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Grinde KE, Browning BL, Reiner AP, Thornton TA, Browning SR. Adjusting for principal components can induce collider bias in genome-wide association studies. PLoS Genet 2024; 20:e1011242. [PMID: 39680601 DOI: 10.1371/journal.pgen.1011242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 11/14/2024] [Indexed: 12/18/2024] Open
Abstract
Principal component analysis (PCA) is widely used to control for population structure in genome-wide association studies (GWAS). Top principal components (PCs) typically reflect population structure, but challenges arise in deciding how many PCs are needed and ensuring that PCs do not capture other artifacts such as regions with atypical linkage disequilibrium (LD). In response to the latter, many groups suggest performing LD pruning or excluding known high LD regions prior to PCA. However, these suggestions are not universally implemented and the implications for GWAS are not fully understood, especially in the context of admixed populations. In this paper, we investigate the impact of pre-processing and the number of PCs included in GWAS models in African American samples from the Women's Health Initiative SNP Health Association Resource and two Trans-Omics for Precision Medicine Whole Genome Sequencing Project contributing studies (Jackson Heart Study and Genetic Epidemiology of Chronic Obstructive Pulmonary Disease Study). In all three samples, we find the first PC is highly correlated with genome-wide ancestry whereas later PCs often capture local genomic features. The pattern of which, and how many, genetic variants are highly correlated with individual PCs differs from what has been observed in prior studies focused on European populations and leads to distinct downstream consequences: adjusting for such PCs yields biased effect size estimates and elevated rates of spurious associations due to the phenomenon of collider bias. Excluding high LD regions identified in previous studies does not resolve these issues. LD pruning proves more effective, but the optimal choice of thresholds varies across datasets. Altogether, our work highlights unique issues that arise when using PCA to control for ancestral heterogeneity in admixed populations and demonstrates the importance of careful pre-processing and diagnostics to ensure that PCs capturing multiple local genomic features are not included in GWAS models.
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Affiliation(s)
- Kelsey E Grinde
- Department of Mathematics, Statistics, and Computer Science, Macalester College, Saint Paul, Minnesota, United States of America
| | - Brian L Browning
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Alexander P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Timothy A Thornton
- Regeneron Genetics Center, Tarrytown, New York, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
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2
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Herrera-Luis E, Martin-Almeida M, Pino-Yanes M. Asthma-Genomic Advances Toward Risk Prediction. Clin Chest Med 2024; 45:599-610. [PMID: 39069324 PMCID: PMC11284279 DOI: 10.1016/j.ccm.2024.03.002] [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] [Indexed: 07/30/2024]
Abstract
Asthma is a common complex airway disease whose prediction of disease risk and most severe outcomes is crucial in clinical practice for adequate clinical management. This review discusses the latest findings in asthma genomics and current obstacles faced in moving forward to translational medicine. While genome-wide association studies have provided valuable insights into the genetic basis of asthma, there are challenges that must be addressed to improve disease prediction, such as the need for diverse representation, the functional characterization of genetic variants identified, variant selection for genetic testing, and refining prediction models using polygenic risk scores.
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Affiliation(s)
- Esther Herrera-Luis
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, 615 N Wolfe Street, Baltimore, MD 21205, USA.
| | - Mario Martin-Almeida
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez, s/n. Facultad de Ciencias, San Cristóbal de La Laguna, S/C de Tenerife La Laguna 38200, Tenerife, Spain
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez, s/n. Facultad de Ciencias, San Cristóbal de La Laguna, S/C de Tenerife La Laguna 38200, Tenerife, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain; Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), San Cristóbal de La Laguna 38200, Tenerife, Spain
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3
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Takahashi I, Ohseto H, Ueno F, Oonuma T, Narita A, Obara T, Ishikuro M, Murakami K, Noda A, Hozawa A, Sugawara J, Tamiya G, Kuriyama S. Genome-wide association study based on clustering by obesity-related variables uncovers a genetic architecture of obesity in the Japanese and the UK populations. Heliyon 2024; 10:e36023. [PMID: 39247266 PMCID: PMC11379603 DOI: 10.1016/j.heliyon.2024.e36023] [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: 06/08/2023] [Revised: 08/06/2024] [Accepted: 08/08/2024] [Indexed: 09/10/2024] Open
Abstract
Whether all obesity-related variants contribute to the onset of obesity or one or a few variants cause obesity in genetically heterogeneous populations remains obscure. Here, we investigated the genetic architecture of obesity by clustering the Japanese and British populations with obesity using obesity-related factors. In Step-1, we conducted a genome-wide association study (GWAS) with body mass index (BMI) as the outcome for eligible participants. In Step-2, we assigned participants with obesity (BMI ≥25 kg/m2) to five clusters based on obesity-related factors. Subsequently, participants from each cluster and those with a BMI <25 kg/m2 were combined. A GWAS was conducted for each cluster. Several previously identified obesity-related genes were verified in Step-1. Of the genes detected in Step-1, unique obesity-related genes were detected separately for each cluster in Step-2. Our novel findings suggest that a smaller sample size with increased homogeneity may provide insights into the genetic architecture of obesity.
