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Zhang H, Zhang H, Yang H, Shuid AN, Sandai D, Chen X. Machine learning-based integrated identification of predictive combined diagnostic biomarkers for endometriosis. Front Genet 2023; 14:1290036. [PMID: 38098472 PMCID: PMC10720908 DOI: 10.3389/fgene.2023.1290036] [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: 09/06/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023] Open
Abstract
Background: Endometriosis (EM) is a common gynecological condition in women of reproductive age, with diverse causes and a not yet fully understood pathogenesis. Traditional diagnostics rely on single diagnostic biomarkers and does not integrate a variety of different biomarkers. This study introduces multiple machine learning techniques, enhancing the accuracy of predictive models. A novel diagnostic approach that combines various biomarkers provides a new clinical perspective for improving the diagnostic efficiency of endometriosis, holding significant potential for clinical application. Methods: In this study, GSE51981 was used as a test set, and 11 machine learning algorithms (Lasso, Stepglm, glmBoost, Support Vector Machine, Ridge, Enet, plsRglm, Random Forest, LDA, XGBoost, and NaiveBayes) were employed to construct 113 predictive models for endometriosis. The optimal model was determined based on the AUC values derived from various algorithms. These genes were then evaluated using nine machine learning algorithms (Random Forest, SVM, Gradient Boosting Machine, LASSO, XGB, NNET, Generalized Linear Model, KNN, and Decision Tree) to assess significance scores and identify diagnostic genes for each algorithm. The diagnostic value of these genes was further validated in external datasets from GSE7305, GSE11691, and GSE120103. Results: Analysis of the GSE51981 dataset revealed 62 DEGs. The Stepglm [Both] and plsRglm algorithms identified 30 genes with the most potential using the AUC evaluation. Subsequently, nine machine learning algorithms were applied to select diagnostic genes, leading to the identification of five key diagnostic genes using the LASSO algorithm. The ADAT1 gene exhibited the best single-gene predictive performance, with an AUC of 0.785. A combination of genes (FOS, EPHX1, DLGAP5, PCSK5, and ADAT1) achieves an AUC of 0.836 in the test dataset. Moreover, these genes consistently exhibited an AUC exceeding 0.78 in all validation datasets, demonstrating superior predictive performance. Furthermore, correlation analysis with immune infiltration strengthened their predictive value by demonstrating the close relationship of the diagnostic genes with immune infiltrating cells. Conclusion: A combination of biomarkers consisting of FOS, EPHX1, DLGAP5, PCSK5, and ADAT1 can serve as a diagnostic tool for endometriosis, enhancing diagnostic efficiency. The association of these genes with immune infiltrating cells reveals their potential role in the pathogenesis of endometriosis, providing new insights for early detection and treatment.
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Affiliation(s)
- Haolong Zhang
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Haoling Zhang
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Huadi Yang
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Ahmad Naqib Shuid
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Doblin Sandai
- Department of Community Health, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Xingbei Chen
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
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Zhang Y, Fan G, Liu X, Skovgaard K, Sturek M, Heegaard PM. The genome of the naturally evolved obesity-prone Ossabaw miniature pig. iScience 2021; 24:103081. [PMID: 34585119 PMCID: PMC8455653 DOI: 10.1016/j.isci.2021.103081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/08/2021] [Accepted: 08/31/2021] [Indexed: 12/03/2022] Open
Abstract
The feral pigs of Ossabaw Island (USA) have an outstanding propensity to obesity and develop complete metabolic syndrome (MetS) upon prolonged high energy dieting. We now report the first high quality genome of the Ossabaw pig with Contig N50 of ∼6.03 Mb, significantly higher than most other published pig genomes. Genomic comparison to Duroc reveals that variations including SNPs, INDELs and one ∼2 Mb inversion identified in Ossabaw pig may be related to its "thrifty" phenotype. Finally, an important positively selected gene (PSG) was found to be LEPR (leptin receptor) containing two positively selected sites which may lead to pseudogenization of this gene with possible significant effects on obesity and inflammation development. This work provides the first complete mapping of a genome representing a naturally 'feast and famine' evolved phenotype of MetS, serving as a blueprint to guide the search for new targets and new biomarkers for obesity comorbidities.
