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Liao G, Yan Q, Zhang M, Zhang X, Yang J, Huang H, Liu X, Jiang Y, Gong J, Zhan S, Li D, Huang X. Integrative analysis of network pharmacology and proteomics reveal the protective effect of Xiaoqinglong Decotion on neutrophilic asthma. JOURNAL OF ETHNOPHARMACOLOGY 2024; 330:118102. [PMID: 38561057 DOI: 10.1016/j.jep.2024.118102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 03/10/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Xiaoqinglong Decotion (XQLD) is a commonly used Chinese herbal formula in clinical practice, especially for allergic diseases such as asthma. However, its intrinsic mechanism for the treatment of neutrophilic asthma (NA) remains unclear. AIM OF THE STUDY The aim of this study was to evaluate the efficacy and potential mechanisms of XQLD on NA using network pharmacology and in vivo experiments. MATERIALS AND METHODS First, the active compounds, potential targets and mechanisms of XQLD against NA were initially elucidated by network pharmacology. Then, OVA/CFA-induced NA mice were treated with XQLD to assess its efficacy. Proteins were then analyzed and quantified using a Tandem Mass Tags approach for differentially expressed proteins (DEPs) to further reveal the mechanisms of NA treatment by XQLD. Finally, the hub genes, critical DEPs and potential pathways were validated. RESULTS 176 active compounds and 180 targets against NA were identified in XQLD. Protein-protein interaction (PPI) network revealed CXCL10, CX3CR1, TLR7, NCF1 and FABP4 as hub genes. In vivo experiments showed that XQLD attenuated inflammatory infiltrates, airway mucus secretion and remodeling in the lungs of NA mice. Moreover, XQLD significantly alleviated airway neutrophil inflammation in NA mice by decreasing the expression of IL-8, MPO and NE. XQLD also reduced the levels of CXCL10, CX3CR1, TLR7, NCF1 and FABP4, which are closely associated with neutrophil inflammation. Proteomics analysis identified 28 overlapping DEPs in the control, NA and XQLD groups, and we found that XQLD inhibited ferroptosis signal pathway (elevated GPX4 and decreased ASCL3) as well as the expression of ARG1, MMP12 and SPP1, while activating the Rap1 signaling pathway. CONCLUSION This study revealed that inhibition of ARG1, MMP12 and SPP1 expression as well as ferroptosis pathways, and activation of the Rap1 signaling pathway contribute to the therapeutic effect of XQLD on NA.
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Affiliation(s)
- Gang Liao
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| | - Qian Yan
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, China; Guangdong Provincial Clinical Research Academy of Chinese Medicine, Guangzhou, China
| | - Miaofen Zhang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, China; Guangdong Provincial Clinical Research Academy of Chinese Medicine, Guangzhou, China
| | - Xinxin Zhang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, China; Guangdong Provincial Clinical Research Academy of Chinese Medicine, Guangzhou, China
| | - Jing Yang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, China; Guangdong Provincial Clinical Research Academy of Chinese Medicine, Guangzhou, China
| | - Huiting Huang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaohong Liu
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yong Jiang
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| | - Jing Gong
- Guangdong Provincial Second Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Shaofeng Zhan
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Detang Li
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Pharmacy, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Xiufang Huang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, China; Guangdong Provincial Clinical Research Academy of Chinese Medicine, Guangzhou, China.
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Bhamidimarri PM, Fuentes D, Salameh L, Mahboub B, Hamoudi R. Assessing the impact of storage conditions on RNA from human saliva and its application to the identification of mRNA biomarkers for asthma. Front Mol Biosci 2024; 11:1363897. [PMID: 38948078 PMCID: PMC11211611 DOI: 10.3389/fmolb.2024.1363897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 05/22/2024] [Indexed: 07/02/2024] Open
Abstract
Introduction: Human saliva was used to develop non-invasive liquid biopsy biomarkers to establish saliva as an alternate to blood and plasma in translational research. The present study focused on understanding the impact of sample storage conditions on the extraction of RNA from saliva and the RNA yield, to be applied in clinical diagnosis. In this study, genes related to asthma were used to test the method developed. Methods: Salivary RNA was extracted from three subjects using the Qiazol® based method and quantified by both spectrophotometric (NanoDrop) and fluorometric (Qubit®) methods. RNA integrity was measured using a bioanalyzer. Quantitative PCR was used to monitor the impact of storage conditions on the expression of housekeeping genes: GAPDH and β-actin, and the asthma related genes: POSTN and FBN2. In addition, an independent cohort of 38 asthmatics and 10 healthy controls were used to validate the expression of POSTN and FBN2 as mRNA salivary biomarkers. Results: Approximately 2 µg of total RNA was obtained from the saliva stored at 40°C without any preservative for 2 weeks showing consistent gene expression with RNA stored at room temperature (RT) for 48 h with RNAlater. Although saliva stored with RNAlater showed a substantial increase in the yield (110 to 234 ng/μL), a similar Cq (15.6 ± 1.4) for the 18s rRNA gene from saliva without preservative showed that the RNA was stable enough. Gene expression analysis from the degraded RNA can be performed by designing the assay using a smaller fragment size spanning a single exon as described below in the case of the POSTN and FBN2 genes in the asthma cohort. Conclusion: This study showed that samples stored at room temperature up to a temperature of 40°C without any preservative for 2 weeks yielded relatively stable RNA. The methodology developed can be employed to transport samples from the point of collection to the laboratory, under non-stringent storage conditions enabling the execution of gene expression studies in a cost effective and efficient manner.
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Affiliation(s)
- Poorna Manasa Bhamidimarri
- Research Institute of Medical and Health Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - David Fuentes
- Research Institute of Medical and Health Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Laila Salameh
- Research Institute of Medical and Health Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Rashid Hospital, Dubai, United Arab Emirates
| | - Bassam Mahboub
- Rashid Hospital, Dubai, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute of Medical and Health Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
- Centre of Excellence for Precision Medicine, Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- BIMAI-Lab, Biomedically Informed Artificial Intelligence Laboratory, University of Sharjah, Sharjah, United Arab Emirates
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Isubakova DS, Litviakov NV, Tsymbal OS, Usova TV, Tsyplenkova MY, Milto IV, Takhauov RM. Search for polymorphic variants of candidate genes contributing to individual radiosensitivity. BULLETIN OF SIBERIAN MEDICINE 2023. [DOI: 10.20538/1682-0363-2022-4-79-87] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Background. Cytogenetic damage (СD) in lymphocytes induced by low doses (up to 0.1 Sv) of ionizing radiation (IR) is the main cytogenetic sign of individual radiosensitivity of the human body. In addition to DNA repair and cell death, which affect the formation of СD and its elimination, IR effects on the cell can be manifested through changes in proliferation of cells with unrepaired DNA damage. The system of cyclins and cyclin-dependent kinases (CDK), which provide coordination of mitotic events during passage of a cell through the cell cycle, plays a crucial role in regulation of cell proliferation.Aim. To evaluate the relationship of single-nucleotide polymorphisms (SNPs) of cell cycle genes with an increased frequency of СD in workers of a nuclear power plant affected by chronic occupational radiation exposure in the dose range of 100–500 mSv.Materials and methods. The object of the study was blood of 55 conditionally healthy workers of Siberian Chemical Plant (SCP) who were affected by chronic occupational radiation exposure (gamma radiation) in the dose range of 100–500 mSv. A standard cytogenetic analysis of blood lymphocytes was performed for all examined individuals. Genomic DNA was isolated from the blood of the workers using the QIAamp DNA Blood Mini Kit (QIAGEN, Germany). DNA was genotyped using 257 SNPs of cyclin genes and neighboring intergenic regions using DNA microarrays from the high-density CytoScan HD Array (Affymetrix, USA).Results. Taking into account the Bonferroni correction, only statistically significant associations of SNPs with the frequency of dicentric chromosomes were found; all other types of chromosomal aberrations did not show statistical significance. The rs803054 CCNI2 was associated with an increased frequency of dicentric chromosomes arising under the influence of chronic occupational radiation exposure.Conclusion. The discovered SNP (rs803054), whose recessive genotype is associated with an increased frequency of dicentric chromosomes in workers of SCP exposed to radiation at doses of 100–500 mSv over a long time, can be considered as a potential marker of individual radiosensitivity. To confirm the identified associations, further validation studies are needed on an expanded sample of people affected by chronic occupational radiation exposure.
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Affiliation(s)
| | - N. V. Litviakov
- Seversk Biophysical Research Center;
Cancer Research Institute of Tomsk National Research Medical Center (NRMC), Russian Academy of Sciences
| | | | | | | | - I. V. Milto
- Seversk Biophysical Research Center;
Siberian State Medical University
| | - R. M. Takhauov
- Seversk Biophysical Research Center;
Siberian State Medical University
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Haas-Neil S, Dvorkin-Gheva A, Forsythe P. Severe, but not moderate asthmatics share blood transcriptomic changes with post-traumatic stress disorder and depression. PLoS One 2022; 17:e0275864. [PMID: 36206293 PMCID: PMC9543640 DOI: 10.1371/journal.pone.0275864] [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: 05/04/2022] [Accepted: 09/23/2022] [Indexed: 11/24/2022] Open
Abstract
Asthma, an inflammatory disorder of the airways, is one of the most common chronic illnesses worldwide and is associated with significant morbidity. There is growing recognition of an association between asthma and mood disorders including post-traumatic stress disorder (PTSD) and major depressive disorder (MDD). Although there are several hypotheses regarding the relationship between asthma and mental health, there is little understanding of underlying mechanisms and causality. In the current study we utilized publicly available datasets of human blood mRNA collected from patients with severe and moderate asthma, MDD, and PTSD. We performed differential expression (DE) analysis and Gene Set Enrichment Analysis (GSEA) on diseased subjects against the healthy subjects from their respective datasets, compared the results between diseases, and validated DE genes and gene sets with 4 more independent datasets. Our analysis revealed that commonalities in blood transcriptomic changes were only found between the severe form of asthma and mood disorders. Gene expression commonly regulated in PTSD and severe asthma, included ORMDL3 a gene known to be associated with asthma risk and STX8, which is involved in TrkA signaling. We also identified several pathways commonly regulated to both MDD and severe asthma. This study reveals gene and pathway regulation that potentially drives the comorbidity between severe asthma, PTSD, and MDD and may serve as foci for future research aimed at gaining a better understanding of both the relationship between asthma and PTSD, and the pathophysiology of the individual disorders.
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Affiliation(s)
- Sandor Haas-Neil
- The Brain Body Institute, St. Joseph’s Hospital, McMaster University, Hamilton, Ontario, Canada
| | - Anna Dvorkin-Gheva
- McMaster Immunology Research Centre, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Paul Forsythe
- Alberta Respiratory Centre, Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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Lee EY, Mak ACY, Hu D, Sajuthi S, White MJ, Keys KL, Eckalbar W, Bonser L, Huntsman S, Urbanek C, Eng C, Jain D, Abecasis G, Kang HM, Germer S, Zody MC, Nickerson DA, Erle D, Ziv E, Rodriguez-Santana J, Seibold MA, Burchard EG. Whole-Genome Sequencing Identifies Novel Functional Loci Associated with Lung Function in Puerto Rican Youth. Am J Respir Crit Care Med 2020; 202:962-972. [PMID: 32459537 PMCID: PMC7528787 DOI: 10.1164/rccm.202002-0351oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/27/2020] [Indexed: 12/22/2022] Open
Abstract
Rationale: Puerto Ricans have the highest childhood asthma prevalence in the United States (23.6%); however, the etiology is uncertain.Objectives: In this study, we sought to uncover the genetic architecture of lung function in Puerto Rican youth with and without asthma who were recruited from the island (n = 836).Methods: We used admixture-mapping and whole-genome sequencing data to discover genomic regions associated with lung function. Functional roles of the prioritized candidate SNPs were examined with chromatin immunoprecipitation sequencing, RNA sequencing, and expression quantitative trait loci data.Measurements and Main Results: We discovered a genomic region at 1q32 that was significantly associated with a 0.12-L decrease in the lung volume of exhaled air (95% confidence interval, -0.17 to -0.07; P = 6.62 × 10-8) with each allele of African ancestry. Within this region, two SNPs were expression quantitative trait loci of TMEM9 in nasal airway epithelial cells and MROH3P in esophagus mucosa. The minor alleles of these SNPs were associated with significantly decreased lung function and decreased TMEM9 gene expression. Another admixture-mapping peak was observed on chromosome 5q35.1, indicating that each Native American ancestry allele was associated with a 0.15-L increase in lung function (95% confidence interval, 0.08-0.21; P = 5.03 × 10-6). The region-based association tests identified four suggestive windows that harbored candidate rare variants associated with lung function.Conclusions: We identified common and rare genetic variants that may play a critical role in lung function among Puerto Rican youth. We independently validated an inflammatory pathway that could potentially be used to develop more targeted treatments and interventions for patients with asthma.
