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Liu K, Liu J, Liu Y, Wang H, Wang Z, Liu J, Wen S. Association study of WNK1 genetic variants and essential hypertension risk in the Northern Han Chinese in Beijing. Front Genet 2023; 14:1234536. [PMID: 37779914 PMCID: PMC10541150 DOI: 10.3389/fgene.2023.1234536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
Background: Essential hypertension (EH) is a complex disorder resulting from interaction of genetic and environmental factors. Lysine deficient protein kinase 1 (WNK1) plays a very important role in maintaining renal potassium, sodium and chlorine ions balance as well as the regulation of blood pressure, so the WNK1 gene is considered a key gene for EH. This study thus sought to evaluate possible genetic associations between the WNK1 genetic variants and EH risk in the Northern Han Chinese population in Beijing. Methods: This study included 476 hypertensive subjects and 491 normotensive subjects. A total of 12 tag SNVs of WNK1 gene were genotyped successfully by TaqMan assay. Comparisons of the genotypic and allelic frequency between cases and controls were made by using the chi-square test. Logistic regression analyses were performed under different genetic models, and haplotype analysis was also conducted. Results: A total of 12 SNVs were identified as the tag SNVs for WNK1 gene. Significant associations were observed between WNK1 gene rs7305099 variant and EH risk, and T allele influenced hypertension risk in a protective manner. After correcting for multiple testing using Bonferroni, the significance remained for the SNV of rs7305099 in three genetic models [allele comparison, p < 0.0002, OR = 0.627, 95%CI (0.491-0.801); homozygote comparison, p < 0.0003, OR = 0.278, 95%CI (0.140-0.552); additive model, p < 0.0003, OR = 0.279, 95%CI (0.140-0.553)]. In the haplotype analyses, we found that the haplotype A-A-A-C-G-G-G was significantly associated with increased risk for EH (p = 0.043, OR = 1.23). Conclusion: Our data suggested that the rs7305099 genetic variant and the haplotype A-A-A-C-G-G-G on WNK1 gene might be associated with the susceptibility of EH in the Northern Han Chinese population. These could provide evidences to the risk assessment, early prevention and individualized therapy of EH to some extent.
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Affiliation(s)
- Kuo Liu
- Department of Hypertension Research, Beijing Anzhen Hospital, Beijing Institute of Heart Lung and Blood Vessel Diseases, Capital Medical University, Beijing, China
| | - Jielin Liu
- Department of Hypertension Research, Beijing Anzhen Hospital, Beijing Institute of Heart Lung and Blood Vessel Diseases, Capital Medical University, Beijing, China
| | - Ya Liu
- Department of Hypertension Research, Beijing Anzhen Hospital, Beijing Institute of Heart Lung and Blood Vessel Diseases, Capital Medical University, Beijing, China
| | - Hao Wang
- Department of Cardiology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| | - Zuoguang Wang
- Department of Hypertension Research, Beijing Anzhen Hospital, Beijing Institute of Heart Lung and Blood Vessel Diseases, Capital Medical University, Beijing, China
| | - Jinghua Liu
- Department of Cardiology, Beijing Anzhen Hospital, Beijing Institute of Heart Lung and Blood Vessel Diseases, Capital Medical University, Beijing, China
| | - Shaojun Wen
- Department of Hypertension Research, Beijing Anzhen Hospital, Beijing Institute of Heart Lung and Blood Vessel Diseases, Capital Medical University, Beijing, China
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Nucleotide-based genetic networks: Methods and applications. J Biosci 2022. [PMID: 36226367 PMCID: PMC9554864 DOI: 10.1007/s12038-022-00290-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Genomic variations have been acclaimed as among the key players in understanding the biological mechanisms behind migration, evolution, and adaptation to extreme conditions. Due to stochastic evolutionary forces, the frequency of polymorphisms is affected by changes in the frequency of nearby polymorphisms in the same DNA sample, making them connected in terms of evolution. This article presents all the ingredients to understand the cumulative effects and complex behaviors of genetic variations in the human mitochondrial genome by analyzing co-occurrence networks of nucleotides, and shows key results obtained from such analyses. The article emphasizes recent investigations of these co-occurrence networks, describing the role of interactions between nucleotides in fundamental processes of human migration and viral evolution. The corresponding co-mutation-based genetic networks revealed genetic signatures of human adaptation in extreme environments. This article provides the methods of constructing such networks in detail, along with their graph-theoretical properties, and applications of the genomic networks in understanding the role of nucleotide co-evolution in evolution of the whole genome.