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Affiliation(s)
- Yaolei Zhang
- Translational Immunology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Kerstin Skovgaard
- Translational Immunology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Michael Sturek
- Department of Anatomy, Cell Biology, & Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Peter M.H. Heegaard
- Translational Immunology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- Innate Immunology Group, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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Taha MM, Saad-Hussein A, Mahdy-Abdallah H. Association of microsomal epoxide hydrolase gene (fast genotype) with lung functions impairment in wood workers. JOURNAL OF COMPLEMENTARY & INTEGRATIVE MEDICINE 2021; 18:609-615. [PMID: 33794079 DOI: 10.1515/jcim-2020-0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 07/09/2020] [Indexed: 06/12/2023]
Abstract
OBJECTIVES Exposure to wood dust may lead to impairment of the lung functions. Microsomal epoxide hydrolase enzyme (EPHX1) was shown to take part in protection against oxidative stress. An alteration in enzyme activity might be associated with its gene polymorphisms. In vitro polymorphisms in exons 3 (His113Tyr) and 4 (Arg139His) lead to reduced activity (slow allele) and increased activity (fast allele). Macrophage inflammatory protein 2 (MIP-2) is produced in rat lung epithelial cells after exposure to fine particles. We aimed to investigate the associations between mEPHX1 polymorphisms (in exon 3 and 4) and lung function in furniture workers and assessment of MIP-2 effect. METHODS Our study was performed on 70 wood dust exposed male workers and 70 matched normal controls subjects. Ventilatory function tests were measured by spirometer, MIP-2 was performed by ELISA methods and EPHX gene was done by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods for each participant. RESULTS Significant reduction in forced vital capacity (FVC%) and forced expiratory volume in the first second (FEV1) levels in Tyr-Tyr and Tyr-Hist genotypes of EPHX (exon 3) was observed. Reduced peak expiratory flow (PEF) levels and significant rise in MIP-2 levels were detected in Tyr-Tyr genotype. While high significant reduction in FVC% and FEV1 levels were shown in different genotypes in exon 4. Significant rise was observed in MIP-2 levels in Hist-Hist genotype of exon 4. An increase in duration of exposure showed positive correlation with fall in ventilatory functions. CONCLUSIONS It was concluded that in Hist139Arg of EPHX gene, fast genotype (Arg-Arg) was associated with impaired ventilatory functions.
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Affiliation(s)
- Mona M Taha
- Department of Environmental and Occupational Medicine, Environmental Research Division, National Research Centre, Giza, Egypt
| | - Amal Saad-Hussein
- Department of Environmental and Occupational Medicine, Environmental Research Division, National Research Centre, Giza, Egypt
| | - Heba Mahdy-Abdallah
- Department of Environmental and Occupational Medicine, Environmental Research Division, National Research Centre, Giza, Egypt
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Feng J, Chen Y, Hua W, Sun X, Chen Y, Liu Y, Fan J, Zhao Y, Zhao L, Xu X, Yang X. The MMP -8 rs11225395 Promoter Polymorphism Increases Cancer Risk of Non-Asian Populations: Evidence from a Meta-Analysis. Biomolecules 2019; 9:E570. [PMID: 31590330 PMCID: PMC6843622 DOI: 10.3390/biom9100570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 12/11/2022] Open
Abstract
This meta-analysis aimed to systematically review the evidence on cancer risk of the MMP-8 rs11225395 promoter polymorphism. Relevant studies published by 12 June 2019 were identified by systematically searching PubMed, Web of Science, Cochrane Library, CNKI and Wanfang databases. R programs and STATA software were used to calculate odds ratio (OR) and 95% confidence interval (CI). In total, 7375 cancer samples and 8117 controls were included by integrating 15 case-control data sets. Pooled estimates from the statistical analysis revealed no statistical significance for the association between this polymorphism and cancer risk. All pooled estimates resulting from subgroup analyses by cancer type and sample size were not materially altered and did not draw significantly different conclusions. The stratified analyses according to geographic region showed the statistical significance for increased cancer risk of the MMP-8 rs11225395 polymorphism in non-Asian populations under the allele model (OR = 1.11, 95% CI: 1.04-1.19), homozygote model (OR = 1.22, 95% CI: 1.05-1.41), heterozygote model (OR = 1.21, 95% CI: 1.07-1.36), and dominant model (OR = 1.21, 95% CI: 1.08-1.35). However, no statistical significance was detected in Asian populations. In conclusion, these findings suggested that the MMP-8 rs11225395 polymorphism is associated with elevated susceptibility to cancer in non-Asian populations.