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Affiliation(s)
- Ippei Takahashi
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Hisashi Ohseto
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Fumihiko Ueno
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomomi Oonuma
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Akira Narita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Taku Obara
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Sendai, Japan
| | - Mami Ishikuro
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Keiko Murakami
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Aoi Noda
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Sendai, Japan
| | - Atsushi Hozawa
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Junichi Sugawara
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Gen Tamiya
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Shinichi Kuriyama
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
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4
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Grinde KE, Browning BL, Reiner AP, Thornton TA, Browning SR. Adjusting for principal components can induce spurious associations in genome-wide association studies in admixed populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587682. [PMID: 38617337 PMCID: PMC11014513 DOI: 10.1101/2024.04.02.587682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/24/2024]
Abstract
Principal component analysis (PCA) is widely used to control for population structure in genome-wide association studies (GWAS). Top principal components (PCs) typically reflect population structure, but challenges arise in deciding how many PCs are needed and ensuring that PCs do not capture other artifacts such as regions with atypical linkage disequilibrium (LD). In response to the latter, many groups suggest performing LD pruning or excluding known high LD regions prior to PCA. However, these suggestions are not universally implemented and the implications for GWAS are not fully understood, especially in the context of admixed populations. In this paper, we investigate the impact of pre-processing and the number of PCs included in GWAS models in African American samples from the Women's Women's Health Initiative SNP Health Association Resource and two Trans-Omics for Precision Medicine Whole Genome Sequencing Project contributing studies (Jackson Heart Study and Genetic Epidemiology of Chronic Obstructive Pulmonary Disease Study). In all three samples, we find the first PC is highly correlated with genome-wide ancestry whereas later PCs often capture local genomic features. The pattern of which, and how many, genetic variants are highly correlated with individual PCs differs from what has been observed in prior studies focused on European populations and leads to distinct downstream consequences: adjusting for such PCs yields biased effect size estimates and elevated rates of spurious associations due to the phenomenon of collider bias. Excluding high LD regions identified in previous studies does not resolve these issues. LD pruning proves more effective, but the optimal choice of thresholds varies across datasets. Altogether, our work highlights unique issues that arise when using PCA to control for ancestral heterogeneity in admixed populations and demonstrates the importance of careful pre-processing and diagnostics to ensure that PCs capturing multiple local genomic features are not included in GWAS models.
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Affiliation(s)
- Kelsey E. Grinde
- Department of Mathematics, Statistics, and Computer Science, Macalester College, Saint Paul, Minnesota, 55105, USA
| | - Brian L. Browning
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, 98195, USA
| | - Alexander P. Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, 98195, USA
| | - Timothy A. Thornton
- Regeneron Genetics Center, Tarrytown, New York, 10591, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, 98195, USA
| | - Sharon R. Browning
- Department of Biostatistics, University of Washington, Seattle, Washington, 98195, USA
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Lu HF, Chou CH, Lin YJ, Uchiyama S, Terao C, Wang YW, Yang JS, Liu TY, Wong HSC, Chen SCC, Tsai FJ. The genome-wide association study of serum IgE levels demonstrated a shared genetic background in allergic diseases. Clin Immunol 2024; 260:109897. [PMID: 38199299 DOI: 10.1016/j.clim.2024.109897] [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: 08/10/2023] [Revised: 12/12/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
Immunoglobulin E (IgE) synthessis is highly related to a variety of atopic diseases, and several genome-wide association studies (GWASs) have demonstrated the association between genes and IgE level. In this study, we conducted the largest genome-wide association study of IgE involving a Taiwanese Han population. Eight independent variants exhibited genome-wide significance. Among them, an intronic SNP of CD28, rs1181388, and an intergenic SNP, rs1002957030, on 11q23.2 were identified as novel signals for IgE. Seven of the loci were replicated successfully in a meta-analysis using data on Japanese population. Among all the human leukocyte antigen (HLA) regions, HLA-DQA1*03:02 - HLA-DQB1*03:03 was the most significant haplotype (OR = 1.25, SE = 0.02, FDR = 1.6 × 10-14), corresponding to HLA-DQA1 Asp160 and HLA-DQB1 Leu87 amino acid residues. The genetic correlation showed significance between IgE and allergic diseases including asthma, atopic dermatitis, and pollinosis. IgE PRS was significantly correlated with total IgE levels. Furthermore, the top decile IgE polygenic risk score (PRS) group had the highest risk of asthma for the Taiwan Biobank and Biobank Japan cohorts. IgE PRS may be used to aid in predicting the occurrence of allergic reactions before symptoms occur and biomarkers are detectable. Our study provided a more comprehensive understanding of the impact of genomic variants, including complex HLA alleles, on serum IgE levels.
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Affiliation(s)
- Hsing-Fang Lu
- Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chen-Hsing Chou
- PhD Program for Health Science and Industry, College of Health Care, China Medical University, Taichung, Taiwan; Department of Health Services Administration, China Medical University, Taichung, Taiwan
| | - Ying-Ju Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan; School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Shunsuke Uchiyama
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan; The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yu-Wen Wang
- Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan
| | - Jai-Sing Yang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, 404327, Taiwan
| | - Ting-Yuan Liu
- Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan
| | - Henry Sung-Ching Wong
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Sean Chun-Chang Chen
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; School of Chinese Medicine, China Medical University, Taichung, Taiwan; Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan.
