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Yu J, Varella Pereira GM, Allen-Brady K, Cuffolo R, Siddharth A, Koch M, Chua JWF, Sorrentino F, Dytko O, Ng KY, Violette P, Khullar V, Wang ZT, Cartwright R. Genetic polymorphisms associated with urinary tract infection in children and adults: a systematic review and meta-analysis. Am J Obstet Gynecol 2024; 230:600-609.e3. [PMID: 38128862 DOI: 10.1016/j.ajog.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
INTRODUCTION The lifetime risk of urinary tract infection is known from first-degree relative studies to be highly heritable. Associations have also been observed across the life course from pediatric urinary tract infection to recurrent urinary tract infection in adulthood, suggesting lifelong susceptibility factors. Candidate gene studies and genome-wide association studies have tested for genetic associations of urinary tract infection; however, no contemporary systematic synthesis of studies is available. OBJECTIVE We conducted a systematic review to identify all genetic polymorphisms tested for an association with urinary tract infection in children and adults; and to assess their strength, consistency, and risk of bias among reported associations. DATA SOURCES AND STUDY ELIGIBILITY CRITERIA PubMed, HuGE Navigator and Embase were searched from January 1, 2005 to November 16, 2023, using a combination of genetic and phenotype key words. STUDY APPRAISAL AND SYNTHESIS METHODS Fixed and random effects meta-analyses were conducted using codominant models of inheritance in metan. The interim Venice criteria were used to assess their credibility of pooled associations. RESULTS After removing 451 duplicates, 1821 studies reports were screened, with 106 selected for full-text review, 22 were included in the meta-analysis (7 adult studies and 15 pediatric studies). Our meta-analyses demonstrated significant pooled associations for pediatric urinary tract infection with variation in CXCR1, IL8, TGF, TLR4 and VDR; all of which have plausible roles in the pathogenesis of urinary tract infection. Our meta-analyses also demonstrated a significant pooled association for adult urinary tract infection with variation in CXCR1. All significant pooled associations were graded according to their epidemiological credibility, sample sizes, heterogeneity between studies, and risk of bias. CONCLUSION This systematic review provides a current synthesis of the known genetic architecture of urinary tract infection in childhood and adulthood; and should provide important information for researchers analysing future genetic association studies. Although, overall, the credibility of pooled associations was weak, the consistency of findings for rs2234671 single nucleotide polymorphisms of CXCR1 in both populations suggest a key role in the urinary tract infection pathogenesis.
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Affiliation(s)
- Jiakun Yu
- University Hospitals Sussex NHS Foundation Trust, Brighton, United Kingdom.
| | - Glaucia Miranda Varella Pereira
- Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, United Kingdom; Department of Urogynaecology, LNWH NHS Trust, London, United Kingdom; Department of Obstetrics and Gynaecology, School of Medical Sciences, University of Campinas, Brazil
| | - Kristina Allen-Brady
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT
| | - Romana Cuffolo
- Department of Obstetrics and Gynaecology, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
| | - Aditi Siddharth
- John Radcliffe Hospital, Headley Way, Headington, Oxford, United Kingdom
| | - Marianne Koch
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - John W F Chua
- Frimley Health NHS Foundation Trust, Frimley, United Kingdom
| | - Felice Sorrentino
- Department of Medical and Surgical Sciences, Institute of Obstetrics and Gynecology, University of Foggia, Foggia, Italy
| | - Oskar Dytko
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
| | - Kaa-Yung Ng
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
| | - Philippe Violette
- Department of Health Research Methods, Evidence and Impact (HEI) and Surgery, McMaster University, Hamilton, Ontario, Canada
| | - Vik Khullar
- Department of Urogynaecology, Imperial College London, United Kingdom
| | - Zhan Tao Wang
- Department of Surgery, Division of Urology, University of Western Ontario, London, Ontario, Canada
| | - Rufus Cartwright
- Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, United Kingdom; Department of Urogynaecology, LNWH NHS Trust, London, United Kingdom; Department of Urogynaecology, Chelsea and Westminster NHS Foundation Trust, London, United Kingdom
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Singh P, Guin D, Pattnaik B, Kukreti R. Mapping the genetic architecture of idiopathic pulmonary fibrosis: Meta-analysis and epidemiological evidence of case-control studies. Gene 2024; 895:147993. [PMID: 37977320 DOI: 10.1016/j.gene.2023.147993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/23/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a rare and devastating fibrotic lung disorder with unknown etiology. Although it is believed that genetic component is an important risk factor for IPF, a comprehensive understanding of its genetic landscape is lacking. Hence, we aimed to highlight the susceptibility genes and pathways implicated in IPF pathogenesis through a two-staged systematic literature search of genetic association studies on IPF, followed by meta-analysis and pathway enrichment analysis. METHODS This study was performed based on PRISMA guidelines (PROSPERO, registration number: CRD42022297970). The first search was performed (using PubMed and Web of Science) retrieving a total of 5642 articles, of which 52 were eligible for inclusion in the first stage. The second search was performed (using PubMed, Web of Science and Scopus) for ten polymorphisms, identified from the first search, with 2 or more studies. Finally, seven polymorphisms, [rs35705950/MUC5B, rs2736100/TERT, rs2609255/FAM13A, rs2076295/DSP, rs12610495/DPP9, rs111521887/TOLLIP and rs1800470/TGF-β1] qualified for meta-analyses. The epidemiological credibility was evaluated using Venice criteria. RESULTS From the systematic review, 222 polymorphisms in 118 genes showed a significant association with IPF susceptibility. Meta-analyses findings revealed significant association of rs35705950/T [OR = 3.92(3.26-4.57)], rs2609255/G [OR = 1.50(1.18-1.82)], rs2076295/G [OR = 1.19(0.82-1.756)], rs12610495/G [OR = 1.28(1.12-1.44)], rs2736100/C [OR = 0.68(0.54-0.82), rs111521887/G [OR = 1.34(1.06-1.61)] and suggestive evidence for rs1800470/T [OR = 1.08(0.82-1.34)] with IPF susceptibility. Four polymorphisms- rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk. Gene ontology and pathway enrichment analysis performed on IPF risk-associated genes identified a critical role of genes in mucin production, immune response and inflammation, host defence, cell-cell adhesion and telomere maintenance. CONCLUSIONS Our findings present the most prominent IPF-associated genetic risk variants involved in alveolar epithelial injuries (MUC5B, TERT, FAM13A, DSP, DPP9) and epithelial-mesenchymal transition (TOLLIP, TGF-β1), providing genetic and biological insights into IPF pathogenesis. However, further experimental research and human studies with larger sample sizes, diverse ethnic representation, and rigorous design are warranted.
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Affiliation(s)
- Pooja Singh
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, India; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Debleena Guin
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, New Delhi, India; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Bijay Pattnaik
- Centre of Excellence for Translational Research in Asthma and Lung Diseases, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India; Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Ritushree Kukreti
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, India; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India.
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Cox EGM, Zhang W, van der Voort PHJ, Lunter G, Keus F, Snieder H. Genetic association studies in critically ill patients: protocol for a systematic review. Syst Rev 2023; 12:233. [PMID: 38093336 PMCID: PMC10716946 DOI: 10.1186/s13643-023-02401-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
INTRODUCTION Patients in the intensive care unit (ICU) are highly heterogeneous in characteristics, their clinical course, and outcomes. Genetic variability may partly explain the variability and similarity in disease courses observed among critically ill patients and may identify clusters of subgroups. The aim of this study is to conduct a systematic review of all genetic association studies of critically ill patients with their outcomes. METHODS AND ANALYSIS This systematic review will be conducted and reported according to the HuGE Review Handbook V1.0. We will search PubMed, Embase, and the Cochrane Library for relevant studies. All types of genetic association studies that included acutely admitted medical and surgical adult ICU patients will be considered for this review. All studies will be selected according to predefined selection criteria, evaluated and assessed for risk of bias independently by two reviewers. Risk of bias will be assessed according to the HuGE Review Handbook V1.0 with some modifications reflecting recent insights. We will provide an overview of all included studies by reporting the characteristics of the study designs, the patients included in the studies, the genetic variables, and the outcomes evaluated. ETHICS AND DISSEMINATION We will use data from peer-reviewed published articles, and hence, there is no requirement for ethics approval. The results of this systematic review will be disseminated through publication in a peer-reviewed scientific journal. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRD42021209744.
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Affiliation(s)
- Eline G M Cox
- Department of Critical Care, University Medical Center Groningen, Groningen, 9713 GZ, the Netherlands.
| | - Wenbo Zhang
- Department of Epidemiology, University Medical Center Groningen, Groningen, 9713 GZ, the Netherlands
| | - Peter H J van der Voort
- Department of Critical Care, University Medical Center Groningen, Groningen, 9713 GZ, the Netherlands
| | - Gerton Lunter
- Department of Epidemiology, University Medical Center Groningen, Groningen, 9713 GZ, the Netherlands
| | - Frederik Keus
- Department of Critical Care, University Medical Center Groningen, Groningen, 9713 GZ, the Netherlands
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, Groningen, 9713 GZ, the Netherlands
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Lumkul L, Wongyikul P, Kulalert P, Sompornrattanaphan M, Lao-Araya M, Chuamanochan M, Nochaiwong S, Phinyo P. Genetic association of beta-lactams-induced hypersensitivity reactions: A systematic review of genome-wide evidence and meta-analysis of candidate genes. World Allergy Organ J 2023; 16:100816. [PMID: 37780578 PMCID: PMC10541471 DOI: 10.1016/j.waojou.2023.100816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/14/2023] [Accepted: 08/29/2023] [Indexed: 10/03/2023] Open
Abstract
Importance Beta-lactams (BLs) are the most prescribed antibiotics, being the most frequent cause of drug allergy. However, the association between BL allergy and genetic variations is still unclear. Objective This systematic review and meta-analysis aimed to summarize the genetic effects of BL-induced hypersensitivity using existing evidence. Methods We searched PubMed, Medline, Scopus, EMBASE, CINAHL, and Cochrane Library from inception to September 15, 2022 with no language restriction. Genetic association studies investigating genetic variant/polymorphism and risk of drug-induced hypersensitivity reactions among individuals receiving BL-antibiotics were included. We excluded studies of acute interstitial nephritis, drug-induced liver injury, serum sickness, and isolated drug fever. Data were comprehensively synthesized and quality of study were assessed using STrengthening the Reporting of Genetic Association Studies (STREGA). The record screening, extraction and quality assessment were performed by two reviewers and discussions were made to resolve discrepancies. The effects of each variant were pooled and evaluated by modified Venice criteria. Results A total of 9276 records were identified, and 31 studies were eligible for inclusion. Twenty-seven were candidate-gene association studies (5416 cases and 5939 controls), while the others were next-generation sequencing (NGS) or genome-wide association studies (GWASs) (119 838 cases and 1 487 111 controls). Forty-nine polymorphisms were identified and most of them located in allergic reaction pathways. Meta-analyses of 15 candidate variants in a mixture of both immediate and non-immediate reactions revealed weak genetic effects of rs1801275 (8 studies; n = 1,560; odd ratio 0.73; 95%CI: 0.57-0.93) and rs20541 (4 studies; n = 1,482; odd ratio 1.34; 95%CI: 1.07-1.68) in IL4R and IL13, respectively. Results from GWASs and NGS identified, and confirmed associations in HLA regions including HLA-DRA, HLA-B, HLA-DQA, HLA-DRB1, and HLA-DRB3. Conclusion Our study summarized genetic evidence influencing BL-induced hypersensitivity and estimated effects of potential variants. We postulated that the genomic studies provide better insights to the mechanism of reactions and suggest potential effects of HLA Class II variants. However, results were inconsistent and unable to generalize in different settings. Further high-throughput studies with a well-defined function, epigenetic interaction, incorporated with clinical factors, would be beneficial for risk identification in BL-induced hypersensitivity.
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Affiliation(s)
- Lalita Lumkul
- Center for Clinical Epidemiology and Clinical Statistics, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Pakpoom Wongyikul
- Center for Clinical Epidemiology and Clinical Statistics, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Prapasri Kulalert
- Department of Clinical Epidemiology, Faculty of Medicine, Thammasat University, Pathum Thani, 12120, Thailand
- Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Thammasat University, Pathum Thani, 12120, Thailand
| | - Mongkhon Sompornrattanaphan
- Division of Allergy and Clinical Immunology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Mongkol Lao-Araya
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Mati Chuamanochan
- Pharmacoepidemiology and Statistics Research Center (PESRC), Chiang Mai University, Chiang Mai, 50200, Thailand
- Division of Dermatology, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Surapon Nochaiwong
- Pharmacoepidemiology and Statistics Research Center (PESRC), Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Pharmaceutical Care, Faculty of Pharmacy, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Phichayut Phinyo
- Center for Clinical Epidemiology and Clinical Statistics, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Family Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Musculoskeletal Science and Translational Research (MSTR), Chiang Mai University, Chiang Mai 50200, Thailand
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Liu T, Yang L, Lv X, Zuo C, Jia C, Yang Z, Fan C, Chen H. Cumulative evidence for associations between genetic variants in interleukin 17 family gene and risk of human diseases. Front Immunol 2022; 13:1008184. [PMID: 36300118 PMCID: PMC9589504 DOI: 10.3389/fimmu.2022.1008184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/20/2022] [Indexed: 12/02/2022] Open
Abstract
Background Genetic association studies have elucidated the link of variants in the interleukin 17 (IL-17) family genes with susceptibility to human diseases, yet have obtained controversial outcomes. Therefore, we sought to update comprehensive synopsis of variants in the IL-17 family genes with susceptibility to human diseases. Methods Our study screened the Pubmed and Web of Science to enroll eligible articles and performed a meta-analysis, then graded the cumulative evidence of significant association using Venice criteria and false-positive report probability test, and finally assessed the function of variants with strong evidence. Results Seven variants in IL-17 family genes had significant relationships with susceptibility to 18 human diseases identified by meta-analyses. Strong evidence was assigned to 4 variants (IL-17A rs2275913, IL-17A rs8193037, IL-17F rs1889570, IL-17F rs763780) with susceptibility to 6 human diseases (lung and cervical cancer, spondyloarthritis, asthma, multiple sclerosis, rheumatoid arthritis), moderate to 2 variants with risk of 5 diseases, weak to 5 variants with risk of 10 diseases. Bioinformatics analysis suggested that the variants with strong evidence might fall in putative functional regions. Additionally, positive relationships for 5 variants with risk of 4 diseases (based on two datasets) and 14 variants with risk of 21 diseases (based on one dataset) were considered noteworthy. Conclusions This study offers updated and comprehensive clues that variants in the IL-17 family genes are significantly linked with susceptibility to cervical, lung cancer, asthma, multiple sclerosis, rheumatoid arthritis and spondyloarthritis, and elucidates the crucial role of the IL-17 regions in the genetic predisposition to cancer or noncancerous diseases.
