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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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2
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Herrera-Luis E, Mak ACY, Perez-Garcia J, Martin-Gonzalez E, Eng C, Beckman KB, Huntsman S, Hu D, González-Pérez R, Hernández-Pérez JM, Mederos-Luis E, Sio YY, Poza-Guedes P, Sardón O, Corcuera P, Sánchez-Machín I, Korta-Murua J, Martínez-Rivera C, Mullol J, Muñoz X, Valero A, Sastre J, Garcia-Aymerich J, Llop S, Torrent M, Casas M, Rodríguez-Santana JR, Villar J, del Pozo V, Lorenzo-Diaz F, Williams LK, Melén E, Chew FT, Borrell LN, Burchard EG, Pino-Yanes M. Admixture mapping of severe asthma exacerbations in Hispanic/Latino children and youth. Thorax 2023; 78:233-241. [PMID: 36180068 PMCID: PMC9957797 DOI: 10.1136/thorax-2022-218755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/04/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND In the USA, genetically admixed populations have the highest asthma prevalence and severe asthma exacerbations rates. This could be explained not only by environmental factors but also by genetic variants that exert ethnic-specific effects. However, no admixture mapping has been performed for severe asthma exacerbations. OBJECTIVE We sought to identify genetic variants associated with severe asthma exacerbations in Hispanic/Latino subgroups by means of admixture mapping analyses and fine mapping, and to assess their transferability to other populations and potential functional roles. METHODS We performed an admixture mapping in 1124 Puerto Rican and 625 Mexican American children with asthma. Fine-mapping of the significant peaks was performed via allelic testing of common and rare variants. We performed replication across Hispanic/Latino subgroups, and the transferability to non-Hispanic/Latino populations was assessed in 1001 African Americans, 1250 Singaporeans and 941 Europeans with asthma. The effects of the variants on gene expression and DNA methylation from whole blood were also evaluated in participants with asthma and in silico with data obtained through public databases. RESULTS Genomewide significant associations of Indigenous American ancestry with severe asthma exacerbations were found at 5q32 in Mexican Americans as well as at 13q13-q13.2 and 3p13 in Puerto Ricans. The single nucleotide polymorphism (SNP) rs1144986 (C5orf46) showed consistent effects for severe asthma exacerbations across Hispanic/Latino subgroups, but it was not validated in non-Hispanics/Latinos. This SNP was associated with DPYSL3 DNA methylation and SCGB3A2 gene expression levels. CONCLUSIONS Admixture mapping study of asthma exacerbations revealed a novel locus that exhibited Hispanic/Latino-specific effects and regulated DPYSL3 and SCGB3A2.
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Affiliation(s)
- Esther Herrera-Luis
- Genomics and Health Group, Department of Biochemistry,
Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna,
Tenerife, Spain
| | - Angel C. Y. Mak
- Department of Medicine, University of California San
Francisco, San Francisco, California, U.S.A
| | - Javier Perez-Garcia
- Genomics and Health Group, Department of Biochemistry,
Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna,
Tenerife, Spain
| | - Elena Martin-Gonzalez
- Genomics and Health Group, Department of Biochemistry,
Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna,
Tenerife, Spain
| | - Celeste Eng
- Department of Medicine, University of California San
Francisco, San Francisco, California, U.S.A
| | | | - Scott Huntsman
- Department of Medicine, University of California San
Francisco, San Francisco, California, U.S.A
| | - Donglei Hu
- Department of Medicine, University of California San
Francisco, San Francisco, California, U.S.A
| | - Ruperto González-Pérez
- Allergy Department, Hospital Universitario de Canarias,
Santa Cruz de Tenerife, Tenerife, Spain,Asthma Unit, Hospital Universitario de Canarias, La Laguna,
Tenerife, Spain
| | - José M. Hernández-Pérez
- Pulmonary Medicine, Hospital Universitario de N.S de
Candelaria, Santa Cruz de Tenerife, Spain,Pulmonary Medicine, Hospital General de La Palma, La Palma,
Santa Cruz de Tenerife, Spain
| | - Elena Mederos-Luis
- Allergy Department, Hospital Universitario de Canarias,