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Affiliation(s)
- Eunice Y. Lee
- Department of Bioengineering and Therapeutic Sciences and
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Angel C. Y. Mak
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Satria Sajuthi
- Department of Pediatrics, Center for Genes, Environment, and Health, and
| | - Marquitta J. White
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Kevin L. Keys
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | - Luke Bonser
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Cydney Urbanek
- Department of Pediatrics, Center for Genes, Environment, and Health, and
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | - Gonçalo Abecasis
- Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
- Regeneron Pharmaceuticals, Tarrytown, New York
| | - Hyun M. Kang
- Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | | | | | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
- Northwest Genomics Center, Seattle, Washington
- Brotman Baty Institute, Seattle, Washington
| | - David Erle
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Elad Ziv
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | - Max A. Seibold
- Department of Pediatrics, Center for Genes, Environment, and Health, and
- Department of Pediatrics, National Jewish Health, Denver, Colorado
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado–Anschutz Medical Campus, Aurora, Colorado
| | - Esteban G. Burchard
- Department of Bioengineering and Therapeutic Sciences and
- Department of Medicine, University of California, San Francisco, San Francisco, California
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6
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Gignoux CR, Torgerson DG, Pino-Yanes M, Uricchio LH, Galanter J, Roth LA, Eng C, Hu D, Nguyen EA, Huntsman S, Mathias RA, Kumar R, Rodriguez-Santana J, Thakur N, Oh SS, McGarry M, Moreno-Estrada A, Sandoval K, Winkler CA, Seibold MA, Padhukasahasram B, Conti DV, Farber HJ, Avila P, Brigino-Buenaventura E, Lenoir M, Meade K, Serebrisky D, Borrell LN, Rodriguez-Cintron W, Thyne S, Joubert BR, Romieu I, Levin AM, Sienra-Monge JJ, Del Rio-Navarro BE, Gan W, Raby BA, Weiss ST, Bleecker E, Meyers DA, Martinez FJ, Gauderman WJ, Gilliland F, London SJ, Bustamante CD, Nicolae DL, Ober C, Sen S, Barnes K, Williams LK, Hernandez RD, Burchard EG. An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos. J Allergy Clin Immunol 2019; 143:957-969. [PMID: 30201514 PMCID: PMC6927816 DOI: 10.1016/j.jaci.2016.08.057] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 08/20/2016] [Accepted: 08/29/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Asthma is a common but complex disease with racial/ethnic differences in prevalence, morbidity, and response to therapies. OBJECTIVE We sought to perform an analysis of genetic ancestry to identify new loci that contribute to asthma susceptibility. METHODS We leveraged the mixed ancestry of 3902 Latinos and performed an admixture mapping meta-analysis for asthma susceptibility. We replicated associations in an independent study of 3774 Latinos, performed targeted sequencing for fine mapping, and tested for disease correlations with gene expression in the whole blood of more than 500 subjects from 3 racial/ethnic groups. RESULTS We identified a genome-wide significant admixture mapping peak at 18q21 in Latinos (P = 6.8 × 10-6), where Native American ancestry was associated with increased risk of asthma (odds ratio [OR], 1.20; 95% CI, 1.07-1.34; P = .002) and European ancestry was associated with protection (OR, 0.86; 95% CI, 0.77-0.96; P = .008). Our findings were replicated in an independent childhood asthma study in Latinos (P = 5.3 × 10-3, combined P = 2.6 × 10-7). Fine mapping of 18q21 in 1978 Latinos identified a significant association with multiple variants 5' of SMAD family member 2 (SMAD2) in Mexicans, whereas a single rare variant in the same window was the top association in Puerto Ricans. Low versus high SMAD2 blood expression was correlated with case status (13.4% lower expression; OR, 3.93; 95% CI, 2.12-7.28; P < .001). In addition, lower expression of SMAD2 was associated with more frequent exacerbations among Puerto Ricans with asthma. CONCLUSION Ancestry at 18q21 was significantly associated with asthma in Latinos and implicated multiple ancestry-informative noncoding variants upstream of SMAD2 with asthma susceptibility. Furthermore, decreased SMAD2 expression in blood was strongly associated with increased asthma risk and increased exacerbations.
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Affiliation(s)
- Christopher R Gignoux
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, Calif; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif.
| | - Dara G Torgerson
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Maria Pino-Yanes
- Department of Medicine, University of California, San Francisco, San Francisco, Calif; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Lawrence H Uricchio
- Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif
| | - Joshua Galanter
- Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif; Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Lindsey A Roth
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Elizabeth A Nguyen
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | | | - Rajesh Kumar
- Ann and Robert H. Lurie Children's Hospital of Chicago, Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | | | - Neeta Thakur
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Meghan McGarry
- Department of Pediatrics, University of California, San Francisco, San Francisco, Calif
| | | | - Karla Sandoval
- Department of Genetics, Stanford University, Palo Alto, Calif
| | - Cheryl A Winkler
- Molecular Genetics Epidemiology Section, Frederick National Laboratory for Cancer Research, Frederick, Md
| | - Max A Seibold
- Integrated Center for Genes, Environment, and Health, Department of Pediatrics, Division of Pulmonary and Critical Care Medicine, National Jewish Health, Denver, Colo
| | - Badri Padhukasahasram
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich
| | - David V Conti
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, Tex
| | - Pedro Avila
- Division of Allergy-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | | | | | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | | | - Luisa N Borrell
- Department of Health Sciences, Graduate Program in Public Health, Lehman College, City University of New York, Bronx, NY
| | | | - Shannon Thyne
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Bonnie R Joubert
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Isabelle Romieu
- Nutritional Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Albert M Levin
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich
| | - Juan-Jose Sienra-Monge
- Departmento de Alergia e Inmunologia, Clinica Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico
| | | | - Weiniu Gan
- Division of Lung Diseases, National Heart, Lung, and Blood Institute, Bethesda, Md
| | - Benjamin A Raby
- Department of Medicine, Harvard Medical School, Boston, Mass
| | - Scott T Weiss
- Department of Medicine, Harvard Medical School, Boston, Mass
| | - Eugene Bleecker
- Center for Genomics & Personalized Medicine Research, Wake Forest University, Winston-Salem, NC
| | - Deborah A Meyers
- Center for Genomics & Personalized Medicine Research, Wake Forest University, Winston-Salem, NC
| | | | - W James Gauderman
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | - Frank Gilliland
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | - Stephanie J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | | | - Dan L Nicolae
- Physical Sciences Division, Department of Statistics, University of Chicago, Chicago, Ill
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Saunak Sen
- Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, Tenn
| | - Kathleen Barnes
- Department of Medicine, Johns Hopkins University, Baltimore, Md
| | - L Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich; Department of Internal Medicine, Henry Ford Health System, Detroit, Mich
| | - Ryan D Hernandez
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, Calif; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif
| | - Esteban G Burchard
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, Calif; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif; Department of Medicine, University of California, San Francisco, San Francisco, Calif
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Tessier L, Côté O, Bienzle D. Sequence variant analysis of RNA sequences in severe equine asthma. PeerJ 2018; 6:e5759. [PMID: 30324028 PMCID: PMC6186407 DOI: 10.7717/peerj.5759] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 09/15/2018] [Indexed: 12/13/2022] Open
Abstract
Background Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. This study aimed to determine the utility of RNA-Seq to call gene sequence variants, and to identify sequence variants of potential relevance to the pathogenesis of asthma. Methods RNA-Seq data were generated from endobronchial biopsies collected from six asthmatic and seven non-asthmatic horses before and after challenge (26 samples total). Sequences were aligned to the equine genome with Spliced Transcripts Alignment to Reference software. Read preparation for sequence variant calling was performed with Picard tools and Genome Analysis Toolkit (GATK). Sequence variants were called and filtered using GATK and Ensembl Variant Effect Predictor (VEP) tools, and two RNA-Seq predicted sequence variants were investigated with both PCR and Sanger sequencing. Supplementary analysis of novel sequence variant selection with VEP was based on a score of <0.01 predicted with Sorting Intolerant from Tolerant software, missense nature, location within the protein coding sequence and presence in all asthmatic individuals. For select variants, effect on protein function was assessed with Polymorphism Phenotyping 2 and screening for non-acceptable polymorphism 2 software. Sequences were aligned and 3D protein structures predicted with Geneious software. Difference in allele frequency between the groups was assessed using a Pearson’s Chi-squared test with Yates’ continuity correction, and difference in genotype frequency was calculated using the Fisher’s exact test for count data. Results RNA-Seq variant calling and filtering correctly identified substitution variants in PACRG and RTTN. Sanger sequencing confirmed that the PACRG substitution was appropriately identified in all 26 samples while the RTTN substitution was identified correctly in 24 of 26 samples. These variants of uncertain significance had substitutions that were predicted to result in loss of function and to be non-neutral. Amino acid substitutions projected no change of hydrophobicity and isoelectric point in PACRG, and a change in both for RTTN. For PACRG, no difference in allele frequency between the two groups was detected but a higher proportion of asthmatic horses had the altered RTTN allele compared to non-asthmatic animals. Discussion RNA-Seq was sensitive and specific for calling gene sequence variants in this disease model. Even moderate coverage (<10–20 counts per million) yielded correct identification in 92% of samples, suggesting RNA-Seq may be suitable to detect sequence variants in low coverage samples. The impact of amino acid alterations in PACRG and RTTN proteins, and possible association of the sequence variants with asthma, is of uncertain significance, but their role in ciliary function may be of future interest.
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Affiliation(s)
- Laurence Tessier
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada.,BenchSci, Toronto, ON, Canada
| | - Olivier Côté
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada.,BioAssay Works, Ijamsville, MD, USA
| | - Dorothee Bienzle
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
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Chen JB, Zhang J, Hu HZ, Xue M, Jin YJ. Polymorphisms of TGFB1, TLE4 and MUC22 are associated with childhood asthma in Chinese population. Allergol Immunopathol (Madr) 2017; 45:432-438. [PMID: 28262390 DOI: 10.1016/j.aller.2016.10.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/31/2016] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To investigate whether the genetic variants of TGFB1, TLE4, MUC22 and IKZF3 are associated with the development of asthma in Chinese children. METHODS 572 adolescent asthma patients and 590 age-matched healthy controls were included in this study. A total of four SNPs were genotyped, including rs2241715 of TGFB1, rs2378383 of TLE4, rs2523924 of MUC22, and rs907092 of IKZF3. Allele frequencies of the patients and the control group were compared by the Chi-square test. The Student t test was used to analyse the relationship between genotypes and clinical feature of the patients. RESULTS Patients were found to have significantly different frequencies of allele A of rs2241715, allele G of rs2378383 and allele A of rs2523924 as compared with the controls (40.4% vs. 45.9%, p=0.01 for rs2241715; 17.2% vs. 13.4%, p=0.01 for rs2378383; 15.3% vs. 11.9%, p=0.02 for rs2523924). For patients with severe asthma, those with genotype AA/AG of rs2241715 had remarkably higher FEV1% as compared with those with genotype GG (59.1±4.3% vs. 55.4±3.7%, p<0.001). Moreover, those with genotype GG/GA of rs2378383 had remarkably lower FEV1% as compared with those with genotype AA (54.6±2.9% vs. 58.6±4.1%, p<0.001). CONCLUSIONS Genes TGFB1, TLE4 and MUC22 are associated with the risk of childhood asthma in Chinese population. Our results associating TGFB1 and TLE4 with clinical features of asthma suggest potential application of these parameters in the management of asthma children.
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Affiliation(s)
- J B Chen
- Department of Paediatrics, Jiangsu Taizhou People's Hospital, Taizhou, China
| | - J Zhang
- Department of Gastroenterology, Jiangsu Taizhou People's Hospital, Taizhou, China
| | - H Z Hu
- Department of Paediatrics, Jiangsu Taizhou People's Hospital, Taizhou, China
| | - M Xue
- Department of Paediatrics, Jiangsu Taizhou People's Hospital, Taizhou, China
| | - Y J Jin
- Department of Paediatrics, Jiangsu Taizhou People's Hospital, Taizhou, China.