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Affiliation(s)
- Jiarong Feng
- Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 199 Ren’ai Road, Suzhou 215123, China (Y.C.); (X.S.); (Y.C.)
| | - Yudi Chen
- Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 199 Ren’ai Road, Suzhou 215123, China (Y.C.); (X.S.); (Y.C.)
| | - Wenxi Hua
- Medical College, Soochow University, 199 Ren’ai Road, Suzhou 215123, China (Y.Z.)
| | - Xiaohan Sun
- Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 199 Ren’ai Road, Suzhou 215123, China (Y.C.); (X.S.); (Y.C.)
| | - Yanjie Chen
- Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 199 Ren’ai Road, Suzhou 215123, China (Y.C.); (X.S.); (Y.C.)
| | - Yu Liu
- Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 199 Ren’ai Road, Suzhou 215123, China (Y.C.); (X.S.); (Y.C.)
| | - Jiaying Fan
- Department of Biotechnology, School of Biology and Basic Medical Sciences, Soochow University, 199 Ren’ai Road, Suzhou 215123, China;
| | - Yuening Zhao
- Medical College, Soochow University, 199 Ren’ai Road, Suzhou 215123, China (Y.Z.)
| | - Lixiang Zhao
- Department of Immunology, School of Biology and Basic Medical Sciences, Soochow University, 199 Ren’ai Road, Suzhou 215123, China
| | - Xiaojing Xu
- Department of Cell Biology, School of Biology and Basic Medical Sciences, Soochow University, 199 Ren’ai Road, Suzhou 215123, China
| | - Xiaoqin Yang
- Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 199 Ren’ai Road, Suzhou 215123, China (Y.C.); (X.S.); (Y.C.)
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Wang B, Liu Y, Li Z, Li Z. Association of indoor air pollution from coal combustion with influenza-like illness in housewives. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 216:646-652. [PMID: 27344085 DOI: 10.1016/j.envpol.2016.06.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/13/2016] [Accepted: 06/15/2016] [Indexed: 05/13/2023]
Abstract
An association of influenza-like illness (ILI) with outdoor air pollution has been reported. However, the effect of indoor air pollution on ILI was rarely investigated. We aimed to determine an association of indoor air pollution from coal combustion (IAPCC) and lifestyle with ILI risk in housewives, and the modification effect of phase II metabolic enzyme genes. We recruited 403 housewives for a cross-sectional study in Shanxi Province, China, including 135 with ILI frequency (≥1 time per year in the past ten years) as the case group and 268 with ILI frequency (<1 times per year) as the control group. Information on their energy usage characteristics and lifestyle was collected by questionnaires, as well as the single nucleotide polymorphisms (SNPs) of epoxide hydrolase 1 (rs1051740 and rs2234922), N-acetyltransferase 2 (rs1041983), and glutathione S-transferase (rs1695). We used exposure index to indicate the level of IAPCC among housewives. Our results revealed that the exposure index was positively correlated with ILI frequency. A significant dose-response trend between the exposure index and ILI risk was found with or without adjusting for confounders. Cooking frequency in kitchen with coal as primary fuel and ventilation frequency in the living room or bedroom with a coal-fueled stove for heating during the heating season were two important risk factors to affect ILI frequency. Only rs1051740 was found to be associated with exposure index, whereas it didn't have interaction effect with exposure index on ILI frequency. In conclusion, IAPCC and SNPs of rs1051740 were both associated with ILI frequency.
