides, rs34660854 (P = 0.019, OR = 1.364, 95% CI 1.052-1.769; P = 0.022, OR = 1.337, 95% CI 1.042-1.716, under Codominant model and Dominant model, respectively) and rs75368165 (P = 0.006, OR = 1.445, 95% CI = 1.114-1.899; P = 0.007, OR = 1.418, 95% CI 1.099-1.831, under Codominant model and Dominant model, respectively) in ATR gene, rs12576279 (P = 0.013, OR = 0.343, 95% CI 0.147-0.800; P = 0.048, OR = 0.437, 95% CI 0.192-0.991, under Codominant model and Dominant model, respectively) and rs540436 (P = 0.012, OR = 1.407, 95% CI 1.077-1.836; P = 0.021, OR = 1.359, 95% CI 1.048-1.762, under Codominant model and Dominant model, respectively) in Chk1 gene, rs3756766 (P = 0.013, OR = 1.455, 95% CI 1.083-1.954; P = 0.009, OR = 1.460, 95% CI 1.098-1.940, under Codominant model and Dominant model, respectively) in Cdc25C gene and rs139245206 (P = 0.022, OR = 5.011, 95% CI 1.267-19.816; P = 0.020, OR = 5.067, 95% CI 1.286-19.970, under Codominant model and Recessive model, respectively) in CDK1 gene were significantly associated with HIV-1 infection under different models. CONCLUSIONS We found that genetic variants of G2/M checkpoint genes had a molecular influence on the occurrence of HIV-1 infection and AIDS progression in a northern Chinese MSM population.
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Affiliation(s)
- Jiawei Wu
- College of Basic Medicine, Harbin Medical University-Daqing Campus, Daqing, Heilongjiang Province, 163319, China
| | - Lidan Xu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang Province, 150081, China
| | - Bangquan Liu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang Province, 150081, China
| | - Yuanting Hu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China
| | - Yi Yang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China
| | - Keer Guo
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China
| | - Xueyuan Jia
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang Province, 150081, China
| | - Haiming Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang Province, 150081, China
| | - Jie Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang Province, 150081, China
| | - Yun Huang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang Province, 150081, China
| | - Wei Ji
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang Province, 150081, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang Province, 150081, China
| | - Yuandong Qiao
- College of Basic Medicine, Harbin Medical University-Daqing Campus, Daqing, Heilongjiang Province, 163319, China.
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China.
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang Province, 150081, China.
| | - Xuelong Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang Province, 150081, China.
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang Province, 150081, China.
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Ribeiro HL, Maia ARS, de Oliveira RTG, Costa MB, Farias IR, de Paula Borges D, de Sousa JC, Magalhães SMM, Pinheiro RF. DNA repair gene expressions are related to bone marrow cellularity in myelodysplastic syndrome. J Clin Pathol 2017; 70:970-980. [DOI: 10.1136/jclinpath-2016-204269] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/21/2017] [Accepted: 04/07/2017] [Indexed: 12/18/2022]
Abstract
ObjectiveTo evaluate the expression of genes related to nuclear excision (ERCC8, XPA and XPC), homologous recombination and non-homologous end-joining (ATM, BRCA1, BRCA2 and LIG4) repair mechanisms, using quantitative PCR methodologies, and it relation with bone marrow cellularity in myelodysplastic syndrome (MDS).Methods and resultsA total of 51 adult de novo patients with MDS (3 refractory anaemia (RA), 11 refractory anaemia with ringed sideroblasts (RARS), 28 refractory cytopenia with multilineage dysplasia (RCMD), 3 refractory anaemia with excess blasts type I (RAEB-I), 5 refractory anaemia with excess blasts type II (RAEB-II), and 1 chronic myelomonocytic leukaemia (CMML) were evaluated. For karyotype, 16.2% patients were defined as very low prognosis, 59.5% low risk, 8.1% intermediate risk, 5.4% high risk and 10.8% very high risk. For bone marrow cellularity, 17.6%, 17.6% and 64.7% presented as hypocellular, normocellular and hypercellular, respectively. Patients with hypocellular MDS had significantly decreased expression of ATM (p=0.000), BRCA1 (p=0.014), BRCA2 (p=0.003), LIG4 (p=0.004) and ERCC8 (p=0.000) than those with normocellular/hypercellular bone marrow, whereas XPA (p=0.049) and XPC (p=0.000) genes were increased. In patients with hypoplastic MDS, a low expression of ATM (p=0.0268), LIG4 (p=0.0199) and ERCC8 (p=0.0493) was significantly associated with the presence of chromosomal abnormalities. We detected positive correlations between BRCA1 and BRCA2 (r=0.416; p=0.007), ATM and LIG4 (r=0.472; p=0.001), LIG4 and BRCA1 (r=0.333; p=0.026), LIG4 and BRCA2 (r=0.334; p=0.025), ATM and XPA (r=0.377; p=0.008), ATM and XPC (r=0.287; p=0.046), LIG4 and XPC (r=0.371; p=0.007) and XPA and XPC genes (r=0.895; p=0.0000). We also found among all patients evaluated that correlation with LIG4 occurred most often.ConclusionsThese correlations demonstrate the important intrinsic relations between single and double DNA strand breaks genes in MDS, emphasising that these genes are related to MDS pathogenesis.