Santa Cruz de Tenerife, Tenerife, Spain
| | - Yang Yie Sio
- Department of Biological Sciences, National University of
Singapore, Singapore
| | - Paloma Poza-Guedes
- Allergy Department, Hospital Universitario de Canarias,
Santa Cruz de Tenerife, Tenerife, Spain,Asthma Unit, Hospital Universitario de Canarias, La Laguna,
Tenerife, Spain
| | - Olaia Sardón
- Division of Pediatric Respiratory Medicine, Hospital
Universitario Donostia, San Sebastián, Spain,Department of Pediatrics, University of the Basque
Country (UPV/EHU), San Sebastián, Spain
| | - Paula Corcuera
- Division of Pediatric Respiratory Medicine, Hospital
Universitario Donostia, San Sebastián, Spain
| | | | - Javier Korta-Murua
- Division of Pediatric Respiratory Medicine, Hospital
Universitario Donostia, San Sebastián, Spain,Department of Pediatrics, University of the Basque
Country (UPV/EHU), San Sebastián, Spain
| | - Carlos Martínez-Rivera
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Servicio de Neumología, Hospital Universitario
Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona,
Spain
| | - Joaquim Mullol
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Rhinology Unit & Smell Clinic, ENT Department;
Clinical & Experimental Respiratory Immunoallergy (IDIBAPS), Universitat de
Barcelona, Barcelona, Spain
| | - Xavier Muñoz
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Servicio de Neumología, Hospital Vall
d’Hebron, Barcelona, Spain
| | - Antonio Valero
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Allergy Unit & Severe Asthma Unit, Pneumonology and
Allergy Department, Hospital Clínic; IDIBAPS; Universitat de
Barcelona.Barcelona, Spain
| | - Joaquín Sastre
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Allergy Department, Hospital Universitario
Fundación Jiménez Díaz, Madrid, Spain
| | - Judith Garcia-Aymerich
- Spanish Consortium for Research on Epidemiology and
Public Health (CIBERESP), Madrid, Spain,ISGlobal, Barcelona, Spain,Universitat Pompeu Fabra, Barcelona, Spain
| | - Sabrina Llop
- Spanish Consortium for Research on Epidemiology and
Public Health (CIBERESP), Madrid, Spain,Epidemiology and Environmental Health Joint Research
Unit, FISABIO–Universitat Jaume I–Universitat de València,
Valencia, Spain
| | | | - Maribel Casas
- ISGlobal, Barcelona, Spain,Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Jesús Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Multidisciplinary Organ Dysfunction Evaluation Research
Network, Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran
Canaria, Spain
| | - Victoria del Pozo
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Immunology Department, Instituto de Investigación
Sanitaria Hospital Universitario Fundación Jiménez Díaz,
Madrid, Spain
| | - Fabian Lorenzo-Diaz
- Genomics and Health Group, Department of Biochemistry,
Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna,
Tenerife, Spain,Instituto Universitario de Enfermedades Tropicales y
Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), La
Laguna, Tenerife, Spain
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research,
Department of Internal Medicine, Henry Ford Health System, Detroit, MI, U.S.A
| | - Erik Melén
- Department of Clinical Sciences and Education,
Södersjukhuset, Karolinska Institutet, Stockholm, Sweden,Sachs’ Children’s Hospital, South General
Hospital, Stockholm, Sweden
| | - Fook Tim Chew
- Department of Biological Sciences, National University of
Singapore, Singapore
| | - Luisa N. Borrell
- Department of Epidemiology & Biostatistics, Graduate
School of Public Health & Health Policy, City University of New York, New York,
NY, U.S.A
| | - Esteban G. Burchard
- UMN Genomics Center, Minneapolis, Minnesota, U.S.A.,Department of Bioengineering and Therapeutic Sciences,
University of California San Francisco, San Francisco, California, U.S.A
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), La Laguna, Spain .,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), La Laguna, Spain
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3
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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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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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