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Zhong C, Wang Y, Liu C, Jiang Y, Kang L. A Novel Single-Nucleotide Polymorphism in WNT4 Promoter Affects Its Transcription and Response to FSH in Chicken Follicles. Genes (Basel) 2022; 13:genes13101774. [PMID: 36292659 PMCID: PMC9602048 DOI: 10.3390/genes13101774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/04/2022] Open
Abstract
The signaling pathway of the wingless-type mouse mammary tumor virus integration site (Wnt) plays an important role in ovarian and follicular development. In our previous study, WNT4 was shown to be involved in the selection and development of chicken follicles by upregulating the expression of follicle-stimulating hormone receptors (FSHR), stimulating the proliferation of follicular granulosa cells, and increasing the secretion of steroidal hormones. FSH also stimulates the expression of WNT4. To further explore the molecular mechanism by which FSH upregulates WNT4 and characterize the cis-elements regulating WNT4 transcription, in this study, we determined the critical regulatory regions affecting chicken WNT4 transcription. We then identified a single-nucleotide polymorphism (SNP) in this region, and finally analyzed the associations of the SNP with chicken production traits. The results showed that the 5′ regulatory region from −3354 to −2689 of WNT4 had the strongest activity and greatest response to FSH stimulation, and we identified one SNP site in this segment, −3015 (G > C), as affecting the binding of NFAT5 (nuclear factor of activated T cells 5) and respones to FSH stimulation. When G was replaced with C at this site, it eliminated the NFAT5 binding. The mRNA level of WNT4 in small yellow follicles of chickens with genotype GG was significantly higher than that of the other two genotypes. Moreover, this locus was found to be significantly associated with comb length in hens. Individuals with the genotype CC had longer combs. Collectively, these data suggested that SNP−3015 (G > C) is involved in the regulation of WNT4 gene expression by responding FSH and affecting the binding of NFAT5 and that it is associated with chicken comb length. The current results provide a reference for further revealing the response mechanism between WNT and FSH.
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Affiliation(s)
- Conghao Zhong
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China
| | - Yiya Wang
- College of Life Science, Qilu Normal University, Jinan 250200, China
| | - Cuiping Liu
- Qishan Animal Husbandry and Veterinary Station, Zhaoyuan 265413, China
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China
| | - Li Kang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China
- Correspondence: ; Tel.: +86-538-8241593
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Kim MH, Lim SH. Matrix Metalloproteinases and Glaucoma. Biomolecules 2022; 12:biom12101368. [PMID: 36291577 PMCID: PMC9599265 DOI: 10.3390/biom12101368] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/19/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are enzymes that decompose extracellular matrix (ECM) proteins. MMPs are thought to play important roles in cellular processes, such as cell proliferation, differentiation, angiogenesis, migration, apoptosis, and host defense. MMPs are distributed in almost all intraocular tissues and are involved in physiological and pathological mechanisms of the eye. MMPs are also associated with glaucoma, a progressive neurodegenerative disease of the eyes. MMP activity affects intraocular pressure control and apoptosis of retinal ganglion cells, which are the pathological mechanisms of glaucoma. It also affects the risk of glaucoma development based on genetic pleomorphism. In addition, MMPs may affect the treatment outcomes of glaucoma, including the success rate of surgical treatment and side effects on the ocular surface due to glaucoma medications. This review discusses the various relationships between MMP and glaucoma.