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Affiliation(s)
- Tianyu Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lei Yang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaolong Lv
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chunjian Zuo
- Department of Thoracic Surgery, Army Medical Center of People’s Liberation Army of China (PLA), Chongqing, China
| | - Chenhao Jia
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zelin Yang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chongqi Fan
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Huanwen Chen,
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Yang L, Yang Z, Zuo C, Lv X, Liu T, Jia C, Chen H. Epidemiological evidence for associations between variants in CHRNA genes and risk of lung cancer and chronic obstructive pulmonary disease. Front Oncol 2022; 12:1001864. [PMID: 36276121 PMCID: PMC9582127 DOI: 10.3389/fonc.2022.1001864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/21/2022] [Indexed: 12/24/2022] Open
Abstract
Background Genetic studies have previously reported that single-nucleotide polymorphisms (SNPs) in CHRNA genes (such as CHRNA3, CHRNA4, CHRNA5, or CHRNA3-CHRNA5-CHRNB4 clusters) are linked to the risk of neoplastic and non-neoplastic diseases. However, these conclusions were controversial and no systematic research synopsis has been available. We aimed to synthesize current knowledge of variants in the CHRNA genes on the risk of diseases. Methods We systematically searched for publications using PubMed, Medline, and Web of Science on or before 25 August 2021. A total of 1,818 publications were identified, of which 29 were deemed eligible for inclusion that could be used to perform meta-analysis based on at least three data sources to assess whether the morbidity associated with neoplastic and non-neoplastic diseases can be attributed to SNPs in CHRNA genes. To further evaluate the authenticity of cumulative evidence proving significant associations, the present study covered the Venice criteria and false-positive report probability tests. Through the Encyclopedia of DNA Elements (ENCODE) project, we created functional annotations for strong associations. Results Meta-analyses were done for nine genetic variants with two diseases {chronic obstructive pulmonary disease (COPD) and lung cancer (LC)}that had at least three data sources. Interestingly, eight polymorphisms were significantly related to changes in the susceptibility COPD and LC (p < 0.05). Of these, strong evidence was assigned to six variants (28 significant associations): CHRNA3 rs1051730, CHRNA3 rs6495309, and CHRNA5 rs16969968 with COPD risk, and CHRNA3 rs1051730, CHRNA3 rs578776, CHRNA3 rs6495309, CHRNA3 rs938682, CHRNA5 rs16969968, and CHRNA5 rs588765 with LC risk; moderate evidence was assigned to five SNPs (12 total associations) with LC or COPD risk. Data from ENCODE and other public databases showed that SNPs with strong evidence may be located in presumptive functional regions. Conclusions Our study summarized comprehensive evidence showing that common mutations in CHRNA genes are strongly related to LC and COPD risk. The study also elucidated the vital function of CHRNA genes in genetic predispositions to human diseases.
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Affiliation(s)
- Lei Yang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zelin Yang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chunjian Zuo
- Department of Thoracic Surgery, Army Medical Center of People’s Liberation Army of China (PLA), Chongqing, China
| | - Xiaolong Lv
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tianyu Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chenhao Jia
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Huanwen Chen,
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Guijosa A, Freyria A, Espinosa‐Fernandez JR, Estrada‐Mena FJ, Armenta‐Quiroga AS, Ortega‐Treviño MF, Catalán R, Antonio‐Aguirre B, Villarreal‐Garza C, Perez‐Ortiz AC. Pharmacogenetics of taxane-induced neurotoxicity in breast cancer: Systematic review and meta-analysis. Clin Transl Sci 2022; 15:2403-2436. [PMID: 35892315 PMCID: PMC9579387 DOI: 10.1111/cts.13370] [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] [Received: 03/04/2022] [Revised: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 01/25/2023] Open
Abstract
Taxane-based chemotherapy regimens are used as first-line treatment for breast cancer. Neurotoxicity, mainly taxane-induced peripheral neuropathy (TIPN), remains the most important dose-limiting adverse event. Multiple genes may be associated with TIPN; however, the strength and direction of the association remain unclear. For this reason, we systematically reviewed observational studies of TIPN pharmacogenetic markers in breast cancer treatment. We conducted a systematic search of terms alluding to breast cancer, genetic markers, taxanes, and neurotoxicity in Ovid, ProQuest, PubMed, Scopus, Virtual Health, and Web of Science. We assessed the quality of evidence and bias profile. We extracted relevant variables and effect measures. Whenever possible, we performed random-effects gene meta-analyses and examined interstudy heterogeneity with meta-regression models and subgroup analyses. This study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and STrengthening the REporting of Genetic Association Studies (STREGA) reporting guidance. A total of 42 studies with 19,431 participants were included. These evaluated 262 single-nucleotide polymorphisms (SNPs) across 121 genes. We conducted meta-analyses on 23 genes with 60 SNPs (19 studies and 6246 participants). Thirteen individual SNPs (ABCB1-rs2032582, ABCB1-rs3213619, BCL6/-rs1903216, /CAND1-rs17781082, CYP1B1-rs1056836, CYP2C8-rs10509681, CYP2C8-rs11572080, EPHA5-rs7349683, EPHA6-rs301927, FZD3-rs7001034, GSTP1-rs1138272, TUBB2A-rs9501929, and XKR4-rs4737264) and the overall SNPs' effect in four genes (CYP3A4, EphA5, GSTP1, and SLCO1B1) were statistically significantly associated with TIPN through meta-analysis. In conclusion, through systematic review and meta-analysis, we found that polymorphisms, and particularly 13 SNPs, are associated with TIPN, suggesting that genetics does play a role in interindividual predisposition. Further studies could potentially use these findings to develop individual risk profiles and guide decision making.
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Affiliation(s)
| | - Ana Freyria
- School of MedicineUniversidad PanamericanaMexico CityMexico
| | | | | | | | | | - Rodrigo Catalán
- School of MedicineUniversidad PanamericanaMexico CityMexico,Thoracic Oncology UnitInstituto Nacional de CancerologíaMexico CityMexico
| | | | - Cynthia Villarreal‐Garza
- Breast Cancer Center, Hospital Zambrano Hellion TecSalud, Tecnologico de MonterreySan Pedro Garza GarcíaNuevo LeónMexico
| | - Andric C. Perez‐Ortiz
- School of MedicineUniversidad PanamericanaMexico CityMexico,Transplant CenterMassachusetts General HospitalBostonMassachusettsUSA
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Genetic architecture of tuberculosis susceptibility: A comprehensive research synopsis, meta-analyses, and epidemiological evidence. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 104:105352. [PMID: 35998870 DOI: 10.1016/j.meegid.2022.105352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/27/2022] [Accepted: 08/17/2022] [Indexed: 02/08/2023]
Abstract
To date, many studies have been conducted to investigate associations between variants and tuberculosis risk; however, the results have been inconclusive. Here, we systematically provide a summary of the understanding of the genetic architecture of tuberculosis susceptibility. We searched PubMed, Embase and Web of Science to identify genetic association studies of tuberculosis published through October 31, 2021. We conducted meta-analyses for the genetic association with tuberculosis risk. We graded levels of cumulative epidemiological evidence of significant associations with risk of tuberculosis and false-positive report probability tests. We performed functional annotations for these variants using data from the Encyclopedia of DNA Elements (ENCODE) Project and other databases. We identified 703 eligible articles comprising 298,074 cases and 879,593 controls through screening a total of 24,398 citations. Meta-analyses were conducted for 614 genetic variants in 469 genes or loci. We found 39 variants that were nominally significantly associated with tuberculosis risk. Cumulative epidemiological evidence for a significant association was graded strong for 9 variants in or near 9 genes. Among them, 5 variants were associated with tuberculosis risk in at least three main ethnicity (African, Asian and White) which together explained approximately 9.59% of the familial relative risk of tuberculosis. Data from ENCODE and other databases suggested that 8 of these 9 genetic variants with strong evidence might fall within putative functional regions. Our study summarizes the current literature on the genetic architecture of tuberculosis susceptibility and provides useful data for designing future studies to investigate the genetic association with tuberculosis risk.
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Comorbidities of Child Malnutrition in Low- and Medium-Income Countries: A Systematic Review. J Pediatr Gastroenterol Nutr 2022; 75:400-410. [PMID: 35809241 DOI: 10.1097/mpg.0000000000003558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The study intended to review the best evidence on prevalence, diagnosis, and treatment outcomes of comorbidities associated with child malnutrition. The study design was a systematic review of quantitative studies. Critical appraisal tools were used to assess the methodological quality of the studies. Data were extracted according to the predetermined data extraction table. Data were further analyzed narratively according to the set study objectives and main concepts. Fifteen studies were eligible to include in the review. All 15 studies reported on the prevalence of 4 child malnutrition-associated comorbidities. Five (n = 5/15) studies reported on length of hospitalization/stay, 10 (n = 10) studies on recovery rate, and 9 (n = 9/15) studies on mortality rate as treatment outcomes of child malnutrition associated comorbidities. The most prevalent child malnutrition associated comorbidities were tuberculosis, pneumonia, gastroenteritis, and anemia. The treatment outcomes identified included the length of hospitalization/stay, recovery rate, and mortality rate. Screening of prevalent comorbidities in children admitted with malnutrition should be standard procedure in practice. More research needs to be done on the diagnosis of under-5 child malnutrition associated comorbidities.
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Zuo C, Lv X, Liu T, Yang L, Yang Z, Yu C, Chen H. Polymorphisms in ERCC4 and ERCC5 and risk of cancers: Systematic research synopsis, meta-analysis, and epidemiological evidence. Front Oncol 2022; 12:951193. [PMID: 36033436 PMCID: PMC9404303 DOI: 10.3389/fonc.2022.951193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/20/2022] [Indexed: 12/24/2022] Open
Abstract
The variants of DNA repair genes have been widely reported to be associated with cancer risk in the past decades. As were two crucial members of nucleotide excision repair pathway, ERCC4 and ERCC5 polymorphisms are linked with susceptibility to multiple cancers, but the conclusions were controversial. In this updated meta-analysis concerned with ERCC4 and ERCC5 single-nucleotide polymorphisms (SNPs), 160 eligible publications were identified, and we exerted the meta-analysis of correlations between 24 variants and 19 types of cancer. Venice criteria and the false-positive report probability were used to evaluate a cumulative evidence of significant associations. We conducted functional annotations for those strong associations using data from the Encyclopedia of DNA Elements (ENCODE) Project. We obtained 11 polymorphisms significantly related to changed susceptibility to 11 cancers (p < 0.05). Strong evidence was assigned to four variant-related cancer risks in Asians (ERCC4 rs744154 with bladder cancer, ERCC5 rs2296147 with esophageal cancer, ERCC5 rs17655 with laryngeal cancer and uterine cancer, and ERCC5 rs751402 with gastric cancer), moderate to six SNPs with a risk of eight cancers, and weak to nine SNPs with nine cancers. Data from ENCODE and other public databases showed that the loci of these SNPs with strong evidence might fall in putative functional regions. In conclusion, this paper summarizes comprehensive evidence that common variants of ERCC4 and ERCC5 genes are strongly associated with the risk of bladder cancer, esophageal cancer, laryngeal cancer, uterine cancer, and gastric cancer and elucidates the crucial role of the DNA repair genes in the genetic predisposition to human cancers.
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Affiliation(s)
- Chunjian Zuo
- Department of Thoracic Surgery, Army Medical Center of PLA, Chongqing, China
| | - Xiaolong Lv
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tianyu Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lei Yang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zelin Yang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Cao Yu
- Department of Cardiothoracic Surgery, The Jiang Jin Central Hospital of Chongqing, Chongqing, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Huanwen Chen,
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Gebrie A. Disease progression role as well as the diagnostic and prognostic value of microRNA-21 in patients with cervical cancer: A systematic review and meta-analysis. PLoS One 2022; 17:e0268480. [PMID: 35895593 PMCID: PMC9328569 DOI: 10.1371/journal.pone.0268480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/01/2022] [Indexed: 02/07/2023] Open
Abstract
Introduction Cervical cancer is the fourth commonest and the fourth leading cause of cancer death in females globally. The upregulated expression of microRNA-21 in cervical cancer has been investigated in numerous studies, yet given the inconsistency on some of the findings, a systematic review and meta-analysis is needed. Therefore, the aim of this systematic review and meta-analysis is to investigate the role in disease progression as well as the diagnostic and prognostic value of microRNA-21 in patients with cervical cancer. Methods Literature search was carried out through visiting several electronic databases including PubMed/MEDLINE/ PubMed Central, Web of Science, Embase, WorldCat, DOAJ, ScienceDirect, and Google Scholar. After extraction, data analysis was carried out using Rev-Man 5.3, STATA 15.0 and Meta-disk 1.4. I2 and meta-bias statistics assessed heterogeneity and publication bias of the included studies, respectively. The area under summary receiver operating characteristic curve and other diagnostic indexes were used to estimate diagnostic accuracy. Result A total of 53 studies were included for this systematic review and meta-analysis. This study summarized that microRNA-21 targets the expression of numerous genes that regulate their subsequent downstream signaling pathways which promote cervical carcinogenesis. The targets addressed in this study included TNF-α, CCL20, PTEN RasA1, TIMP3, PDCD-4, TPM-1, FASL, BTG-2, GAS-5, and VHL. In addition, the meta-analysis of reports from 6 eligible studies has demonstrated that the overall area under the curve (AUC) of summary receiver operating characteristic (SROC) of microRNA-21 as a diagnostic accuracy index for cervical cancer was 0.80 (95% CI: 0.75, 0.86). In addition, evidence from studies revealed that upregulated microRNA-21 led to worsening progression and poor prognosis in cervical cancer patients. Conclusion microRNA-21 is an oncogenic microRNA molecule playing a key role in the development and progression of cervical malignancy. It has good diagnostic accuracy in the diagnosis of cervical cancer. In addition, the upregulation of microRNA-21 could predict a worse outcome in terms of prognosis in cervical cancer patients.
