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Ma N, Sun Y, Kong Y, Jin Y, Yu F, Liu L, Yang L, Liu W, Gao X, Liu D, Zhang X, Li L. Comprehensive investigating of mismatch repair genes (MMR) polymorphisms in participants with chronic hepatitis B virus infection. Front Genet 2023; 14:1077297. [PMID: 36816025 PMCID: PMC9928949 DOI: 10.3389/fgene.2023.1077297] [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: 10/22/2022] [Accepted: 01/13/2023] [Indexed: 02/04/2023] Open
Abstract
Background and aim: In this study, we focused on the relationship between single nucleotide polymorphisms in MMR genes and the occurrence and development of HBV infection. Materials and methods: A total of 3,128 participants were divided into five groups: negative control group (NeC), spontaneous clearance group (SC), chronic hepatitis B group (CHB), liver cirrhosis group (LC) and hepatocellular carcinoma group (HCC), CHB, liver cirrhosis and hepatocellular carcinoma constitute HLD. We conducted three case-control studies: NeC (840 cases) vs. HLD (1792 cases), SC (486 cases) vs. HLD (1792 cases) and CHB + LC (1,371 cases) vs. HCC (421 cases). 11 polymorphic loci in MLH1, MLH3, MSH5, PMS1 and PMS2 were involved in genotyping by Sequenom MassArray. The SNPStats performed Hardy-Weinberg equilibrium test. Linkage disequilibrium patterns were visualized using Haploview4.2. The GMDR (v0.9) was conducted to generalized multifactor dimension reduction analysis. The correlation, multiplicative interaction and additive interaction analyses were calculated by Logistic Regression through SPSS21.0. Matrix and programmed excel were also involved in the calculation of additive interaction. Results: In NeC vs. HLD group, MSH5-rs1150793(G) was a risk base to HBV susceptibility (nominal p = 0.002, OR = 1.346). We found multiplicative interaction between MLH1-rs1540354 (AA + AT) and PMS1-rs1233255 (AA) (nominal p = 0.024, OR = 1.240). There was additive interaction between PMS1-rs1233255 (AA) and PMS1-rs256554(CA + CC). In SC vs. HLD group, MLH1-rs1540354 (TT) was a risk genotype (nominal p < 0.05, OR>1). Through haplotype analysis, we found the linkage disequilibrium of three loci in MLH1. The results of GMDR showed the optimal five-locus model about the spontaneous clearance of HBV. In CHB + LC vs. HCC group, PMS2-rs12112229(A) was related to the cancerization of liver. Conclusion: We found rs1150793(G), rs1540354(T) and rs12112229(A) were significantly related to HBV susceptibility, spontaneous clearance of HBV and cancerization after infection, respectively.
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Affiliation(s)
- Ning Ma
- Department of Social Medicine and HealthCare Management, School of Public Health, Hebei Medical University, Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, China
| | - Yucheng Sun
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, China
| | - Yanan Kong
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, China
| | - Yiyao Jin
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, China
| | - Fengxue Yu
- Division of gastroenterology, The Second Hospital of Hebei Medical University, The Hebei Key Laboratory of Gastroenterology, Shijiazhuang, China
| | - Lianfeng Liu
- Department of Pediatrics, Shijiazhuang Maternal and Child Health Hospital, Shijiazhuang, China
| | - Lei Yang
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, China
| | - Wenxuan Liu
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, China
| | - Xia Gao
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, China
| | - Dianwu Liu
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, China
| | - Xiaolin Zhang
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, China,*Correspondence: Xiaolin Zhang, ; Lu Li,
| | - Lu Li
- Department of Social Medicine and HealthCare Management, School of Public Health, Hebei Medical University, Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, China,*Correspondence: Xiaolin Zhang, ; Lu Li,
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Liu WX, Yang L, Yan HM, Yan LN, Zhang XL, Ma N, Tang LM, Gao X, Liu DW. Germline Variants and Genetic Interactions of Several EMT Regulatory Genes Increase the Risk of HBV-Related Hepatocellular Carcinoma. Front Oncol 2021; 11:564477. [PMID: 34178612 PMCID: PMC8226114 DOI: 10.3389/fonc.2021.564477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) plays an important role in the development of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). We hypothesized that germline variants in the major EMT regulatory genes (SNAIL1, ZEB1, ZEB2, TWIST1) may influence the development of HBV-related HCC. We included 421 cases of HBsAg-positive patients with HCC, 1371 cases of HBsAg-positive subjects without HCC [patients with chronic hepatitis B (CHB) or liver cirrhosis (LC)] and 618 cases of healthy controls in the case-control study. Genotype, allele, and haplotype associations in the major EMT regulatory genes were tested. Environment-gene and gene-gene interactions were analysed using the non-parametric model-free multifactor dimensionality reduction (MDR) method. The SNAIL1rs4647958T>C was associated with a significantly increased risk of both HCC (CT+CC vs. TT: OR=1.559; 95% confidence interval [CI], 1.073-2.264; P=0.020) and CHB+LC (CT+CC vs. TT: OR=1.509; 95% CI, 1.145-1.988; P=0.003). Carriers of the TWIST1rs2285681G>C (genotypes CT+CC) had an increased risk of HCC (CG+CC vs. GG: OR=1.407; 95% CI, 1.065-1.858; P=0.016). The ZEB2rs3806475T>C was associated with significantly increased risk of both HCC (P recessive =0.001) and CHB+LC (P recessive<0.001). The CG haplotype of the rs4647958/rs1543442 haplotype block was associated with significant differences between healthy subjects and HCC patients (P=0.0347). Meanwhile, the CT haplotype of the rs2285681/rs2285682 haplotype block was associated with significant differences between CHB+LC and HCC patients (P=0.0123). In MDR analysis, the combination of TWIST1rs2285681, ZEB2rs3806475, SNAIL1rs4647958 exhibited the most significant association with CHB+LC and Health control in the three-locus model. Our results suggest significant single-gene associations and environment-gene/gene-gene interactions of EMT-related genes with HBV-related HCC.