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9
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Rahmani E, Shenhav L, Schweiger R, Yousefi P, Huen K, Eskenazi B, Eng C, Huntsman S, Hu D, Galanter J, Oh SS, Waldenberger M, Strauch K, Grallert H, Meitinger T, Gieger C, Holland N, Burchard EG, Zaitlen N, Halperin E. Genome-wide methylation data mirror ancestry information. Epigenetics Chromatin 2017; 10:1. [PMID: 28149326 PMCID: PMC5267476 DOI: 10.1186/s13072-016-0108-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/14/2016] [Indexed: 11/15/2022] Open
Abstract
Background Genetic data are known to harbor information about human demographics, and genotyping data are commonly used for capturing ancestry information by leveraging genome-wide differences between populations. In contrast, it is not clear to what extent population structure is captured by whole-genome DNA methylation data. Results We demonstrate, using three large-cohort 450K methylation array data sets, that ancestry information signal is mirrored in genome-wide DNA methylation data and that it can be further isolated more effectively by leveraging the correlation structure of CpGs with cis-located SNPs. Based on these insights, we propose a method, EPISTRUCTURE, for the inference of ancestry from methylation data, without the need for genotype data. Conclusions EPISTRUCTURE can be used to infer ancestry information of individuals based on their methylation data in the absence of corresponding genetic data. Although genetic data are often collected in epigenetic studies of large cohorts, these are typically not made publicly available, making the application of EPISTRUCTURE especially useful for anyone working on public data. Implementation of EPISTRUCTURE is available in GLINT, our recently released toolset for DNA methylation analysis at: http://glint-epigenetics.readthedocs.io. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0108-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elior Rahmani
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Liat Shenhav
- Department of Statistics, Tel Aviv University, Tel Aviv, Israel
| | - Regev Schweiger
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Paul Yousefi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA USA
| | - Karen Huen
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA USA
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Scott Huntsman
- Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Joshua Galanter
- Department of Medicine, University of California San Francisco, San Francisco, CA USA.,Department of Bioengineering and Therapeutic Science, University of California San Francisco, San Francisco, CA USA
| | - Sam S Oh
- Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany.,Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Nina Holland
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA USA.,Department of Bioengineering and Therapeutic Science, University of California San Francisco, San Francisco, CA USA
| | - Noah Zaitlen
- Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Eran Halperin
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA USA.,Department of Anesthesiology and Perioperative Medicine, University of California Los Angeles, Los Angeles, CA USA
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10
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Gupta J, Johansson E, Bernstein JA, Chakraborty R, Khurana Hershey GK, Rothenberg ME, Mersha TB. Resolving the etiology of atopic disorders by using genetic analysis of racial ancestry. J Allergy Clin Immunol 2016; 138:676-699. [PMID: 27297995 PMCID: PMC5014679 DOI: 10.1016/j.jaci.2016.02.045] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 02/09/2016] [Accepted: 02/25/2016] [Indexed: 12/23/2022]
Abstract
Atopic dermatitis (AD), food allergy, allergic rhinitis, and asthma are common atopic disorders of complex etiology. The frequently observed atopic march from early AD to asthma, allergic rhinitis, or both later in life and the extensive comorbidity of atopic disorders suggest common causal mechanisms in addition to distinct ones. Indeed, both disease-specific and shared genomic regions exist for atopic disorders. Their prevalence also varies among races; for example, AD and asthma have a higher prevalence in African Americans when compared with European Americans. Whether this disparity stems from true genetic or race-specific environmental risk factors or both is unknown. Thus far, the majority of the genetic studies on atopic diseases have used populations of European ancestry, limiting their generalizability. Large-cohort initiatives and new analytic methods, such as admixture mapping, are currently being used to address this knowledge gap. Here we discuss the unique and shared genetic risk factors for atopic disorders in the context of ancestry variations and the promise of high-throughput "-omics"-based systems biology approach in providing greater insight to deconstruct their genetic and nongenetic etiologies. Future research will also focus on deep phenotyping and genotyping of diverse racial ancestry, gene-environment, and gene-gene interactions.
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Affiliation(s)
- Jayanta Gupta
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Elisabet Johansson
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Jonathan A Bernstein
- Division of Immunology/Allergy Section, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Ranajit Chakraborty
- Center for Computational Genomics, Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Tex
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio.
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11
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Luo W, Obeidat M, Di Narzo AF, Chen R, Sin DD, Paré PD, Hao K. Airway Epithelial Expression Quantitative Trait Loci Reveal Genes Underlying Asthma and Other Airway Diseases. Am J Respir Cell Mol Biol 2016; 54:177-87. [PMID: 26102239 DOI: 10.1165/rcmb.2014-0381oc] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified loci that are robustly associated with asthma and related phenotypes; however, the molecular mechanisms underlying these associations need to be explored. The most relevant tissues to study the functional consequences of asthma are the airways. We used publically available data to derive expression quantitative trait loci (eQTLs) for human epithelial cells from small and large airways and applied the eQTLs in the interpretation of GWAS results of asthma and related phenotypes. For the small airways (n = 105), we discovered 660 eQTLs at a 10% false discovery rate (FDR), among which 315 eQTLs were not previously reported in a large-scale eQTL study of whole lung tissue. A large fraction of the identified eQTLs is supported by data from Encyclopedia of DNA Elements (ENCODE) showing that the eQTLs reside in regulatory elements (57.5 and 67.6% of cis- and trans-eQTLs, respectively). Published pulmonary GWAS hits were enriched as airway epithelial eQTLs (9.2-fold). Further, genes regulated by asthma GWAS loci in epithelium are significantly enriched in immune response pathways, such as IL-4 signaling (FDR, 5.2 × 10(-4)). The airway epithelial eQTLs described in this study are complementary to previously reported lung eQTLs and represent a powerful resource to link GWAS-associated variants to their regulatory function and thus elucidate the molecular mechanisms underlying asthma and airway-related conditions.
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Affiliation(s)
- Wei Luo
- 1 College of Computer Science and Technology, Huaqiao University, Xiamen, China.,2 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ma'en Obeidat
- 3 The University of British Columbia Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,4 Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Antonio Fabio Di Narzo
- 2 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,5 Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; and
| | - Rong Chen
- 2 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,5 Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; and
| | - Don D Sin
- 3 The University of British Columbia Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,4 Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter D Paré
- 3 The University of British Columbia Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,4 Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ke Hao
- 2 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,5 Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; and.,6 Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
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12
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Lavoie-Charland E, Bérubé JC, Boulet LP, Bossé Y. Asthma susceptibility variants are more strongly associated with clinically similar subgroups. J Asthma 2016; 53:907-13. [PMID: 27058054 DOI: 10.3109/02770903.2016.1165699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE Genome-wide association studies (GWAS) identified single nucleotide polymorphisms (SNPs) reproducibly associated with asthma. This study evaluated whether GWAS-nominated SNPs are more strongly associated with asthma patients sharing the same clinical characteristics in order to refine the role of recently identified genes. METHODS Analyses were performed in unrelated French Canadian subjects (566 cases and 416 controls) with data collected on lung function, blood cell counts, atopy, disease history and medication. Previously defined asthma subgroups were used for analysis: 1) older patients with low atopy and low lung function, 2) high atopy, 3) young non-smoking women and 4) high smoking history. Allele frequencies of 68 GWAS-nominated SNPs were compared between controls and cases or controls and subgroups of cases defined by cluster analysis. RESULTS Twelve GWAS-nominated SNPs demonstrated evidence of replication (p value < 0.05) for association with asthma. In phenotypically similar asthma patients, rs10197862, located in IL1RL1/IL18R1, was the most strongly associated SNP with the high atopy subgroup (p = 0.0009). SNPs located at the IL33 and the STARD3/PGAP3 loci were also associated with the high atopy subgroup. Two SNPs, rs1544791 (PDE4D) and rs3806932 (TSLP), were more strongly associated with the high smoking history subgroup than with asthma or any other subgroups. All 10 SNPs that replicated for asthma per se and within subgroups had lower p values in subgroups. Moreover, 12 SNPs were only replicated in a subgroup. CONCLUSION This study shows that the majority of GWAS-nominated SNPs are more strongly associated with homogeneous subgroups of asthma than broadly defined asthma.
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Affiliation(s)
| | | | - Louis-Philippe Boulet
- a Institut Universitaire de Cardiologie et de Pneumologie de Québec , Québec , Canada
| | - Yohan Bossé
- a Institut Universitaire de Cardiologie et de Pneumologie de Québec , Québec , Canada.,b Department of Molecular Medicine , Université Laval , Québec , Canada
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13
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Mersha TB. Mapping asthma-associated variants in admixed populations. Front Genet 2015; 6:292. [PMID: 26483834 PMCID: PMC4586512 DOI: 10.3389/fgene.2015.00292] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/03/2015] [Indexed: 12/19/2022] Open
Abstract
Admixed populations arise when two or more previously isolated populations interbreed. Mapping asthma susceptibility loci in an admixed population using admixture mapping (AM) involves screening the genome of individuals of mixed ancestry for chromosomal regions that have a higher frequency of alleles from a parental population with higher asthma risk as compared with parental population with lower asthma risk. AM takes advantage of the admixture created in populations of mixed ancestry to identify genomic regions where an association exists between genetic ancestry and asthma (in contrast to between the genotype of the marker and asthma). The theory behind AM is that chromosomal segments of affected individuals contain a significantly higher-than-average proportion of alleles from the high-risk parental population and thus are more likely to harbor disease-associated loci. Criteria to evaluate the applicability of AM as a gene mapping approach include: (1) the prevalence of the disease differences in ancestral populations from which the admixed population was formed; (2) a measurable difference in disease-causing alleles between the parental populations; (3) reduced linkage disequilibrium (LD) between unlinked loci across chromosomes and strong LD between neighboring loci; (4) a set of markers with noticeable allele-frequency differences between parental populations that contributes to the admixed population (single nucleotide polymorphisms (SNPs) are the markers of choice because they are abundant, stable, relatively cheap to genotype, and informative with regard to the LD structure of chromosomal segments); and (5) there is an understanding of the extent of segmental chromosomal admixtures and their interactions with environmental factors. Although genome-wide association studies have contributed greatly to our understanding of the genetic components of asthma, the large and increasing degree of admixture in populations across the world create many challenges for further efforts to map disease-causing genes. This review, summarizes the historical context of admixed populations and AM, and considers current opportunities to use AM to map asthma genes. In addition, we provide an overview of the potential limitations and future directions of AM in biomedical research, including joint admixture and association mapping for asthma and asthma-related disorders.
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Affiliation(s)
- Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati Cincinnati, OH, USA
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14
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Çalışkan M, Baker SW, Gilad Y, Ober C. Host genetic variation influences gene expression response to rhinovirus infection. PLoS Genet 2015; 11:e1005111. [PMID: 25874939 PMCID: PMC4395341 DOI: 10.1371/journal.pgen.1005111] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 03/01/2015] [Indexed: 01/17/2023] Open
Abstract
Rhinovirus (RV) is the most prevalent human respiratory virus and is responsible for at least half of all common colds. RV infections may result in a broad spectrum of effects that range from asymptomatic infections to severe lower respiratory illnesses. The basis for inter-individual variation in the response to RV infection is not well understood. In this study, we explored whether host genetic variation is associated with variation in gene expression response to RV infections between individuals. To do so, we obtained genome-wide genotype and gene expression data in uninfected and RV-infected peripheral blood mononuclear cells (PBMCs) from 98 individuals. We mapped local and distant genetic variation that is associated with inter-individual differences in gene expression levels (eQTLs) in both uninfected and RV-infected cells. We focused specifically on response eQTLs (reQTLs), namely, genetic associations with inter-individual variation in gene expression response to RV infection. We identified local reQTLs for 38 genes, including genes with known functions in viral response (UBA7, OAS1, IRF5) and genes that have been associated with immune and RV-related diseases (e.g., ITGA2, MSR1, GSTM3). The putative regulatory regions of genes with reQTLs were enriched for binding sites of virus-activated STAT2, highlighting the role of condition-specific transcription factors in genotype-by-environment interactions. Overall, we suggest that the 38 loci associated with inter-individual variation in gene expression response to RV-infection represent promising candidates for affecting immune and RV-related respiratory diseases.
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Affiliation(s)
- Minal Çalışkan
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Samuel W. Baker
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Yoav Gilad
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
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15
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Parker MM, Foreman MG, Abel HJ, Mathias RA, Hetmanski JB, Crapo JD, Silverman EK, Beaty TH. Admixture mapping identifies a quantitative trait locus associated with FEV1/FVC in the COPDGene Study. Genet Epidemiol 2014; 38:652-9. [PMID: 25112515 DOI: 10.1002/gepi.21847] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 06/30/2014] [Accepted: 07/03/2014] [Indexed: 12/31/2022]
Abstract
African Americans are admixed with genetic contributions from European and African ancestral populations. Admixture mapping leverages this information to map genes influencing differential disease risk across populations. We performed admixture and association mapping in 3,300 African American current or former smokers from the COPDGene Study. We analyzed estimated local ancestry and SNP genotype information to identify regions associated with FEV1 /FVC, the ratio of forced expiratory volume in one second to forced vital capacity, measured by spirometry performed after bronchodilator administration. Global African ancestry inversely associated with FEV1 /FVC (P = 0.035). Genome-wide admixture analysis, controlling for age, gender, body mass index, current smoking status, pack-years smoked, and four principal components summarizing the genetic background of African Americans in the COPDGene Study, identified a region on chromosome 12q14.1 associated with FEV1 /FVC (P = 2.1 × 10(-6) ) when regressed on local ancestry. Allelic association in this region of chromosome 12 identified an intronic variant in FAM19A2 (rs348644) as associated with FEV1 /FVC (P = 1.76 × 10(-6) ). By combining admixture and association mapping, a marker on chromosome 12q14.1 was identified as being associated with reduced FEV1 /FVC ratio among African Americans in the COPDGene Study.
