1
|
Costa IB, Santana-da-Silva MN, Nogami PY, Santos e Santos CDJ, Pereira LMS, França EDS, Freire ABC, Ramos FLDP, Monteiro TAF, Macedo O, Sousa RCM, Freitas FB, Vallinoto ACR, Brasil-Costa I. Immunogenetic Profile Associated with Patients Living with HIV-1 and Epstein-Barr Virus (EBV) in the Brazilian Amazon Region. Viruses 2024; 16:1012. [PMID: 39066175 PMCID: PMC11281405 DOI: 10.3390/v16071012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/14/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Viral coinfection among HIV-positive patients, coupled with the development of AIDS, remains a major public health problem. The synergism between the presence of HIV and other viruses has consequences in relation to changes in the severity of the infection, as well as changes in the natural course of both infections. Several polymorphisms present in genes that encode cytokines have a relevant influence on their transcription and consequently on the production of such immunological molecules. The present study evaluated the influence of SNPs located in the promoter regions of genes encoding the cytokines INF-ɣ, TNF, IL-6, IL-4, and IL-2, as well as their respective plasma concentrations, in patients infected with HIV and/or EBV in the state of Pará. Additionally, this study described the epidemiological profile and compared CD4+ and CD8+ T lymphocyte counts among the groups studied. The associative analysis between the SNPs and plasma cytokine concentrations in different groups showed statistical relevance for three polymorphisms: rs2069762 (IL2), where the GG genotype demonstrated higher IL-2 levels in HIV mono-infected individuals; rs2243250 (IL4), where the CT genotype showed higher IL-4 levels in the control group; and rs2069705 (IFNG), where the TT genotype showed higher IFN-γ levels in the coinfected group. Regarding SNP associations with CD4+/CD8+ counts, significant findings were observed in HIV mono-infected individuals: the rs2069705 (IFNG) polymorphism was linked to higher CD4+ counts with the CT genotype, and rs1799964 (TNF) was associated with higher CD8+ counts with the CC genotype. Therefore, this study provides evidence that the rs2069705 (IFNG) SNP is associated with elevated IFN-γ levels, which may have pathogenic consequences, as depletion of this cytokine is concerning for people living with HIV due to its antiviral properties.
Collapse
Affiliation(s)
- Iran Barros Costa
- Epstein-Barr Virus Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (I.B.C.); (M.N.S.-d.-S.); (P.Y.N.); (C.d.J.S.e.S.); (E.d.S.F.); (T.A.F.M.)
- Immunology Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil
| | - Mayara Natália Santana-da-Silva
- Epstein-Barr Virus Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (I.B.C.); (M.N.S.-d.-S.); (P.Y.N.); (C.d.J.S.e.S.); (E.d.S.F.); (T.A.F.M.)
- Immunology Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil
| | - Patrícia Yuri Nogami
- Epstein-Barr Virus Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (I.B.C.); (M.N.S.-d.-S.); (P.Y.N.); (C.d.J.S.e.S.); (E.d.S.F.); (T.A.F.M.)
- Immunology Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil
| | - Carolinne de Jesus Santos e Santos
- Epstein-Barr Virus Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (I.B.C.); (M.N.S.-d.-S.); (P.Y.N.); (C.d.J.S.e.S.); (E.d.S.F.); (T.A.F.M.)
- Immunology Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil
| | - Leonn Mendes Soares Pereira
- Virology Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil; (L.M.S.P.); (A.C.R.V.)
| | - Eliane dos Santos França
- Epstein-Barr Virus Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (I.B.C.); (M.N.S.-d.-S.); (P.Y.N.); (C.d.J.S.e.S.); (E.d.S.F.); (T.A.F.M.)
| | - Amaury Bentes Cunha Freire
- Epidemiology and Surveillance Service, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (A.B.C.F.); (F.L.d.P.R.)
| | - Francisco Lúzio de Paula Ramos
- Epidemiology and Surveillance Service, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (A.B.C.F.); (F.L.d.P.R.)
| | - Talita Antonia Furtado Monteiro
- Epstein-Barr Virus Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (I.B.C.); (M.N.S.-d.-S.); (P.Y.N.); (C.d.J.S.e.S.); (E.d.S.F.); (T.A.F.M.)
- Immunology Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil
| | - Olinda Macedo
- Retrovirus Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (O.M.); (F.B.F.)
| | | | - Felipe Bonfim Freitas
- Retrovirus Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (O.M.); (F.B.F.)
| | - Antonio Carlos Rosário Vallinoto
- Virology Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil; (L.M.S.P.); (A.C.R.V.)
| | - Igor Brasil-Costa
- Epstein-Barr Virus Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (I.B.C.); (M.N.S.-d.-S.); (P.Y.N.); (C.d.J.S.e.S.); (E.d.S.F.); (T.A.F.M.)
- Immunology Laboratory, Virology Department, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil
| |
Collapse
|
2
|
Khanam UA, Gao Z, Adamko D, Kusalik A, Rennie DC, Goodridge D, Chu L, Lawson JA. A scoping review of asthma and machine learning. J Asthma 2023; 60:213-226. [PMID: 35171725 DOI: 10.1080/02770903.2022.2043364] [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: 10/19/2022]
Abstract
OBJECTIVE The objective of this study was to determine the extent of machine learning (ML) application in asthma research and to identify research gaps while mapping the existing literature. DATA SOURCES We conducted a scoping review. PubMed, ProQuest, and Embase Scopus databases were searched with an end date of September 18, 2020. STUDY SELECTION DistillerSR was used for data management. Inclusion criteria were an asthma focus, human participants, ML techniques, and written in English. Exclusion criteria were abstract only, simulation-based, not human based, or were reviews or commentaries. Descriptive statistics were presented. RESULTS A total of 6,317 potential articles were found. After removing duplicates, and reviewing the titles and abstracts, 102 articles were included for the full text analysis. Asthma episode prediction (24.5%), asthma phenotype classification (16.7%), and genetic profiling of asthma (12.7%) were the top three study topics. Cohort (52.9%), cross-sectional (20.6%), and case-control studies (11.8%) were the study designs most frequently used. Regarding the ML techniques, 34.3% of the studies used more than one technique. Neural networks, clustering, and random forests were the most common ML techniques used where they were used in 20.6%, 18.6%, and 17.6% of studies, respectively. Very few studies considered location of residence (i.e. urban or rural status). CONCLUSIONS The use of ML in asthma studies has been increasing with most of this focused on the three major topics (>50%). Future research using ML could focus on gaps such as a broader range of study topics and focus on its use in additional populations (e.g. location of residence). Supplemental data for this article is available online at http://dx.doi.org/ .