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Affiliation(s)
- Moo Hyun Kim
- Department of Ophthalmology, Daegu Premier Eye Center, Suseong-ro 197, Suseong-Gu, Daegu 42153, Korea
| | - Su-Ho Lim
- Department of Ophthalmology, Daegu Veterans Health Service Medical Center, 60 Wolgok-Ro, Dalseo-Gu, Daegu 42835, Korea
- Correspondence: ; Tel.: +82-53-630-7572
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Lee KY, Leung KS, Ma SL, So HC, Huang D, Tang NLS, Wong MH. Genome-Wide Search for SNP Interactions in GWAS Data: Algorithm, Feasibility, Replication Using Schizophrenia Datasets. Front Genet 2020; 11:1003. [PMID: 33133133 PMCID: PMC7505102 DOI: 10.3389/fgene.2020.01003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/06/2020] [Indexed: 11/13/2022] Open
Abstract
In this study, we looked for potential gene-gene interaction in susceptibility to schizophrenia by an exhaustive searching for SNP-SNP interactions in 3 GWAS datasets (phs000021:phg000013, phs000021:phg000014, phs000167) using our recently published algorithm. The search space for SNP-SNP interaction was confined to 8 biologically plausible ways of interaction under dominant-dominant or recessive-recessive modes. First, we performed our search of all pair-wise combination of 729,454 SNPs after filtering by SNP genotype quality. All possible pairwise interactions of any 2 SNPs (5 × 1011) were exhausted to search for significant interaction which was defined by p-value of chi-square tests. Nine out the top 10 interactions, protein coding genes were partnered with non-coding RNA (ncRNA) which suggested a new alternative insight into interaction biology other than the frequently sought-after protein-protein interaction. Therefore, we extended to look for replication among the top 10,000 interaction SNP pairs and high proportion of concurrent genes forming the interaction pairs were found. The results indicated that an enrichment of signals over noise was present in the top 10,000 interactions. Then, replications of SNP-SNP interaction were confirmed for 14 SNPs-pairs in both replication datasets. Biological insight was highlighted by a potential binding between FHIT (protein coding gene) and LINC00969 (lncRNA) which showed a replicable interaction between their SNPs. Both of them were reported to have expression in brain. Our study represented an early attempt of exhaustive interaction analysis of GWAS data which also yield replicated interaction and new insight into understanding of genetic interaction in schizophrenia.
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Affiliation(s)
- Kwan-Yeung Lee
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwong-Sak Leung
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Suk Ling Ma
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China
| | - Hon Cheong So
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China.,School of Biomedical Science, The Chinese University of Hong Kong, Hong Kong, China.,Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Kunming Institute of Zoology, The Chinese University of Hong Kong, Hong Kong, China.,Margaret K.L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Brain and Mind Institute, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Nelson Leung-Sang Tang
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology and Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Functional Genomics and Biostatistical Computing Laboratory, CUHK Shenzhen Research Institute, Shenzhen, China
| | - Man-Hon Wong
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
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Wang H, Liu J, Liu K, Liu Y, Wen J, Wang Z, Wen S. Association of ECE1 gene polymorphisms and essential hypertension risk in the Northern Han Chinese: A case-control study. Mol Genet Genomic Med 2020; 8:e1188. [PMID: 32107880 PMCID: PMC7196447 DOI: 10.1002/mgg3.1188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 01/30/2023] Open
Abstract
Background The ECE1 gene polymorphisms have been studied as a candidate gene in essential hypertension, but no consensus has been reached. To systematically explore their possible association, a case‒control study was conducted. Methods This study included 398 hypertensive subjects and 596 healthy volunteers as control subjects in the Northern Han Chinese. A total of 10 tag SNPs of ECE1 gene were genotyped successfully by TaqMan assay. Results A total of 10 SNPs (rs212544, rs2076280, rs115071, rs2076283, rs9426748, rs11590928, rs212515, rs2236847, rs2282715, and rs2774028) were identified as the tag SNPs for ECE1 gene. Although no positive connection has been found in general population, several SNPs have been found to be related to EH risk in gender‐stratified subgroup analysis. In males, rs115071 T allele influenced EH risk in a protective manner, with dominant model (TT+TC vs. CC: p = .032, OR = 0.655, 95% CI = 0.445–0.965), additive model (TT vs. TC vs. CC: p = .019, OR = 0.616, 95% CI = 0.411–0.924), as well as allele comparison (T vs. C: p = .045, OR = 0.702, 95% CI = 0.496–0.992). While, in females, rs212544 AA genotype would increase the onset risk of EH (recessive model: AA vs. GA+GG, p = .024, OR = 1.847, 95% CI = 1.086–3.142). In the three haplotype blocks identified, rs2076283‐rs2236847 C‐T haplotype was associated with a decreased risk of EH (OR = 0.558, p = .046). Conclusion The current case‒control study suggested that several SNPs and related haplotypes on ECE1 gene might be associated with the susceptibility of EH in certain gender subgroups in the Northern Han Chinese population.