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6
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Xu Z, Forno E, Sun Y, Manni ML, Han YY, Kim S, Yue M, Vonk JM, Kersten ETM, Acosta-Perez E, Canino G, Koppelman GH, Chen W, Celedón JC. Nasal epithelial gene expression and total IgE in children and adolescents with asthma. J Allergy Clin Immunol 2024; 153:122-131. [PMID: 37742934 PMCID: PMC10842443 DOI: 10.1016/j.jaci.2023.09.014] [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: 02/28/2023] [Revised: 08/15/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Little is known about nasal epithelial gene expression and total IgE in youth. OBJECTIVE We aimed to identify genes whose nasal epithelial expression differs by total IgE in youth, and group them into modules that could be mapped to airway epithelial cell types. METHODS We conducted a transcriptome-wide association study of total IgE in 469 Puerto Ricans aged 9 to 20 years who participated in the Epigenetic Variation and Childhood Asthma in Puerto Ricans study, separately in all subjects and in those with asthma. We then attempted to replicate top findings for each analysis using data from 3 cohorts. Genes with a Benjamini-Hochberg-adjusted P value of less than .05 in the Epigenetic Variation and Childhood Asthma in Puerto Ricans study and a P value of less than .05 in the same direction of association in 1 or more replication cohort were considered differentially expressed genes (DEGs). DEGs for total IgE in subjects with asthma were further dissected into gene modules using coexpression analysis, and such modules were mapped to specific cell types in airway epithelia using public single-cell RNA-sequencing data. RESULTS A higher number of DEGs for total IgE were identified in subjects with asthma (n = 1179 DEGs) than in all subjects (n = 631 DEGs). In subjects with asthma, DEGs were mapped to 11 gene modules. The top module for positive correlation with total IgE was mapped to myoepithelial and mucus secretory cells in lower airway epithelia and was regulated by IL-4, IL5, IL-13, and IL-33. Within this module, hub genes included CDH26, FETUB, NTRK2, CCBL1, CST1, and CST2. Furthermore, an enrichment analysis showed overrepresentation of genes in signaling pathways for synaptogenesis, IL-13, and ferroptosis, supporting interactions between interleukin- and acetylcholine-induced responses. CONCLUSIONS Our findings for nasal epithelial gene expression support neuroimmune coregulation of total IgE in youth with asthma.
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Affiliation(s)
- Zhongli Xu
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa; School of Medicine, Tsinghua University, Beijing, China
| | - Erick Forno
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Yidan Sun
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands
| | - Michelle L Manni
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Yueh Ying Han
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Soyeon Kim
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Molin Yue
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Judith M Vonk
- GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands; Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Elin T M Kersten
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands
| | - Edna Acosta-Perez
- Behavioral Sciences Research Institute of Puerto Rico, University of Puerto Rico, San Juan, Puerto Rico
| | - Glorisa Canino
- Behavioral Sciences Research Institute of Puerto Rico, University of Puerto Rico, San Juan, Puerto Rico; Department of Pediatrics, Medical Science Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands
| | - Wei Chen
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Juan C Celedón
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa.
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7
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Zhang Y. From gene identifications to therapeutic targets for asthma: Focus on great potentials of TSLP, ORMDL3, and GSDMB. CHINESE MEDICAL JOURNAL PULMONARY AND CRITICAL CARE MEDICINE 2023; 1:139-147. [PMID: 39171126 PMCID: PMC11332877 DOI: 10.1016/j.pccm.2023.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Indexed: 08/23/2024]
Abstract
Asthma is a chronic respiratory disease, and clinically, asthma exacerbations remain difficult to treat. The disease is caused by combinations of and interactions between genetic and environmental factors. Genomic and genetic approaches identified many novel genes to treat asthma and brought new insights into the disease. The products of the genes have functional roles in regulating physiological or pathophysiological processes in airway structural cells and immune system cells. Genetic factors also interact with environmental factors such as air pollutants, and bacterial and viral infections to trigger the disease. Thymic stromal lymphopoietin (TSLP), orosomucoid-like 3 (ORMDL3), and gasdermin B (GSDMB) are three genes identified by genetic studies to have a great potential as therapeutic targets of asthma. TSLP is an important driver of type 2 inflammation. ORMDL3 mediates cell stress, sphingolipid synthesis, and viral and bacterial infections. GSDMB regulates cell pyroptosis through its N and C terminals and can bind sulfatides to influence inflammatory response. Investigating inhibitors or modulators for these pathways would bring a new landscape for therapeutics of asthma in future.
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Affiliation(s)
- Youming Zhang
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London SW3 6LY, UK
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8
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Pushpamithran G, Skoglund C, Olsson F, Méndez-Aranda M, Schön T, Segelmark M, Stendahl O, Gilman RH, Blomgran R. No impact of helminth coinfection in patients with smear positive tuberculosis on immunoglobulin levels using a novel method measuring Mycobacterium tuberculosis-specific antibodies. ALLERGY, ASTHMA, AND CLINICAL IMMUNOLOGY : OFFICIAL JOURNAL OF THE CANADIAN SOCIETY OF ALLERGY AND CLINICAL IMMUNOLOGY 2023; 19:55. [PMID: 37386541 DOI: 10.1186/s13223-023-00808-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 06/11/2023] [Indexed: 07/01/2023]
Abstract
Helminth/tuberculosis (TB)-coinfection can reduce cell-mediated immunity against Mycobacterium tuberculosis (Mtb) and increase disease severity, although the effects are highly helminth species dependent. Mtb have long been ranked as the number one single infectious agent claiming the most lives. The only licensed vaccine for TB (BCG) offers highly variable protection against TB, and almost no protection against transmission of Mtb. In recent few years the identification of naturally occurring antibodies in humans that are protective during Mtb infection has reignited the interest in adaptive humoral immunity against TB and its possible implementation in novel TB vaccine design. The effects of helminth/TB coinfection on the humoral response against Mtb during active pulmonary TB are however still unclear, and specifically the effect by globally prevalent helminth species such as Ascaris lumbricoides, Strongyloides stercoralis, Ancylostoma duodenale, Trichuris trichiura. Plasma samples from smear positive TB patients were used to measure both total and Mtb-specific antibody responses in a Peruvian endemic setting where these helminths are dominating. Mtb-specific antibodies were detected by a novel approach coating ELISA-plates with a Mtb cell-membrane fraction (CDC1551) that contains a broad range of Mtb surface proteins. Compared to controls without helminths or TB, helminth/TB coinfected patients had high levels of Mtb-specific IgG (including an IgG1 and IgG2 subclass response) and IgM, which were similarly increased in TB patients without helminth infection. These data, indicate that helminth/TB coinfected have a sustained humoral response against Mtb at the level of active TB only. More studies on the species-specific impact of helminths on the adaptive humoral response against Mtb using a larger sample size, and in relation to TB disease severity, are needed.