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Affiliation(s)
- Margaret M Parker
- Department of Epidemiology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland, United States of America
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16
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Light N, Adoue V, Ge B, Chen SH, Kwan T, Pastinen T. Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping. Epigenetics 2014; 9:1238-51. [PMID: 25055051 DOI: 10.4161/epi.29920] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Allele-specific (AS) assessment of chromatin has the potential to elucidate specific cis-regulatory mechanisms, which are predicted to underlie the majority of the known genetic associations to complex disease. However, development of chromatin landscapes at allelic resolution has been challenging since sites of variable signal strength require substantial read depths not commonly applied in sequencing based approaches. In this study, we addressed this by performing parallel analyses of input DNA and chromatin immunoprecipitates (ChIP) on high-density Illumina genotyping arrays. Allele-specificity for the histone modifications H3K4me1, H3K4me3, H3K27ac, H3K27me3, and H3K36me3 was assessed using ChIP samples generated from 14 lymphoblast and 6 fibroblast cell lines. AS-ChIP SNPs were combined into domains and validated using high-confidence ChIP-seq sites. We observed characteristic patterns of allelic-imbalance for each histone-modification around allele-specifically expressed transcripts. Notably, we found H3K4me1 to be significantly anti-correlated with allelic expression (AE) at transcription start sites, indicating H3K4me1 allelic imbalance as a marker of AE. We also found that allelic chromatin domains exhibit population and cell-type specificity as well as heritability within trios. Finally, we observed that a subset of allelic chromatin domains is regulated by DNase I-sensitive quantitative trait loci and that these domains are significantly enriched for genome-wide association studies hits, with autoimmune disease associated SNPs specifically enriched in lymphoblasts. This study provides the first genome-wide maps of allelic-imbalance for five histone marks. Our results provide new insights into the role of chromatin in cis-regulation and highlight the need for high-depth sequencing in ChIP-seq studies along with the need to improve allele-specificity of ChIP-enrichment.
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Affiliation(s)
- Nicholas Light
- Department of Human Genetics; McGill University; Montréal, QC Canada; McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
| | - Véronique Adoue
- Institut National de la Santé et de la Recherche Médicale (Inserm); U1043; Toulouse, France
| | - Bing Ge
- McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
| | - Shu-Huang Chen
- McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
| | - Tony Kwan
- Department of Human Genetics; McGill University; Montréal, QC Canada; McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
| | - Tomi Pastinen
- Department of Human Genetics; McGill University; Montréal, QC Canada; McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
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17
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Ortega VE, Meyers DA. Pharmacogenetics: implications of race and ethnicity on defining genetic profiles for personalized medicine. J Allergy Clin Immunol 2014; 133:16-26. [PMID: 24369795 DOI: 10.1016/j.jaci.2013.10.040] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/22/2013] [Accepted: 10/23/2013] [Indexed: 01/06/2023]
Abstract
Pharmacogenetics is being used to develop personalized therapies specific to subjects from different ethnic or racial groups. To date, pharmacogenetic studies have been primarily performed in trial cohorts consisting of non-Hispanic white subjects of European descent. A "bottleneck" or collapse of genetic diversity associated with the first human colonization of Europe during the Upper Paleolithic period, followed by the recent mixing of African, European, and Native American ancestries, has resulted in different ethnic groups with varying degrees of genetic diversity. Differences in genetic ancestry might introduce genetic variation, which has the potential to alter the therapeutic efficacy of commonly used asthma therapies, such as β2-adrenergic receptor agonists (β-agonists). Pharmacogenetic studies of admixed ethnic groups have been limited to small candidate gene association studies, of which the best example is the gene coding for the receptor target of β-agonist therapy, the β2-adrenergic receptor (ADRB2). Large consortium-based sequencing studies are using next-generation whole-genome sequencing to provide a diverse genome map of different admixed populations, which can be used for future pharmacogenetic studies. These studies will include candidate gene studies, genome-wide association studies, and whole-genome admixture-based approaches that account for ancestral genetic structure, complex haplotypes, gene-gene interactions, and rare variants to detect and replicate novel pharmacogenetic loci.
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Affiliation(s)
- Victor E Ortega
- Center for Genomics and Personalized Medicine, Wake Forest School of Medicine, Winston-Salem, NC
| | - Deborah A Meyers
- Center for Genomics and Personalized Medicine, Wake Forest School of Medicine, Winston-Salem, NC.
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18
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Al-Daghri NM, Abd-Alrahman S, Draz H, Alkharfy K, Mohammed AK, Clerici MS, Alokail MS. Increased IL-4 mRNA expression and poly-aromatic hydrocarbon concentrations from children with asthma. BMC Pediatr 2014; 14:17. [PMID: 24450480 PMCID: PMC3912936 DOI: 10.1186/1471-2431-14-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 01/14/2014] [Indexed: 01/31/2023] Open
Abstract
Background Asthma is the most common chronic childhood disease. Imbalance of cytokines released from T helper cells and environmental factors, such as exposure to poly-aromatic hydrocarbon (PAH), play pivotal roles in the pathogenesis of asthma. The aim of this study was to compare the mRNA expression patterns of Interleukin (IL)-4, interferon (IFN)-γ and Acyl Co A long chain 3 (ACSL3) in peripheral blood leukocytes of children with and without asthma. To correlate the obtained mRNA data with serum IL-4, IFN-γ and PAH levels. Further, to determine the effect of in vivo exposure to PAH on mRNA expression of IL-4, IFN-γ and ACSL3 genes in a rat model. Methods A total of 170 children below 16 years (85 pediatric asthma patients and 85 matched healthy controls) were randomly selected from the Riyadh Cohort, Saudi Arabia. Gene expression analysis was performed using qRTPCR. Serum IL-4, IFN-γ and PAH were measured using LINCOplex (human multiplex immunoassay kit) and HPLC respectively. Results IL-4 mRNA expression was significantly increased (P < 0.05) in children with asthma compared to healthy control group whereas no differences were observed for either IFN-γ or ACSL3 mRNA. Similarly, serum IL- 4 and PAHs concentration was significantly higher as well in children with asthma in whom IFN-γ was also significantly lower. Results obtained in rats showed that exposure to the benzopyrene prototype PAH resulted in a 2.6 fold (P < 0.001) increased IL-4 mRNA expression in blood. Conclusion Peripheral blood IL-4 mRNA levels, serum concentration of this cytokine are elevated in children with asthma. Also, elevated levels of PAH were observed in children with asthma. Additionally, PAH administration in rodents resulted in an increased IL-4 mRNA which is supposed to partly mediate the inflammatory response noted in asthma.
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Affiliation(s)
- Nasser M Al-Daghri
- Biomarkers Research Program, Biochemistry Department, College of Science, King Saud University, PO Box, 2455, 11451 Riyadh, Saudi Arabia.
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19
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Shang Y, Das S, Rabold R, Sham JSK, Mitzner W, Tang WY. Epigenetic alterations by DNA methylation in house dust mite-induced airway hyperresponsiveness. Am J Respir Cell Mol Biol 2013; 49:279-87. [PMID: 23526225 DOI: 10.1165/rcmb.2012-0403oc] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Asthma is one of the most prevalent chronic lung diseases, affecting 235 million individuals around the world, with its related morbidity and mortality increasing steadily over the last 20 years. Exposure to the environmental allergen, house dust mite (HDM), results in airway inflammation with a variable degree of airway obstruction. Although there has been much experimental work in the past using HDM challenge models to understand mechanistic details in allergic inflammation and airway hyperresponsiveness (AHR), there has been no study on reprogramming of lung or airways mediated through epigenetic mechanisms in response to an acute HDM exposure. Male mice, 6 weeks of age, were administrated HDM extracts or saline at Days 1, 14, and 21. Exposure of mice to HDM extracts caused significant airway inflammation and increased AHR. These HDM-challenged mice also exhibited a change in global DNA methylation as compared with saline-exposed (control) mice. Next, by employing methylation-sensitive restriction fingerprinting, we identified a set of genes, showing aberrant methylation status, associated with the HDM-induced AHR. These candidate genes are known to be involved in cAMP signaling (pde4 d), Akt-signaling (akt1 s1), ion transport (tm6 sf1, pom121l2, and slc8a3), and fatty acid metabolism (acsl3). Slc8a3 and acsl3 were down-regulated, whereas pde4 d, akt1 s1, tm6 sf1, and pom121l2 were up-regulated in the mice exposed to HDM. Hence, our results suggest that HDM exposure induces a series of aberrant methylated genes that are potentially important for the development of allergic AHR.
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Affiliation(s)
- Yan Shang
- Department of Respiratory Diseases, Changhai Hospital, Second Military Medical University, Shanghai, China
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20
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Huen K, Harley K, Beckman K, Eskenazi B, Holland N. Associations of PON1 and genetic ancestry with obesity in early childhood. PLoS One 2013; 8:e62565. [PMID: 23658746 PMCID: PMC3643931 DOI: 10.1371/journal.pone.0062565] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 03/22/2013] [Indexed: 12/03/2022] Open
Abstract
Obesity in children has become an epidemic in the U.S. and is particularly prominent in minority populations such as Mexican-Americans. In addition to physical activity and diet, genetics also plays a role in obesity etiology. A few studies in adults and adolescents suggest a link between obesity and paraoxonase 1 (PON1), a multifunctional enzyme that can metabolize organophosphate pesticides and also has antioxidant properties. We determined PON1192 genotype and arylesterase levels (ARYase, measure of PON1 enzyme quantity), to characterize the relationship between PON1 and obesity in young Mexican-American children (n = 373) living in an agricultural community in California. Since PON1 polymorphisms and obesity both vary between ethnic groups, we estimated proportional genetic ancestry using 106 ancestral informative markers (AIMs). Among children, PON1192 allele frequencies were 0.5 for both alleles, and the prevalence of obesity was high (15% and 33% at ages two and five, respectively). The average proportion of European, African, and Native American ancestry was 0.40, 0.09, and 0.51, yet there was wide inter-individual variation. We found a significantly higher odds of obesity (9.3 and 2.5- fold) in PON1192QQ children compared to PON1192RR children at ages two and five, respectively. Similar relationships were seen with BMI Z-scores at age two and waist circumference at age five. After adjusting for genetic ancestry in models of PON1 and BMI Z-score, effect estimates for PON1192 genotype changed 15% and 9% among two and five year old children, respectively, providing evidence of genetic confounding by population stratification. However even after adjustment for genetic ancestry, the trend of increased BMI Z-scores with increased number of PON1192 Q alleles remained. Our findings suggest that PON1 may play a role in obesity independent of genetic ancestry and that studies of PON1 and health outcomes, especially in admixed populations, should account for differences due to population stratification.
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Affiliation(s)
- Karen Huen
- Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America.
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21
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Vergara C, Murray T, Rafaels N, Lewis R, Campbell M, Foster C, Gao L, Faruque M, Oliveira RR, Carvalho E, Araujo MI, Cruz AA, Watson H, Mercado D, Knight-Madden J, Ruczinski I, Dunston G, Ford J, Caraballo L, Beaty TH, Mathias RA, Barnes KC. African ancestry is a risk factor for asthma and high total IgE levels in African admixed populations. Genet Epidemiol 2013; 37:393-401. [PMID: 23554133 DOI: 10.1002/gepi.21702] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 11/21/2012] [Accepted: 11/22/2012] [Indexed: 12/16/2022]
Abstract
Characterization of genetic admixture of populations in the Americas and the Caribbean is of interest for anthropological, epidemiological, and historical reasons. Asthma has a higher prevalence and is more severe in populations with a high African component. Association of African ancestry with asthma has been demonstrated. We estimated admixture proportions of samples from six trihybrid populations of African descent and determined the relationship between African ancestry and asthma and total serum IgE levels (tIgE). We genotyped 237 ancestry informative markers in asthmatics and nonasthmatic controls from Barbados (190/277), Jamaica (177/529), Brazil (40/220), Colombia (508/625), African Americans from New York (207/171), and African Americans from Baltimore/Washington, D.C. (625/757). We estimated individual ancestries and evaluated genetic stratification using Structure and principal component analysis. Association of African ancestry and asthma and tIgE was evaluated by regression analysis. Mean ± SD African ancestry ranged from 0.76 ± 0.10 among Barbadians to 0.33 ± 0.13 in Colombians. The European component varied from 0.14 ± 0.05 among Jamaicans and Barbadians to 0.26 ± 0.08 among Colombians. African ancestry was associated with risk for asthma in Colombians (odds ratio (OR) = 4.5, P = 0.001) Brazilians (OR = 136.5, P = 0.003), and African Americans of New York (OR: 4.7; P = 0.040). African ancestry was also associated with higher tIgE levels among Colombians (β = 1.3, P = 0.04), Barbadians (β = 3.8, P = 0.03), and Brazilians (β = 1.6, P = 0.03). Our findings indicate that African ancestry can account for, at least in part, the association between asthma and its associated trait, tIgE levels.