Collapse
Affiliation(s)
- Ulfat A Khanam
- Health Sciences Program, College of Medicine, Canadian Centre for Health and Safety in Agriculture, Respiratory Research Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Zhiwei Gao
- Department of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Darryl Adamko
- Department of Paediatrics, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anthony Kusalik
- Department of Computer Science, College of Arts and Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Donna C Rennie
- College of Nursing and Canadian Centre for Health and Safety in Agriculture, University of Saskatchewan, Saskatoon, SK, Canada
| | - Donna Goodridge
- Department of Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Luan Chu
- Provincial Research Data Services, Alberta Health Service, Calgary, AB, Canada
| | - Joshua A Lawson
- Department of Medicine, Canadian Centre for Health and Safety in Agriculture, and Respiratory Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| |
Collapse
|
3
|
Hanton AJ, Scott F, Stenzel K, Nausch N, Zdesenko G, Mduluza T, Mutapi F. Frequency distribution of cytokine and associated transcription factor single nucleotide polymorphisms in Zimbabweans: Impact on schistosome infection and cytokine levels. PLoS Negl Trop Dis 2022; 16:e0010536. [PMID: 35759449 PMCID: PMC9236240 DOI: 10.1371/journal.pntd.0010536] [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: 12/08/2021] [Accepted: 05/25/2022] [Indexed: 11/18/2022] Open
Abstract
Cytokines mediate T-helper (TH) responses that are crucial for determining the course of infection and disease. The expression of cytokines is regulated by transcription factors (TFs). Here we present the frequencies of single nucleotide polymorphisms (SNPs) in cytokine and TF genes in a Zimbabwean population, and further relate SNPs to susceptibility to schistosomiasis and cytokine levels. Individuals (N = 850) were genotyped for SNPs across the cytokines IL4, IL10, IL13, IL33, and IFNG, and their TFs STAT4, STAT5A/B, STAT6, GATA3, FOXP3, and TBX21 to determine allele frequencies. Circulatory levels of systemic and parasite-specific IL-4, IL-5, IL-10, IL-13, and IFNγ were quantified via enzyme-linked immunosorbent assay. Schistosoma haematobium infection was determined by enumerating parasite eggs excreted in urine by microscopy. SNP allele frequencies were related to infection status by case-control analysis and logistic regression, and egg burdens and systemic and parasite-specific cytokine levels by analysis of variance and linear regression. Novel findings were i) IL4 rs2070874*T’s association with protection from schistosomiasis, as carriage of ≥1 allele gave an odds ratio of infection of 0.597 (95% CIs, 0.421–0.848, p = 0.0021) and IFNG rs2069727*G’s association with susceptibility to schistosomiasis as carriage of ≥1 allele gave an odds ratio of infection of 1.692 (1.229–2.33, p = 0.0013). Neither IL4 rs2070874*T nor IFNG rs2069727*G were significantly associated with cytokine levels. This study found TH2-upregulating SNPs were more frequent among the Zimbabwean sample compared to African and European populations, highlighting the value of immunogenetic studies of African populations in the context of infectious diseases and other conditions, including allergic and atopic disease. In addition, the identification of novel infection-associated alleles in both TH1- and TH2-associated genes highlights the role of both in regulating and controlling responses to Schistosoma.
Collapse
Affiliation(s)
- Andrew John Hanton
- Institute of Immunology & Infection Research, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
- NIHR Global Health Research Unit Tackling Infections to Benefit Africa (TIBA), University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
- * E-mail:
| | - Fiona Scott
- Institute of Immunology & Infection Research, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
- NIHR Global Health Research Unit Tackling Infections to Benefit Africa (TIBA), University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Katharina Stenzel
- Institute of Immunology & Infection Research, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Norman Nausch
- Institute of Immunology & Infection Research, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Grace Zdesenko
- Institute of Immunology & Infection Research, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
- NIHR Global Health Research Unit Tackling Infections to Benefit Africa (TIBA), University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Takafira Mduluza
- Department of Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - Francisca Mutapi
- Institute of Immunology & Infection Research, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
- NIHR Global Health Research Unit Tackling Infections to Benefit Africa (TIBA), University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| |
Collapse
|
4
|
Komlósi ZI, van de Veen W, Kovács N, Szűcs G, Sokolowska M, O'Mahony L, Akdis M, Akdis CA. Cellular and molecular mechanisms of allergic asthma. Mol Aspects Med 2021; 85:100995. [PMID: 34364680 DOI: 10.1016/j.mam.2021.100995] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 12/21/2022]
Abstract
Asthma is a chronic disease of the airways, which affects more than 350 million people worldwide. It is the most common chronic disease in children, affecting at least 30 million children and young adults in Europe. Asthma is a complex, partially heritable disease with a marked heterogeneity. Its development is influenced both by genetic and environmental factors. The most common, as well as the most well characterized subtype of asthma is allergic eosinophilic asthma, which is characterized by a type 2 airway inflammation. The prevalence of asthma has substantially increased in industrialized countries during the last 60 years. The mechanisms underpinning this phenomenon are incompletely understood, however increased exposure to various environmental pollutants probably plays a role. Disease inception is thought to be enabled by a disadvantageous shift in the balance between protective and harmful lifestyle and environmental factors, including exposure to protective commensal microbes versus infection with pathogens, collectively leading to airway epithelial cell damage and disrupted barrier integrity. Epithelial cell-derived cytokines are one of the main drivers of the type 2 immune response against innocuous allergens, ultimately leading to infiltration of lung tissue with type 2 T helper (TH2) cells, type 2 innate lymphoid cells (ILC2s), M2 macrophages and eosinophils. This review outlines the mechanisms responsible for the orchestration of type 2 inflammation and summarizes the novel findings, including but not limited to dysregulated epithelial barrier integrity, alarmin release and innate lymphoid cell stimulation.