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Affiliation(s)
- Alemu Gebrie
- Department of Biomedical Sciences, School of Medicine, Debre Markos University, Debre Markos, Ethiopia
- * E-mail:
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12
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Tian J, Wang Y, Dong Y, Chang J, Wu Y, Chang S, Che G. Cumulative Evidence for Relationships Between Multiple Variants in the TERT and CLPTM1L Region and Risk of Cancer and Non-Cancer Disease. Front Oncol 2022; 12:946039. [PMID: 35847915 PMCID: PMC9279858 DOI: 10.3389/fonc.2022.946039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/30/2022] [Indexed: 12/01/2022] Open
Abstract
Background Genetic studies previously reported that variants in TERT-CLPTM1L genes were related to susceptibility of cancer and non-cancer diseases. However, conclusions were not always concordant. Methods We performed meta-analyses to assess correlations between 23 variants within TERT-CLPTM1L region and susceptibility to 12 cancers and 1 non-cancer disease based on data in 109 papers (involving 139,510 cases and 208,530 controls). Two approaches (false-positive report probability test and Venice criteria) were adopted for assessing the cumulative evidence of significant associations. Current study evaluated the potential role of these variants based on data in Encyclopedia of DNA Elements (ENCODE) Project. Results Thirteen variants were statistically associated with susceptibility to 11 cancers and 1 non-cancer disease (p < 0.05). Besides, 12 variants with eight cancers and one non-cancer disease were rated as strong evidence (rs2736098, rs401681, and rs402710 in bladder cancer; rs2736100, rs2853691, and rs401681 in esophageal cancer; rs10069690 in gastric cancer; rs2736100 and rs2853676 in glioma; rs2242652, rs2736098, rs2736100, rs2853677, rs31489, rs401681, rs402710, rs465498, and rs4975616 in lung cancer; rs2736100 in idiopathic pulmonary fibrosis and myeloproliferative neoplasms; and rs401681 in pancreatic and skin cancer). According to data from ENCODE and other public databases, 12 variants with strong evidence might fall within putative functional regions. Conclusions This paper demonstrated that common variants of TERT-CLPTM1L genes were related to susceptibility to bladder, esophageal, gastric, lung, pancreatic, and skin cancer, as well as to glioma, myeloproliferative neoplasms, and idiopathic pulmonary fibrosis, and, besides, the crucial function of the TERT-CLPTM1L region in the genetic predisposition to human diseases is elucidated.
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Affiliation(s)
- Jie Tian
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Wang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yingxian Dong
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Junke Chang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yongming Wu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Shuai Chang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Guowei Che
- Department of Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Guowei Che,
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Worldwide Prevalence of mcr-mediated Colistin-Resistance Escherichia coli in Isolates of Clinical Samples, Healthy Humans, and Livestock-A Systematic Review and Meta-Analysis. Pathogens 2022; 11:pathogens11060659. [PMID: 35745513 PMCID: PMC9230117 DOI: 10.3390/pathogens11060659] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Antimicrobial resistance is a serious public-health problem throughout the world. Escherichia coli, the most common Gram-negative microorganism, has developed different resistance mechanisms, making treating infections difficult. Colistin is considered a last-resort drug in the treatment of infections caused by E. coli. Plasmid-mediated mobile-colistin-resistant (mcr) genes in E. coli, now disseminated globally, are considered a major public-health threat. Humans, chickens, and pigs are the main reservoirs for E. coli and the sources of antibiotic resistance. Hence, an up-to-date and precise estimate of the global prevalence of mcr resistance genes in these reservoirs is necessary to understand more precisely the worldwide spread and to more effectively implement control and prevention strategies. Methodology: Publications were identified in the PubMed database on the basis of the PRISMA guidelines. English full-text articles were selected from December 2014 to March 2021. Descriptive statistics and a meta-analysis were performed in Excel and R software, respectively. Colistin resistance was defined as the molecular-genetic detection of the mcr genes. The crude and estimated prevalence were calculated for each host and continent. The studies were divided into two groups; community-based when they involved isolates from healthy humans, chickens, or pigs, and clinical studies when they involved only hospital, outpatient, or laboratory isolates. Results: A total of 1278 studies were identified and 218 were included in this systematic review and meta-analysis, divided into community studies (159 studies) and clinical studies (59 studies). The general prevalence of mcr-mediated colistin-resistant E. coli (mcrMCRE) was 6.51% (n = 11,583/177,720), reported in 54 countries and on five continents; Asia with 119 studies followed by Europe with 61 studies registered the most articles. Asia reported the major diversity of mcr-variants (eight of nine, except mcr-2). Worldwide, chickens and pigs proved to be the principal reservoir of mcr with an estimated prevalence of 15.8% and 14.9%, respectively. Healthy humans and clinical isolates showed a lower prevalence with 7.4% and 4.2% respectively. Conclusions: In this systematic review and meta-analysis, the worldwide prevalence of mcr in E. coli isolated from healthy humans, chickens, and pigs was investigated. A wide prevalence and distribution of mcr genes was demonstrated on all continents in E. coli isolates from the selected reservoirs. Understanding the epidemiology and occurrence in the reservoirs of mcr in E. coli on different continents of the world facilitates tracing how mcr genes are transmitted and determining the infection risks for humans. This knowledge can be used to reduce the incidence of zoonotic transmission by implementing the appropriate control programs.
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Bai N, Liu W, Xiang T, Zhou Q, Pu J, Zhao J, Luo D, Liu X, Liu H. Genetic association of ANRIL with susceptibility to Ischemic stroke: A comprehensive meta-analysis. PLoS One 2022; 17:e0263459. [PMID: 35653368 PMCID: PMC9162336 DOI: 10.1371/journal.pone.0263459] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 01/19/2022] [Indexed: 11/18/2022] Open
Abstract
Background
Ischemic stroke (IS) is a complex polygenic disease with a strong genetic background. The relationship between the ANRIL (antisense non-coding RNA in the INK4 locus) in chromosome 9p21 region and IS has been reported across populations worldwide; however, these studies have yielded inconsistent results. The aim of this study is to clarify the types of single-nucleotide polymorphisms on the ANRIL locus associated with susceptibility to IS using meta-analysis and comprehensively assess the strength of the association.
Methods
Relevant studies were identified by comprehensive and systematic literature searches. The quality of each study was assessed using the Newcastle-Ottawa Scale. Allele and genotype frequencies were extracted from each of the included studies. Odds ratios with corresponding 95% confidence intervals of combined analyses were calculated under three genetic models (allele frequency comparison, dominant model, and recessive model) using a random-effects or fixed-effects model. Heterogeneity was tested using the chi-square test based on the Cochran Q statistic and I2 metric, and subgroup analyses and a meta-regression model were used to explore sources of heterogeneity. The correction for multiple testing used the false discovery rate method proposed by Benjamini and Hochberg. The assessment of publication bias employed funnel plots and Egger’s test.
Results
We identified 25 studies (15 SNPs, involving a total of 11,527 cases and 12,216 controls maximum) and performed a meta-analysis. Eight SNPs (rs10757274, rs10757278, rs2383206, rs1333040, rs1333049, rs1537378, rs4977574, and rs1004638) in ANRIL were significantly associated with IS risk. Six of these SNPs (rs10757274, rs10757278, rs2383206, rs1333040, rs1537378, and rs4977574) had a significant relationship to the large artery atherosclerosis subtype of IS. Two SNPs (rs2383206 and rs4977574) were associated with IS mainly in Asians, and three SNPs (rs10757274, rs1333040, and rs1333049) were associated with susceptibility to IS mainly in Caucasians. Sensitivity analyses confirmed the reliability of the original results. Ethnicity and individual studies may be the main sources of heterogeneity in ANRIL.
Conclusions
Our results suggest that some single-nucleotide polymorphisms on the ANRIL locus may be associated with IS risk. Future studies with larger sample numbers are necessary to confirm this result. Additional functional analyses of causal effects of these polymorphisms on IS subtypes are also essential.
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Affiliation(s)
- Na Bai
- Department of Neurology, The Third People’s Hospital of Chengdu & The Affiliated Hospital of Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Wei Liu
- Institute of Neuroscience, Kunming Medical University, Kunming, Yunnan, China
- Department of Neurology, Nanbu People’s Hospital, Nanbu, Sichuan, China
| | - Tao Xiang
- Department of Neurology, The Third People’s Hospital of Chengdu & The Affiliated Hospital of Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Qiang Zhou
- Department of Neurology, The Third People’s Hospital of Chengdu & The Affiliated Hospital of Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Jun Pu
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Jing Zhao
- Department of Neurology, Nanbu People’s Hospital, Nanbu, Sichuan, China
| | - Danyang Luo
- Nuclear Industry 416 Hospital & The Second Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Xindong Liu
- Nuclear Industry 416 Hospital & The Second Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Hua Liu
- Department of Neurology, The Third People’s Hospital of Chengdu & The Affiliated Hospital of Southwest Jiaotong University, Chengdu, Sichuan, China
- * E-mail:
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15
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Yang J, Shi Y, Jiang J. Thoracic endovascular aortic repair or best medical therapy for uncomplicated type B aortic dissection? A meta-analysis. THE JOURNAL OF CARDIOVASCULAR SURGERY 2022; 63:288-298. [PMID: 25658975 DOI: 10.23736/s0021-9509.16.08594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
INTRODUCTION The aim of this meta-analysis was to investigate all studies comparing thoracic endovascular aortic repair (TEVAR) and best medical therapy (BMT) for the treatment of uncomplicated type B aortic dissection (TBAD). EVIDENCE ACQUISITION PubMed/Medline and Web of Knowledge were searched until September 2014 for relevant studies published in English. Pooled odds ratio (OR) and its corresponding 95% CI were analyzed with Cochrane Review Manager (RevMan v.5.3). EVIDENCE SYNTHESIS Our analysis showed that compared with BMT, TEVAR did not significantly affect 30-day (hospital) mortality. A significantly lower 1-year and 2- or 3-year survival rates was observed with TEVAR vs. BMT. Interestingly, a trend just short of statistical significance towards higher 4- or 5-year survival was found with TEVAR treatment (P=0.08). No significant differences were found in false lumen (FL) thrombosis formation with TEVAR vs. BMT treatment. However, a trend toward less incomplete or no FL thrombosis was noted with TEVAR. No significantly impact on the risk of later re-intervention was found with TEVAR vs. BMT. CONCLUSIONS TEVAR did not provide obvious early survival advantage for uncomplicated TBAD over BMT, especially in the patients using TEVAR alone. It may remain a treatment option in uncomplicated TBAD patients with high risks for later complications. More randomized, prospective, long-term studies are needed to further clarify whether TEVAR could be a better first-line treatment strategy vs. BMT for uncomplicated TBAD.
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Affiliation(s)
- Jue Yang
- Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yun Shi
- Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Junhao Jiang
- Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China -
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Hamilton FW, Somers J, Mitchell RE, Ghazal P, Timpson NJ. HMOX1 genetic polymorphisms and outcomes in infectious disease: A systematic review. PLoS One 2022; 17:e0267399. [PMID: 35551540 PMCID: PMC9098073 DOI: 10.1371/journal.pone.0267399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 04/07/2022] [Indexed: 11/18/2022] Open
Abstract
Introduction
Heme-oxygenase 1 (HMOX1) is a critical stress response gene that catalyzes the multistep oxidation of heme. A GT(n) repeat of variable length in the promoter in has been associated with a wide range of human diseases, including infections. This paper aims to summarise and systematically review associations between the length of the HMOX1 GT(n) promoter and infectious disease in humans.
Methods
A search using relevant terms was performed in PubMED and EMBASE through to 15/01/21 identifying all research that studied an association between the HMOX1 GT(n) repeat polymorphism and the incidence and/or outcome of any human infectious disease. Citations were screened for additional studies. Potential studies were screened for inclusion by two authors. Data was extracted on allele frequency, genotype, strength of association, mechanism of genotyping, and potential biases. A narrative review was performed across each type of infection.
Results
1,533 studies were identified in the search, and one via citation screening. Sixteen studies were ultimately included, seven in malaria, three in HIV, three in sepsis, and one each in pneumonia, hepatitis C, and acute respiratory distress syndrome (ARDS). Sample sizes for nearly all studies were small (biggest study, n = 1,646). Allelic definition was different across all included studies. All studies were at some risk of bias. In malaria, three studies suggested that longer alleles were associated with reduced risk of severe malaria, particularly malaria-induced renal dysfunction, with four studies identifying a null association. In sepsis, two studies suggested an association with longer alleles and better outcomes.
Conclusions
Despite the importance of HMOX1 in survival from infection, and the association between repeat length and gene expression, the clinical data supporting an association between repeat length and incidence and/or outcome of infection remain inconclusive.