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Affiliation(s)
- Candelaria Vergara
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University (JHU), Baltimore, MD, USA
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22
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Quanjer PH, Stanojevic S, Cole TJ, Baur X, Hall GL, Culver BH, Enright PL, Hankinson JL, Ip MSM, Zheng J, Stocks J. Multi-ethnic reference values for spirometry for the 3-95-yr age range: the global lung function 2012 equations. Eur Respir J 2012; 40:1324-43. [PMID: 22743675 PMCID: PMC3786581 DOI: 10.1183/09031936.00080312] [Citation(s) in RCA: 3809] [Impact Index Per Article: 317.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The aim of the Task Force was to derive continuous prediction equations and their lower limits of normal for spirometric indices, which are applicable globally. Over 160,000 data points from 72 centres in 33 countries were shared with the European Respiratory Society Global Lung Function Initiative. Eliminating data that could not be used (mostly missing ethnic group, some outliers) left 97,759 records of healthy nonsmokers (55.3% females) aged 2.5-95 yrs. Lung function data were collated and prediction equations derived using the LMS method, which allows simultaneous modelling of the mean (mu), the coefficient of variation (sigma) and skewness (lambda) of a distribution family. After discarding 23,572 records, mostly because they could not be combined with other ethnic or geographic groups, reference equations were derived for healthy individuals aged 3-95 yrs for Caucasians (n=57,395), African-Americans (n=3,545), and North (n=4,992) and South East Asians (n=8,255). Forced expiratory value in 1 s (FEV(1)) and forced vital capacity (FVC) between ethnic groups differed proportionally from that in Caucasians, such that FEV(1)/FVC remained virtually independent of ethnic group. For individuals not represented by these four groups, or of mixed ethnic origins, a composite equation taken as the average of the above equations is provided to facilitate interpretation until a more appropriate solution is developed. Spirometric prediction equations for the 3-95-age range are now available that include appropriate age-dependent lower limits of normal. They can be applied globally to different ethnic groups. Additional data from the Indian subcontinent and Arabic, Polynesian and Latin American countries, as well as Africa will further improve these equations in the future.
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Affiliation(s)
- Philip H Quanjer
- Dept of Pulmonary Diseases and Dept of Paediatrics, Erasmus Medical Centre, Erasmus University, Rotterdam, the Netherlands
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23
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Hao K, Bossé Y, Nickle DC, Paré PD, Postma DS, Laviolette M, Sandford A, Hackett TL, Daley D, Hogg JC, Elliott WM, Couture C, Lamontagne M, Brandsma CA, van den Berge M, Koppelman G, Reicin AS, Nicholson DW, Malkov V, Derry JM, Suver C, Tsou JA, Kulkarni A, Zhang C, Vessey R, Opiteck GJ, Curtis SP, Timens W, Sin DD. Lung eQTLs to help reveal the molecular underpinnings of asthma. PLoS Genet 2012; 8:e1003029. [PMID: 23209423 PMCID: PMC3510026 DOI: 10.1371/journal.pgen.1003029] [Citation(s) in RCA: 222] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 08/14/2012] [Indexed: 12/26/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified loci reproducibly associated with pulmonary diseases; however, the molecular mechanism underlying these associations are largely unknown. The objectives of this study were to discover genetic variants affecting gene expression in human lung tissue, to refine susceptibility loci for asthma identified in GWAS studies, and to use the genetics of gene expression and network analyses to find key molecular drivers of asthma. We performed a genome-wide search for expression quantitative trait loci (eQTL) in 1,111 human lung samples. The lung eQTL dataset was then used to inform asthma genetic studies reported in the literature. The top ranked lung eQTLs were integrated with the GWAS on asthma reported by the GABRIEL consortium to generate a Bayesian gene expression network for discovery of novel molecular pathways underpinning asthma. We detected 17,178 cis- and 593 trans- lung eQTLs, which can be used to explore the functional consequences of loci associated with lung diseases and traits. Some strong eQTLs are also asthma susceptibility loci. For example, rs3859192 on chr17q21 is robustly associated with the mRNA levels of GSDMA (P = 3.55×10−151). The genetic-gene expression network identified the SOCS3 pathway as one of the key drivers of asthma. The eQTLs and gene networks identified in this study are powerful tools for elucidating the causal mechanisms underlying pulmonary disease. This data resource offers much-needed support to pinpoint the causal genes and characterize the molecular function of gene variants associated with lung diseases. Recent genome-wide association studies (GWAS) have identified genetic variants associated with lung diseases. The challenge now is to find the causal genes in GWAS–nominated chromosomal regions and to characterize the molecular function of disease-associated genetic variants. In this paper, we describe an international effort to systematically capture the genetic architecture of gene expression regulation in human lung. By studying lung specimens from 1,111 individuals of European ancestry, we found a large number of genetic variants affecting gene expression in the lung, or lung expression quantitative trait loci (eQTL). These lung eQTLs will serve as an important resource to aid in the understanding of the molecular underpinnings of lung biology and its disruption in disease. To demonstrate the utility of this lung eQTL dataset, we integrated our data with previous genetic studies on asthma. Through integrative techniques, we identified causal variants and genes in GWAS–nominated loci and found key molecular drivers for asthma. We feel that sharing our lung eQTLs dataset with the scientific community will leverage the impact of previous large-scale GWAS on lung diseases and function by providing much needed functional information to understand the molecular changes introduced by the susceptibility genetic variants.
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Affiliation(s)
- Ke Hao
- Merck Research Laboratories, Boston, Massachusetts, United States of America
- Merck, Rahway, New Jersey, United States of America
- Genetics, Rosetta Inpharmatics, Merck, Seattle, Washington, United States of America
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec City, Canada
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec City, Canada
| | - David C. Nickle
- Merck Research Laboratories, Boston, Massachusetts, United States of America
- Merck, Rahway, New Jersey, United States of America
- Genetics, Rosetta Inpharmatics, Merck, Seattle, Washington, United States of America
- * E-mail:
| | - Peter D. Paré
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Dirkje S. Postma
- Department of Pulmonology, University Medical Center Groningen, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Michel Laviolette
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec City, Canada
| | - Andrew Sandford
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Tillie L. Hackett
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
| | - Denise Daley
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - James C. Hogg
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - W. Mark Elliott
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
| | - Christian Couture
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec City, Canada
| | - Maxime Lamontagne
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec City, Canada
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University Medical Center Groningen, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Department of Pulmonology, University Medical Center Groningen, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Gerard Koppelman
- Department of Pediatric Pulmonology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | | | | | - Christine Suver
- Sage Bionetworks, Seattle, Washington, United States of America
| | | | | | | | | | | | | | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Don D. Sin
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, Canada
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Myers RA, Himes BE, Gignoux CR, Yang JJ, Gauderman WJ, Rebordosa C, Xie J, Torgerson DG, Levin AM, Baurley J, Graves PE, Mathias RA, Romieu I, Roth LA, Conti D, Avila L, Eng C, Vora H, LeNoir MA, Soto-Quiros M, Liu J, Celedón JC, Galanter JM, Farber HJ, Kumar R, Avila PC, Meade K, Serebrisky D, Thyne S, Rodriguez-Cintron W, Rodriguez-Santana JR, Borrell LN, Lemanske RF, Bleecker ER, Meyers DA, London SJ, Barnes KC, Raby BA, Martinez FD, Gilliland FD, Williams LK, Burchard EG, Weiss ST, Nicolae DL, Ober C. Further replication studies of the EVE Consortium meta-analysis identifies 2 asthma risk loci in European Americans. J Allergy Clin Immunol 2012; 130:1294-301. [PMID: 23040885 DOI: 10.1016/j.jaci.2012.07.054] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 07/27/2012] [Accepted: 07/31/2012] [Indexed: 11/26/2022]
Abstract
BACKGROUND Genome-wide association studies of asthma have implicated many genetic risk factors, with well-replicated associations at approximately 10 loci that account for only a small proportion of the genetic risk. OBJECTIVES We aimed to identify additional asthma risk loci by performing an extensive replication study of the results from the EVE Consortium meta-analysis. METHODS We selected 3186 single nucleotide polymorphisms for replication based on the P values from the EVE Consortium meta-analysis. These single nucleotide polymorphisms were genotyped in ethnically diverse replication samples from 9 different studies, totaling 7202 cases, 6426 controls, and 507 case-parent trios. Association analyses were conducted within each participating study, and the resulting test statistics were combined in a meta-analysis. RESULTS Two novel associations were replicated in European Americans: rs1061477 in the KLK3 gene on chromosome 19 (combined odds ratio = 1.18; 95% CI, 1.10-1.25) and rs9570077 (combined odds ratio =1.20; 95% CI, 1.12-1.29) on chromosome 13q21. We could not replicate any additional associations in the African Americans or Latinos. CONCLUSIONS This extended replication study identified 2 additional asthma risk loci in populations of European descent. The absence of additional loci for African Americans and Latinos highlights the difficulty in replicating associations in admixed populations.
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Affiliation(s)
- Rachel A Myers
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
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Nguyen EA, Burchard EG. Asthma Research for All of the United States. PEDIATRIC ALLERGY IMMUNOLOGY AND PULMONOLOGY 2012; 25:128-131. [PMID: 22970422 DOI: 10.1089/ped.2012.0173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/12/2012] [Indexed: 01/08/2023]
Abstract
Asthma disproportionally affects different ethnic/racial groups, with Puerto Ricans and African Americans suffering the highest asthma prevalence and morbidity, Mexicans the lowest, and non-Hispanic whites in between. Genome-wide association studies of asthma have found both shared and race/ethnic-specific genetic risks factors for asthma. However, the majority of genetic asthma research is performed in populations of European descent, which limits the benefits of genetic research to European populations. It is important to biomedical and clinical research to include more diverse and underrepresented populations. The rich genetic diversity of all populations can be leveraged to scientific advantage. For example, admixture mapping provides a more powerful approach than traditional genome-wide allelic association studies in discovering genetic associations for complex diseases. By being more inclusive we can achieve a better understanding of the genetics of asthma, address health disparities, and ensure that scientific advances will benefit populations worldwide.
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26
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Tang WY, Levin L, Talaska G, Cheung YY, Herbstman J, Tang D, Miller RL, Perera F, Ho SM. Maternal exposure to polycyclic aromatic hydrocarbons and 5'-CpG methylation of interferon-γ in cord white blood cells. ENVIRONMENTAL HEALTH PERSPECTIVES 2012; 120:1195-200. [PMID: 22562770 PMCID: PMC3440069 DOI: 10.1289/ehp.1103744] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 05/04/2012] [Indexed: 05/17/2023]
Abstract
BACKGROUND Maternal factors are implicated in the onset of childhood asthma. Differentiation of naïve CD4+ T lymphocytes into pro-allergic T-helper 2 cells induces interleukin (IL)4 expression and inhibits interferon (IFN)γ expression accompanied by concordant methylation changes in the promoters of these genes. However, it has yet to be established whether maternal exposure to polycyclic aromatic hydrocarbons (PAHs) can alter these gene promoters epigenetically during fetal development. OBJECTIVES In this study we sought to elucidate the relationship between maternal PAH exposure and promoter methylation status of IFNγ and IL4. METHODS We assessed the effects of benzo[a]pyrene (BaP), a representative airborne PAH, on the methylation status of the IFNγ and IL4 promoters in Jurkat cells and two lung adenocarcinoma cell lines, and on gene expression. In addition, we evaluated methylation status of the IFNγ promoter in cord white blood cells from 53 participants in the Columbia Center for Children's Environmental Health cohort. Maternal PAH exposure was estimated by personal air monitoring during pregnancy. RESULTS In vitro exposure of the cell models to low, noncytotoxic doses (0.1 and 1 nM) of BaP elicited increased promoter hypermethylation and reduced expression of IFNγ, but not IL4. IFNγ promoter methylation in cord white blood cells was associated with maternal PAH exposure in the cohort study subsample. CONCLUSION Consistent with the results for the cell lines, maternal exposure to PAHs was associated with hypermethylation of IFNγ in cord blood DNA from cohort children. These findings support a potential role of epigenetics in fetal reprogramming by PAH-induced environmental diseases.