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Affiliation(s)
- Giggil Pushpamithran
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University Campus US, Building 420 Floor 12, 581 85, Linköping, SE, Sweden
| | - Camilla Skoglund
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Fanny Olsson
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University Campus US, Building 420 Floor 12, 581 85, Linköping, SE, Sweden
- Laboratorio de Investigación en Enfermedades Infecciosas, LID, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Melissa Méndez-Aranda
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University Campus US, Building 420 Floor 12, 581 85, Linköping, SE, Sweden
- Laboratorio de Investigación en Enfermedades Infecciosas, LID, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Thomas Schön
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University Campus US, Building 420 Floor 12, 581 85, Linköping, SE, Sweden
- Department of Infectious Diseases, County of Östergötland and Kalmar, Linköping University, Linköping, Sweden
| | - Mårten Segelmark
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
- Department of Clinical Sciences, Lund University and Department of Nephrology, Skane University Hospital, Lund, Sweden
| | - Olle Stendahl
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University Campus US, Building 420 Floor 12, 581 85, Linköping, SE, Sweden
| | - Robert H Gilman
- Laboratorio de Investigación en Enfermedades Infecciosas, LID, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, Mayland, USA
| | - Robert Blomgran
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University Campus US, Building 420 Floor 12, 581 85, Linköping, SE, Sweden.
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9
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Cooper PJ, Figueiredo CA, Rodriguez A, dos Santos LM, Ribeiro‐Silva RC, Carneiro VL, Costa G, Magalhães T, dos Santos de Jesus T, Rios R, da Silva HBF, Costa R, Chico ME, Vaca M, Alcantara‐Neves N, Rodrigues LC, Cruz AA, Barreto ML. Understanding and controlling asthma in Latin America: A review of recent research informed by the SCAALA programme. Clin Transl Allergy 2023; 13:e12232. [PMID: 36973960 PMCID: PMC10041090 DOI: 10.1002/clt2.12232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 02/01/2023] [Accepted: 02/15/2023] [Indexed: 03/29/2023] Open
Abstract
Asthma is an important health concern in Latin America (LA) where it is associated with variable prevalence and disease burden between countries. High prevalence and morbidity have been observed in some regions, particularly marginalized urban populations. Research over the past 10 years from LA has shown that childhood disease is primarily non-atopic. The attenuation of atopy may be explained by enhanced immune regulation induced by intense exposures to environmental factors such as childhood infections and poor environmental conditions of the urban poor. Non-atopic symptoms are associated with environmental and lifestyle factors including poor living conditions, respiratory infections, psychosocial stress, obesity, and a diet of highly processed foods. Ancestry (particularly African) and genetic factors increase asthma risk, and some of these factors may be specific to LA settings. Asthma in LA tends to be poorly controlled and depends on access to health care and medications. There is a need to improve management and access to medication through primary health care. Future research should consider the heterogeneity of asthma to identify relevant endotypes and underlying causes. The outcome of such research will need to focus on implementable strategies relevant to populations living in resource-poor settings where the disease burden is greatest.