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Affiliation(s)
- Fergus W. Hamilton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Infection Sciences, North Bristol NHS Trust, Bristol, United Kingdom
- * E-mail:
| | - Julia Somers
- Knight Cancer Research Building, Oregon Health and Sciences University, Portland, Oregon, United States of America
| | - Ruth E. Mitchell
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Peter Ghazal
- System Immunity Research Institute, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
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17
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Yang K, Scott JG. A Phenome-Wide Association Study and the Discovery of a New Clinical Spectrum of Hereditary Cancer Genes. JAMA Oncol 2022; 8:827-828. [PMID: 35446339 DOI: 10.1001/jamaoncol.2022.0361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, Ohio
| | - Jacob G Scott
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, Ohio.,Department of Translational Hematology and Oncology Research, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
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18
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Zhang M, Bai Y, Wang Y, Cui H, Tang M, Wang L, Wang X, Gu D. Cumulative Evidence for Associations Between Genetic Variants in Interleukin 6 Receptor Gene and Human Diseases and Phenotypes. Front Immunol 2022; 13:860703. [PMID: 35493452 PMCID: PMC9046675 DOI: 10.3389/fimmu.2022.860703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/14/2022] [Indexed: 12/12/2022] Open
Abstract
Background Genetic studies have linked polymorphisms in the interleukin 6 receptor (IL6R) gene to the risk of multiple human diseases and phenotypes, yet have reported inconsistent results. We aimed to synthesize current knowledge of variants in the IL6R gene on the risk of diseases and phenotypes. Methods We searched the Medline and Embase databases to identify relevant publications. Meta-analysis was performed utilizing DerSimonian and Laird random-effects model. We also graded cumulative evidence for significant associations. Furthermore, phenome-wide analyses and functional annotations were performed for variants with strong evidence. Results We included 155 studies for evaluating the associations between 80 polymorphisms in the IL6R gene and the risk of 102 human diseases and 98 phenotypes. We conducted 58 main meta-analyses, and 41 significant associations were identified. Strong evidence was assigned to 29 associations that investigated ten variants (rs2228145, rs4129267, rs7529229, rs4537545, rs7518199, rs4845625, rs4553185, rs4845618, rs4845371, and rs6667434) related to the risk of four cardiovascular diseases (coronary heart disease, coronary artery disease, atherosclerosis, and abdominal aortic aneurysms), four inflammatory diseases (rheumatoid arthritis, Crohn’s disease, dermatitis, and asthma), and concentration of four phenotypes (C-reactive protein, fibrinogen, IL-6, and sIL-6R). Furthermore, phenome-wide analysis verified that rs2228145 associated with asthma and dermatitis risk. Functional analyses indicated that these polymorphisms fall within exon, enhancer regions. Conclusions Our study comprehensively summarizes current data on the genetic architecture of the IL6R gene and highlights the pharmacological targeting potential of IL-6R on cardiovascular and inflammatory diseases.
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Affiliation(s)
- Min Zhang
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Ye Bai
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Yutong Wang
- Department of Epidemiology and Medicine, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Huijie Cui
- Department of Epidemiology and Medicine, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Mingshuang Tang
- Department of Epidemiology and Medicine, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Lanbing Wang
- Division of Medical Affairs, The First Affiliated Hospital of Army Military Medical University, Chongqing, China
| | - Xin Wang
- Department of Epidemiology and Medicine, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Dongqing Gu
- Department of Infectious Diseases, First Affiliated Hospital, Army Medical University, Chongqing, China
- *Correspondence: Dongqing Gu,
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Genetic Association of Beta-Lactams-Induced Hypersensitivity Reactions: A Protocol for Systematic Review and Meta-Analysis. Genes (Basel) 2022; 13:genes13040681. [PMID: 35456487 PMCID: PMC9032758 DOI: 10.3390/genes13040681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 02/01/2023] Open
Abstract
Beta-lactam (BL) antibiotics are among the drugs commonly related to hypersensitivity reactions. Several candidate gene studies and genome-wide association studies have reported associations of genetic variants and hypersensitivity reactions induced by BL antibiotics. However, the results were inconclusive. This protocol details a comprehensive systematic review of genetic factors associated with BL-induced hypersensitivity. A systematic search of literature related to genetic associations of BL-induced hypersensitivity will be performed through PubMed, Medline, Scopus, EMBASE, Web of Science, CINAHL, and the Cochrane central register of Controlled Trials (CENTRAL) from their inception dates with no language restrictions. Two reviewers will independently screen, extract, and appraise the risk of bias. Frequencies of genetic variants that comply with Hardy–Weinberg equilibrium will be extracted and pooled. Genetic models will be applied to variant effect calculation as per allele and genotype analysis. Based on statistical heterogeneity among studies, common effect estimation (odds ratio) and its corresponding 95% confidence interval will be analyzed. Sensitivity and subgroup analyses will be performed to determine the robustness of eligible studies. This systematic review and meta-analysis will provide comprehensive evidence of genetic effects regarding BL-induced hypersensitivity. The findings will enlighten the determination of disease-related genotypes that would potentially reveal allergy profiling in patients.
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Mabhida SE, Muhamed B, Sharma JR, Apalata T, Nomatshila S, Mabasa L, Benjeddou M, Masilela C, Ziqubu K, Shabalala S, Johnson R. Methylenetetrahydrofolate Reductase Polymorphism (rs1801133) and the Risk of Hypertension among African Populations: A Narrative Synthesis of Literature. Genes (Basel) 2022; 13:genes13040631. [PMID: 35456437 PMCID: PMC9027465 DOI: 10.3390/genes13040631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 02/07/2023] Open
Abstract
In this review, we have gathered and analyzed the available genetic evidence on the association between the methylenetetrahydrofolate reductase gene (MTHFR), rs1801133 and the risk of Hypertension (HTN) in African populations, which was further compared to the global data evidence. This review was reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol and Human Genome Epidemiology Network (HuGENet) guidelines. Literature was retrieved through major search databases, including PubMed, Scopus, Web of Science, and African Journal Online. We identified 64 potential studies, of which 4 studies were from the African continent and 60 studies were reported globally. Among the studies conducted in Africa, only two (n = 2) reported a significant association between the MTHFR (rs1801133) and the risk of developing HTN. Only one (n = 1) study population was purely composed of black Africans, while others were of other ethnicities. Among studies conducted in other continents (n = 60), forty-seven (n = 47) studies reported a positive association between MTHFR (rs1801133) and the risk of developing HTN, whereas the remaining studies (n = 14) did not show a significant association. Available literature suggests an apparent association between rs1801133 and HTN in global regions; however, such information is still scarce in Africa, especially in the black African population.
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Affiliation(s)
- Sihle E. Mabhida
- Biomedical Research and Innovation Platform, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (S.E.M.); (J.R.S.); (L.M.); (S.S.)
- Department of Biotechnology, Faculty of Natural Science, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
| | - Babu Muhamed
- Division of Infections Disease, University of Tennessee Health Sciences Center (UTHSC), Memphis, TN 38163, USA;
| | - Jyoti R. Sharma
- Biomedical Research and Innovation Platform, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (S.E.M.); (J.R.S.); (L.M.); (S.S.)
| | - Teke Apalata
- Division of Medical Microbiology, Department of Laboratory-Medicine and Pathology, Faculty of Health Sciences, Walter Sisulu University, Mthatha 5100, South Africa;
- National Health Laboratory Services, Mthatha 5100, South Africa
| | - Sibusiso Nomatshila
- Division of Preventive Medicine and Health Behavior, Department of Public Health, Faculty of Health Sciences, Walter Sisulu University, Mthatha 5100, South Africa;
| | - Lawrence Mabasa
- Biomedical Research and Innovation Platform, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (S.E.M.); (J.R.S.); (L.M.); (S.S.)
| | - Mongi Benjeddou
- Department of Biotechnology, Faculty of Natural Science, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
| | - Charity Masilela
- Department of Biochemistry, North-West University, Mafikeng Campus, Mmabatho 2735, South Africa; (C.M.); (K.Z.)
| | - Khanyisani Ziqubu
- Department of Biochemistry, North-West University, Mafikeng Campus, Mmabatho 2735, South Africa; (C.M.); (K.Z.)
| | - Samukelisiwe Shabalala
- Biomedical Research and Innovation Platform, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (S.E.M.); (J.R.S.); (L.M.); (S.S.)
- Division of Medical Microbiology, Department of Laboratory-Medicine and Pathology, Faculty of Health Sciences, Walter Sisulu University, Mthatha 5100, South Africa;
- National Health Laboratory Services, Mthatha 5100, South Africa
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (S.E.M.); (J.R.S.); (L.M.); (S.S.)
- Centre for Cardio-Metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
- Correspondence: ; Tel.: +27-21-938-0866
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de Araújo JLF, Menezes D, de Aguiar RS, de Souza RP. IFITM3, FURIN, ACE1, and TNF-α Genetic Association With COVID-19 Outcomes: Systematic Review and Meta-Analysis. Front Genet 2022; 13:775246. [PMID: 35432458 PMCID: PMC9010674 DOI: 10.3389/fgene.2022.775246] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/11/2022] [Indexed: 12/18/2022] Open
Abstract
Human polymorphisms may contribute to SARS-CoV-2 infection susceptibility and COVID-19 outcomes (asymptomatic presentation, severe COVID-19, death). We aimed to evaluate the association of IFITM3, FURIN, ACE1, and TNF-α genetic variants with both phenotypes using meta-analysis. The bibliographic search was conducted on the PubMed and Scielo databases covering reports published until February 8, 2022. Two independent researchers examined the study quality using the Q-Genie tool. Using the Mantel–Haenszel weighted means method, odds ratios were combined under both fixed- and random-effect models. Twenty-seven studies were included in the systematic review (five with IFITM3, two with Furin, three with TNF-α, and 17 with ACE1) and 22 in the meta-analysis (IFITM3 n = 3, TNF-α, and ACE1 n = 16). Meta-analysis indicated no association of 1) ACE1 rs4646994 and susceptibility, 2) ACE1 rs4646994 and asymptomatic COVID-19, 3) IFITM3 rs12252 and ICU hospitalization, and 4) TNF-α rs1800629 and death. On the other hand, significant results were found for ACE1 rs4646994 association with COVID-19 severity (11 studies, 692 severe cases, and 1,433 nonsevere controls). The ACE1 rs4646994 deletion allele showed increased odds for severe manifestation (OR: 1.45; 95% CI: 1.26–1.66). The homozygous deletion was a risk factor (OR: 1.49, 95% CI: 1.22–1.83), while homozygous insertion presented a protective effect (OR: 0.57, 95% CI: 0.45–0.74). Further reports are needed to verify this effect on populations with different ethnic backgrounds.Systematic Review Registration: https://www.crd.york.ac.uk/prosperodisplay_record.php?ID=CRD42021268578, identifier CRD42021268578
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Nautiyal H, Imam SS, Alshehri S, Ghoneim MM, Afzal M, Alzarea SI, Güven E, Al-Abbasi FA, Kazmi I. Polycystic Ovarian Syndrome: A Complex Disease with a Genetics Approach. Biomedicines 2022; 10:biomedicines10030540. [PMID: 35327342 PMCID: PMC8945152 DOI: 10.3390/biomedicines10030540] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 01/27/2023] Open
Abstract
Polycystic ovarian syndrome (PCOS) is a complex endocrine disorder affecting females in their reproductive age. The early diagnosis of PCOS is complicated and complex due to overlapping symptoms of this disease. The most accepted diagnostic approach today is the Rotterdam Consensus (2003), which supports the positive diagnosis of PCOS when patients present two out of the following three symptoms: biochemical and clinical signs of hyperandrogenism, oligo, and anovulation, also polycystic ovarian morphology on sonography. Genetic variance, epigenetic changes, and disturbed lifestyle lead to the development of pathophysiological disturbances, which include hyperandrogenism, insulin resistance, and chronic inflammation in PCOS females. At the molecular level, different proteins and molecular and signaling pathways are involved in disease progression, which leads to the failure of a single genetic diagnostic approach. The genetic approach to elucidate the mechanism of pathogenesis of PCOS was recently developed, whereby four phenotypic variances of PCOS categorize PCOS patients into classic, ovulatory, and non-hyperandrogenic types. Genetic studies help to identify the root cause for the development of this PCOS. PCOS genetic inheritance is autosomal dominant but the latest investigations revealed it as a multigene origin disease. Different genetic loci and specific genes have been identified so far as being associated with this disease. Genome-wide association studies (GWAS) and related genetic studies have changed the scenario for the diagnosis and treatment of this reproductive and metabolic condition known as PCOS. This review article briefly discusses different genes associated directly or indirectly with disease development and progression.
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Affiliation(s)
- Himani Nautiyal
- Siddhartha Institute of Pharmacy, Near IT-Park, Sahastradhara Road, Dehradun 248001, India;
| | - Syed Sarim Imam
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.S.I.); (S.A.)
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.S.I.); (S.A.)
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia;
| | - Muhammad Afzal
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia;
- Correspondence: (M.A.); (I.K.)
| | - Sami I. Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia;
| | - Emine Güven
- Biomedical Engineering Department, Faculty of Engineering, Düzce University, Düzce 81620, Turkey;
| | - Fahad A. Al-Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Correspondence: (M.A.); (I.K.)
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Tian J, Dong Y, Chang S, Wang Y, Shen C, Che G. Epidemiological evidence for associations between variants in microRNA and cancer risk. Carcinogenesis 2022; 43:321-337. [PMID: 35084494 DOI: 10.1093/carcin/bgac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/16/2022] [Accepted: 01/25/2022] [Indexed: 02/05/2023] Open
Abstract
Numerous papers have reported variants in microRNAs associated with cancer risk; these results, however, are controversial. We seek to offer an updated, comprehensive synopsis of genetic associations between single nucleotide polymorphisms (SNPs) in microRNAs (miRNAs) and cancer risk. We did systematic a field synopsis and meta-analysis to investigate 29 SNPs in 24 miRNAs associated with risk of 18 different kinds of cancer based on data from 247 eligible articles. We graded levels of cumulative epidemiological evidence of significant association using Venice criteria and a false-positive report probability (FPRP) test. We constructed functional annotations for these variants using data from the Encyclopedia of DNA Elements Project. We used FPRP to find additional noteworthy associations between 278 SNPs in 117 miRNAs and risk of 26 cancers based on each SNP with one data source. 16 SNPs were statistically associated with risk of 17 cancers. We graded the cumulative epidemiological evidence as strong for statistical associations between 10 SNPs in eight miRNAs and risk of 11 cancers, moderate for nine SNPs with 12 cancers, and weak for 11 SNPs with 11 cancers. Bioinformatics analysis suggested that the SNPs with strong evidence might fall in putative functional regions. In addition, 38 significant associations were observed in 38 SNPs and risk of 13 cancers. This study offered the a comprehensive research on miRNA gene variants and cancer risk and provided referenced information for the genetic predisposition to cancer risk in future research.