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Affiliation(s)
- Wan-yee Tang
- Division of Environmental Genetics and Molecular Toxicology, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
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27
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Torgerson DG, Gignoux CR, Galanter JM, Drake KA, Roth LA, Eng C, Huntsman S, Torres R, Avila PC, Chapela R, Ford JG, Rodríguez-Santana JR, Rodríguez-Cintrón W, Hernandez RD, Burchard EG. Case-control admixture mapping in Latino populations enriches for known asthma-associated genes. J Allergy Clin Immunol 2012; 130:76-82.e12. [PMID: 22502797 PMCID: PMC3593143 DOI: 10.1016/j.jaci.2012.02.040] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Revised: 12/20/2011] [Accepted: 02/02/2012] [Indexed: 12/22/2022]
Abstract
BACKGROUND Polymorphisms in more than 100 genes have been associated with asthma susceptibility, yet much of the heritability remains to be explained. Asthma disproportionately affects different racial and ethnic groups in the United States, suggesting that admixture mapping is a useful strategy to identify novel asthma-associated loci. OBJECTIVE We sought to identify novel asthma-associated loci in Latino populations using case-control admixture mapping. METHODS We performed genome-wide admixture mapping by comparing levels of local Native American, European, and African ancestry between children with asthma and nonasthmatic control subjects in Puerto Rican and Mexican populations. Within candidate peaks, we performed allelic tests of association, controlling for differences in local ancestry. RESULTS Between the 2 populations, we identified a total of 62 admixture mapping peaks at a P value of less than 10(-3) that were significantly enriched for previously identified asthma-associated genes (P= .0051). One of the peaks was statistically significant based on 100 permutations in the Mexican sample (6q15); however, it was not significant in Puerto Rican subjects. Another peak was identified at nominal significance in both populations (8q12); however, the association was observed with different ancestries. CONCLUSION Case-control admixture mapping is a promising strategy for identifying novel asthma-associated loci in Latino populations and implicates genetic variation at 6q15 and 8q12 regions with asthma susceptibility. This approach might be useful for identifying regions that contribute to both shared and population-specific differences in asthma susceptibility.
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Affiliation(s)
- Dara G Torgerson
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA.
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28
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Torgerson DG, Capurso D, Ampleford EJ, Li X, Moore WC, Gignoux CR, Hu D, Eng C, Mathias RA, Busse WW, Castro M, Erzurum SC, Fitzpatrick AM, Gaston B, Israel E, Jarjour NN, Teague WG, Wenzel SE, Rodríguez-Santana JR, Rodríguez-Cintrón W, Avila PC, Ford JG, Barnes KC, Burchard EG, Howard TD, Bleecker ER, Meyers DA, Cox NJ, Ober C, Nicolae DL. Genome-wide ancestry association testing identifies a common European variant on 6q14.1 as a risk factor for asthma in African American subjects. J Allergy Clin Immunol 2012; 130:622-629.e9. [PMID: 22607992 DOI: 10.1016/j.jaci.2012.03.045] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 02/22/2012] [Accepted: 03/06/2012] [Indexed: 12/14/2022]
Abstract
BACKGROUND Genetic variants that contribute to asthma susceptibility might be present at varying frequencies in different populations, which is an important consideration and advantage for performing genetic association studies in admixed populations. OBJECTIVE We sought to identify asthma-associated loci in African American subjects. METHODS We compared local African and European ancestry estimated from dense single nucleotide polymorphism genotype data in African American adults with asthma and nonasthmatic control subjects. Allelic tests of association were performed within the candidate regions identified, correcting for local European admixture. RESULTS We identified a significant ancestry association peak on chromosome 6q. Allelic tests for association within this region identified a single nucleotide polymorphism (rs1361549) on 6q14.1 that was associated with asthma exclusively in African American subjects with local European admixture (odds ratio, 2.2). The risk allele is common in Europe (42% in the HapMap population of Utah residents with Northern and Western European ancestry from the Centre d'Etude du Polymorphisme Humain collection) but absent in West Africa (0% in the HapMap population of Yorubans in Ibadan, Nigeria), suggesting the allele is present in African American subjects because of recent European admixture. We replicated our findings in Puerto Rican subjects and similarly found that the signal of association is largely specific to subjects who are heterozygous for African and non-African ancestry at 6q14.1. However, we found no evidence for association in European American or Puerto Rican subjects in the absence of local African ancestry, suggesting that the association with asthma at rs1361549 is due to an environmental or genetic interaction. CONCLUSION We identified a novel asthma-associated locus that is relevant to admixed populations with African ancestry and highlight the importance of considering local ancestry in genetic association studies of admixed populations.
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Affiliation(s)
- Dara G Torgerson
- Department of Human Genetics, University of Chicago, Chicago, Il 60637, USA
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Avena S, Via M, Ziv E, Pérez-Stable EJ, Gignoux CR, Dejean C, Huntsman S, Torres-Mejía G, Dutil J, Matta JL, Beckman K, Burchard EG, Parolin ML, Goicoechea A, Acreche N, Boquet M, Ríos Part MDC, Fernández V, Rey J, Stern MC, Carnese RF, Fejerman L. Heterogeneity in genetic admixture across different regions of Argentina. PLoS One 2012; 7:e34695. [PMID: 22506044 PMCID: PMC3323559 DOI: 10.1371/journal.pone.0034695] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 03/05/2012] [Indexed: 01/15/2023] Open
Abstract
The population of Argentina is the result of the intermixing between several groups, including Indigenous American, European and African populations. Despite the commonly held idea that the population of Argentina is of mostly European origin, multiple studies have shown that this process of admixture had an impact in the entire Argentine population. In the present study we characterized the distribution of Indigenous American, European and African ancestry among individuals from different regions of Argentina and evaluated the level of discrepancy between self-reported grandparental origin and genetic ancestry estimates. A set of 99 autosomal ancestry informative markers (AIMs) was genotyped in a sample of 441 Argentine individuals to estimate genetic ancestry. We used non-parametric tests to evaluate statistical significance. The average ancestry for the Argentine sample overall was 65% European (95%CI: 63-68%), 31% Indigenous American (28-33%) and 4% African (3-4%). We observed statistically significant differences in European ancestry across Argentine regions [Buenos Aires province (BA) 76%, 95%CI: 73-79%; Northeast (NEA) 54%, 95%CI: 49-58%; Northwest (NWA) 33%, 95%CI: 21-41%; South 54%, 95%CI: 49-59%; p<0.0001] as well as between the capital and immediate suburbs of Buenos Aires city compared to more distant suburbs [80% (95%CI: 75-86%) versus 68% (95%CI: 58-77%), p = 0.01]. European ancestry among individuals that declared all grandparents born in Europe was 91% (95%CI: 88-94%) compared to 54% (95%CI: 51-57%) among those with no European grandparents (p<0.001). Our results demonstrate the range of variation in genetic ancestry among Argentine individuals from different regions in the country, highlighting the importance of taking this variation into account in genetic association and admixture mapping studies in this population.
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Affiliation(s)
- Sergio Avena
- Departamento de Antropología, University of Buenos Aires, Buenos Aires, Argentina
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnósticos, Universidad Maimónides, Buenos Aires, Provincia de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires, Argentina
| | - Marc Via
- Division of Pulmonary and Critical Care, University of California San Francisco, San Francisco, California, United States of America
- Unit of Anthropology, Department of Animal Biology, Universitat de Barcelona, Barcelona, Spain
| | - Elad Ziv
- Division of General Internal Medicine, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | - Eliseo J. Pérez-Stable
- Division of General Internal Medicine, University of California San Francisco, San Francisco, California, United States of America
- Medical Effectiveness Research Center for Diverse Populations, University of California San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | - Christopher R. Gignoux
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Cristina Dejean
- Departamento de Antropología, University of Buenos Aires, Buenos Aires, Argentina
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnósticos, Universidad Maimónides, Buenos Aires, Provincia de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires, Argentina
| | - Scott Huntsman
- Division of General Internal Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Gabriela Torres-Mejía
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Julie Dutil
- Department of Biochemistry, Ponce School of Medicine and Health Sciences, Ponce, Puerto Rico
| | - Jaime L. Matta
- Department of Physiology and Pharmacology, Ponce School of Medicine and Health Sciences, Ponce, Puerto Rico
| | - Kenneth Beckman
- Deptartment of Genetics, Cell Biology and Developmental Biology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Esteban González Burchard
- Division of Pulmonary and Critical Care, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - María Laura Parolin
- Departamento de Antropología, University of Buenos Aires, Buenos Aires, Argentina
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnósticos, Universidad Maimónides, Buenos Aires, Provincia de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires, Argentina
| | - Alicia Goicoechea
- Departamento de Antropología, University of Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires, Argentina
| | - Noemí Acreche
- Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
| | - Mariel Boquet
- Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia, Esquel, Chubut, Argentina
| | | | - Vanesa Fernández
- Servicio de Hemoterapia Hospital Penna de Bahía Blanca, Bahía Blanca, Buenos Aires, Argentina
| | - Jorge Rey
- Servicio de Hemoterapia Hospital de Clínicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariana C. Stern
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Raúl F. Carnese
- Departamento de Antropología, University of Buenos Aires, Buenos Aires, Argentina
| | - Laura Fejerman
- Division of General Internal Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Weiss ST, Silverman EK. Pro: Genome-wide association studies (GWAS) in asthma. Am J Respir Crit Care Med 2012; 184:631-3. [PMID: 21920925 DOI: 10.1164/rccm.201103-0485ed] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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31
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Torgerson DG, Ampleford EJ, Chiu GY, Gauderman WJ, Gignoux CR, Graves PE, Himes BE, Levin AM, Mathias RA, Hancock DB, Baurley JW, Eng C, Stern DA, Celedón JC, Rafaels N, Capurso D, Conti DV, Roth LA, Soto-Quiros M, Togias A, Li X, Myers RA, Romieu I, Van Den Berg DJ, Hu D, Hansel NN, Hernandez RD, Israel E, Salam MT, Galanter J, Avila PC, Avila L, Rodriquez-Santana JR, Chapela R, Rodriguez-Cintron W, Diette GB, Adkinson NF, Abel RA, Ross KD, Shi M, Faruque MU, Dunston GM, Watson HR, Mantese VJ, Ezurum SC, Liang L, Ruczinski I, Ford JG, Huntsman S, Chung KF, Vora H, Li X, Calhoun WJ, Castro M, Sienra-Monge JJ, del Rio-Navarro B, Deichmann KA, Heinzmann A, Wenzel SE, Busse WW, Gern JE, Lemanske RF, Beaty TH, Bleecker ER, Raby BA, Meyers DA, London SJ, Gilliland FD, Burchard EG, Martinez FD, Weiss ST, Williams LK, Barnes KC, Ober C, Nicolae DL. Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations. Nat Genet 2011; 43:887-92. [PMID: 21804549 PMCID: PMC3445408 DOI: 10.1038/ng.888] [Citation(s) in RCA: 619] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 06/16/2011] [Indexed: 11/09/2022]
Abstract
Asthma is a common disease with a complex risk architecture including both genetic and environmental factors. We performed a meta-analysis of North American genome-wide association studies of asthma in 5,416 individuals with asthma (cases) including individuals of European American, African American or African Caribbean, and Latino ancestry, with replication in an additional 12,649 individuals from the same ethnic groups. We identified five susceptibility loci. Four were at previously reported loci on 17q21, near IL1RL1, TSLP and IL33, but we report for the first time, to our knowledge, that these loci are associated with asthma risk in three ethnic groups. In addition, we identified a new asthma susceptibility locus at PYHIN1, with the association being specific to individuals of African descent (P = 3.9 × 10(-9)). These results suggest that some asthma susceptibility loci are robust to differences in ancestry when sufficiently large samples sizes are investigated, and that ancestry-specific associations also contribute to the complex genetic architecture of asthma.
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Affiliation(s)
- Dara G Torgerson
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
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The use of race, ethnicity and ancestry in human genetic research. THE HUGO JOURNAL 2011; 5:47-63. [PMID: 22276086 PMCID: PMC3237839 DOI: 10.1007/s11568-011-9154-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 04/27/2011] [Accepted: 06/17/2011] [Indexed: 01/04/2023]
Abstract
Post-Human Genome Project progress has enabled a new wave of population genetic research, and intensified controversy over the use of race/ethnicity in this work. At the same time, the development of methods for inferring genetic ancestry offers more empirical means of assigning group labels. Here, we provide a systematic analysis of the use of race/ethnicity and ancestry in current genetic research. We base our analysis on key published recommendations for the use and reporting of race/ethnicity which advise that researchers: explain why the terms/categories were used and how they were measured, carefully define them, and apply them consistently. We studied 170 population genetic research articles from high impact journals, published 2008–2009. A comparative perspective was obtained by aligning study metrics with similar research from articles published 2001–2004. Our analysis indicates a marked improvement in compliance with some of the recommendations/guidelines for the use of race/ethnicity over time, while showing that important shortfalls still remain: no article using ‘race’, ‘ethnicity’ or ‘ancestry’ defined or discussed the meaning of these concepts in context; a third of articles still do not provide a rationale for their use, with those using ‘ancestry’ being the least likely to do so. Further, no article discussed potential socio-ethical implications of the reported research. As such, there remains a clear imperative for highlighting the importance of consistent and comprehensive reporting on human populations to the genetics/genomics community globally, to generate explicit guidelines for the uses of ancestry and genetic ancestry, and importantly, to ensure that guidelines are followed.