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Mekli K, Nazroo JY, Marshall AD, Kumari M, Pendleton N. Proinflammatory genotype is associated with the frailty phenotype in the English Longitudinal Study of Ageing. Aging Clin Exp Res 2016; 28:413-21. [PMID: 26248682 PMCID: PMC4877432 DOI: 10.1007/s40520-015-0419-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 07/08/2015] [Indexed: 01/22/2023]
Abstract
Background Frailty is a state of increased vulnerability to poor resolution of homeostasis after a stressor event, which increases the risk of adverse outcomes including falls, disability and death. The underlying pathophysiological pathways of frailty are not known but the hypothalamic–pituitary–adrenal axis and heightened chronic systemic inflammation appear to be major contributors. Methods We used the English Longitudinal Study of Ageing dataset of 3160 individuals over the age of 50 and assessed their frailty status according to the Fried-criteria. We selected single nucleotide polymorphisms in genes involved in the steroid hormone or inflammatory pathways and performed linear association analysis using age and sex as covariates. To support the biological plausibility of any genetic associations, we selected biomarker levels for further analyses to act as potential endophenotypes of our chosen genetic loci. Results The strongest association with frailty was observed in the Tumor Necrosis Factor (TNF) (rs1800629, P = 0.001198, β = 0.0894) and the Protein Tyrosine Phosphatase, Receptor type, J (PTPRJ) (rs1566729, P = 0.001372, β = 0.09397) genes. Rs1800629 was significantly associated with decreased levels of high-density lipoprotein (HDL) (P = 0.00949) and cholesterol levels (P = 0.00315), whereas rs1566729 was associated with increased levels of HDL (P = 0.01943). After correcting for multiple testing none of the associations remained significant. Conclusions We provide potential evidence for the involvement of a multifunctional proinflammatory cytokine gene (TNF) in the frailty phenotype. The implication of this gene is further supported by association with the endophenotype biomarker results. Electronic supplementary material The online version of this article (doi:10.1007/s40520-015-0419-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Krisztina Mekli
- Cathie Marsh Institute for Social Research, School of Social Sciences, University of Manchester, Humanities Bridgeford Street, Oxford Road, Manchester, M13 9PL, UK.
| | - James Y Nazroo
- Cathie Marsh Institute for Social Research, School of Social Sciences, University of Manchester, Humanities Bridgeford Street, Oxford Road, Manchester, M13 9PL, UK
| | - Alan D Marshall
- Cathie Marsh Institute for Social Research, School of Social Sciences, University of Manchester, Humanities Bridgeford Street, Oxford Road, Manchester, M13 9PL, UK
| | - Meena Kumari
- Department of Epidemiology and Public Health, University College London, London, UK
- Institute for Social and Economic Research, University of Essex, Essex, UK
| | - Neil Pendleton
- Clinical and Cognitive Neurosciences, Institute of Brain, Behaviour and Mental Health, University of Manchester, Manchester, UK
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Baca-López K, Mayorga M, Hidalgo-Miranda A, Gutiérrez-Nájera N, Hernández-Lemus E. The role of master regulators in the metabolic/transcriptional coupling in breast carcinomas. PLoS One 2012; 7:e42678. [PMID: 22952604 PMCID: PMC3428335 DOI: 10.1371/journal.pone.0042678] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/10/2012] [Indexed: 12/24/2022] Open
Abstract
Metabolic transformations have been reported as involved in neoplasms survival. This suggests a role of metabolic pathways as potential cancer pharmacological targets. Modulating tumor's energy production pathways may become a substantial research area for cancer treatment. The significant role of metabolic deregulation as inducing transcriptional instabilities and consequently whole-system failure, is thus of foremost importance. By using a data integration approach that combines experimental evidence for high-throughput genome wide gene expression, a non-equilibrium thermodynamics analysis, nonlinear correlation networks as well as database mining, we were able to outline the role that transcription factors MEF2C and MNDA may have as main master regulators in primary breast cancer phenomenology, as well as the possible interrelationship between malignancy and metabolic dysfunction. The present findings are supported by the analysis of 1191 whole genome gene expression experiments, as well as probabilistic inference of gene regulatory networks, and non-equilibrium thermodynamics of such data. Other evidence sources include pathway enrichment and gene set enrichment analyses, as well as motif comparison with a comprehensive gene regulatory network (of homologue genes) in Arabidopsis thaliana. Our key finding is that the non-equilibrium free energies provide a realistic description of transcription factor activation that when supplemented with gene regulatory networks made us able to find deregulated pathways. These analyses also suggest a novel potential role of transcription factor energetics at the onset of primary tumor development. Results are important in the molecular systems biology of cancer field, since deregulation and coupling mechanisms between metabolic activity and transcriptional regulation can be better understood by taking into account the way that master regulators respond to physicochemical constraints imposed by different phenotypic conditions.
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Affiliation(s)
- Karol Baca-López
- Computational Genomics Department, National Institute of Genomic Medicine, México City, México
- School of Sciences, Autonomous University of the State of México, Toluca, México
| | - Miguel Mayorga
- School of Sciences, Autonomous University of the State of México, Toluca, México
| | | | - Nora Gutiérrez-Nájera
- Proteomics Core Facility, National Institute of Genomic Medicine, México City, México
| | - Enrique Hernández-Lemus
- Computational Genomics Department, National Institute of Genomic Medicine, México City, México
- Center for Complexity Sciences, National Autonomous University of México, México City, México
- * E-mail:
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