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Affiliation(s)
- Jie Tian
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Guoxuexiang, Chengdu, China
| | - Yingxian Dong
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Guoxuexiang, Chengdu, China
| | - Shuai Chang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Guoxuexiang, Chengdu, China
| | - Yan Wang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Guoxuexiang, Chengdu, China
| | - Cheng Shen
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Guoxuexiang, Chengdu, China
| | - Guowei Che
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Guoxuexiang, Chengdu, China
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Cahill S, Chandola T, Hager R. Genetic Variants Associated With Resilience in Human and Animal Studies. Front Psychiatry 2022; 13:840120. [PMID: 35669264 PMCID: PMC9163442 DOI: 10.3389/fpsyt.2022.840120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/19/2022] [Indexed: 11/15/2022] Open
Abstract
Resilience is broadly defined as the ability to maintain or regain functioning in the face of adversity and is influenced by both environmental and genetic factors. The identification of specific genetic factors and their biological pathways underpinning resilient functioning can help in the identification of common key factors, but heterogeneities in the operationalisation of resilience have hampered advances. We conducted a systematic review of genetic variants associated with resilience to enable the identification of general resilience mechanisms. We adopted broad inclusion criteria for the definition of resilience to capture both human and animal model studies, which use a wide range of resilience definitions and measure very different outcomes. Analyzing 158 studies, we found 71 candidate genes associated with resilience. OPRM1 (Opioid receptor mu 1), NPY (neuropeptide Y), CACNA1C (calcium voltage-gated channel subunit alpha1 C), DCC (deleted in colorectal carcinoma), and FKBP5 (FKBP prolyl isomerase 5) had both animal and human variants associated with resilience, supporting the idea of shared biological pathways. Further, for OPRM1, OXTR (oxytocin receptor), CRHR1 (corticotropin-releasing hormone receptor 1), COMT (catechol-O-methyltransferase), BDNF (brain-derived neurotrophic factor), APOE (apolipoprotein E), and SLC6A4 (solute carrier family 6 member 4), the same allele was associated with resilience across divergent resilience definitions, which suggests these genes may therefore provide a starting point for further research examining commonality in resilience pathways.
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Affiliation(s)
- Stephanie Cahill
- Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.,Faculty of Humanities, Cathie Marsh Institute for Social Research, The University of Manchester, Manchester, United Kingdom
| | - Tarani Chandola
- Faculty of Humanities, Cathie Marsh Institute for Social Research, The University of Manchester, Manchester, United Kingdom.,Methods Hub, Department of Sociology, Faculty of Social Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Reinmar Hager
- Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
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25
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Genetic Variants Associated with Thyroid Cancer Risk: Comprehensive Research Synopsis, Meta-Analysis, and Cumulative Epidemiological Evidence. JOURNAL OF ONCOLOGY 2021; 2021:9967599. [PMID: 34950210 PMCID: PMC8691982 DOI: 10.1155/2021/9967599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/09/2021] [Accepted: 11/20/2021] [Indexed: 11/28/2022]
Abstract
Purpose With the increasing incidence of thyroid cancer (TC), associations between genetic polymorphisms and TC risk have attracted a lot of attention. Considering that the results of associations of genetic variants with TC were usually inconsistent based on publications until now, we attempted to comprehensively evaluate the real evidence of associations between single nucleotide polymorphisms (SNPs) and TC risk. Method We performed meta-analyses on 36 SNPs in 23 genes associated with TC susceptibility based on the data from 99 articles and comprehensively valued the epidemiological evidence of significant associations through the Venice criteria and false-positive report probability (FPRP) test. OR and P value were also calculated for 19 SNPs in 13 genes based on the insufficient data from 22 articles. Results 19 SNPs were found significantly associated with TC susceptibility. Of these, strong epidemiological evidence of associations was identified for the following seven SNPs: POU5F1B rs6983267, FOXE1 rs966423, TERT rs2736100, NKX2-1 rs944289, FOXE1 rs1867277, FOXE1 rs2439302, and RET rs1799939, in which moderate associations were found in four SNPs and weak associations were found in eight SNPs. In addition, probable significant associations with TC were found in nine SNPs. Conclusion Our study systematically evaluated associations between SNPs and TC risk and offered reference information for further understanding of polymorphisms and TC susceptibility.
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Van Goethem N, Danwang C, Bossuyt N, Van Oyen H, Roosens NHC, Robert A. A systematic review and meta-analysis of host genetic factors associated with influenza severity. BMC Genomics 2021; 22:912. [PMID: 34930124 PMCID: PMC8686082 DOI: 10.1186/s12864-021-08240-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/07/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The severity of influenza disease can range from mild symptoms to severe respiratory failure and can partly be explained by host genetic factors that predisposes the host to severe influenza. Here, we aimed to summarize the current state of evidence that host genetic variants play a role in the susceptibility to severe influenza infection by conducting a systematic review and performing a meta-analysis for all markers with at least three or more data entries. RESULTS A total of 34 primary human genetic association studies were identified that investigated a total of 20 different genes. The only significant pooled ORs were retrieved for the rs12252 polymorphism: an overall OR of 1.52 (95% CI [1.06-2.17]) for the rs12252-C allele compared to the rs12252-T allele. A stratified analysis by ethnicity revealed opposite effects in different populations. CONCLUSION With exception for the rs12252 polymorphism, we could not identify specific genetic polymorphisms to be associated with severe influenza infection in a pooled meta-analysis. This advocates for the use of large, hypothesis-free, genome-wide association studies that account for the polygenic nature and the interactions with other host, pathogen and environmental factors.
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Affiliation(s)
- Nina Van Goethem
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Brussels, Belgium
| | - Célestin Danwang
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Brussels, Belgium
| | - Nathalie Bossuyt
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Herman Van Oyen
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Public Health and Primary Care, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Annie Robert
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Brussels, Belgium
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27
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Singh S, Brandenburg JT, Choudhury A, Gómez-Olivé FX, Ramsay M. Systematic Review of Genomic Associations with Blood Pressure and Hypertension in Populations with African-Ancestry. Front Genet 2021; 12:699445. [PMID: 34745203 PMCID: PMC8564494 DOI: 10.3389/fgene.2021.699445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/10/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Despite hypertension being highly prevalent in individuals with African-ancestry, they are under-represented in large genome-wide association studies. Inclusion of African participants is essential to better understand genetic associations with blood pressure-related traits in Africans. This systematic review critically evaluates existing studies with African-ancestry participants and identifies knowledge gaps. Methods: We followed the PRISMA protocol, HuGE Review handbook to identify literature on original research, in English, on genetic association studies for blood pressure-related traits (systolic and diastolic blood pressure, pulse and mean-arterial pressure, and hypertension) in populations with African-ancestry (January 2007 to April 2020). A narrative synthesis of the evidence was conducted. Results: Twelve studies with African-ancestry participants met the eligibility criteria, within which 10 studies met the additional genetic association data criteria (i.e., reporting only on African-ancestry participants). Across the five blood pressure-related traits, 26 genome-wide significantly associated SNPs were identified, with six SNPs linked to more than one trait, illustrating pleiotropic effects. Among the SNP associations, 12 had not previously been described in non-African studies. Discussion: The limited number of relevant studies highlights the dearth of genomic association studies on participants with African-ancestry, especially those located within Africa. Variations in study methodology, participant inclusion, adjustment for covariates (e.g., antihypertensive medication) and relatively small sample sizes make comparisons challenging, and have resulted in fewer significant associations, compared to large European studies. Regional variation in the prevalence and associated risk factors of hypertension across Africa makes a compelling argument to develop African cohorts to facilitate large genomic studies, using African-centric arrays. Data harmonisation and comparable study designs, such as described in the H3Africa CHAIR initiative, provide a good example toward achieving this goal. Other relevant information: SS and J-TB were funded by the South African National Research Foundation. MR is a South African Research Chair in Genomics and Bioinformatics of African populations hosted by the University of the Witwatersrand, funded by the Department of Science and Innovation, and administered by the NRF. This review was registered at PROSPERO (registration number: CRD42020179221) and OSF (registration DOI: 10.17605/OSF.IO/QT2HA).
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Affiliation(s)
- S Singh
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J-T Brandenburg
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A Choudhury
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - F X Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - M Ramsay
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Pabalan N, Chaweeborisuit P, Tharabenjasin P, Tasanarong A, Jarjanazi H, Eiamsitrakoon T, Tapanadechopone P. Associations of CB1 cannabinoid receptor (CNR1) gene polymorphisms with risk for alcohol dependence: Evidence from meta-analyses of genetic and genome-wide association studies. Medicine (Baltimore) 2021; 100:e27343. [PMID: 34713823 PMCID: PMC8556036 DOI: 10.1097/md.0000000000027343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 09/08/2021] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES Reported associations of the cannabinoid receptor 1 (CNR1) single nucleotide polymorphisms (SNPs) with alcohol dependence (AD) have been inconsistent, prompting a meta-analysis to obtain more precise estimates. METHODS A Boolean search of 4 databases (PubMed, Scopus, Google Scholar, and Mednar) sought articles that evaluated the association between CNR1 polymorphisms and risk of AD. We selected the articles with sufficient genotype frequency data to enable calculation of odds ratios (ORs) and 95% confidence intervals (CIs). Using the Population Intervention Comparators Outcome elements, AD patients (P) were compared by genotype data between AD-participants (I) and non-AD-participants (C) in order to determine the risk of AD (O) attributed to the CNR1 SNPs. Analyzing 4 SNPs (rs1049353, rs1535255, rs2023239, and rs806379) using standard genetic models, we examined associations where multiple comparisons were Holm-Bonferroni corrected. The pooled ORs were assessed for aggregate statistical power and robustness (sensitivity analysis). Subgroups were Caucasians and African-Americans. RESULTS From 32 comparisons, 14 were significant indicating increased risk, from which 5 outcomes (P-value for association [Pa] = .003 to <.001) survived the Holm-Bonferroni-correction, which were deemed robust. In the rs1535255 outcomes, the codominant effect (OR = 1.43, 95% CIs = 1.24-1.65, Pa < .001) had greater statistical power than the dominant effect (OR = 1.30, 95% CI = 1.08-1.57, Pa = .006). In contrast, the rs2023239 codominant outcome was underpowered. Significance of both rs806379 Caucasian outcomes (ORs = 1.20-1.43, 95% CIs = 1.07-1.57, Pa = .003) contrasted with the null effects in African-Americans (ORs = 0.98-1.08, 95% CIs = 0.70-1.53). CONCLUSIONS Three CNR1 SNPs (rs1535255, rs2023239, and rs806379) were implicated in their associations with development of AD: based on aggregate statistical power, rs1535255 presented greater evidence for associations than rs2023239; rs806379 implicated the Caucasian subgroup. Multiple statistical and meta-analytical features (consistency, robustness, and high significance) underpinned the strengths of these outcomes. Our findings could render the CNR1 polymorphisms useful in the clinical genetics of AD.
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Affiliation(s)
- Noel Pabalan
- Chulabhorn International College of Medicine, Thammasat University, Pathumthani, Thailand
| | | | - Phuntila Tharabenjasin
- Chulabhorn International College of Medicine, Thammasat University, Pathumthani, Thailand
| | - Adis Tasanarong
- Chulabhorn International College of Medicine, Thammasat University, Pathumthani, Thailand
| | - Hamdi Jarjanazi
- Environmental Monitoring and Reporting Branch, Ontario Ministry of the Environment, Conservation and Parks, 125 Resources Road, Toronto, Ontario, Canada
| | - Thanee Eiamsitrakoon
- Chulabhorn International College of Medicine, Thammasat University, Pathumthani, Thailand
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Duan F, Song C, Shi J, Wang P, Ye H, Dai L, Zhang J, Wang K. Identification and epidemiological evaluation of gastric cancer risk factors: based on a field synopsis and meta-analysis in Chinese population. Aging (Albany NY) 2021; 13:21451-21469. [PMID: 34491229 PMCID: PMC8457565 DOI: 10.18632/aging.203484] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 08/11/2021] [Indexed: 12/16/2022]
Abstract
To summarize and assess the credibility and strength of non-genetic factors and genetic variation on gastric cancer risk, we performed a field synopsis and meta-analysis to identify the risk of gastric cancer in Chinese population. Cumulative evidence was graded according to the Venice criteria, and attributable risk percentage (ARP) and population attributable risk percentage (PARP) were used to evaluate the epidemiological effect. A total of 956 studies included non-genetic (404 studies) and genetic factors (552 studies) were quantified, and data on 1161 single nucleotide polymorphisms (SNPs) were available. We identified 14 non-genetic factors were significantly associated with gastric cancer risk. For the analysis of time trends, H. pylori infection rate in gastric cancer and population showed a downward trend. Meanwhile 22 variants were identified significantly associated with gastric cancer: 3 (PLCE1 rs2274223, PSCA rs2976392, MUC1 rs4072037) were high and 19 SNPs were intermediate level of summary evidence, respectively. For non-genetic factors, the top three for ARP were 54.75% (pickled food), 65.87% (stomach disease), and 49.75% (smoked and frying). For PARP were 34.22% (pickled food), 34.24% (edible hot food) and 23.66%(H. pylori infection). On the basis of ARP and PARP associated with SNPs of gastric cancer, the top three for ARP were 53.91% (NAT2, rs1799929),53.05% (NAT2 phenotype), and 42.85% (IL-10, rs1800896). For PARP (Chinese Han in Beijing) were 36.96% (VDR, rs731236), 25.58% (TGFBR2, rs3773651) and 20.56% (MUC1, rs4072037). Our study identified non-genetic risk factors and high-quality biomarkers of gastric cancer susceptibility and their contribution to gastric cancer.
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Affiliation(s)
- Fujiao Duan
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China.,Key Laboratory of Tumor Epidemiology of Henan Province, Zhengzhou, Henan Province, China.,Medical Research Office, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Chunhua Song
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China.,Key Laboratory of Tumor Epidemiology of Henan Province, Zhengzhou, Henan Province, China
| | - Jiachen Shi
- Department of Internal Medicine, The First Affiliated Hospital of Zhengzhou University,Zhengzhou, Henan Province, China
| | - Peng Wang
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China.,Key Laboratory of Tumor Epidemiology of Henan Province, Zhengzhou, Henan Province, China
| | - Hua Ye
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China.,Key Laboratory of Tumor Epidemiology of Henan Province, Zhengzhou, Henan Province, China
| | - Liping Dai
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China.,Key Laboratory of Tumor Epidemiology of Henan Province, Zhengzhou, Henan Province, China
| | - Jianying Zhang
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China.,Key Laboratory of Tumor Epidemiology of Henan Province, Zhengzhou, Henan Province, China
| | - Kaijuan Wang
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China.,Key Laboratory of Tumor Epidemiology of Henan Province, Zhengzhou, Henan Province, China
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30
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Riley M. Critical review of the evidence base regarding theories conceptualising the aetiology of psychosis. ACTA ACUST UNITED AC 2021; 29:1030-1037. [PMID: 32972234 DOI: 10.12968/bjon.2020.29.17.1030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A critical review of literature related to the aetiology of psychosis was conducted with specific emphasis on genetics. It was found that, although many published articles were retrieved via database searches, the format of the information was disparate in presentation leading to unnecessary inconsistences. This suggests the need for insightful collaboration by authors and standardisation of published articles to prevent academic and specialism barriers remaining as a discouragement to non-specialists wishing to access this information.