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Affiliation(s)
- Wen-Xuan Liu
- Department of Epidemiology and Statistics & Hebei Province Key Laboratory of Environment and Human Health, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Lei Yang
- Department of Epidemiology and Statistics & Hebei Province Key Laboratory of Environment and Human Health, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Hui-Min Yan
- Department of Laboratory Medicine, Shijiazhuang Fifth Hospital, Shijiazhuang, China
| | - Li-Na Yan
- Department of Epidemiology and Statistics & Hebei Province Key Laboratory of Environment and Human Health, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Xiao-Lin Zhang
- Department of Epidemiology and Statistics & Hebei Province Key Laboratory of Environment and Human Health, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Ning Ma
- Department of Social Medicine and Health Care Management & Hebei Province Key Laboratory of Environment and Human Health, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Long-Mei Tang
- Department of Epidemiology and Statistics & Hebei Province Key Laboratory of Environment and Human Health, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Xia Gao
- Department of Epidemiology and Statistics & Hebei Province Key Laboratory of Environment and Human Health, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Dian-Wu Liu
- Department of Epidemiology and Statistics & Hebei Province Key Laboratory of Environment and Human Health, School of Public Health, Hebei Medical University, Shijiazhuang, China
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Lian Q, Wang B, Fan L, Sun J, Wang G, Zhang J. DNA methylation data-based molecular subtype classification and prediction in patients with gastric cancer. Cancer Cell Int 2020; 20:349. [PMID: 32742196 PMCID: PMC7388223 DOI: 10.1186/s12935-020-01253-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/10/2020] [Indexed: 01/29/2023] Open
Abstract
Background Genetic and epigenetic alterations have been indicated to be closely correlated with the carcinogenesis, DNA methylation is one of most frequently occurring molecular behavior that take place early during this complicated process in gastric cancer (GC). Methods In this study, 398 samples were collected from the cancer genome atlas (TCGA) database and were analyzed, so as to mine the specific DNA methylation sites that affected the prognosis for GC patients. Moreover, the 23,588 selected CpGs that were markedly correlated with patient prognosis were used for consistent clustering of the samples into 6 subgroups, and samples in each subgroup varied in terms of M, Stage, Grade, and Age. In addition, the levels of methylation sites in each subgroup were calculated, and 347 methylation sites (corresponding to 271 genes) were screened as the intrasubgroup specific methylation sites. Meanwhile, genes in the corresponding promoter regions that the above specific methylation sites were located were performed signaling pathway enrichment analysis. Results The specific genes were enriched to the biological pathways that were reported to be closely correlated with GC; moreover, the subsequent transcription factor enrichment analysis discovered that, these genes were mainly enriched into the cell response to transcription factor B, regulation of MAPK signaling pathways, and regulation of cell proliferation and metastasis. Eventually, the prognosis prediction model for GC patients was constructed using the Random Forest Classifier model, and the training set and test set data were carried out independent verification and test. Conclusions Such specific classification based on specific DNA methylation sites can well reflect the heterogeneity of GC tissues, which contributes to developing the individualized treatment and accurately predicting patient prognosis.