Collapse
Affiliation(s)
- Zsolt I Komlósi
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad Sqr. 4, 1089, Budapest, Hungary.
| | - Willem van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Nóra Kovács
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad Sqr. 4, 1089, Budapest, Hungary; Lung Health Hospital, Munkácsy Mihály Str. 70, 2045, Törökbálint, Hungary
| | - Gergő Szűcs
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad Sqr. 4, 1089, Budapest, Hungary; Department of Pulmonology, Semmelweis University, Tömő Str. 25-29, 1083, Budapest, Hungary
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Liam O'Mahony
- Department of Medicine and School of Microbiology, APC Microbiome Ireland, University College Cork, Ireland
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| |
Collapse
|
5
|
Wu X, Wang P, Zhang Y, Gao L, Zheng B, Xu Y, Mo J. Toll-Like Receptor Characterization Correlates with Asthma and Is Predictive of Diagnosis. DNA Cell Biol 2020; 39:1313-1321. [PMID: 32543891 DOI: 10.1089/dna.2020.5543] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Toll-like receptors (TLRs) play crucial roles in the recognition of invading pathogens and the immune system. However, the effect of TLRs in asthma is still not fully known. This study was performed to better understand the role of TLR signatures in asthma. Blood samples from case-control studies (study 1: 348 asthmas and 39 normal controls and validation study 2: 411 asthmas and 87 normal controls) were enrolled. The single-sample gene set enrichment analysis method was performed to quantify the abundance of 21 TLR signatures. Gene ontology analysis and pathway function analysis were conducted for functional analysis, and a protein-protein interaction network was constructed. The area under the curve (AUC) value was used to assess the diagnostic capacity. In this study, TLR2/TLR3/TLR4 pathway, MyD88-dependent/independent TLR pathway, positive regulation of TLR4 pathway, and TLR binding signatures were significantly higher in asthma. Functional analysis showed that biological processes and pathways were still involved in TLR cascades and TLR signaling pathway. Eleven hub TLR-related genes were identified, and further validation demonstrated that the combination of TLR-related genes was a good diagnostic biomarker for asthma (AUC = 0.8). Our study provided more insight into the underlying immune mechanism of how TLR signatures affected asthma. The use of the easy-to-apply TLR-related genes might represent a promising blood-based biomarker for early detection of asthma.
Collapse
Affiliation(s)
- Xiaoyu Wu
- Department of Clinical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Pan Wang
- Department of Clinical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Yaqiong Zhang
- Department of Clinical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Lin Gao
- Department of Clinical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Beijia Zheng
- Department of Clinical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Youwen Xu
- Department of Clinical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Jinggang Mo
- The First Clinical College of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Department of Hepatobiliary Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| |
Collapse
|
6
|
Zhang X, Yang H, Zhang J, Gao F, Dai L. HSD17B4, ACAA1, and PXMP4 in Peroxisome Pathway Are Down-Regulated and Have Clinical Significance in Non-small Cell Lung Cancer. Front Genet 2020; 11:273. [PMID: 32265992 PMCID: PMC7103649 DOI: 10.3389/fgene.2020.00273] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/06/2020] [Indexed: 12/25/2022] Open
Abstract
To explore the potential functions and clinical significances of peroxisomes during lung cancer development and progression, we investigated the expressional profiles of peroxisome pathway genes and their correlations with clinical features in non-small cell lung cancer (NSCLC). The RNA-seq data of NSCLC including lung squamous carcinoma (LUSC) and lung adenocarcinoma (LUAD) patients with their clinical information were downloaded from The Cancer Genome Atlas (TCGA). Gene expression comparisons between tumor and normal samples were performed with edgeR package in R software and the results of the 83 peroxisome pathway genes were extracted. Through Venn diagram analysis, 38 common differentially expressed peroxisome pathway genes (C-DEPGs) in NSCLC were identified. Principal components analysis (PCA) was performed and the 38 C-DEPGs could discriminate NSCLC tumors from the non-tumor controls well. Through Kaplan-Meier survival and Cox regression analyses, 11 of the C-DEPGs were shown to have prognostic effects on NSCLC overall survival (OS) and were considered as key C-DEPGs (K-DEPGs). Through Oncomine, Human Protein Atlas (HPA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC), three K-DEPGs (HSD17B4, ACAA1, and PXMP4) were confirmed to be down-regulated in NSCLC at both mRNA and protein level. Their dy-regulation mechanisms were revealed through their correlations with their copy number variations and methylation status. Their potential functions in NSCLC were explored through their NSCLC-specific co-expression network analysis, their correlations with immune infiltrations, immunomodulator gene expressions, MKI67 expression and their associations with anti-cancer drug sensitivity. Our findings suggested that HSD17B4, ACAA1, and PXMP4 might be new markers for NSCLC diagnosis and prognosis and might provide new clues for NSCLC treatment.
Collapse
Affiliation(s)
- Xiuzhi Zhang
- Department of Pathology, Henan Medical College, Zhengzhou, China.,Institute of Cancer Research, Henan Medical College, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hongmei Yang
- Department of Pathology, Henan Medical College, Zhengzhou, China.,Institute of Cancer Research, Henan Medical College, Zhengzhou, China
| | - Jinzhong Zhang
- Institute of Cancer Research, Henan Medical College, Zhengzhou, China
| | - Fenglan Gao
- Department of Pathology, Henan Medical College, Zhengzhou, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
7
|
Shao Y, Zhang Y, Liu M, Fernandez-Beros ME, Qian M, Reibman J. Gene-Environment Interaction between the IL1RN Variants and Childhood Environmental Tobacco Smoke Exposure in Asthma Risk. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17062036. [PMID: 32204425 PMCID: PMC7142766 DOI: 10.3390/ijerph17062036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/14/2022]
Abstract
(1) Background: Variants of the interleukin-1 receptor antagonist (IL1RN) gene, encoding an anti-inflammatory cytokine, are associated with asthma. Asthma is a chronic inflammatory disease of the airway influenced by interactions between genetic variants and environmental factors. We discovered a gene-environment interaction (GEI) of IL1RN polymorphisms with childhood environmental tobacco smoke (ETS) exposure on asthma susceptibility in an urban adult population. (2) Methods: DNA samples from the NYU/Bellevue Asthma Registry were genotyped for tag SNPs in IL1RN in asthma cases and unrelated healthy controls. Logistic regressions were used to study the GEI between IL1RN variants and childhood ETS exposures on asthma and early onset asthma, respectively, adjusting for population admixture and other covariates. (3) Results: Whereas the rare genotypes of IL1RN SNPs (e.g., GG in SNP rs2234678) were associated with decreased risk for asthma among those without ETS exposure (odds ratio OR = 0.215, p = 0.021), they are associated with increased risk for early onset asthma among those with childhood ETS (OR = 4.467, p = 0.021). (4) Conclusions: We identified a GEI between polymorphisms of IL1RN and childhood ETS exposure in asthma. Analysis of GEI indicated that childhood ETS exposure disrupted the protective effect of some haplotypes/genotypes of IL1RN for asthma and turned them into high-risk polymorphisms for early onset asthma.