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Affiliation(s)
- Miv Riley
- Senior Care Co-ordinator, Early Intervention Service (Psychosis), Lancashire Care Foundation Trust and Manchester University
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Aasdahl L, Nilsen TIL, Meisingset I, Nordstoga AL, Evensen KAI, Paulsen J, Mork PJ, Skarpsno ES. Genetic variants related to physical activity or sedentary behaviour: a systematic review. Int J Behav Nutr Phys Act 2021; 18:15. [PMID: 33482856 PMCID: PMC7821484 DOI: 10.1186/s12966-020-01077-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Research shows that part of the variation in physical activity and sedentary behaviour may be explained by genetic factors. Identifying genetic variants associated with physical activity and sedentary behaviour can improve causal inference in physical activity research. The aim of this systematic review was to provide an updated overview of the evidence of genetic variants associated with physical activity or sedentary behaviour. METHODS We performed systematic literature searches in PubMed and Embase for studies published from 1990 to April 2020 using keywords relating to "physical activity", "exercise", "sedentariness" and "genetics". Physical activity phenotypes were either based on self-report (e.g., questionnaires, diaries) or objective measures (e.g., accelerometry, pedometer). We considered original studies aiming to i) identify new genetic variants associated with physical activity or sedentary behaviour (i.e., genome wide association studies [GWAS]), or ii) assess the association between known genetic variants and physical activity or sedentary behaviour (i.e., candidate gene studies). Study selection, data extraction, and critical appraisal were carried out by independent researchers, and risk of bias and methodological quality was assessed for all included studies. RESULTS Fifty-four out of 5420 identified records met the inclusion criteria. Six of the included studies were GWAS, whereas 48 used a candidate gene approach. Only one GWAS and three candidate gene studies were considered high-quality. The six GWAS discovered up to 10 single nucleotide polymorphisms (SNPs) associated with physical activity or sedentariness that reached genome-wide significance. In total, the candidate gene studies reported 30 different genes that were associated (p < 0.05) with physical activity or sedentary behaviour. SNPs in or close to nine candidate genes were associated with physical activity or sedentary behaviour in more than one study. CONCLUSION GWAS have reported up to 10 loci associated with physical activity or sedentary behaviour. Candidate gene studies have pointed to some interesting genetic variants, but few have been replicated. Our review highlights the need for high-quality GWAS in large population-based samples, and with objectively assessed phenotypes, in order to establish robust genetic instruments for physical activity and sedentary behaviour. Furthermore, consistent replications in GWAS are needed to improve credibility of genetic variants. TRIAL REGISTRATION Prospero CRD42019119456 .
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Affiliation(s)
- Lene Aasdahl
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway. .,Unicare Helsefort Rehabilitation Centre, Rissa, Norway.
| | - Tom Ivar Lund Nilsen
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway.,Clinic of Anaesthesia and Intensive Care, St. Olavs Hospital, Trondheim, Norway
| | - Ingebrigt Meisingset
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway
| | - Anne Lovise Nordstoga
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway
| | - Kari Anne I Evensen
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway.,Department of Clinical and Molecular Medicine, NTNU, Trondheim, Norway.,Department of Physiotherapy, Oslo Metropolitan University, Oslo, Norway.,Unit for Physiotherapy Services, Trondheim, Norway
| | - Julie Paulsen
- Department of Medical Genetics, St. Olavs Hospital, Trondheim, Norway
| | - Paul Jarle Mork
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway
| | - Eivind Schjelderup Skarpsno
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway.,Department of Neurology and Clinical Neurophysiology, St. Olavs Hospital, Trondheim, Norway
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Elucidation of the Genomic-Epigenomic Interaction Landscape of Aggressive Prostate Cancer. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6641429. [PMID: 33511206 PMCID: PMC7825361 DOI: 10.1155/2021/6641429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/31/2020] [Indexed: 12/16/2022]
Abstract
Background Majority of prostate cancer (PCa) deaths are attributed to localized high-grade aggressive tumours which progress rapidly to metastatic disease. A critical unmet need in clinical management of PCa is discovery and characterization of the molecular drivers of aggressive tumours. The development and progression of aggressive PCa involve genetic and epigenetic alterations occurring in the germline, somatic (tumour), and epigenomes. To date, interactions between genes containing germline, somatic, and epigenetic mutations in aggressive PCa have not been characterized. The objective of this investigation was to elucidate the genomic-epigenomic interaction landscape in aggressive PCa to identify potential drivers aggressive PCa and the pathways they control. We hypothesized that aggressive PCa originates from a complex interplay between genomic (both germline and somatic mutations) and epigenomic alterations. We further hypothesized that these complex arrays of interacting genomic and epigenomic factors affect gene expression, molecular networks, and signaling pathways which in turn drive aggressive PCa. Methods We addressed these hypotheses by performing integrative data analysis combining information on germline mutations from genome-wide association studies with somatic and epigenetic mutations from The Cancer Genome Atlas using gene expression as the intermediate phenotype. Results The investigation revealed signatures of genes containing germline, somatic, and epigenetic mutations associated with aggressive PCa. Aberrant DNA methylation had effect on gene expression. In addition, the investigation revealed molecular networks and signalling pathways enriched for germline, somatic, and epigenetic mutations including the STAT3, PTEN, PCa, ATM, AR, and P53 signalling pathways implicated in aggressive PCa. Conclusions The study demonstrated that integrative analysis combining diverse omics data is a powerful approach for the discovery of potential clinically actionable biomarkers, therapeutic targets, and elucidation of oncogenic interactions between genomic and epigenomic alterations in aggressive PCa.
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McAuley ABT, Hughes DC, Tsaprouni LG, Varley I, Suraci B, Roos TR, Herbert AJ, Kelly AL. The association of the ACTN3 R577X and ACE I/D polymorphisms with athlete status in football: a systematic review and meta-analysis. J Sports Sci 2021; 39:200-211. [PMID: 32856541 DOI: 10.1080/02640414.2020.1812195] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of this review was to assess the association of ACTN3 R577X and ACE I/D polymorphisms with athlete status in football and determine which allele and/or genotypes are most likely to influence this phenotype via a meta-analysis. A comprehensive search identified 17 ACTN3 and 19 ACE studies. Significant associations were shown between the presence of the ACTN3 R allele and professional footballer status (OR = 1.35, 95% CI: 1.18-1.53) and the ACE D allele and youth footballers (OR = 1.18, 95% CI: 1.01-1.38). More specifically, the ACTN3 RR genotype (OR = 1.48, 95% CI: 1.23-1.77) and ACE DD genotype (OR = 1.29, 95% CI: 1.02-1.63) exhibited the strongest associations, respectively. These findings may be explained by the association of the ACTN3 RR genotype and ACE DD genotype with power-orientated phenotypes and the relative contribution of power-orientated phenotypes to success in football. As such, the results of this review provide further evidence that individual genetic variation may contribute towards athlete status and can differentiate athletes of different competitive playing statuses in a homogenous team-sport cohort. Moreover, the ACTN3 R577X and ACE I/D polymorphisms are likely (albeit relatively minor) contributing factors that influence athlete status in football.
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Affiliation(s)
- Alexander B T McAuley
- Faculty of Health, Education and Life Sciences, Birmingham City University , Birmingham, UK
| | - David C Hughes
- Faculty of Health, Education and Life Sciences, Birmingham City University , Birmingham, UK
| | - Loukia G Tsaprouni
- Faculty of Health, Education and Life Sciences, Birmingham City University , Birmingham, UK
| | - Ian Varley
- Department of Sport Science, Nottingham Trent University , Nottingham, UK
| | - Bruce Suraci
- Academy Coaching Department, AFC Bournemouth , Bournemouth, UK
| | - Thomas R Roos
- The International Academy of Sports Science and Technology (AISTS), University of Lausanne , Lausanne, Switzerland
| | - Adam J Herbert
- Faculty of Health, Education and Life Sciences, Birmingham City University , Birmingham, UK
| | - Adam L Kelly
- Faculty of Health, Education and Life Sciences, Birmingham City University , Birmingham, UK
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Delineation of the Germline and Somatic Mutation Interaction Landscape in Triple-Negative and Non-Triple-Negative Breast Cancer. Int J Genomics 2020; 2020:2641370. [PMID: 32724790 PMCID: PMC7364202 DOI: 10.1155/2020/2641370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/26/2020] [Accepted: 06/09/2020] [Indexed: 11/18/2022] Open
Abstract
Background Breast cancer development and progression involve both germline and somatic mutations. High-throughput genotyping and next-generation sequencing technologies have enabled discovery of genetic risk variants and acquired somatic mutations driving the disease. However, the possible oncogenic interactions between germline genetic risk variants and somatic mutations in triple-negative breast cancer (TNBC) and non-triple-negative breast cancer (non-TNBC) have not been characterized. Here, we delineated the possible oncogenic interactions between genes containing germline and somatic mutations in TNBC and non-TNBC and investigated whether there are differences in gene expression and mutation burden between the two types of breast cancer. Methods We addressed this problem by integrating germline mutation information from genome-wide association studies with somatic mutation information from next-generation sequencing using gene expression data as the intermediated phenotype. We performed network and pathway analyses to discover molecular networks and signalling pathways enriched for germline and somatic mutations. Results The investigation revealed signatures of differentially expressed and differentially somatic mutated genes between TNBC and non-TNBC. Network and pathway analyses revealed functionally related genes interacting in gene regulatory networks and multiple signalling pathways enriched for germline and somatic mutations for each type of breast cancer. Among the signalling pathways discovered included the DNA repair and Androgen and ATM signalling pathways for TNBC and the DNA damage response, molecular mechanisms of cancer, and ATM and GP6 signalling pathways for non-TNBC. Conclusions The results show that integrative genomics is a powerful approach for delineating oncogenic interactions between genes containing germline and genes containing somatic mutations in TNBC and non-TNBC and establishes putative functional bridges between genetic and somatic alterations and the pathways they control in the two types of breast cancer.
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Abstract
Mycetoma is one of the badly neglected tropical diseases, characterised by subcutaneous painless swelling, multiple sinuses, and discharge containing aggregates of the infecting organism known as grains. Risk factors conferring susceptibility to mycetoma include environmental factors and pathogen factors such as virulence and the infecting dose, in addition to host factors such as immunological and genetic predisposition. Epidemiological evidence suggests that host genetic factors may regulate susceptibility to mycetoma and other fungal infections, but they are likely to be complex genetic traits in which multiple genes interact with each other and environmental factors, as well as the pathogen, to cause disease. This paper reviews what is known about genetic predisposition to fungal infections that might be relevant to mycetoma, as well as all studies carried out to explore host genetic susceptibility to mycetoma. Most studies were investigating polymorphisms in candidate genes related to the host immune response. A total of 13 genes had allelic variants found to be associated with mycetoma, and these genes lie in different pathways and systems such as innate and adaptive immune systems, sex hormone biosynthesis, and some genes coding for host enzymes. None of these studies have been replicated. Advances in genomic science and the supporting technology have paved the way for large-scale genome-wide association and next generation sequencing (NGS) studies, underpinning a new strategy to systematically interrogate the genome for variants associated with mycetoma. Dissecting the contribution of host genetic variation to susceptibility to mycetoma will enable the identification of pathways that are potential targets for new treatments for mycetoma and will also enhance the ability to stratify ‘at-risk’ individuals, allowing the possibility of developing preventive and personalised clinical care strategies in the future.
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Affiliation(s)
- Rayan S. Ali
- The Mycetoma Research Centre, University of Khartoum, Khartoum, Sudan
- Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, Brighton, United Kingdom
- * E-mail:
| | - Melanie J. Newport
- Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, Brighton, United Kingdom
| | - Sahar Mubarak Bakhiet
- The Mycetoma Research Centre, University of Khartoum, Khartoum, Sudan
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
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Muhamed B, Shaboodien G, Engel ME. Genetic variants in rheumatic fever and rheumatic heart disease. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:159-177. [PMID: 32083395 DOI: 10.1002/ajmg.c.31773] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 12/16/2022]
Abstract
Genetic association studies in rheumatic heart disease (RHD) have the potential to contribute toward our understanding of the pathogenetic mechanism, and may shed light on controversies about RHD etiology. Furthermore, genetic association studies may uncover biomarkers that can be used to identify susceptible individuals, and contribute toward developing vaccine and novel therapeutic targets. Genetic predisposition to rheumatic fever and RHD has been hypothesized by findings from familial studies and observed associations between genes located in the human leukocyte antigens on chromosome 6p21.3 and elsewhere in the genome. We sought to summarize, from published Genetic association studies in RHD, evidence on genetic variants implicated in RHD susceptibility. Using HuGENet™ systematic review methods, we evaluated 66 studies reporting on 42 genes. Existing meta-analyses of candidate gene studies suggest that TGF-β1 [rs1800469], and IL-1β [rs2853550] single nucleotide polymorphisms (SNPs) contribute to susceptibility to RHD, whereas the TNF-α [rs1800629 and rs361525], TGF-β1 [rs1800470 and rs4803457], IL-6 [rs1800795], IL-10 [rs1800896] were not associated with RHD. However, candidate gene studies in RF/RHD are relatively small, thus lacking statistical power to identify reliable and reproducible findings, emphasizing the need for large-scale multicenter studies with different populations.