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Affiliation(s)
- Hao Wang
- Department of Hypertension Research, Beijing Anzhen Hospital, Capital Medical University and Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, People's Republic of China
| | - Jielin Liu
- Department of Hypertension Research, Beijing Anzhen Hospital, Capital Medical University and Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, People's Republic of China
| | - Kuo Liu
- Department of Hypertension Research, Beijing Anzhen Hospital, Capital Medical University and Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, People's Republic of China
| | - Ya Liu
- Department of Hypertension Research, Beijing Anzhen Hospital, Capital Medical University and Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, People's Republic of China
| | - Jie Wen
- Department of Hypertension Research, Beijing Anzhen Hospital, Capital Medical University and Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, People's Republic of China
| | - Zuoguang Wang
- Department of Hypertension Research, Beijing Anzhen Hospital, Capital Medical University and Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, People's Republic of China
| | - Shaojun Wen
- Department of Hypertension Research, Beijing Anzhen Hospital, Capital Medical University and Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, People's Republic of China
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Jiao H, Zang Y, Zhang M, Zhang Y, Wang Y, Wang K, Price RA, Li WD. Genome-Wide Interaction and Pathway Association Studies for Body Mass Index. Front Genet 2019; 10:404. [PMID: 31118946 PMCID: PMC6504780 DOI: 10.3389/fgene.2019.00404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 04/12/2019] [Indexed: 11/24/2022] Open
Abstract
Objective: We investigated gene interactions (epistasis) for body mass index (BMI) in a European-American adult female cohort via genome-wide interaction analyses (GWIA) and pathway association analyses. Methods: Genome-wide pairwise interaction analyses were carried out for BMI in 493 extremely obese cases (BMI > 35 kg/m2) and 537 never-overweight controls (BMI < 25 kg/m2). To further validate the results, specific SNPs were selected based on the GWIA results for haplotype-based association studies. Pathway-based association analyses were performed using a modified Gene Set Enrichment Algorithm (GSEA) (GenGen program) to further explore BMI-related pathways using our genome wide association study (GWAS) data set, GIANT, ENGAGE, and DIAGRAM Consortia. Results: The EXOC4-1q23.1 interaction was associated with BMI, with the most significant epistasis between rs7800006 and rs10797020 (P = 2.63 × 10-11). In the pathway-based association analysis, Tob1 pathway showed the most significant association with BMI (empirical P < 0.001, FDR = 0.044, FWER = 0.040). These findings were further validated in different populations. Conclusion: Genome-wide pairwise SNP-SNP interaction and pathway analyses suggest that EXOC4 and TOB1-related pathways may contribute to the development of obesity.
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Affiliation(s)
- Hongxiao Jiao
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yong Zang
- Department of Genetics, College of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Miaomiao Zhang
- Department of Genetics, College of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuan Zhang
- Department of Genetics, College of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yaogang Wang
- College of Public Health, Tianjin Medical University, Tianjin, China
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Laboratory Medicine, Department of Pathology, University of Pennsylvania, Philadelphia, PA, United States
| | - R. Arlen Price
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Wei-Dong Li
- Department of Genetics, College of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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Dong SS, Yao S, Chen YX, Guo Y, Zhang YJ, Niu HM, Hao RH, Shen H, Tian Q, Deng HW, Yang TL. Detecting epistasis within chromatin regulatory circuitry reveals CAND2 as a novel susceptibility gene for obesity. Int J Obes (Lond) 2018; 43:450-456. [PMID: 29717274 DOI: 10.1038/s41366-018-0069-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/14/2018] [Accepted: 02/13/2018] [Indexed: 01/03/2023]
Abstract