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Affiliation(s)
- Qixin Lian
- Oncology Department, First Affiliated Hospital of Jiamusi University, 154002 Qiqihar, Heilongjiang China
| | - Bo Wang
- Oncology Department, First Affiliated Hospital of Jiamusi University, 154002 Qiqihar, Heilongjiang China
| | - Lijun Fan
- Gastroenterology Department, The First Hospital of Qiqihar, The Affiliate Qiqihar Hospital of Southern Medical University, Longsha District, 30 of Park Road, Qiqihar, Heilongjiang 161005 China
| | - Junqiang Sun
- Radiotherapy and Chemotherapy, The First Hospital of Dandong, Liaoning, 118000 China
| | - Guilai Wang
- General Surgery, The First Hospital of Qiqihar, The Affiliate Qiqihar Hospital of Southern Medical University, Longsha District, 30 of Park Road, Qiqihar, Heilongjiang 161005 China
| | - Jidong Zhang
- Gastroenterology Department, The First Hospital of Qiqihar, The Affiliate Qiqihar Hospital of Southern Medical University, Longsha District, 30 of Park Road, Qiqihar, Heilongjiang 161005 China
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Chattopadhyay A, Lu TP. Gene-gene interaction: the curse of dimensionality. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:813. [PMID: 32042829 DOI: 10.21037/atm.2019.12.87] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Identified genetic variants from genome wide association studies frequently show only modest effects on the disease risk, leading to the "missing heritability" problem. An avenue, to account for a part of this "missingness" is to evaluate gene-gene interactions (epistasis) thereby elucidating their effect on complex diseases. This can potentially help with identifying gene functions, pathways, and drug targets. However, the exhaustive evaluation of all possible genetic interactions among millions of single nucleotide polymorphisms (SNPs) raises several issues, otherwise known as the "curse of dimensionality". The dimensionality involved in the epistatic analysis of such exponentially growing SNPs diminishes the usefulness of traditional, parametric statistical methods. With the immense popularity of multifactor dimensionality reduction (MDR), a non-parametric method, proposed in 2001, that classifies multi-dimensional genotypes into one- dimensional binary approaches, led to the emergence of a fast-growing collection of methods that were based on the MDR approach. Moreover, machine-learning (ML) methods such as random forests and neural networks (NNs), deep-learning (DL) approaches, and hybrid approaches have also been applied profusely, in the recent years, to tackle this dimensionality issue associated with whole genome gene-gene interaction studies. However, exhaustive searching in MDR based approaches or variable selection in ML methods, still pose the risk of missing out on relevant SNPs. Furthermore, interpretability issues are a major hindrance for DL methods. To minimize this loss of information, Python based tools such as PySpark can potentially take advantage of distributed computing resources in the cloud, to bring back smaller subsets of data for further local analysis. Parallel computing can be a powerful resource that stands to fight this "curse". PySpark supports all standard Python libraries and C extensions thus making it convenient to write codes to deliver dramatic improvements in processing speed for extraordinarily large sets of data.
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Affiliation(s)
- Amrita Chattopadhyay
- Institute of Epidemiology and Preventive Medicine, Department of Public Health, National Taiwan University, Taipei
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, Department of Public Health, National Taiwan University, Taipei
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Choi S, Lee S, Kim Y, Hwang H, Park T. HisCoM-GGI: Hierarchical structural component analysis of gene-gene interactions. J Bioinform Comput Biol 2018; 16:1840026. [PMID: 30567476 DOI: 10.1142/s0219720018400267] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although genome-wide association studies (GWAS) have successfully identified thousands of single nucleotide polymorphisms (SNPs) associated with common diseases, these observations are limited for fully explaining "missing heritability". Determining gene-gene interactions (GGI) are one possible avenue for addressing the missing heritability problem. While many statistical approaches have been proposed to detect GGI, most of these focus primarily on SNP-to-SNP interactions. While there are many advantages of gene-based GGI analyses, such as reducing the burden of multiple-testing correction, and increasing power by aggregating multiple causal signals across SNPs in specific genes, only a few methods are available. In this study, we proposed a new statistical approach for gene-based GGI analysis, "Hierarchical structural CoMponent analysis of Gene-Gene Interactions" (HisCoM-GGI). HisCoM-GGI is based on generalized structured component analysis, and can consider hierarchical structural relationships between genes and SNPs. For a pair of genes, HisCoM-GGI first effectively summarizes all possible pairwise SNP-SNP interactions into a latent variable, from which it then performs GGI analysis. HisCoM-GGI can evaluate both gene-level and SNP-level interactions. Through simulation studies, HisCoM-GGI demonstrated higher statistical power than existing gene-based GGI methods, in analyzing a GWAS of a Korean population for identifying GGI associated with body mass index. Resultantly, HisCoM-GGI successfully identified 14 potential GGI, two of which, (NCOR2 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>×</mml:mo></mml:math> SPOCK1) and (LINGO2 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>×</mml:mo></mml:math> ZNF385D) were successfully replicated in independent datasets. We conclude that HisCoM-GGI method may be a valuable tool for genome to identify GGI in missing heritability, allowing us to better understand the biological genetic mechanisms of complex traits. We conclude that HisCoM-GGI method may be a valuable tool for genome to identify GGI in missing heritability, allowing us to better understand biological genetic mechanisms of complex traits. An implementation of HisCoM-GGI can be downloaded from the website ( http://statgen.snu.ac.kr/software/hiscom-ggi ).
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Affiliation(s)
- Sungkyoung Choi
- Department of Pharmacology, Yonsei University College of Medicine, 50-1 Yonsei-ro Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Sungyoung Lee
- Center for Precision Medicine, Seoul National University Hospital, 71 Daehak-ro Jongno-gu, Seoul 03082, Republic of Korea
| | - Yongkang Kim
- Department of Statistics, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul 08826, Republic of Korea.,Department of Psychology, McGill University, 2001 Avenue McGill College, Montreal, Quebec H3A 1G1, Canada
| | - Heungsun Hwang
- Department of Psychology, McGill University, 2001 Avenue McGill College, Montreal, Quebec H3A 1G1, Canada
| | - Taesung Park
- Department of Statistics, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul 08826, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul 08826, Republic of Korea
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