Collapse
Affiliation(s)
- Yongzhao Shao
- Division of Biostatistics, Department of Population Health, School of Medicine (SOM), New York University, New York, NY 10016, USA; (Y.Z.); (M.L.); (M.Q.)
- Department of Environmental Medicine, SOM, New York University, New York, NY 10016, USA
- Correspondence: (Y.S.); (J.R.)
| | - Yian Zhang
- Division of Biostatistics, Department of Population Health, School of Medicine (SOM), New York University, New York, NY 10016, USA; (Y.Z.); (M.L.); (M.Q.)
- Department of Environmental Medicine, SOM, New York University, New York, NY 10016, USA
| | - Mengling Liu
- Division of Biostatistics, Department of Population Health, School of Medicine (SOM), New York University, New York, NY 10016, USA; (Y.Z.); (M.L.); (M.Q.)
- Department of Environmental Medicine, SOM, New York University, New York, NY 10016, USA
| | - Maria-Elena Fernandez-Beros
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, SOM, New York University, New York, NY 10016, USA;
| | - Meng Qian
- Division of Biostatistics, Department of Population Health, School of Medicine (SOM), New York University, New York, NY 10016, USA; (Y.Z.); (M.L.); (M.Q.)
| | - Joan Reibman
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, SOM, New York University, New York, NY 10016, USA;
- Correspondence: (Y.S.); (J.R.)
| |
Collapse
|
8
|
Choi H, Tabashidze N, Rossner P, Dostal M, Pastorkova A, Kong SW, Gmuender H, Sram RJ. Altered vulnerability to asthma at various levels of ambient Benzo[a]Pyrene by CTLA4, STAT4 and CYP2E1 polymorphisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:1134-1144. [PMID: 28807506 DOI: 10.1016/j.envpol.2017.07.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Within fossil- and solid-fuel dependent geographic locations, mechanisms of air pollution-induced asthma remains unknown. In particular, sources of greater genetic susceptibility to airborne carcinogen, namely, benzo[a]pyrene (B[a]P) has never been investigated beyond that of a few well known genes. OBJECTIVES To deepen our understanding on how the genotypic variations within the candidate genes contribute to the variability in the children's susceptibility to ambient B[a]P on doctor-diagnosed asthma. METHODS Clinically confirmed asthmatic versus healthy control children (aged, 7-15) were enrolled from historically polluted and rural background regions in Czech Republic. Contemporaneous ambient B[a]P concentration was obtained from the routine monitoring network. The sputum DNA was genotyped for 95 genes. B[a]P interaction with SNPs was studied by two-stage, semi-agnostic screening of 621 SNPs. RESULTS The median B[a]P within the highly polluted urban center was 8-times higher than that in the background region (7.8 vs. 1.1 ng/m3) during the period of investigation. Within the baseline model, which considered B[a]P exposure-only, the second tertile range was associated with a significantly reduced odds (aOR = 0.28) of asthma (95% CI, 0.16 to 0.50) compared to those at the lowest range. However, the highest range of B[a]P was associated with 3.18-times greater odds of the outcome (95% CI, 1.77 to 5.71). Within the gene-environment interaction models, joint occurrence of a high B[a]P exposure range and having a high-risk genotype at CTLA4 gene (rs11571316) was associated with 9-times greater odds (95% CI, 4.56-18.36) of the asthma diagnosis. Similarly, rs11571319 at CTLA4 and a high B[a]P exposure range was associated with a 8-times greater odds (95% CI, 3.95-14.27) of asthma diagnosis. Furthermore, having TG + GG genotypes on rs1031509 near STAT4 was associated with 5-times (95% CI, 3.03-8.55) greater odds of asthma diagnosis at the highest B[a]P range, compared to the odds at the reference range. Also CYP2E1 AT + TT genotypes (rs2070673) was associated with 5-times (95% CI, 3.1-8.8) greater odds of asthma diagnosis at the highest B[a]P exposure. CONCLUSIONS The children, who jointly experience a high B[a]P exposure (6.3-8.5 ng/m3) as well as susceptible genotypes in CTLA4 (rs11571316 and rs11571319), STAT4 (rs1031509), and CYP2E1 (rs2070673), respectively, are associated with a significantly greater odds of having doctor-diagnosed asthma, compared to those with neither risk factors.
Collapse
Affiliation(s)
- Hyunok Choi
- Departments of Environmental Health Sciences, Epidemiology, and Biostatistics University at Albany School of Public Health, One University Place, Room 153, Rensselaer, NY 12144-3456, USA.
| | - Nana Tabashidze
- Department of Genetic Ecotoxicology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic.
| | - Pavel Rossner
- Department of Genetic Ecotoxicology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic.
| | - Miroslav Dostal
- Department of Genetic Ecotoxicology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic.
| | - Anna Pastorkova
- Department of Genetic Ecotoxicology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Sek Won Kong
- Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115, USA.
| | - Hans Gmuender
- Genedata AG, Margarethenstrasse 38, CH-4053, Basel, Switzerland.
| | - Radim J Sram
- Department of Genetic Ecotoxicology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic.