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Affiliation(s)
- Philip J. Cooper
- Escuela de MedicinaUniversidad Internacional del EcuadorQuitoEcuador
- Institute of Infection and ImmunitySt George's University of LondonLondonUK
| | | | | | | | | | | | - Gustavo Costa
- Center for Data Knowledge and Integration for Health (CIDACS)Fundação Oswaldo CruzBahiaSalvadorBrazil
- Universidade Salvador (UNIFACS)SalvadorBahiaBrazil
| | - Thiago Magalhães
- Instituto de Saúde ColetivaUniversidade Federal da BahiaSalvadorBrazil
| | | | - Raimon Rios
- Instituto de Ciências da SaúdeUniversidade Federal da BahiaSalvadorBrazil
| | | | - Ryan Costa
- Instituto de Ciências da SaúdeUniversidade Federal da BahiaSalvadorBrazil
| | - Martha E. Chico
- Fundacion Ecuatoriana para la Investigacion en Salud (FEPIS)EsmeraldasEcuador
| | - Maritza Vaca
- Instituto de Saúde ColetivaUniversidade Federal da BahiaSalvadorBrazil
- Fundacion Ecuatoriana para la Investigacion en Salud (FEPIS)EsmeraldasEcuador
| | | | - Laura C Rodrigues
- Faculty of Epidemiology and Population HealthLondon School of Hygiene and Tropical MedicineLondonUK
| | - Alvaro A. Cruz
- Universidade Federal da Bahia and Fundação ProARSalvadorBrazil
| | - Mauricio L. Barreto
- Center for Data Knowledge and Integration for Health (CIDACS)Fundação Oswaldo CruzBahiaSalvadorBrazil
- Instituto de Saúde ColetivaUniversidade Federal da BahiaSalvadorBrazil
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10
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Udemgba C, Sarkaria SK, Gleeson P, Bryant-Stephens T, Ogbogu PU, Khoury P, Apter AJ. New considerations of health disparities within allergy and immunology. J Allergy Clin Immunol 2023; 151:314-323. [PMID: 36503854 PMCID: PMC9905264 DOI: 10.1016/j.jaci.2022.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022]
Abstract
The pandemic, political upheavals, and social justice efforts in our society have resulted in attention to persistent health disparities and the urgent need to address them. Using a scoping review, we describe published updates to address disparities and targets for interventions to improve gaps in care within allergy and immunology. These disparities-related studies provide a broad view of our current understanding of how social determinants of health threaten patient outcomes and our ability to advance health equity efforts in our field. We outline next steps to improve access to care and advance health equity for patients with allergic/immunologic diseases through actions taken at the individual, community, and policy levels, which could be applied outside of our field. Key among these are efforts to increase the diversity among our trainees, providers, and scientific teams and enhancing efforts to participate in advocacy work and public health interventions. Addressing health disparities requires advancing our understanding of the interplay between social and structural barriers to care and enacting the needed interventions in various key areas to effect change.
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Affiliation(s)
- Chioma Udemgba
- National Institute of Allergic and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sandeep K Sarkaria
- Section of Allergy and Immunology, Department of Pulmonary & Critical Care, Case Western Reserve University, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Patrick Gleeson
- Section of Allergy & Immunology, Division of Pulmonary, Allergy, & Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pa
| | - Tyra Bryant-Stephens
- Department of Pediatrics, Division of General Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pa
| | - Princess U Ogbogu
- Division of Pediatric Allergy, Immunology, and Rheumatology, University Hospitals Rainbow Babies and Children's Hospital, Cleveland, Ohio; Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Paneez Khoury
- National Institute of Allergic and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrea J Apter
- Section of Allergy & Immunology, Division of Pulmonary, Allergy, & Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pa.
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11
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Baloh CH, Mathias RA. Recent progress in the genetic and epigenetic underpinnings of atopy. J Allergy Clin Immunol 2023; 151:60-69. [PMID: 36608983 PMCID: PMC9987265 DOI: 10.1016/j.jaci.2022.10.027] [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: 09/14/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 01/05/2023]
Abstract
In the past 2 years, there continue to be advances in our understanding of the genetic and epigenetic underpinnings of atopy pertaining to disease risk and disease severity. The joint role of genetics and the environment has been emphasized in multiple studies. Combining genetics with family history, biomarkers, and comorbidities is further refining our ability to predict the development of individual atopic diseases as well as the advancement of the atopic march. Polygenic risk scores will be an important next step for the field moving toward clinical translation of the genetic findings thus far. A systems biology approach, as illustrated by studies of the microbiome and epigenome, will be necessary to fully understand disease development and to develop increasingly targeted therapeutics.
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Affiliation(s)
- Carolyn H Baloh
- The Immune Tolerance Network, Benaroya Research Institute at Virginia Mason, Seattle, Wash; Department of Medicine, Harvard Medical School, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass
| | - Rasika A Mathias
- Department of Medicine, School of Medicine, Johns Hopkins University, Division of Allergy and Clinical Immunology, Baltimore, Md.
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12
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Lee S, Prokopenko D, Kelly RS, Lutz S, Ann Lasky-Su J, Cho MH, Laurie C, Celedón JC, Lange C, Weiss ST, Hecker J, DeMeo DL. Zinc finger protein 33B demonstrates sex interaction with atopy-related markers in childhood asthma. Eur Respir J 2023; 61:2200479. [PMID: 35953101 PMCID: PMC10124713 DOI: 10.1183/13993003.00479-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/14/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Sex differences related to immune responses can influence atopic manifestations in childhood asthma. While genome-wide association studies have investigated a sex-specific genetic architecture of the immune response, gene-by-sex interactions have not been extensively analysed for atopy-related markers including allergy skin tests, IgE and eosinophils in asthmatic children. METHODS We performed a genome-wide gene-by-sex interaction analysis for atopy-related markers using whole-genome sequencing data based on 889 trios from the Genetic Epidemiology of Asthma in Costa Rica Study (GACRS) and 284 trios from the Childhood Asthma Management Program (CAMP). We also tested the findings in UK Biobank participants with self-reported childhood asthma. Furthermore, downstream analyses in GACRS integrated gene expression to disentangle observed associations. RESULTS Single nucleotide polymorphism (SNP) rs1255383 at 10q11.21 demonstrated a genome-wide significant gene-by-sex interaction (pinteraction=9.08×10-10) for atopy (positive skin test) with opposite direction of effects between females and males. In the UK Biobank participants with a history of childhood asthma, the signal was consistently observed with the same sex-specific effect directions for high eosinophil count (pinteraction=0.0058). Gene expression of ZNF33B (zinc finger protein 33B), located at 10q11.21, was moderately associated with atopy in girls, but not in boys. CONCLUSIONS We report SNPs in/near a zinc finger gene as novel sex-differential loci for atopy-related markers with opposite effect directions in females and males. A potential role for ZNF33B should be studied further as an important driver of sex-divergent features of atopy in childhood asthma.