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Affiliation(s)
- Babu Muhamed
- Department of Medicine, University of Cape Town, Cape Town, South Africa.,Hatter Institute for Cardiovascular Diseases Research in Africa, Observatory, South Africa.,Division of Cardiology, Children's National Health System, Washington, District of Columbia
| | - Gasnat Shaboodien
- Department of Medicine, University of Cape Town, Cape Town, South Africa.,Hatter Institute for Cardiovascular Diseases Research in Africa, Observatory, South Africa
| | - Mark E Engel
- Department of Medicine, University of Cape Town, Cape Town, South Africa
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Liu G, Tian J, Zuo C, Li Y, Fu K, Chen H. Epidemiological evidence for associations between variants in microRNA or biosynthesis genes and lung cancer risk. Cancer Med 2020; 9:1937-1950. [PMID: 31910330 PMCID: PMC7050065 DOI: 10.1002/cam4.2645] [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: 07/04/2019] [Revised: 09/29/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022] Open
Abstract
In the past decade, the studies involving single nucleotide polymorphisms (SNPs) in microRNAs (miRNAs) with lung cancer (LC) risk have been performed, however, these results are inconsistent, and a systematic research synopsis has not been performed yet. Therefore, we attempted to perform comprehensive meta‐analyses to assess the relationships between SNPs in miRNAs or biosynthesis genes and LC risk and further evaluate the epidemiological credibility of these significant associations. We used PubMed, Medline, and Web of Science to search for relevant articles published before 30 May 2019 that assessed relationships between SNPs in miRNAs or biosynthesis genes and LC risk. The cumulative epidemiological evidence of statistical relationships was further assessed combining Venice Criteria and a false‐positive report probability test. Based on 20 publications with 15 969 cases and 17 174 controls, we found that six variants in miRNAs or biosynthesis genes that proved significant associations with LC risk, whereas five proved no association. Subgroup analyses by ethnicity and genetic models were performed, suggesting that four associations were rated as demonstrating strong evidence of relationship with LC risk, including miRNA‐146a rs2910164 in all populations under dominant model and in Asians under dominant and recessive models, and AGO1 rs595961 in Asians under allelic model. Three associations were graded as moderate, and seven associations were rated as weak. This study presents the relationships between SNPs in miRNAs or biosynthesis genes and LC risk, subsequently demonstrates the credibility of these significant associations, and highlights the role in the pathogenesis of LC.
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Affiliation(s)
- Guanchu Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Tian
- Department of Thoracic Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
| | - Chunjian Zuo
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yufu Li
- Department of Cardiothoracic Surgery, The People's Hospital of Chongqing Tongnan, Chongqing, China
| | - Kui Fu
- Department of Cardiothoracic Surgery, Traditional Chinese Medicine Hospital, Dianjiang, Chongqing, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Asamoah EA, Obirikorang C, Acheampong E, Annani-Akollor ME, Laing EF, Owiredu EW, Anto EO. Heritability and Genetics of Type 2 Diabetes Mellitus in Sub-Saharan Africa: A Systematic Review and Meta-Analysis. J Diabetes Res 2020; 2020:3198671. [PMID: 32685554 PMCID: PMC7352126 DOI: 10.1155/2020/3198671] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/08/2020] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVES Sub-Saharan Africa (SSA) is observing an accelerating prevalence rate of type 2 diabetes mellitus (T2DM) influenced by gene-environment interaction of modifiable and nonmodifiable factors. We conducted a systematic review and meta-analysis on the heritability and genetic risk of T2DM in SSA. METHODS We reviewed all published articles on T2DM in SSA between January 2000 and December 2019 and available in PubMed, Scopus, and Web of Science. Studies that reported on the genetics and/or heritability of T2DM or indicators of glycaemia were included. Data extracted included the study design, records of family history, pattern and characteristics of inheritance, genetic determinants, and effects estimates. RESULTS The pattern and characteristics of T2DM heritability in SSA are preference for maternal aggregation, higher among first degree compared to second-degree relatives; early age-onset (<50 years), and inherited abnormalities of beta-cell function/mass. The overall prevalence of T2DM was 28.2% for the population with a positive family history (PFH) and 11.2% for the population with negative family history (NFH). The pooled odds ratio of the impact of PFH on T2DM was 3.29 (95% CI: 2.40-4.52). Overall, 28 polymorphisms in 17 genes have been investigated in relation with T2DM in SSA. Almost all studies used the candidate gene approach with most (45.8%) of genetic studies published between 2011 and 2015. Polymorphisms in ABCC8, Haptoglobin, KCNJ11, ACDC, ENPP1, TNF-α, and TCF7L2 were found to be associated with T2DM, with overlapping effect on specific cardiometabolic traits. Genome-wide studies identified ancestry-specific signals (AGMO-rs73284431, VT11A-rs17746147, and ZRANB3) and TCF7L2-rs7903146 as the only transferable genetic risk variants to SSA population. TCF7L2-rs7903146 polymorphism was investigated in multiple studies with consistent effects and low-moderate statistical heterogeneity. Effect sizes were modestly strong [odds ratio = 6.17 (95% CI: 2.03-18.81), codominant model; 2.27 (95% CI: 1.50-3.44), additive model; 1.75 (95% CI: 1.18-2.59), recessive model]. Current evidence on the heritability and genetic markers of T2DM in SSA populations is limited and largely insufficient to reliably inform the genetic architecture of T2DM across SSA regions.
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Affiliation(s)
- Evans Adu Asamoah
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Ghana
| | - Christian Obirikorang
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Ghana
| | - Emmanuel Acheampong
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Ghana
| | - Max Efui Annani-Akollor
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Ghana
| | - Edwin Ferguson Laing
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Ghana
| | - Eddie-Williams Owiredu
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Ghana
| | - Enoch Odame Anto
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Ghana
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Lipunova N, Wesselius A, Cheng KK, van Schooten FJ, Cazier JB, Bryan RT, Zeegers MP. Systematic Review: Genetic Associations for Prognostic Factors of Urinary Bladder Cancer. BIOMARKERS IN CANCER 2019; 11:1179299X19897255. [PMID: 31908559 PMCID: PMC6937527 DOI: 10.1177/1179299x19897255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 12/03/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Many germline associations have been reported for urinary bladder cancer (UBC) outcomes and prognostic characteristics. It is unclear whether there are overlapping genetic patterns for various prognostic endpoints. We aimed to review contemporary literature on genetic associations with UBC prognostic outcomes and to identify potential overlap in reported genes. METHODS EMBASE, MEDLINE, and PubMed databases were queried for relevant articles in English language without date restrictions. The initial search identified 1346 articles. After exclusions, 112 studies have been summarized. Cumulatively, 316 single-nucleotide polymorphisms (SNPs) were reported across prognostic outcomes (recurrence, progression, death) and characteristics (tumor stage, grade, size, age, risk group). There were considerable differences between studied outcomes in the context of genetic associations. The most commonly reported SNPs were located in OGG1, TP53, and MDM2. For outcomes with the highest number of reported associations (ie, recurrence and death), functional enrichment annotation yields different terms, potentially indicating separate biological mechanisms. CONCLUSIONS Our study suggests that all UBC prognostic outcomes may have different biological origins with limited overlap. Further validation of these observations is essential to target a phenotype that could best predict patient outcome and advance current management practices.
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Affiliation(s)
- Nadezda Lipunova
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Department of Complex Genetics, Maastricht University, Maastricht, The Netherlands
- Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Anke Wesselius
- Department of Complex Genetics, Maastricht University, Maastricht, The Netherlands
| | - Kar K Cheng
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | | | - Jean-Baptiste Cazier
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Richard T Bryan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Maurice P Zeegers
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Department of Complex Genetics, Maastricht University, Maastricht, The Netherlands
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Mamidi TKK, Wu J, Hicks C. Mapping the Germline and Somatic Mutation Interaction Landscape in Indolent and Aggressive Prostate Cancers. JOURNAL OF ONCOLOGY 2019; 2019:4168784. [PMID: 31814827 PMCID: PMC6878815 DOI: 10.1155/2019/4168784] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/19/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND A majority of prostate cancers (PCas) are indolent and cause no harm even without treatment. However, a significant proportion of patients with PCa have aggressive tumors that progress rapidly to metastatic disease and are often lethal. PCa develops through somatic mutagenesis, but emerging evidence suggests that germline genetic variation can markedly contribute to tumorigenesis. However, the causal association between genetic susceptibility and tumorigenesis has not been well characterized. The objective of this study was to map the germline and somatic mutation interaction landscape in indolent and aggressive tumors and to discover signatures of mutated genes associated with each type and distinguishing the two types of PCa. MATERIALS AND METHODS We integrated germline mutation information from genome-wide association studies (GWAS) with somatic mutation information from The Cancer Genome Atlas (TCGA) using gene expression data from TCGA on indolent and aggressive PCas as the intermediate phenotypes. Germline and somatic mutated genes associated with each type of PCa were functionally characterized using network and pathway analysis. RESULTS We discovered gene signatures containing germline and somatic mutations associated with each type and distinguishing the two types of PCa. We discovered multiple gene regulatory networks and signaling pathways enriched with germline and somatic mutations including axon guidance, RAR, WINT, MSP-RON, STAT3, PI3K, TR/RxR, and molecular mechanisms of cancer, NF-kB, prostate cancer, GP6, androgen, and VEGF signaling pathways for indolent PCa and MSP-RON, axon guidance, RAR, adipogenesis, and molecular mechanisms of cancer and NF-kB signaling pathways for aggressive PCa. CONCLUSION The investigation revealed germline and somatic mutated genes associated with indolent and aggressive PCas and distinguishing the two types of PCa. The study revealed multiple gene regulatory networks and signaling pathways dysregulated by germline and somatic alterations. Integrative analysis combining germline and somatic mutations is a powerful approach to mapping germline and somatic mutation interaction landscape.
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Affiliation(s)
- Tarun Karthik Kumar Mamidi
- Informatics Institute, University of Alabama at Birmingham, School of Medicine, 1720 2nd Avenue South, Birmingham, AL 35294-3412, USA
| | - Jiande Wu
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar, New Orleans, LA-70112, USA
| | - Chindo Hicks
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar, New Orleans, LA-70112, USA
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Cui H, Tang M, Zhang M, Liu S, Chen S, Zeng Z, Shen Z, Song B, Lu J, Jia H, Gu D, Zhang B. Variants in the PSCA gene associated with risk of cancer and nonneoplastic diseases: systematic research synopsis, meta-analysis and epidemiological evidence. Carcinogenesis 2019; 40:70-83. [PMID: 30407486 DOI: 10.1093/carcin/bgy151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 10/01/2018] [Indexed: 12/19/2022] Open
Abstract
Variants in the prostate stem cell antigen (PSCA) gene have been linked with risk of multiple cancers and other diseases. But results have been inconclusive and no systematic research synopsis has been available. We did a comprehensive meta-analysis to investigate associations between variants in this gene and risk of nine cancers and four nonneoplastic diseases based on data from 55 publications including 81 961 cases and 442 932 controls. We graded levels of cumulative epidemiological evidence of a significant association using the Venice criteria and false-positive report probability tests. We performed functional annotation for these variants using data from the Encyclopedia of DNA Elements Project and other public databases. We found that six variants were nominally significantly associated with an increased or reduced risk of three cancers and three nonneoplastic diseases (P < 0.05). Cumulative evidence of an association was graded as strong for rs2294008 [odds ratio (OR) = 1.32, P = 5.1 × 10-33], rs2976392 (OR = 1.29, P = 1.8 × 10-8), rs9297976 (OR = 0.75, P = 1.4 × 10-7), rs2976391 (OR = 1.38, P = 6.1 × 10-5) and rs138377917 (OR = 0.53, P = 0.008) with gastric cancer, rs2294008 with bladder cancer (OR = 1.15, P = 8.0 × 10-19), gastritis (OR = 1.35, P = 1.2 × 10-5), duodenal ulcer (OR = 0.68, P = 2.4 × 10-57) and gastric ulcer (OR = 0.88, P = 1.7 × 10-7). Data from the Encyclopedia of DNA Elements Project and other databases showed that these variants and other variants correlated with them might fall in putative functional regions. In conclusion, this study provides summary evidence that variants in the PSCA gene are associated with risk of gastric and bladder cancer, gastritis, as well as duodenal and gastric ulcer and highlights the significant role of this gene in the pathogenesis of these diseases.
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Affiliation(s)
- Huijie Cui
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Min Zhang
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Shanshan Liu
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Siyu Chen
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Ziqian Zeng
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Zhuozhi Shen
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Bin Song
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Jiachun Lu
- Department of Epidemiology, School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Hong Jia
- Department of Epidemiology, School of Public Health, Southwest Medical University, Luzhou, China
| | - Dongqing Gu
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China.,Department of Epidemiology, School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China.,Department of Epidemiology, School of Public Health, Southwest Medical University, Luzhou, China.,Department of Epidemiology, School of Public Health, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Wu J, Mamidi TKK, Zhang L, Hicks C. Deconvolution of the Genomic and Epigenomic Interaction Landscape of Triple-Negative Breast Cancer. Cancers (Basel) 2019; 11:cancers11111692. [PMID: 31683572 PMCID: PMC6896043 DOI: 10.3390/cancers11111692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/07/2019] [Accepted: 10/19/2019] [Indexed: 12/26/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive form of breast cancer. Emerging evidenced suggests that both genetics and epigenetic factors play a role in the pathogenesis of TNBC. However, oncogenic interactions and cooperation between genomic and epigenomic variation have not been characterized. The objective of this study was to deconvolute the genomic and epigenomic interaction landscape in TNBC using an integrative genomics approach, which integrates information on germline, somatic, epigenomic and gene expression variation. We hypothesized that TNBC originates from a complex interplay between genomic (both germline and somatic variation) and epigenomic variation. We further hypothesized that these complex arrays of interacting genomic and epigenomic factors affect entire molecular networks and signaling pathways which, in turn, drive TNBC. We addressed these hypotheses using germline variation from genome-wide association studies and somatic, epigenomic and gene expression variation from The Cancer Genome Atlas (TCGA). The investigation revealed signatures of functionally related genes containing germline, somatic and epigenetic variations. DNA methylation had an effect on gene expression. Network and pathway analysis revealed molecule networks and signaling pathways enriched for germline, somatic and epigenomic variation, among them: Role of BRCA1 in DNA Damage Response, Hereditary Breast Cancer Signaling, Molecular Mechanisms of Cancer, Estrogen-Dependent Breast Cancer, p53, MYC Mediated Apoptosis, and PTEN Signaling pathways. The investigation revealed that integrative genomics is a powerful approach for deconvoluting the genomic-epigenomic interaction landscape in TNBC. Further studies are needed to understand the biological mechanisms underlying oncogenic interactions between genomic and epigenomic factors in TNBC.