| |
Collapse
|
9
|
Hosoki K, Boldogh I, Aguilera-Aguirre L, Sun Q, Itazawa T, Hazra T, Brasier AR, Kurosky A, Sur S. Myeloid differentiation protein 2 facilitates pollen- and cat dander-induced innate and allergic airway inflammation. J Allergy Clin Immunol 2015; 137:1506-1513.e2. [PMID: 26586036 DOI: 10.1016/j.jaci.2015.09.036] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/08/2015] [Accepted: 09/23/2015] [Indexed: 11/17/2022]
Abstract
BACKGROUND The National Health and Nutrition Examination Survey identified several pollens and cat dander as among the most common allergens that induce allergic sensitization and allergic diseases. We recently reported that ragweed pollen extract (RWPE) requires Toll-like receptor 4 (TLR4) to stimulate CXCL-mediated innate neutrophilic inflammation, which in turn facilitates allergic sensitization and airway inflammation. Myeloid differentiation protein 2 (MD2) is a TLR4 coreceptor, but its role in pollen- and cat dander-induced innate and allergic inflammation has not been critically evaluated. OBJECTIVE We sought to elucidate the role of MD2 in inducing pollen- and cat dander-induced innate and allergic airway inflammation. METHODS TCM(Null) (TLR4(Null), CD14(Null), MD2(Null)), TLR4(Hi), and TCM(Hi) cells and human bronchial epithelial cells with small interfering RNA-induced downregulation of MD2 were stimulated with RWPE, other pollen allergic extracts, or cat dander extract (CDE), and activation of nuclear factor κB (NF-κB), secretion of the NF-κB-dependent CXCL8, or both were quantified. Wild-type mice or mice with small interfering RNA knockdown of lung MD2 were challenged intranasally with RWPE or CDE, and innate and allergic inflammation was quantified. RESULTS RWPE stimulated MD2-dependent NF-κB activation and CXCL secretion. Likewise, Bermuda, rye, timothy, pigweed, Russian thistle, cottonwood, walnut, and CDE stimulated MD2-dependent CXCL secretion. RWPE and CDE challenge induced MD2-dependent and CD14-independent innate neutrophil recruitment. RWPE induced MD2-dependent allergic sensitization and airway inflammation. CONCLUSIONS MD2 plays an important role in induction of allergic sensitization to cat dander and common pollens relevant to human allergic diseases.
Collapse
Affiliation(s)
- Koa Hosoki
- Department of Internal Medicine, Division of Allergy and Immunology, University of Texas Medical Branch, Galveston, Tex
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Tex; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Tex
| | | | - Qian Sun
- Department of Internal Medicine, Division of Allergy and Immunology, University of Texas Medical Branch, Galveston, Tex
| | - Toshiko Itazawa
- Department of Internal Medicine, Division of Allergy and Immunology, University of Texas Medical Branch, Galveston, Tex
| | - Tapas Hazra
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Tex; Department of Internal Medicine, Division of Pulmonary Critical Care & Sleep Medicine, University of Texas Medical Branch, Galveston, Tex
| | - Allan R Brasier
- Department of Internal Medicine, Division of Allergy and Immunology, University of Texas Medical Branch, Galveston, Tex; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Tex
| | - Alexander Kurosky
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Tex; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Tex
| | - Sanjiv Sur
- Department of Internal Medicine, Division of Allergy and Immunology, University of Texas Medical Branch, Galveston, Tex; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Tex.
| |
Collapse
|
10
|
Baines KJ, Wright TK, Simpson JL, McDonald VM, Wood LG, Parsons KS, Wark PA, Gibson PG. Airway β-Defensin-1 Protein Is Elevated in COPD and Severe Asthma. Mediators Inflamm 2015; 2015:407271. [PMID: 26568662 PMCID: PMC4629049 DOI: 10.1155/2015/407271] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 09/18/2015] [Accepted: 09/28/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Innate immune antimicrobial peptides, including β-defensin-1, promote the chemotaxis and activation of several immune cells. The role of β-defensin-1 in asthma and chronic obstructive pulmonary disease (COPD) remains unclear. METHODS Induced sputum was collected from healthy controls and individuals with asthma or COPD. β-defensin-1 protein in sputum supernatant was quantified by ELISA. Biomarker potential was examined using receiver operating characteristic curves. β-defensin-1 release from primary bronchial epithelial cells (pBECs) was investigated in culture with and without cigarette smoke extract (CSE). RESULTS Airway β-defensin-1 protein was elevated in COPD participants compared to asthma participants and healthy controls. Inflammatory phenotype had no effect on β-defensin-1 levels in asthma or COPD. β-defensin-1 protein was significantly higher in severe asthma compared to controlled and uncontrolled asthma. β-defensin-1 protein could predict the presence of COPD from both healthy controls and asthma patients. Exposure of pBECs to CSE decreased β-defensin-1 production in healthy controls; however in pBECs from COPD participants the level of β-defensin-1 remanied unchanged. CONCLUSIONS Elevated β-defensin-1 protein is a feature of COPD and severe asthma regardless of inflammatory phenotype. β-defensin-1 production is dysregulated in the epithelium of patients with COPD and may be an effective biomarker and potential therapeutic target.
Collapse
Affiliation(s)
- Katherine J. Baines
- Priority Research Centre for Asthma and Respiratory Diseases, Hunter Medical Research Institute, The University of Newcastle, New Lambton Heights, NSW 2305, Australia
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia
| | - Thomas K. Wright
- Priority Research Centre for Asthma and Respiratory Diseases, Hunter Medical Research Institute, The University of Newcastle, New Lambton Heights, NSW 2305, Australia
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia
| | - Jodie L. Simpson
- Priority Research Centre for Asthma and Respiratory Diseases, Hunter Medical Research Institute, The University of Newcastle, New Lambton Heights, NSW 2305, Australia
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia
| | - Vanessa M. McDonald
- Priority Research Centre for Asthma and Respiratory Diseases, Hunter Medical Research Institute, The University of Newcastle, New Lambton Heights, NSW 2305, Australia
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia
| | - Lisa G. Wood
- Priority Research Centre for Asthma and Respiratory Diseases, Hunter Medical Research Institute, The University of Newcastle, New Lambton Heights, NSW 2305, Australia
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia
| | - Kristy S. Parsons
- Priority Research Centre for Asthma and Respiratory Diseases, Hunter Medical Research Institute, The University of Newcastle, New Lambton Heights, NSW 2305, Australia
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia
| | - Peter A. Wark
- Priority Research Centre for Asthma and Respiratory Diseases, Hunter Medical Research Institute, The University of Newcastle, New Lambton Heights, NSW 2305, Australia
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia
| | - Peter G. Gibson
- Priority Research Centre for Asthma and Respiratory Diseases, Hunter Medical Research Institute, The University of Newcastle, New Lambton Heights, NSW 2305, Australia
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia
| |
Collapse
|
11
|
Genetic association of key Th1/Th2 pathway candidate genes, IRF2, IL6, IFNGR2, STAT4 and IL4RA, with atopic asthma in the Indian population. J Hum Genet 2015; 60:443-8. [PMID: 25994869 DOI: 10.1038/jhg.2015.45] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 04/06/2015] [Accepted: 04/10/2015] [Indexed: 02/01/2023]
Abstract
Asthma is a complex, multifactorial disease resulting due to dysregulated immune responses. Genetic factors contribute significantly to asthma pathogenesis, and identification of these factors is one of the major goals in understanding the disease. Th1/Th2 helper differentiation has a critical role in modulating the phenotypes associated with atopic asthma. This study was aimed at identifying genetic modifiers of asthma in selected genes involved in T helper differentiation. A total of 354 single-nucleotide polymorphisms (SNPs) in 33 candidate genes were genotyped in a case-control cohort (cases=147, controls=199) and families (n=247) using Illumina's Golden Gate Assay. Five SNPs, rs3733475A/C (IRF2), rs2069832A/G (IL6), rs2012075G/A (IFNGR2) and rs1400656G/A (STAT4) and rs1805011C/A (IL4RA) were found to be associated with asthma in family based as well as in case-control analyses (P=0.002, P=0.001, P=0.004, P=0.003 and P=0.001, respectively). Interestingly, the minor alleles at these loci showed a protective effect. A five loci haplotype, TAACG, in IRF2 gene, was significantly associated with asthma in families (P=1.1 × 10(-6)) and in case-control cohort (P=0.01). In conclusion, our studies led to identification of some key candidate genes, namely IRF2, IL6, IFNGR2, STAT4 and IL4RA that modulate genetic susceptibility to asthma in the Indian population. Also, this is the first report of independent association of IL6 gene polymorphism with atopic asthma.