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Affiliation(s)
- Bin Wang
- Institute of Reproductive and Child Health/Ministry of Health Key Laboratory of Reproductive Health, School of Public Health, Peking University, Beijing 100191, PR China; Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Yingying Liu
- Institute of Reproductive and Child Health/Ministry of Health Key Laboratory of Reproductive Health, School of Public Health, Peking University, Beijing 100191, PR China; Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Zhenjiang Li
- Institute of Reproductive and Child Health/Ministry of Health Key Laboratory of Reproductive Health, School of Public Health, Peking University, Beijing 100191, PR China; Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Zhiwen Li
- Institute of Reproductive and Child Health/Ministry of Health Key Laboratory of Reproductive Health, School of Public Health, Peking University, Beijing 100191, PR China; Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China.
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Kim JH, Lee MR, Hong YC. Modification of the association of bisphenol A with abnormal liver function by polymorphisms of oxidative stress-related genes. ENVIRONMENTAL RESEARCH 2016; 147:324-30. [PMID: 26922413 DOI: 10.1016/j.envres.2016.02.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/26/2016] [Accepted: 02/18/2016] [Indexed: 05/22/2023]
Abstract
Some studies suggested oxidative stress as a possible mechanism for the relation between exposure to bisphenol A (BPA) and liver damage. Therefore, we evaluated modification of genetic polymorphisms of cyclooxygenase 2 (COX2 or PTGS2), epoxide hydrolase 1 (EPHX1), catalase (CAT), and superoxide dismutase 2 (SOD2 or MnSOD), which are oxidative stress-related genes, on the relation between exposure to BPA and liver function in the elderly. We assessed the association of visit-to-visit variations in BPA exposure with abnormal liver function by each genotype or haplotype after controlling for age, sex, BMI, alcohol consumption, exercise, urinary cotinine levels, and low density lipoprotein cholesterol using a GLIMMIX model. A significant association of BPA with abnormal liver function was observed only in participants with COX2 GG genotype at rs5277 (odds ratio (OR)=3.04 and p=0.0231), CAT genotype at rs769218 (OR=4.16 and p=0.0356), CAT CT genotype at rs769217 (OR=4.19 and p=0.0348), SOD2 TT genotype at rs4880 (OR=2.59 and p=0.0438), or SOD2 GG genotype at rs2758331 (OR=2.57 and p=0.0457). Moreover, we also found higher OR values in participants with a pair of G-G haplotypes for COX2 (OR=2.81 and p=0.0384), G-C-A haplotype for EPHX1 (OR=4.63 and p=0.0654), A-T haplotype for CAT (OR=4.48 and p=0.0245), or T-G-A haplotype for SOD2 (OR=2.91 and p=0.0491) compared with those with the other pair of haplotypes for each gene. Furthermore, the risk score composed of 4 risky pair of haplotypes showed interactive effect with BPA on abnormal liver function (p=0.0057). Our study results suggest that genetic polymorphisms of COX2, EPHX1, CAT, and SOD2 modify the association of BPA with liver function.
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Affiliation(s)
- Jin Hee Kim
- Department of Environmental Health, Graduate School of Public Health, Seoul National University, Seoul 151-742, Republic of Korea; Department of Bioscience and Bioengineering, Sejong University, Seoul, 05006, Republic of Korea
| | - Mee-Ri Lee
- (c)Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Yun-Chul Hong
- (c)Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea; (d)Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul 110-799, Republic of Korea.