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Affiliation(s)
- Sanghun Lee
- Department of Medical Consilience, Division of Medicine, Graduate School, Dankook University, Yongin, South Korea
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- NH Institute for Natural Product Research, Myungji Hospital, Goyang-si, South Korea
| | - Dmitry Prokopenko
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sharon Lutz
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jessica Ann Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Christoph Lange
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Julian Hecker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
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13
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Dapas M, Thompson EE, Wentworth-Sheilds W, Clay S, Visness CM, Calatroni A, Sordillo JE, Gold DR, Wood RA, Makhija M, Khurana Hershey GK, Sherenian MG, Gruchalla RS, Gill MA, Liu AH, Kim H, Kattan M, Bacharier LB, Rastogi D, Altman MC, Busse WW, Becker PM, Nicolae D, O’Connor GT, Gern JE, Jackson DJ, Ober C. Multi-omic association study identifies DNA methylation-mediated genotype and smoking exposure effects on lung function in children living in urban settings. PLoS Genet 2023; 19:e1010594. [PMID: 36638096 PMCID: PMC9879483 DOI: 10.1371/journal.pgen.1010594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 01/26/2023] [Accepted: 12/23/2022] [Indexed: 01/14/2023] Open
Abstract
Impaired lung function in early life is associated with the subsequent development of chronic respiratory disease. Most genetic associations with lung function have been identified in adults of European descent and therefore may not represent those most relevant to pediatric populations and populations of different ancestries. In this study, we performed genome-wide association analyses of lung function in a multiethnic cohort of children (n = 1,035) living in low-income urban neighborhoods. We identified one novel locus at the TDRD9 gene in chromosome 14q32.33 associated with percent predicted forced expiratory volume in one second (FEV1) (p = 2.4x10-9; βz = -0.31, 95% CI = -0.41- -0.21). Mendelian randomization and mediation analyses revealed that this genetic effect on FEV1 was partially mediated by DNA methylation levels at this locus in airway epithelial cells, which were also associated with environmental tobacco smoke exposure (p = 0.015). Promoter-enhancer interactions in airway epithelial cells revealed chromatin interaction loops between FEV1-associated variants in TDRD9 and the promoter region of the PPP1R13B gene, a stimulator of p53-mediated apoptosis. Expression of PPP1R13B in airway epithelial cells was significantly associated the FEV1 risk alleles (p = 1.3x10-5; β = 0.12, 95% CI = 0.06-0.17). These combined results highlight a potential novel mechanism for reduced lung function in urban youth resulting from both genetics and smoking exposure.
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Affiliation(s)
- Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | - Emma E. Thompson
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | | | - Selene Clay
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | | | | | - Joanne E. Sordillo
- Department of Population Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Diane R. Gold
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert A. Wood
- Department of Pediatrics, Johns Hopkins University Medical Center, Baltimore, Maryland, United States of America
| | - Melanie Makhija
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children’s Hospital, Chicago, Illinois, United States of America
| | - Gurjit K. Khurana Hershey
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Michael G. Sherenian
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Rebecca S. Gruchalla
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michelle A. Gill
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Andrew H. Liu
- Department of Allergy and Immunology, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Haejin Kim
- Department of Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Meyer Kattan
- Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Leonard B. Bacharier
- Monroe Carell Jr. Children’s Hospital at Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Deepa Rastogi
- Children’s National Health System, Washington, District of Columbia, United States of America
| | - Matthew C. Altman
- Department of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - William W. Busse
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Dan Nicolae
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - George T. O’Connor
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - James E. Gern
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Daniel J. Jackson
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
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14
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Swart Y, van Eeden G, Uren C, van der Spuy G, Tromp G, Möller M. GWAS in the southern African context. PLoS One 2022; 17:e0264657. [PMID: 36170230 PMCID: PMC9518849 DOI: 10.1371/journal.pone.0264657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/06/2022] [Indexed: 11/18/2022] Open
Abstract
Researchers would generally adjust for the possible confounding effect of population structure by considering global ancestry proportions or top principle components. Alternatively, researchers would conduct admixture mapping to increase the power to detect variants with an ancestry effect. This is sufficient in simple admixture scenarios, however, populations from southern Africa can be complex multi-way admixed populations. Duan et al. (2018) first described local ancestry adjusted allelic (LAAA) analysis as a robust method for discovering association signals, while producing minimal false positive hits. Their simulation study, however, was limited to a two-way admixed population. Realizing that their findings might not translate to other admixture scenarios, we simulated a three- and five-way admixed population to compare the LAAA model to other models commonly used in genome-wide association studies (GWAS). We found that, given our admixture scenarios, the LAAA model identifies the most causal variants in most of the phenotypes we tested across both the three-way and five-way admixed populations. The LAAA model also produced a high number of false positive hits which was potentially caused by the ancestry effect size that we assumed. Considering the extent to which the various models tested differed in their results and considering that the source of a given association is unknown, we recommend that researchers use multiple GWAS models when analysing populations with complex ancestry.