Collapse
|
12
|
Abstract
Complex multifactorial diseases such as allergic rhinitis and asthma are not only becoming an increasing burden to healthcare systems, but especially affect the life quality of children and families suffering from their allergic symptoms. Also physicians are challenged by the multifaceted diseases as their work involves not only the often difficult decisions on case-adapted diagnostics, treatment, and monitoring, but also possible preventive measures. This review gives an outline of the latest scientific developments related to the etiology, diagnosis, and management of allergic airway diseases in childhood, as well as prenatal and early life risk factors and strategies for prevention.
Collapse
Affiliation(s)
- Stephanie Hofmaier
- Department of Paediatric Pneumology & Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
13
|
Cipriani F, Dondi A, Ricci G. Recent advances in epidemiology and prevention of atopic eczema. Pediatr Allergy Immunol 2014; 25:630-8. [PMID: 25406640 DOI: 10.1111/pai.12309] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/14/2014] [Indexed: 12/22/2022]
Abstract
Atopic dermatitis (AD), named also atopic eczema, is a chronic relapsing inflammatory skin disease with a considerable social and economic burden. The primum movens of AD is in most cases a genetic and/or immune-supported defect of the skin barrier, facilitating penetration and sensitization to food or airborne allergens, as well as infections by Staphylococcus aureus, herpes simplex virus, or other microbes. New pathogenetic concepts have generated new approaches to prevention and therapy of AD. In particular, the daily use of emollients in newborns at high risk of AD has shown interesting results, with a reduction in the cumulative incidence of AD ranging from 32% to 50% of the treated infants. On the other hand, the AD preventive efficacy of food and/or inhalant allergen avoidance has been questioned, and supplementation strategies (vitamin D, probiotics, or other compounds) need to be further investigated.
Collapse
Affiliation(s)
- Francesca Cipriani
- Pediatric Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | | | | |
Collapse
|
14
|
Esposito S, Ierardi V, Daleno C, Scala A, Terranova L, Tagliabue C, Rios WP, Pelucchi C, Principi N. Genetic polymorphisms and risk of recurrent wheezing in pediatric age. BMC Pulm Med 2014; 14:162. [PMID: 25326706 PMCID: PMC4210469 DOI: 10.1186/1471-2466-14-162] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 09/22/2014] [Indexed: 12/30/2022] Open
Abstract
Background Wheezing during early life is a very common disorder, but the reasons underlying the different wheezing phenotypes are still unclear. The aims of this study were to analyse the potential correlations between the risk of developing recurrent wheezing and the presence of specific polymorphisms of some genes regulating immune system function, and to study the relative importance of the associations of different viruses and genetic polymorphisms in causing recurrent episodes. Methods The study involved 119 otherwise healthy infants admitted to hospital for a first episode of wheezing (74 of whom subsequently experienced recurrent episodes) and 119 age- and sex-matched subjects without any history of respiratory problem randomly selected from those attending our outpatient clinic during the study period. All of the study subjects were followed up for two years, and 47 single nucleotide polymorphisms (SNPs) in 33 candidate genes were genotyped on whole blood using an ABI PRISM 7900 HT Fast Real-time instrument. Results IL8-rs4073AT, VEGFA-rs833058CT, MBL2-rs1800450CT and IKBKB-rs3747811AT were associated with a significantly increased risk of developing wheezing (p = 0.02, p = 0.03, p = 0.05 and p = 0.0018), whereas CTLA4-rs3087243AG and NFKBIB-rs3136641TT were associated with a significantly reduced risk (p = 0.05 and p = 0.04). IL8-rs4073AT, VEGFA-rs2146323AA and NFKBIA-rs2233419AG were associated with a significantly increased risk of developing recurrent wheezing (p = 0.04, p = 0.04 and p = 0.03), whereas TLR3-rs3775291TC was associated with a significantly reduced risk (p = 0.03). Interestingly, the study of gene-environment interactions showed that rhinovirus was significantly associated with recurrent wheezing in the presence of IL4Ra-rs1801275GG and G (odds ratio [OR] 6.03, 95% confidence interval [CI]: 1.21-30.10, p = 0.03) and MAP3K1-rs702689AA (OR 4.09, 95% CI: 1.14-14.61, p = 0.03). Conclusions This study shows a clear relationship between the risk of wheezing and polymorphisms of some genes involved in the immune response. Although further studies are needed to confirm the results, these findings may be useful for the early identification of children at the highest risk of developing recurrent episodes and possibly subsequent asthma.