BACKGROUND Genome-wide association studies have identified many susceptibility loci for obesity. However, missing heritability problem is still challenging and ignorance of genetic interactions is believed to be an important cause. Current methods for detecting interactions usually do not consider regulatory elements in non-coding regions. Interaction analyses within chromatin regulatory circuitry may identify new susceptibility loci. METHODS We developed a pipeline named interaction analyses within chromatin regulatory circuitry (IACRC), to identify genetic interactions impacting body mass index (BMI). Potential interacting SNP pairs were obtained based on Hi-C datasets, PreSTIGE (Predicting Specific Tissue Interactions of Genes and Enhancers) algorithm, and super enhancer regions. SNP × SNP analyses were next performed in three GWAS datasets, including 2286 unrelated Caucasians from Kansas City, 3062 healthy Caucasians from the Gene Environment Association Studies initiative, and 3164 Hispanic subjects from the Women's Health Initiative. RESULTS A total of 16,643,227 SNP × SNP analyses were performed. Meta-analyses showed that two SNP pairs, rs6808450-rs9813534 (combined P = 2.39 × 10-9) and rs6808450-rs3773306 (combined P = 2.89 × 10-9) were associated with BMI after multiple testing corrections. Single-SNP analyses did not detect significant association signals for these three SNPs. In obesity relevant cells, rs6808450 is located in intergenic enhancers, while rs9813534 and rs3773306 are located in the region of strong transcription regions of CAND2 and RPL32, respectively. The expression of CAND2 was significantly downregulated after the differentiation of human Simpson-Golabi-Behmel syndrome (SGBS) preadipocyte cells (P = 0.0241). Functional validation in the International Mouse Phenotyping Consortium database showed that CAND2 was associated with increased lean body mass and decreased total body fat amount. CONCLUSIONS Detecting epistasis within chromatin regulatory circuitry identified CAND2 as a novel obesity susceptibility gene. We hope IACRC could facilitate the interaction analyses for complex diseases and offer new insights into solving the missing heritability problem.
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Affiliation(s)
- Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Yu-Jie Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Hui-Min Niu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Ruo-Han Hao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Hui Shen
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Qing Tian
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Hong-Wen Deng
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.
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Mao JJ, Wu LX, Wang W, Ye YY, Yang J, Chen H, Yang QF, Zhang XY, Wang B, Chen WX. Nucleotide variation in ATG4A and susceptibility to cervical cancer in Southwestern Chinese women. Oncol Lett 2017; 15:2992-3000. [PMID: 29435029 PMCID: PMC5778867 DOI: 10.3892/ol.2017.7663] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/25/2017] [Indexed: 12/19/2022] Open
Abstract
Early detection of human papillomavirus (HPV) is important for the clinical diagnosis of cervical cancer. However, to date, the pathogenesis of cervical cancer is still unclear. Autophagy is a dynamic process that contributes to the maintenance of cellular homeostasis. Here, we investigate whether variants of autophagy genes affect the occurrence of cervical cancer. In this study, our results indicate that single nucleotide polymorphisms (SNPs) of autophagy-related protein 4 (ATG4), including rs4036579, rs5973822, rs807181, rs807182 and rs807183, have a significant relationship with cervical cancer risk. Furthermore, stratified analysis suggests that the homozygous variant genotype could decrease the risk of cervical cancer and should be considered when investigating the role of HPV in cervical cancer. We aim to investigate whether SNPs of ATG4A contribute to HPV infection in the population of Southwestern China. The association of both single SNPs and SNP-SNP interactions with HPV was evaluated in a sample of cancer cases and healthy control subjects. The interaction of rs807181 and rs807183 was associated with HPV infection in case and control subjects (combined P=2.00×10−3 and 3.22×10−2, respectively). This result showed that ATG4A SNP interactions may affect HPV infection in the population of Southwestern China. Notably, the autophagy gene ATG4A may contribute to cervical cancer.
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Affiliation(s)
- Jin-Ju Mao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 410010, P.R. China
| | - Li-Xiang Wu
- Department of Laboratory Medicine, Chongqing Cancer Institute, Chongqing 400030, P.R. China
| | - Wei Wang
- Department of Laboratory Medicine, Chongqing Cancer Institute, Chongqing 400030, P.R. China
| | - Yuan-Yuan Ye
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 410010, P.R. China
| | - Jun Yang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 410010, P.R. China
| | - Hong Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 410010, P.R. China
| | - Qian-Fan Yang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 410010, P.R. China
| | - Xiu-Yu Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 410010, P.R. China
| | - Bo Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 410010, P.R. China
| | - Wei-Xian Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 410010, P.R. China
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