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Affiliation(s)
- Yolandi Swart
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerald van Eeden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Gian van der Spuy
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, Cape Town, South Africa
| | - Gerard Tromp
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
- SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, Cape Town, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
- * E-mail:
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15
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Corona-Rivera J, Peña-Padilla C, Morales-Domínguez GE, Romero-Bolaño YM. [Genetic aspects involved in asthma]. REVISTA ALERGIA MÉXICO 2022; 69:21-30. [PMID: 36927748 DOI: 10.29262/ram.v69i1.1031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 01/03/2022] [Indexed: 11/24/2022] Open
Abstract
Asthma is an etiologically heterogeneous disease resulting from a complex interaction between genetic. The genetic aspects involved in asthma, which were analyzed from the perspective of the traditional model of multifactorial inheritance, were susceptibility, host factors, and environmental exposures. In the present paper, studies on their family aggregation, concordance in twins, and heritability were analized; as well as the current knowledge about candidate genes, genome wide association studies, and epigenomics contributions and other omic studies that have increased our knowledge about their pathophysiology and environmental interactions.
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Affiliation(s)
- Jorge Corona-Rivera
- Universidad de Guadalajara, Centro Universitario de Ciencias de la Salud, Departamento de Biología Mole-cular y Genómica, Instituto de Genética Humana Dr. Enrique Corona-Rivera, Guadalajara, Jalisco, México.
| | - Christian Peña-Padilla
- Hospital Civil de Guadalajara Dr. Juan I. Menchaca, División de Pediatría, Servicio de Genética, Guadalajara, Jalisco, México
| | | | - Yaneris Maibeth Romero-Bolaño
- Hospital Civil de Guadalajara Dr. Juan I. Menchaca, División de Pediatría, Servicio de Genética, Guadalajara, Jalisco, México
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16
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Forno E, Brandenburg DD, Castro-Rodriguez JA, Celis-Preciado CA, Holguin F, Licskai C, Lovinsky-Desir S, Pizzichini M, Teper A, Yang C, Celedón JC. Asthma in the Americas: An Update: A Joint Perspective from the Brazilian Thoracic Society, Canadian Thoracic Society, Latin American Thoracic Society, and American Thoracic Society. Ann Am Thorac Soc 2022; 19:525-535. [PMID: 35030062 PMCID: PMC8996271 DOI: 10.1513/annalsats.202109-1068cme] [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: 09/20/2021] [Accepted: 01/14/2022] [Indexed: 11/20/2022] Open
Abstract
Asthma affects a large number of people living in the Americas, a vast and diverse geographic region comprising 35 nations in the Caribbean and North, Central, and South America. The marked variability in the prevalence, morbidity, and mortality from asthma across and within nations in the Americas offers a unique opportunity to improve our understanding of the risk factors and management of asthma phenotypes and endotypes in children and adults. Moreover, a better assessment of the causes and treatment of asthma in less economically developed regions in the Americas would help diagnose and treat individuals migrating from those areas to Canada and the United States. In this focused review, we first assess the epidemiology of asthma, review known and potential risk factors, and examine commonalities and differences in asthma management across the Americas. We then discuss future directions in research and health policies to improve the prevention, diagnosis, and management of pediatric and adult asthma in the Americas, including standardized and periodic assessment of asthma burden across the region; large-scale longitudinal studies including omics and comprehensive environmental data on racially and ethnically diverse populations; and dissemination and implementation of guidelines for asthma management across the spectrum of disease severity. New initiatives should recognize differences in socioeconomic development and health care systems across the region while paying particular attention to novel or more impactful risk factors for asthma in the Americas, including indoor pollutants such as biomass fuel, tobacco use, infectious agents and the microbiome, and psychosocial stressor and chronic stress.
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Affiliation(s)
- Erick Forno
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh School of Medicine and Pediatric Asthma Center, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Diego D. Brandenburg
- Department of Pediatrics, Pediatric Pulmonology Unit, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Jose A. Castro-Rodriguez
- Department of Pediatric Pulmonology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos A. Celis-Preciado
- Pulmonary Unit, Internal Medicine Department, Hospital Universitario San Ignacio and Faculty of Medicine, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Fernando Holguin
- Division of Pulmonary Sciences and Critical Care, University of Colorado Denver, Denver, Colorado
| | - Christopher Licskai
- Department of Medicine, Western University Canada, Schulich School of Medicine and Dentistry, London Health Sciences Centre, London, Ontario, Canada
| | - Stephanie Lovinsky-Desir
- Division of Pediatric Pulmonary Medicine, Columbia University Irving Medical Center, New York, New York
| | - Marcia Pizzichini
- Post-Graduate Program of Medical Sciences, Federal University of Santa Catarina, Florianopolis, Santa Catarina, Brazil
| | - Alejandro Teper
- Respiratory Center, Hospital de Niños Dr. Ricardo Gutiérrez, Ciudad Autónoma de Buenos Aires, Argentina; and
| | - Connie Yang
- Division of Respiratory Medicine, University of British Columbia, British Columbia Children’s Hospital, Vancouver, British Columbia, Canada
| | - Juan C. Celedón
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh School of Medicine and Pediatric Asthma Center, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
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17
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Gysens F, Mestdagh P, de Bony de Lavergne E, Maes T. Unlocking the secrets of long non-coding RNAs in asthma. Thorax 2022; 77:514-522. [PMID: 35246486 PMCID: PMC9016255 DOI: 10.1136/thoraxjnl-2021-218359] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/21/2022] [Indexed: 12/15/2022]
Abstract
Asthma is a very heterozygous disease, divided in subtypes, such as eosinophilic and neutrophilic asthma. Phenotyping and endotyping of patients, especially patients with severe asthma who are refractory to standard treatment, are crucial in asthma management and are based on a combination of clinical and biological features. Nevertheless, the quest remains to find better biomarkers that distinguish asthma subtypes in a more clear and objective manner and to find new therapeutic targets to treat people with therapy-resistant asthma. In the past, research to identify asthma subtypes mainly focused on expression profiles of protein-coding genes. However, advances in RNA-sequencing technologies and the discovery of non-coding RNAs as important post-transcriptional regulators have provided an entire new field of research opportunities in asthma. This review focusses on long non-coding RNAs (lncRNAs) in asthma; these are non-coding RNAs with a length of more than 200 nucleotides. Many lncRNAs are differentially expressed in asthma, and several have been associated with asthma severity or inflammatory phenotype. Moreover, in vivo and in vitro functional studies have identified the mechanisms of action of specific lncRNAs. Although lncRNAs remain not widely studied in asthma, the current studies show the potential of lncRNAs as biomarkers and therapeutic targets as well as the need for further research.