Collapse
Affiliation(s)
- Susanna Esposito
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122 Milan, Italy.
| | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Estus JL, Fardo DW. Combining genetic association study designs: a GWAS case study. Front Genet 2013; 4:186. [PMID: 24098305 PMCID: PMC3784826 DOI: 10.3389/fgene.2013.00186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 09/03/2013] [Indexed: 01/06/2023] Open
Abstract
Genome-wide association studies (GWAS) explore the relationship between genome variability and disease susceptibility with either population- or family-based data. Here, we have evaluated the utility of combining population- and family-based statistical association tests and have proposed a method for reducing the burden of multiple testing. Unrelated singleton and parent-offspring trio cases and controls from the Genetics of Kidneys in Diabetes (GoKinD) study were analyzed for genetic association with diabetic nephropathy (DN) in type 1 diabetics (T1D). The Cochran-Armitage test for trend and the family-based association test were employed using either unrelated cases and controls or trios, respectively. In addition to combining single nucleotide polymorphism (SNP) p-values across these tests via Fisher's method, we employed a novel screening approach to rank SNPs based on conditional power for more efficient testing. Using either the population-based or family-based subset alone predictably limited resolution to detect DN SNPs. For 384,197 SNPs passing quality control (QC), none achieved strict genome-wide significance (1.4 × 10−7) using 1171 singletons (577/594 cases/controls) or 1738 pooled singletons and offspring probands (841/897). Similarly, none of the 352,004 SNPs passing QC in 567 family trios (264/303 case/control proband trios) reached genome-wide significance. Testing the top 10 SNPs ranked using aggregated conditional power resulted in two SNPs reaching genome-wide significance, rs11645147 on chromosome 16 (p = 1.74 × 10−4 < 0.05/10 = 0.005) and rs7866522 on chromosome 9 (p = 0.0033). Efficient usage of mixed designs incorporating both unrelated and family-based data may help to uncover associations otherwise difficult to detect in the presence of massive multiple testing corrections. Capitalizing on the strengths of both types while using screening approaches may be useful especially in light of large-scale, next-generation sequencing and rare variant studies.
Collapse
Affiliation(s)
- Janice L Estus
- Department of Biostatistics, University of Kentucky Lexington, KY, USA
| | | | | |
Collapse
|
16
|
Roetker NS, Page CD, Yonker JA, Chang V, Roan CL, Herd P, Hauser TS, Hauser RM, Atwood CS. Assessment of genetic and nongenetic interactions for the prediction of depressive symptomatology: an analysis of the Wisconsin Longitudinal Study using machine learning algorithms. Am J Public Health 2013; 103 Suppl 1:S136-44. [PMID: 23927508 DOI: 10.2105/ajph.2012.301141] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES We examined depression within a multidimensional framework consisting of genetic, environmental, and sociobehavioral factors and, using machine learning algorithms, explored interactions among these factors that might better explain the etiology of depressive symptoms. METHODS We measured current depressive symptoms using the Center for Epidemiologic Studies Depression Scale (n = 6378 participants in the Wisconsin Longitudinal Study). Genetic factors were 78 single nucleotide polymorphisms (SNPs); environmental factors-13 stressful life events (SLEs), plus a composite proportion of SLEs index; and sociobehavioral factors-18 personality, intelligence, and other health or behavioral measures. We performed traditional SNP associations via logistic regression likelihood ratio testing and explored interactions with support vector machines and Bayesian networks. RESULTS After correction for multiple testing, we found no significant single genotypic associations with depressive symptoms. Machine learning algorithms showed no evidence of interactions. Naïve Bayes produced the best models in both subsets and included only environmental and sociobehavioral factors. CONCLUSIONS We found no single or interactive associations with genetic factors and depressive symptoms. Various environmental and sociobehavioral factors were more predictive of depressive symptoms, yet their impacts were independent of one another. A genome-wide analysis of genetic alterations using machine learning methodologies will provide a framework for identifying genetic-environmental-sociobehavioral interactions in depressive symptoms.
Collapse
Affiliation(s)
- Nicholas S Roetker
- Nicholas S. Roetker, James A. Yonker, Vicky Chang, Carol L. Roan, Pamela Herd, Taissa S. Hauser, and Robert M. Hauser are with the Department of Sociology, University of Wisconsin-Madison. Pamela Herd is also with La Follete School of Public Affairs, University of Wisconsin-Madison. C. David Page is with the Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison. Craig S. Atwood is with the Geriatric Research, Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI, and the Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Current world literature. Curr Opin Allergy Clin Immunol 2013; 13:119-24. [PMID: 23242117 DOI: 10.1097/aci.0b013e32835cb509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
18
|
Dahlin A, Tantisira KG. Integrative systems biology approaches in asthma pharmacogenomics. Pharmacogenomics 2013; 13:1387-404. [PMID: 22966888 DOI: 10.2217/pgs.12.126] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In order to improve therapeutic outcomes, there is a tremendous need to identify patients who are likely to respond to a given asthma treatment. Pharmacogenomic studies have explained a portion of the variability in drug response and provided an increasing list of candidate genes and SNPs. However, as phenotypic variation arises from a network of complex interactions among genetic and environmental factors, rather than individual genes or SNPs, a multidisciplinary, systems-level approach is required in order to understand the inter-relationships among these factors. Systems biology, which seeks to capture interactions between genetic factors and other variables, offers a promising approach to improved therapeutic outcomes in asthma. This aritcle will review and update progress in the pharmacogenomics of asthma and then discuss the application of systems biology approaches to asthma pharmacogenomics.
Collapse
Affiliation(s)
- Amber Dahlin
- Channing Laboratory, Brigham & Women's Hospital & Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
| | | |
Collapse
|
19
|
Li X, Hawkins GA, Ampleford EJ, Moore WC, Li H, Hastie AT, Howard TD, Boushey HA, Busse WW, Calhoun WJ, Castro M, Erzurum SC, Israel E, Lemanske RF, Szefler SJ, Wasserman SI, Wenzel SE, Peters SP, Meyers DA, Bleecker ER. Genome-wide association study identifies TH1 pathway genes associated with lung function in asthmatic patients. J Allergy Clin Immunol 2013; 132:313-20.e15. [PMID: 23541324 DOI: 10.1016/j.jaci.2013.01.051] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 12/18/2012] [Accepted: 01/18/2013] [Indexed: 11/17/2022]
Abstract
BACKGROUND Recent meta-analyses of genome-wide association studies in general populations of European descent have identified 28 loci for lung function. OBJECTIVE We sought to identify novel lung function loci specifically for asthma and to confirm lung function loci identified in general populations. METHODS Genome-wide association studies of lung function (percent predicted FEV1 [ppFEV1], percent predicted forced vital capacity, and FEV1/forced vital capacity ratio) were performed in 4 white populations of European descent (n = 1544), followed by meta-analyses. RESULTS Seven of 28 previously identified lung function loci (HHIP, FAM13A, THSD4, GSTCD, NOTCH4-AGER, RARB, and ZNF323) identified in general populations were confirmed at single nucleotide polymorphism (SNP) levels (P < .05). Four of 32 loci (IL12A, IL12RB1, STAT4, and IRF2) associated with ppFEV1 (P < 10(-4)) belong to the TH1 or IL-12 cytokine family pathway. By using a linear additive model, these 4 TH1 pathway SNPs cumulatively explained 2.9% to 7.8% of the variance in ppFEV1 values in 4 populations (P = 3 × 10(-11)). Genetic scores of these 4 SNPs were associated with ppFEV1 values (P = 2 × 10(-7)) and the American Thoracic Society severe asthma classification (P = .005) in the Severe Asthma Research Program population. TH2 pathway genes (IL13, TSLP, IL33, and IL1RL1) conferring asthma susceptibility were not associated with lung function. CONCLUSION Genes involved in airway structure/remodeling are associated with lung function in both general populations and asthmatic subjects. TH1 pathway genes involved in anti-virus/bacterial infection and inflammation modify lung function in asthmatic subjects. Genes associated with lung function that might affect asthma severity are distinct from those genes associated with asthma susceptibility.