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Zhang Y, Lin X, Desrosiers M, Zhang W, Meng N, Zhao L, Han D, Zhang L. Association pattern of interleukin-1 receptor-associated kinase-4 gene polymorphisms with allergic rhinitis in a Han Chinese population. PLoS One 2011; 6:e21769. [PMID: 21738793 PMCID: PMC3128076 DOI: 10.1371/journal.pone.0021769] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 06/07/2011] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVE Interleukin-1 receptor-associated kinase-4 (IRAK-4) encodes a kinase that is essential for NF-kB activation in Toll-like receptor and T-cell receptor signaling pathways, indicating a possible crosstalk between innate and acquired immunities. We attempted to determine whether the polymorphisms in the Interleukin-1 receptor-associated kinase-4 (IRAK-4) gene are associated with allergic rhinitis (AR) in the Han Chinese population. METHODS A population of 379 patients with AR and 333 healthy controls was studied. Blood was drawn for DNA extraction and total serum immunoglobulin E (IgE). A total of 11 single nucleotide polymorphisms (SNPs) in IRAK-4 were selected and individually genotyped. RESULTS Significant allelic differences between cases and controls were obtained for the SNP of rs3794262 in the IRAK-4 gene. In the stratified analysis for gender, two SNPs (rs4251431 and rs6582484) in males appeared as significant associations. Subgroup analysis for the presence of different allergen sensitivities displayed associations only in the house dust mite-allergic cohorts (rs3794262, rs4251481). None of the selected SNPs in IRAK-4 was associated with total IgE level. The haplotype analysis indicated GCCTGCGA was significantly associated with AR. The SNP-SNP interaction information analysis indicated that the selected sets of polymorphisms had no synergistic effect. CONCLUSIONS Our findings did not support the potential contribution of the IRAK-4 gene to serum IgE levels. However, the results demonstrated a gender- and allergen-dependant association pattern between polymorphisms in IRAK-4 and AR in Chinese population.
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Affiliation(s)
- Yuan Zhang
- Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education of China, Beijing Institute of Otorhinolaryngology, Beijing, People's Republic of China
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Xiaoping Lin
- Center of Allergy and Immunotherapy, The General Hospital of Shenyang Military Command, Shengyang, Liaoning, People's Republic of China
| | - Martin Desrosiers
- Department of Otolaryngology, Hotel-Dieu Hospital, University of Montreal, Montreal, Quebec, Canada
- Department of Otolaryngology-Head and Neck Surgery, Montreal General Hospital, McGill University, Montreal, Quebec, Canada
| | - Wei Zhang
- Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education of China, Beijing Institute of Otorhinolaryngology, Beijing, People's Republic of China
| | - Na Meng
- Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education of China, Beijing Institute of Otorhinolaryngology, Beijing, People's Republic of China
| | - Liping Zhao
- Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education of China, Beijing Institute of Otorhinolaryngology, Beijing, People's Republic of China
| | - Demin Han
- Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education of China, Beijing Institute of Otorhinolaryngology, Beijing, People's Republic of China
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Luo Zhang
- Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education of China, Beijing Institute of Otorhinolaryngology, Beijing, People's Republic of China
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, People's Republic of China
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Freidin MB, Bragina EY, Fedorova OS, Deev IA, Kulikov ES, Ogorodova LM, Puzyrev VP. Genome-wide association study of allergic diseases in Russians of West Siberia. Mol Biol 2011. [DOI: 10.1134/s0026893311020075] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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Reibman J, Liu M. Genetics and asthma disease susceptibility in the US Latino population. ACTA ACUST UNITED AC 2011; 77:140-8. [PMID: 20309924 DOI: 10.1002/msj.20171] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The US Latino population is heterogeneous with diversity in environmental exposures and socioeconomic status. Moreover, the US Hispanic population derives from numerous countries previously under Spanish rule, and many Hispanics have complex proportions of European, Native American, and African ancestry. Disparities in asthma severity and control are due to complex interactions between environmental exposures, socioeconomic factors, and genetic variations. In addition, diseases within the Latino community may also differ by country of origin. Although US Census data show low asthma rates in the Hispanic population as a whole, there is a lot of variability in the prevalence and morbidity of asthma, with a prevalence of 5.0% in Mexican Americans versus 17.0% in Puerto Ricans. The diversity and population admixture make the study of the genetics of asthma complex in Latino populations. However, an understanding of the genetics of asthma in all populations, including the Latino population, can enhance risk identification, help us to target pharmacological therapy, and guide environmental regulations, all of which can promote a reduction in health disparities. The inclusion of markers of ancestral diversity and the incorporation of techniques to adjust for stratification now make these studies feasible in complex populations, including the Latino population. To date, studies using linkage analyses, genome-wide associations, or candidate gene analyses have identified an association of asthma or asthma-related phenotypes with candidate genes, including interleukin 13, beta-2 adrenergic receptor, a disintegrin and metalloproteinase 33, orosomucoid 1-like 3, and thymic stromal lymphopoietin. As reviewed here, although these genes have been identified in diverse populations, limited studies have been performed in Latino populations, and they have had variable replication. There is a need for the development of registries with well-phenotyped pediatric and adult Latino populations and subgroups for inclusion in the rapidly expanding field of genetic studies, and these studies need to be used to reduce health disparities.
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Affiliation(s)
- Joan Reibman
- New York University School of Medicine, New York, NY, USA.
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36
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Marsh LM, Pfefferle PI, Pinkenburg O, Renz H. Maternal signals for progeny prevention against allergy and asthma. Cell Mol Life Sci 2011; 68:1851-62. [PMID: 21369709 PMCID: PMC11115134 DOI: 10.1007/s00018-011-0644-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 02/08/2011] [Accepted: 02/15/2011] [Indexed: 01/04/2023]
Abstract
Allergy and asthma are chronic inflammatory diseases which result from complex gene-environment interactions. Recent evidence indicates the importance of prenatal and postnatal developmental processes in terms of maturation of balanced immune responses. According to the current view, gene-environment interactions during a restricted time frame are responsible for programming of the immune system in favor of allergic immune mechanisms later in life. The interaction between genes and environment is complex and only partially understood; however, heritable epigenetic modifications including chemical additions in and alternative packaging of the DNA have been shown to play a crucial role in this context. Novel data indicate that epigenetic mechanisms contribute to the development of T-helper cell function. Environmental factors, including diesel exhaust particles (DEP), vitamins and tobacco smoke, operate through such mechanisms. Furthermore, the role of environmental microbes provides another and maybe even more important group of exogenous exposures which operates in this critical time frame.
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Affiliation(s)
- Leigh Matthew Marsh
- Department of Clinical Chemistry and Molecular Diagnostics, Philipps-University of Marburg, 35043 Marburg, Germany
| | - Petra Ina Pfefferle
- Department of Clinical Chemistry and Molecular Diagnostics, Philipps-University of Marburg, 35043 Marburg, Germany
| | - Olaf Pinkenburg
- Department of Clinical Chemistry and Molecular Diagnostics, Philipps-University of Marburg, 35043 Marburg, Germany
| | - Harald Renz
- Institute for Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Medical Faculty, Philipps University of Marburg, Baldingerstraße 1, 35043 Marburg, Germany
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AKHABIR LOUBNA, SANDFORD ANDREWJ. Genome-wide association studies for discovery of genes involved in asthma. Respirology 2011; 16:396-406. [DOI: 10.1111/j.1440-1843.2011.01939.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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38
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Pugach I, Matveyev R, Wollstein A, Kayser M, Stoneking M. Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biol 2011; 12:R19. [PMID: 21352535 PMCID: PMC3188801 DOI: 10.1186/gb-2011-12-2-r19] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 01/13/2011] [Accepted: 02/25/2011] [Indexed: 12/31/2022] Open
Abstract
We describe a PCA-based genome scan approach to analyze genome-wide admixture structure, and introduce wavelet transform analysis as a method for estimating the time of admixture. We test the wavelet transform method with simulations and apply it to genome-wide SNP data from eight admixed human populations. The wavelet transform method offers better resolution than existing methods for dating admixture, and can be applied to either SNP or sequence data from humans or other species.
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Affiliation(s)
- Irina Pugach
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D-04103, Germany.
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39
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Holt RJ, Zhang Y, Binia A, Dixon AL, Vandiedonck C, Cookson WO, Knight JC, Moffatt MF. Allele-specific transcription of the asthma-associated PHD finger protein 11 gene (PHF11) modulated by octamer-binding transcription factor 1 (Oct-1). J Allergy Clin Immunol 2011; 127:1054-62.e1-2. [PMID: 21320718 DOI: 10.1016/j.jaci.2010.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 11/26/2010] [Accepted: 12/14/2010] [Indexed: 10/18/2022]
Abstract
BACKGROUND Asthma is a common, chronic inflammatory airway disease of major public health importance with multiple genetic determinants. Previously, we found by positional cloning that PHD finger protein 11 (PHF11) on chromosome 13q14 modifies serum immunoglobulin E (IgE) concentrations and asthma susceptibility. No coding variants in PHF11 were identified. OBJECTIVE Here we investigate the 3 single nucleotide polymorphisms (SNPs) in this gene most significantly associated with total serum IgE levels--rs3765526, rs9526569, and rs1046295--for a role in transcription factor binding. METHODS We used electrophoretic mobility shift assays to examine the effect of the 3 SNPs on transcription factor binding in 3 cell lines relevant to asthma pathogenesis. Relative preferential expression of alleles was investigated by using the allelotyping method. RESULTS Electrophoretic mobility shift assays show that rs1046295 modulates allele-specific binding by the octamer-binding transcription factor 1 (Oct-1). Analysis of the relative expression levels of the 2 alleles of this SNP in heterozygous individuals showed a modest, but highly significant (P = 6.5 × 10(-16)), preferential expression of the A allele consistent with a functional role for rs1046295. CONCLUSION These results suggest a mechanism by which rs1046295 may act as a regulatory variant modulating transcription at this locus and altering asthma susceptibility.
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Affiliation(s)
- Richard J Holt
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
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Zhang G, Goldblatt J, Lesouëf P. Findings in genome-wide association studies on asthma lack generalisation. CLINICAL RESPIRATORY JOURNAL 2011; 4:e8-9. [PMID: 20887339 DOI: 10.1111/j.1752-699x.2010.00213.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guicheng Zhang
- School of Paediatrics and Child Health, Faculty of Medicine, Faculty of Medicine and Dentistry, The University of Western Australia, Perth, Australia
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Abstract
Allergy and asthma are chronic inflammatory diseases that result from complex gene-environment interactions. Recent evidence points to the importance of prenatal and postnatal developmental processes in the maturation of balanced immune responses. Novel data indicate that epigenetic mechanisms contribute to the development of T-helper-cell function. Environmental factors, including diesel exhaust particles, vitamins, and tobacco smoke, operate through such mechanisms. Furthermore, the role of environmental microbes provides another-and maybe an even more important-group of exogenous exposures that operate in this critical time frame. A better understanding of fetal immuno-maturation conditions will provide the basis for the development of novel allergo-protective clinical strategies.
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42
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Ferreira MAR, McRae AF, Medland SE, Nyholt DR, Gordon SD, Wright MJ, Henders AK, Madden PA, Visscher PM, Wray NR, Heath AC, Montgomery GW, Duffy DL, Martin NG. Association between ORMDL3, IL1RL1 and a deletion on chromosome 17q21 with asthma risk in Australia. Eur J Hum Genet 2010; 19:458-64. [PMID: 21150878 DOI: 10.1038/ejhg.2010.191] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Genome-wide association studies followed by replication provide a powerful approach to map genetic risk factors for asthma. We sought to search for new variants associated with asthma and attempt to replicate the association with four loci reported previously (ORMDL3, PDE4D, DENND1B and IL1RL1). Genome-wide association analyses of individual single nucleotide polymorphisms (SNPs), rare copy number variants (CNVs) and overall CNV burden were carried out in 986 asthma cases and 1846 asthma-free controls from Australia. The most-associated locus in the SNP analysis was ORMDL3 (rs6503525, P = 4.8 × 10⁻⁷). Five other loci were associated with P < 10⁻⁵, most notably the chemokine CXC motif ligand 14 (CXCL14) gene (rs31263, P = 7.8 × 10⁻⁶). We found no evidence for association with the specific risk variants reported recently for PDE4D, DENND1B and ILR1L1. However, a variant in IL1RL1 that is in low linkage disequilibrium with that reported previously was associated with asthma risk after accounting for all variants tested (rs10197862, gene wide P = 0.01). This association replicated convincingly in an independent cohort (P = 2.4 × 10⁻⁴). A 300-kb deletion on chromosome 17q21 was associated with asthma risk, but this did not reach experiment-wide significance. Asthma cases and controls had comparable CNV rates, length and number of genes affected by deletions or duplications. In conclusion, we confirm the association between asthma risk and variants in ORMDL3 and identify a novel risk variant in IL1RL1. Follow-up of the 17q21 deletion in larger cohorts is warranted.