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Affiliation(s)
- Fien Gysens
- OncoRNALab, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- OncoRNALab, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Tania Maes
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
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18
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Suarez-Pajes E, Díaz-García C, Rodríguez-Pérez H, Lorenzo-Salazar JM, Marcelino-Rodríguez I, Corrales A, Zheng X, Callero A, Perez-Rodriguez E, Garcia-Robaina JC, González-Montelongo R, Flores C, Guillen-Guio B. Targeted analysis of genomic regions enriched in African ancestry reveals novel classical HLA alleles associated with asthma in Southwestern Europeans. Sci Rep 2021; 11:23686. [PMID: 34880287 PMCID: PMC8654850 DOI: 10.1038/s41598-021-02893-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/24/2021] [Indexed: 12/30/2022] Open
Abstract
Despite asthma has a considerable genetic component, an important proportion of genetic risks remain unknown, especially for non-European populations. Canary Islanders have the largest African genetic ancestry observed among Southwestern Europeans and the highest asthma prevalence in Spain. Here we examined broad chromosomal regions previously associated with an excess of African genetic ancestry in Canary Islanders, with the aim of identifying novel risk variants associated with asthma susceptibility. In a two-stage cases-control study, we revealed a variant within HLA-DQB1 significantly associated with asthma risk (rs1049213, meta-analysis p = 1.30 × 10–7, OR [95% CI] = 1.74 [1.41–2.13]) previously associated with asthma and broad allergic phenotype. Subsequent fine-mapping analyses of classical HLA alleles revealed a novel allele significantly associated with asthma protection (HLA-DQA1*01:02, meta-analysis p = 3.98 × 10–4, OR [95% CI] = 0.64 [0.50–0.82]) that had been linked to infectious and autoimmune diseases, and peanut allergy. HLA haplotype analyses revealed a novel haplotype DQA1*01:02-DQB1*06:04 conferring asthma protection (meta-analysis p = 4.71 × 10–4, OR [95% CI] = 0.47 [0.29– 0.73]).
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Affiliation(s)
- Eva Suarez-Pajes
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Claudio Díaz-García
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Itahisa Marcelino-Rodríguez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ariel Callero
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Eva Perez-Rodriguez
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jose C Garcia-Robaina
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | | | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain. .,Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain. .,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain. .,Department of Health Sciences, University of Leicester, Leicester, UK.
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Multiethnic genome-wide and HLA association study of total serum IgE level. J Allergy Clin Immunol 2021; 148:1589-1595. [PMID: 34536413 PMCID: PMC8665111 DOI: 10.1016/j.jaci.2021.09.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/26/2021] [Accepted: 09/01/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Total serum IgE (tIgE) is an important intermediate phenotype of allergic disease. Whole genome genetic association studies across ancestries may identify important determinants of IgE. OBJECTIVE We aimed to increase understanding of genetic variants affecting tIgE production across the ancestry and allergic disease spectrum by leveraging data from the National Heart, Lung and Blood Institute Trans-Omics for Precision Medicine program; the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA); and the Atopic Dermatitis Research Network (N = 21,901). METHODS We performed genome-wide association within strata of study, disease, and ancestry groups, and we combined results via a meta-regression approach that models heterogeneity attributable to ancestry. We also tested for association between HLA alleles called from whole genome sequence data and tIgE, assessing replication of associations in HLA alleles called from genotype array data. RESULTS We identified 6 loci at genome-wide significance (P < 5 × 10-9), including 4 loci previously reported as genome-wide significant for tIgE, as well as new regions in chr11q13.5 and chr15q22.2, which were also identified in prior genome-wide association studies of atopic dermatitis and asthma. In the HLA allele association study, HLA-A∗02:01 was associated with decreased tIgE level (Pdiscovery = 2 × 10-4; Preplication = 5 × 10-4; Pdiscovery+replication = 4 × 10-7), and HLA-DQB1∗03:02 was strongly associated with decreased tIgE level in Hispanic/Latino ancestry populations (PHispanic/Latino discovery+replication = 8 × 10-8). CONCLUSION We performed the largest genome-wide association study and HLA association study of tIgE focused on ancestrally diverse populations and found several known tIgE and allergic disease loci that are relevant in non-European ancestry populations.
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