Collapse
Affiliation(s)
- Xingnan Li
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Chen J, Pande M, Huang YJ, Wei C, Amos CI, Talseth-Palmer BA, Meldrum CJ, Chen WV, Gorlov IP, Lynch PM, Scott RJ, Frazier ML. Cell cycle-related genes as modifiers of age of onset of colorectal cancer in Lynch syndrome: a large-scale study in non-Hispanic white patients. Carcinogenesis 2012; 34:299-306. [PMID: 23125224 DOI: 10.1093/carcin/bgs344] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Heterogeneity in age of onset of colorectal cancer in individuals with mutations in DNA mismatch repair genes (Lynch syndrome) suggests the influence of other lifestyle and genetic modifiers. We hypothesized that genes regulating the cell cycle influence the observed heterogeneity as cell cycle-related genes respond to DNA damage by arresting the cell cycle to provide time for repair and induce transcription of genes that facilitate repair. We examined the association of 1456 single nucleotide polymorphisms (SNPs) in 128 cell cycle-related genes and 31 DNA repair-related genes in 485 non-Hispanic white participants with Lynch syndrome to determine whether there are SNPs associated with age of onset of colorectal cancer. Genotyping was performed on an Illumina GoldenGate platform, and data were analyzed using Kaplan-Meier survival analysis, Cox regression analysis and classification and regression tree (CART) methods. Ten SNPs were independently significant in a multivariable Cox proportional hazards regression model after correcting for multiple comparisons (P < 5 × 10(-4)). Furthermore, risk modeling using CART analysis defined combinations of genotypes for these SNPs with which subjects could be classified into low-risk, moderate-risk and high-risk groups that had median ages of colorectal cancer onset of 63, 50 and 42 years, respectively. The age-associated risk of colorectal cancer in the high-risk group was more than four times the risk in the low-risk group (hazard ratio = 4.67, 95% CI = 3.16-6.92). The additional genetic markers identified may help in refining risk groups for more tailored screening and follow-up of non-Hispanic white patients with Lynch syndrome.
Collapse
Affiliation(s)
- Jinyun Chen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Effects of psychological stress on innate immunity and metabolism in humans: a systematic analysis. PLoS One 2012; 7:e43232. [PMID: 23028447 PMCID: PMC3446986 DOI: 10.1371/journal.pone.0043232] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 07/18/2012] [Indexed: 01/01/2023] Open
Abstract
Stress is perhaps easiest to conceptualize as a process which allows an organism to accommodate for the demands of its environment such that it can adapt to the prevailing set of conditions. Psychological stress is an important component with the potential to affect physiology adversely as has become evident from various studies in the area. Although these studies have established numerous effects of psychological stress on physiology, a global strategy for the correlation of these effects has yet to begin. Our comparative and systematic analysis of the published literature has unraveled certain interesting molecular mechanisms as clues to account for some of the observed effects of psychological stress on human physiology. In this study, we attempt to understand initial phase of the physiological response to psychological stress by analyzing interactions between innate immunity and metabolism at systems level by analyzing the data available in the literature. In light of our gene association-networks and enrichment analysis we have identified candidate genes and molecular systems which might have some associative role in affecting psychological stress response system or even producing some of the observed terminal effects (such as the associated physiological disorders). In addition to the already accepted role of psychological stress as a perturbation that can disrupt physiological homeostasis, we speculate that it is potentially capable of causing deviation of certain biological processes from their basal level activity after which they can return back to their basal tones once the effects of stress diminish. Based on the derived inferences of our comparative analysis, we have proposed a probabilistic mechanism for how psychological stress could affect physiology such that these adaptive deviations are sometimes not able to bounce back to their original basal tones, and thus increase physiological susceptibility to metabolic and immune imbalance.
Collapse
|
22
|
Sordillo JE, Sharma S, Poon A, Lasky-Su J, Belanger K, Milton DK, Bracken MB, Triche EW, Leaderer BP, Gold DR, Litonjua AA. Effects of endotoxin exposure on childhood asthma risk are modified by a genetic polymorphism in ACAA1. BMC MEDICAL GENETICS 2011; 12:158. [PMID: 22151743 PMCID: PMC3252252 DOI: 10.1186/1471-2350-12-158] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 12/08/2011] [Indexed: 11/24/2022]
Abstract
Background Polymorphisms in the endotoxin-mediated TLR4 pathway genes have been associated with asthma and atopy. We aimed to examine how genetic polymorphisms in innate immunity pathways interact with endotoxin to influence asthma risk in children. Methods In a previous analysis of 372 children from the Boston Home Allergens and the Connecticut Childhood Asthma studies, 7 SNPs in 6 genes (CARD15, TGFB1, LY96, ACAA1, DEFB1 and IFNG) involved in innate immune pathways were associated with asthma, and 5 SNPs in 3 genes (CD80, STAT4, IRAK2) were associated with eczema. We tested these SNPs for interaction with early life endotoxin exposure (n = 291), in models for asthma and eczema by age 6. Results We found a significant interaction between endotoxin and a SNP (rs156265) in ACAA1 (p = 0.0013 for interaction). Increased endotoxin exposure (by quartile) showed protective effects for asthma in individuals with at least one copy of the minor allele (OR = 0.39 per quartile increase in endotoxin, 95% CI 0.15 to 1.01). Endotoxin exposure did not reduce the risk of asthma in children homozygous for the major allele. Conclusion Our findings suggest that protective effects of endotoxin exposure on asthma may vary depending upon the presence or absence of a polymorphism in ACAA1.
Collapse
Affiliation(s)
- Joanne E Sordillo
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|