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Affiliation(s)
- Jiande Wu
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
| | - Tarun Karthik Kumar Mamidi
- Graduate Biomedical Sciences, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35233, USA.
| | - Lu Zhang
- Department of Public Health Sciences, Clemson University, 513 Edwards Hall, Clemson, SC 29634, USA.
| | - Chindo Hicks
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
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The Genetics of Polycystic Ovary Syndrome: An Overview of Candidate Gene Systematic Reviews and Genome-Wide Association Studies. J Clin Med 2019; 8:jcm8101606. [PMID: 31623391 PMCID: PMC6832583 DOI: 10.3390/jcm8101606] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 09/26/2019] [Accepted: 09/30/2019] [Indexed: 01/08/2023] Open
Abstract
Polycystic Ovary Syndrome (PCOS) is a complex condition with mechanisms likely to involve the interaction between genetics and lifestyle. Familial clustering of PCOS symptoms is well documented, providing evidence for a genetic contribution to the condition. This overview aims firstly to systematically summarise the current literature surrounding genetics and PCOS, and secondly, to assess the methodological quality of current systematic reviews and identify limitations. Four databases were searched to identify candidate gene systematic reviews, and quality was assessed with the AMSTAR tool. Genome-wide association studies (GWAS) were identified by a semi structured literature search. Of the candidate gene systematic reviews, 17 were of high to moderate quality and four were of low quality. A total of 19 gene loci have been associated with risk of PCOS in GWAS, and 11 of these have been replicated across two different ancestries. Gene loci were located in the neuroendocrine, metabolic, and reproductive pathways. Overall, the gene loci with the most robust findings were THADA, FSHR, INS-VNTR, and DENND1A, that now require validation. This overview also identified limitations of the current literature and important methodological considerations for future genetic studies. Much work remains to identify causal variants and functional relevance of genes associated with PCOS.
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Muhamed B, Parks T, Sliwa K. Genetics of rheumatic fever and rheumatic heart disease. Nat Rev Cardiol 2019; 17:145-154. [PMID: 31519994 DOI: 10.1038/s41569-019-0258-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 12/13/2022]
Abstract
Rheumatic heart disease (RHD) is a complication of group A streptococcal infection that results from a complex interaction between the genetic make-up of the host, the infection itself and several other environmental factors, largely reflecting poverty. RHD is estimated to affect 33.4 million people and results in 10.5 million disability-adjusted life-years lost globally. The disease has long been considered heritable but still little is known about the host genetic factors that increase or reduce the risk of developing RHD. In the 1980s and 1990s, several reports linked the disease to the human leukocyte antigen (HLA) locus on chromosome 6, followed in the 2000s by reports implicating additional candidate regions elsewhere in the genome. Subsequently, the search for susceptibility loci has been reinvigorated by the use of genome-wide association studies (GWAS) through which millions of variants can be tested for association in thousands of individuals. Early findings implicate not only HLA, particularly the HLA-DQA1 to HLA-DQB1 region, but also the immunoglobulin heavy chain locus, including the IGHV4-61 gene segment, on chromosome 14. In this Review, we assess the emerging role of GWAS in assessing RHD, outlining both the advantages and disadvantages of this approach. We also highlight the potential use of large-scale, publicly available data and the value of international collaboration to facilitate comprehensive studies that produce findings that have implications for clinical practice.
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Affiliation(s)
- Babu Muhamed
- Hatter Institute for Cardiovascular Diseases Research in Africa, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Tom Parks
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Karen Sliwa
- Hatter Institute for Cardiovascular Diseases Research in Africa, Department of Medicine, University of Cape Town, Cape Town, South Africa.
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Edris A, den Dekker HT, Melén E, Lahousse L. Epigenome-wide association studies in asthma: A systematic review. Clin Exp Allergy 2019; 49:953-968. [PMID: 31009112 DOI: 10.1111/cea.13403] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/29/2019] [Accepted: 04/10/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Asthma is a common chronic respiratory airway disease influenced by environmental factors and possibly their interaction with the human genome causing epigenetic changes. Epigenome-wide association studies (EWAS) have mainly investigated DNA methylation and its association with disease or traits, exposure factors or gene expression. This systematic review aimed to identify all EWAS assessing differentially methylated sites associated with asthma in humans. DESIGN Structured systematic literature search following PRISMA guidelines, Newcastle-Ottawa Scale (NOS) for cohort studies was used for bias assessment. DATA SOURCES We searched PubMed and Embase databases from 2005 to 2019. ELIGIBILITY CRITERIA Epigenome-wide association studies testing association between differential methylation and asthma in humans. RESULTS Overall, we identified 16 EWAS studies complying with our search criteria. Twelve studies were conducted on children, and 10 were conducted on sample sizes <150 subjects. Four hundred and nineteen CpGs were reported in children studies after correction for multiple testing. In the adult studies, thousands of differentially methylated sites were identified. Differential methylation in inflammatory-related genes correlated with higher levels of gene expressions of inflammatory modulators in asthma. Differentially methylated genes associated with asthma included SMAD3, SERPINC1, PROK1, IL13, RUNX3 and TIGIT. Forty-one CpGs were replicated at least once in blood samples, and 28 CpGs were replicated in nasal samples. CONCLUSION Although many differentially methylated CpGs in genes known to be involved in asthma have been identified in EWAS to date, we conclude that further studies of larger sample sizes and analyses of differential methylation between different phenotypes are needed in order to comprehensively evaluate the role of epigenetic factors in the pathophysiology and heterogeneity of asthma, and the potential clinical utility to predict or classify patients with asthma.
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Affiliation(s)
- Ahmed Edris
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Herman T den Dekker
- The Generation R Study Group, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands.,Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Sachs' Children's Hospital, Södersjukhuset, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Lies Lahousse
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
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Citterio F, Romano F, Ferrarotti F, Gualini G, Aimetti M. Quality of methods and reporting in association studies of chronic periodontitis and IL1A -889 and IL1B +3953/4 SNPs: A systematic review. J Periodontal Res 2019; 54:457-467. [PMID: 30982982 DOI: 10.1111/jre.12655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/30/2018] [Accepted: 12/10/2018] [Indexed: 11/29/2022]
Abstract
OBJECTIVE The aim of this systematic review was to evaluate the quality of reporting and methodology in genetic association studies between IL1A -889 and IL1B +3954 polymorphisms and chronic periodontitis. BACKGROUND Evidence provided by periodontal research on genetic risk factors is of uttermost importance in clinical practice as a possible diagnostic and prognostic tool for periodontitis. Inadequate reporting of results as well as high risk of bias due to methodological inconsistency hampers the integration of evidence in terms of clinical applicability. METHODS This review includes case-control studies in humans published between 1997 and July 2017. Searching was conducted through MEDLINE, EMBASE, and search handing. Specific scoring systems have been developed to evaluate the quality of methods and reporting. Each article was scored according to its adequacy, and then, the total number and the percentage of items positively qualified for both methods and reporting were calculated. The quality of methods in studies scoring 0-6, 7-12, and 13-16 was, respectively, considered poor, moderate, and good. For reporting, scores of 0-9, 10-18, and 19-26 were deemed of poor, moderate, and good quality, respectively. Pearson's correlation coefficient was calculated to explore the correlation between the year of publication and the quality in terms of methods and reporting. RESULTS From the 531 screened studies, 52 met the inclusion criteria and were thus included in the study. The quality of methods and reporting of published genetic association papers on IL1 and chronic periodontitis is moderate. On a scale from 0 to 16, the mean score for methods of the reviewed studies was 8.19 ± 1.93. The items more frequently considered inadequate concerned the handling of confounders in statistical analysis, especially oral hygiene habits, socioeconomic status, subgingival colonization of specific periodontal pathogens, and stress. A significant positive correlation was found between the year of publication and the quality scores in terms of method (r = 0.401, P = 0.003). In terms of reporting, the mean score was 14.83 ± 3.04 on a scale from 0 to 26 and it was considered overall moderate. No statistically significant correlation was found between the year of publication and the quality of reporting (P = 0.266). CONCLUSIONS The association between IL1A -889 and IL1B +3954 polymorphisms and chronic periodontitis is questionable due to methodological inconsistency. Evidence arising from meta-analysis is unreliable due to high risk of bias and moderate quality in terms of reporting.
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Affiliation(s)
- Filippo Citterio
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Federica Romano
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Francesco Ferrarotti
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Giacomo Gualini
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Mario Aimetti
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
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Huang ZS, Guo XW, Zhang G, Liang LX, Nong B. The Diagnostic and Prognostic Value of miR-200c in Gastric Cancer: A Meta-Analysis. DISEASE MARKERS 2019; 2019:8949618. [PMID: 31089400 PMCID: PMC6476052 DOI: 10.1155/2019/8949618] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 02/04/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND The role of miR-200c in gastric cancer remains controversial. This study is aimed at clarifying the diagnostic and prognostic value of miR-200c in gastric cancer through a meta-analysis. METHODS A comprehensive literature search of PubMed, Embase, and Ovid library databases was conducted. The studies included were those conducted before December 2017. The sensitivity and specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under curve (AUC) were used to estimate the diagnostic value of miR-200c. Meanwhile, the pooled hazard ratio (HR) was used to estimate the prognostic value of miR-200c. RESULTS For the diagnostic value of miR-200c, six studies that included 202 patients with gastric cancer and 250 normal controls were analyzed. The sensitivity, specificity, PLR, NLR, DOR, and AUC were 0.74, 0.66, 2.20, 0.40, 5.34, and 0.75, respectively. Subgroup analysis showed no significant difference in the type of the sample, method for testing miR-200c, and ethnicity among the patients. Meanwhile, for the prognostic value of miR-200c, seven studies comprising 935 patients with gastric cancer were analyzed. The pooled results showed that miR-200c expression was associated with overall survival (HR = 2.19) and disease-free survival (HR = 1.73), but not with progression-free survival (HR = 1.64) in patients with gastric cancer. There was no publication bias across the studies. CONCLUSIONS Both serum and tissue miR-200c have moderate diagnostic accuracy in gastric cancer. miR-200c could also be used as a valuable indicator for predicting the prognosis of gastric cancer patients.
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Affiliation(s)
- Zong-Sheng Huang
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xian-Wen Guo
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Guo Zhang
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Lie-Xin Liang
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Bing Nong
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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Lan T, Yang B, Zhang X, Wang T, Lu Q. Statistical Methods and Software for Substance Use and Dependence Genetic Research. Curr Genomics 2019; 20:172-183. [PMID: 31929725 PMCID: PMC6935956 DOI: 10.2174/1389202920666190617094930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/16/2019] [Accepted: 05/24/2019] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Substantial substance use disorders and related health conditions emerged dur-ing the mid-20th century and continue to represent a remarkable 21st century global burden of disease. This burden is largely driven by the substance-dependence process, which is a complex process and is influenced by both genetic and environmental factors. During the past few decades, a great deal of pro-gress has been made in identifying genetic variants associated with Substance Use and Dependence (SUD) through linkage, candidate gene association, genome-wide association and sequencing studies. METHODS Various statistical methods and software have been employed in different types of SUD ge-netic studies, facilitating the identification of new SUD-related variants. CONCLUSION In this article, we review statistical methods and software that are currently available for SUD genetic studies, and discuss their strengths and limitations.
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Affiliation(s)
| | | | | | - Tong Wang
- Address correspondence to these authors at the Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, China; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA; Tel/ Fax: ++1-517-353-8623; E-mails: ;
| | - Qing Lu
- Address correspondence to these authors at the Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, China; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA; Tel/ Fax: ++1-517-353-8623; E-mails: ;
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50
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Wu J, Mamidi TKK, Zhang L, Hicks C. Integrating Germline and Somatic Mutation Information for the Discovery of Biomarkers in Triple-Negative Breast Cancer. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16061055. [PMID: 30909550 PMCID: PMC6466377 DOI: 10.3390/ijerph16061055] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 12/22/2022]
Abstract
Recent advances in high-throughput genotyping and the recent surge of next generation sequencing of the cancer genomes have enabled discovery of germline mutations associated with an increased risk of developing breast cancer and acquired somatic mutations driving the disease. Emerging evidence indicates that germline mutations may interact with somatic mutations to drive carcinogenesis. However, the possible oncogenic interactions and cooperation between germline and somatic alterations in triple-negative breast cancer (TNBC) have not been characterized. The objective of this study was to investigate the possible oncogenic interactions and cooperation between genes containing germline and somatic mutations in TNBC. Our working hypothesis was that genes containing germline mutations associated with an increased risk developing breast cancer also harbor somatic mutations acquired during tumorigenesis, and that these genes are functionally related. We further hypothesized that TNBC originates from a complex interplay among and between genes containing germline and somatic mutations, and that these complex array of interacting genetic factors affect entire molecular networks and biological pathways which in turn drive the disease. We tested this hypothesis by integrating germline mutation information from genome-wide association studies (GWAS) with somatic mutation information on TNBC from The Cancer Genome Atlas (TCGA) using gene expression data from 110 patients with TNBC and 113 controls. We discovered a signature of 237 functionally related genes containing both germline and somatic mutations. We discovered molecular networks and biological pathways enriched for germline and somatic mutations. The top pathways included the hereditary breast cancer and role of BRCA1 in DNA damage response signaling pathways. In conclusion, this is the first large-scale and comprehensive analysis delineating possible oncogenic interactions and cooperation among and between genes containing germline and somatic mutations in TNBC. Genetic and somatic mutations, along with the genes discovered in this study, will require experimental functional validation in different ethnic populations. Functionally validated genetic and somatic variants will have important implications for the development of novel precision prevention strategies and discovery of prognostic markers in TNBC.
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Affiliation(s)
- Jiande Wu
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
| | - Tarun Karthik Kumar Mamidi
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
| | - Lu Zhang
- Louisiana Tumor Registry, Louisiana State University Health Sciences Center, School of Public Health, 2020 Gravier Street, New Orleans, LA 70112, USA.
| | - Chindo Hicks
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
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