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Abstract
PURPOSE OF REVIEW Asthma and allergic diseases are common and disproportionately affect racial and ethnic minorities. Large-scale research efforts and the expense committed to multiple genomewide association studies (GWAS) have led to the identification of numerous susceptibility loci for the allergic diseases, but few successes have been reported in populations that are not of European ancestry. RECENT FINDINGS Of the more than two dozen GWAS for asthma and allergic disease performed to date, very few have included racial/ethnic minorities. Lessons learned from the studies conducted so far suggest that the GWAS approach must include considerations unique to the ancestral populations represented in the sample, population stratification due to admixture, and recognition that the current coverage of common variants both in the public database and on commercially available single-nucleotide polymorphism chips is inadequate to detect true genetic associations among ethnic/racial groups. SUMMARY Advancements in the GWAS technology for identifying genes relevant to asthma and allergic disease among under-represented ethnic and racial minorities who suffer most will facilitate the identification and confirmation of validated genetic risk factors that are both unique to minority groups as well as confirm risk factors that are generic to the population at large.
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Affiliation(s)
- Kathleen C Barnes
- Johns Hopkins Asthma and Allergy Center, Baltimore, Maryland 21224, USA.
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44
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Environmental epigenetics of asthma: an update. J Allergy Clin Immunol 2010; 126:453-65. [PMID: 20816181 DOI: 10.1016/j.jaci.2010.07.030] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 07/27/2010] [Accepted: 07/29/2010] [Indexed: 12/29/2022]
Abstract
Asthma, a chronic inflammatory disorder of the airway, is influenced by interplay between genetic and environmental factors now known to be mediated by epigenetics. Aberrant DNA methylation, altered histone modifications, specific microRNA expression, and other chromatin alterations orchestrate a complex early-life reprogramming of immune T-cell response, dendritic cell function, macrophage activation, and a breach of airway epithelial barrier that dictates asthma risk and severity in later life. Adult-onset asthma is under analogous regulation. The sharp increase in asthma prevalence over the past 2 or 3 decades and the large variations among populations of similar racial/ethnic background but different environmental exposures favors a strong contribution of environmental factors. This review addresses the fundamental question of whether environmental influences on asthma risk, severity, and steroid resistance are partly due to differential epigenetic modulations. Current knowledge on the epigenetic effects of tobacco smoke, microbial allergens, oxidants, airborne particulate matter, diesel exhaust particles, polycyclic aromatic hydrocarbons, dietary methyl donors and other nutritional factors, and dust mites is discussed. Exciting findings have been generated by rapid technological advances and well-designed experimental and population studies. The discovery and validation of epigenetic biomarkers linked to exposure, asthma, or both might lead to better epigenotyping of risk, prognosis, treatment prediction, and development of novel therapies.
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Halapi E, Bjornsdottir US. Overview on the current status of asthma genetics. CLINICAL RESPIRATORY JOURNAL 2010; 3:2-7. [PMID: 20298365 DOI: 10.1111/j.1752-699x.2008.00119.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Asthma is a complex heterogeneous and mutifactorial disease occurring at the interface of multiple genes that interact with various environmental stimuli insulting the immune system at different levels and different times of disease susceptibility. OBJECTIVE The present paper is a review of the current status of the genetics of asthma. RESULTS Sequence variants in hundreds of genes have been associated with asthma using both family-based and case control screening methods. CONCLUSION As the number of genes known to be associated with asthma risk is rapidly growing, it is essential to begin integrating epidemiologic, genetic and genomic strategies to unravel the relationships between genotype and phenotype, and elucidate the pathogenesis of asthma with the goal to make clinical use of these discoveries.
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Affiliation(s)
- Eva Halapi
- deCODE Genetics Inc., Sturlugata, Reykjavik, Iceland.
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Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proc Natl Acad Sci U S A 2010; 107 Suppl 2:8954-61. [PMID: 20445096 DOI: 10.1073/pnas.0914618107] [Citation(s) in RCA: 289] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped on the Illumina 610-Quad arrays and 112 Mexicans genotyped on Affymetrix 500K platform. Intersecting these data with previously collected high-density SNP data from 4,305 individuals, we use principal component analysis and clustering methods FRAPPE and STRUCTURE to investigate genome-wide patterns of African, European, and Native American population structure within and among Hispanic/Latino populations. Comparing autosomal, X and Y chromosome, and mtDNA variation, we find evidence of a significant sex bias in admixture proportions consistent with disproportionate contribution of European male and Native American female ancestry to present-day populations. We also find that patterns of linkage-disequilibria in admixed Hispanic/Latino populations are largely affected by the admixture dynamics of the populations, with faster decay of LD in populations of higher African ancestry. Finally, using the locus-specific ancestry inference method LAMP, we reconstruct fine-scale chromosomal patterns of admixture. We document moderate power to differentiate among potential subcontinental source populations within the Native American, European, and African segments of the admixed Hispanic/Latino genomes. Our results suggest future genome-wide association scans in Hispanic/Latino populations may require correction for local genomic ancestry at a subcontinental scale when associating differences in the genome with disease risk, progression, and drug efficacy, as well as for admixture mapping.
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Fejerman L, Romieu I, John EM, Lazcano-Ponce E, Huntsman S, Beckman KB, Pérez-Stable EJ, González Burchard E, Ziv E, Torres-Mejía G. European ancestry is positively associated with breast cancer risk in Mexican women. Cancer Epidemiol Biomarkers Prev 2010; 19:1074-82. [PMID: 20332279 DOI: 10.1158/1055-9965.epi-09-1193] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The incidence of breast cancer is 35% lower in Hispanic women living in the San Francisco Bay Area than in non-Hispanic White women. We have previously described a significant association between genetic ancestry and risk for breast cancer in a sample of U.S. Hispanics/Latinas. We retested the association in women residing in Mexico because of the possibility that the original finding may be confounded by U.S. specific unmeasured environmental exposures. We genotyped a set of 106 ancestry informative markers in 846 Mexican women with breast cancer and 1,035 unaffected controls and estimated genetic ancestry using a maximum likelihood method. Odds ratios and 95% confidence intervals (95% CI) for ancestry modeled as a categorical and continuous variable were estimated using logistic regression and adjusted for reproductive and other known risk factors. Greater European ancestry was associated with increased breast cancer risk in this new and independent sample of Mexican women residing in Mexico. Compared with women with 0% to 25% European ancestry, the risk was increased for women with 51% to 75% and 76% to 100% European ancestry [odds ratios, 1.35 (95% CI, 0.96-1.91) and 2.44 (95% CI, 0.94-6.35), respectively; P for trend = 0.044]. For every 25% increase in European ancestry (modeled as a continuous variable), there was a 20% increase in risk for breast cancer (95% CI, 1.03-1.41; P = 0.019). These results suggest that nongenetic factors play a crucial role in explaining the difference in breast cancer incidence between Latinas and non-Latina White women, and it also points out to the possibility of a genetic component to this difference.
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Affiliation(s)
- Laura Fejerman
- Division of General Internal Medicine, Department of Medicine, Institute for Human Genetics, University of California, San Francisco, California, USA
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Oleksyk TK, Smith MW, O'Brien SJ. Genome-wide scans for footprints of natural selection. Philos Trans R Soc Lond B Biol Sci 2010; 365:185-205. [PMID: 20008396 PMCID: PMC2842710 DOI: 10.1098/rstb.2009.0219] [Citation(s) in RCA: 233] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Detecting recent selected ‘genomic footprints’ applies directly to the discovery of disease genes and in the imputation of the formative events that molded modern population genetic structure. The imprints of historic selection/adaptation episodes left in human and animal genomes allow one to interpret modern and ancestral gene origins and modifications. Current approaches to reveal selected regions applied in genome-wide selection scans (GWSSs) fall into eight principal categories: (I) phylogenetic footprinting, (II) detecting increased rates of functional mutations, (III) evaluating divergence versus polymorphism, (IV) detecting extended segments of linkage disequilibrium, (V) evaluating local reduction in genetic variation, (VI) detecting changes in the shape of the frequency distribution (spectrum) of genetic variation, (VII) assessing differentiating between populations (FST), and (VIII) detecting excess or decrease in admixture contribution from one population. Here, we review and compare these approaches using available human genome-wide datasets to provide independent verification (or not) of regions found by different methods and using different populations. The lessons learned from GWSSs will be applied to identify genome signatures of historic selective pressures on genes and gene regions in other species with emerging genome sequences. This would offer considerable potential for genome annotation in functional, developmental and evolutionary contexts.
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Affiliation(s)
- Taras K Oleksyk
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez 00681, Puerto Rico.
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Via M, Ziv E, Burchard EG. Recent advances of genetic ancestry testing in biomedical research and direct to consumer testing. Clin Genet 2010; 76:225-35. [PMID: 19793051 DOI: 10.1111/j.1399-0004.2009.01263.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In the post-Human Genome Project era, the debate on the concept of race/ethnicity and its implications for biomedical research are dependent on two critical issues: whether and how to classify individuals and whether biological factors play a role in health disparities. The advent of reliable estimates of genetic (or biogeographic) ancestry has provided this debate with a quantitative and more objective tool. The estimation of genetic ancestry allows investigators to control for population stratification in association studies and helps to detect biological causation behind population-specific differences in disease and drug response. New techniques such as admixture mapping can specifically detect population-specific risk alleles for a disease in admixed populations. However, researchers have to be mindful of the correlation between genetic ancestry and socioeconomic and environmental factors that could underlie these differences. More importantly, researchers must avoid the stigmatization of individuals based on perceived or real genetic risks. The latter point will become increasingly sensitive as several 'for profit companies' are offering ancestry and genetic testing directly to consumers and the consequences of the spread of the services of these companies are still unforeseeable.
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Affiliation(s)
- M Via
- Institute for Human Genetics, University of California, San Francisco, CA 94143-2911, USA.
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Gold DR, Bloomberg GR, Cruikshank WW, Visness CM, Schwarz J, Kattan M, O'Connor GT, Wood RA, Burger MS, Wright RJ, Witter F, Lee-Parritz A, Sperling R, Sadovsky Y, Togias A, Gern JE. Parental characteristics, somatic fetal growth, and season of birth influence innate and adaptive cord blood cytokine responses. J Allergy Clin Immunol 2009; 124:1078-87. [PMID: 19895995 DOI: 10.1016/j.jaci.2009.08.021] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 08/03/2009] [Accepted: 08/04/2009] [Indexed: 12/14/2022]
Abstract
BACKGROUND Immunologic responses at birth likely relate to subsequent risks for allergic diseases and wheezing in infancy; however, the influences of parental characteristics and prenatal factors on neonatal immune responses are incompletely understood. OBJECTIVE This study investigates potential correlations between urban parental, prenatal, and perinatal factors on innate and adaptive stimuli-induced cytokine responses. METHODS Five hundred sixty and 49 children of parents with and without allergic disease or asthma, respectively, were enrolled into a prospective birth cohort study (Urban Environment and Childhood Asthma). Cord blood mononuclear cells were incubated with innate and adaptive immune stimuli, and cytokine responses (ELISA) were compared with season of birth, parental characteristics, in utero stressors, and fetal growth. RESULTS Many cytokine responses varied by season of birth, including 2-fold to 3-fold fluctuations with specific IFN-alpha and IFN-gamma responses. Birth weight was inversely associated with IFN-gamma responses to respiratory syncytial virus (R = -0.16), but positively associated with IL-8 responses to a variety of innate stimuli (R = 0.08-0.12). Respiratory syncytial virus-induced cytokine responses were 21% to 54% lower in children of mothers with asthma. Cytokine responses were generally lower in babies born to parents with allergy/asthma. CONCLUSIONS Innate cytokine responses are associated with parental allergic or airway disease, somatic fetal growth, ethnicity, and season of birth. Collectively, these findings suggest that urban prenatal exposures and familial factors affect the development of the fetal immune system.
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Affiliation(s)
- Diane R Gold
- Channing Laboratory, Brigham and Women's Hospital, Boston, Mass, USA
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