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Zhang P, Zhang Y, Yang H, Li W, Chen X, Long F. Association between EPHX1 rs1051740 and lung cancer susceptibility: a meta-analysis. Int J Clin Exp Med 2015; 8:17941-17949. [PMID: 26770388 PMCID: PMC4694288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 09/06/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Microsomal epoxide hydrolase 1 (EPHX1) may play an important role in epigenetic change and DNA repair concerned with lung cancer. Several studies have investigated the association between EPHX1 rs1051740 and lung cancer risk, but there is no consensus. Therefore, we performed a meta-analysis to further identify the relationship. METHODS The Pubmed and Embase databases were searched for eligible studies. An odds ratio (OR) with 95% confidence intervals (CIs) was used to assess the correlation between EPHX1 rs1051740 polymorphism and lung cancer risk through a meta-analysis. RESULTS Overall, no significant relationship was found between EPHX1 rs1051740 and lung cancer risk (CC vs. TT: OR=1.10, 95% CI=0.88-1.36; CC+CT vs. TT: OR=1.02, 95% CI=0.88-1.18; CC vs. TT+CT: OR=1.08, 95% CI=0.91-1.27; C vs. T: OR=1.04, 95% CI=0.93-1.17; CT vs. TT: OR=0.98, 95% CI=0.85-1.13). Nevertheless, further subgroup analysis by ethnicity demonstrated that EPHX1 rs1051740 with CC genotype or C allele was an increased risk for lung cancer in Asians (CC vs. TT: OR=1.54, 95% CI=1.23-1.94; CC vs. TT+CT: OR=1.43, 95% CI=1.20-1.71; C vs. T: OR=1.26, 95% CI=1.08-1.47). CONCLUSIONS This meta-analysis indicates that EPHX1 rs1051740 with CC genotype or C allele may be a risk factor in Asians.
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Affiliation(s)
- Peng Zhang
- Department of Respiratory Medicine, Huashan Hospital North, Fudan University Shanghai 201907, China
| | - Youzhi Zhang
- Department of Respiratory Medicine, Huashan Hospital North, Fudan University Shanghai 201907, China
| | - Haihua Yang
- Department of Respiratory Medicine, Huashan Hospital North, Fudan University Shanghai 201907, China
| | - Wenjing Li
- Department of Respiratory Medicine, Huashan Hospital North, Fudan University Shanghai 201907, China
| | - Xiaodong Chen
- Department of Respiratory Medicine, Huashan Hospital North, Fudan University Shanghai 201907, China
| | - Feng Long
- Department of Respiratory Medicine, Huashan Hospital North, Fudan University Shanghai 201907, China
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Cress WD, Chiappori A, Santiago P, Muñoz-Antonia T. Lung cancer mutations and use of targeted agents in Hispanics. Rev Recent Clin Trials 2014; 9:225-32. [PMID: 25626064 PMCID: PMC4441412 DOI: 10.2174/1574887110666150127103555] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/02/2014] [Accepted: 12/08/2014] [Indexed: 12/12/2022]
Abstract
Hispanic/Latinos (H/L) are expected to grow to over 24% of the USA population by 2050 and lung cancer is the number one cause of cancer death among H/L men. Due to the information that is becoming available via genetic testing, lung cancer molecular profiling is allowing for increasing application of personalized lung cancer therapies. However, to benefit the most people, development of these therapies and genetic tests must include research on as many racial and ethnic groups as possible. The purpose of this review is to bring attention to the fact that the mutations driving lung cancer in H/Ls differ in frequency and nature relative to the non-Hispanic White (WNH) majority that dominate current databases and participate in clinical trials that test new therapies. Clinical trials using new agents targeting genetic alterations (driver mutations) in lung cancer have demonstrated significant improvements in patient outcomes (for example, gefitinib, erlotinib or crizotinib for lung adenocarcinomas harboring EGFR mutations or EML4-ALK fusions, respectively). The nature and frequencies of some lung cancer driver mutations have been shown to be considerably different among racial and ethnic groups. This is particularly true for H/Ls. For example, several reports suggest a dramatic shift in the mutation pattern from predominantly KRAS in a WNH population to predominantly EGFR in multiple H/L populations. However, these studies are limited, and the effects of racial and ethnic differences on the incidence of mutations in lung cancer remain incompletely understood. This review serves as a call to address this problem.
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