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Hong X, Jiang M, Kho AT, Tiwari A, Guo H, Wang AL, McGeachie MJ, Weiss ST, Tantisira KG, Li J. Circulating miRNAs associate with historical childhood asthma hospitalization in different serum vitamin D groups. Respir Res 2024; 25:118. [PMID: 38459594 PMCID: PMC10921757 DOI: 10.1186/s12931-024-02737-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/17/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Vitamin D may help to alleviate asthma exacerbation because of its anti-inflammation effect, but the evidence is inconsistent in childhood asthma. MiRNAs are important mediators in asthma pathogenesis and also excellent non-invasive biomarkers. We hypothesized that circulating miRNAs are associated with asthma exacerbation and modified by vitamin D levels. METHODS We sequenced baseline serum miRNAs from 461 participants in the Childhood Asthma Management Program (CAMP). Logistic regression was used to associate miRNA expression with asthma exacerbation through interaction analysis first and then stratified by vitamin D insufficient and sufficient groups. Microarray from lymphoblastoid B-cells (LCLs) treated by vitamin D or sham of 43 subjects in CAMP were used for validation in vitro. The function of miRNAs was associated with gene modules by weighted gene co-expression network analysis (WGCNA). RESULTS We identified eleven miRNAs associated with asthma exacerbation with vitamin D effect modification. Of which, five were significant in vitamin D insufficient group and nine were significant in vitamin D sufficient group. Six miRNAs, including hsa-miR-143-3p, hsa-miR-192-5p, hsa-miR-151a-5p, hsa-miR-24-3p, hsa-miR-22-3p and hsa-miR-451a were significantly associated with gene modules of immune-related functions, implying miRNAs may mediate vitamin D effect on asthma exacerbation through immune pathways. In addition, hsa-miR-143-3p and hsa-miR-451a are potential predictors of childhood asthma exacerbation at different vitamin D levels. CONCLUSIONS miRNAs are potential mediators of asthma exacerbation and their effects are directly impacted by vitamin D levels.
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Affiliation(s)
- Xiaoning Hong
- Clinical Big Data Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Mingye Jiang
- Clinical Big Data Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Alvin T Kho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Anshul Tiwari
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Haiyan Guo
- Department of Respiratory and Critical Care Medicine, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Disease, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Alberta L Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Partners Personalized Medicine, Partners Healthcare, Boston, MA, USA
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pediatrics, Division of Respiratory Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Jiang Li
- Clinical Big Data Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China.
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Shenzhen Key Laboratory of Chinese Medicine Active Substance Screening and Translational Research, Shenzhen, Guangdong, China.
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Li J, Hong X, Jiang M, Kho AT, Tiwari A, Wang AL, Chase RP, Celedón JC, Weiss ST, McGeachie MJ, Tantisira KG. A novel piwi-interacting RNA associates with type 2-high asthma phenotypes. J Allergy Clin Immunol 2024; 153:695-704. [PMID: 38056635 DOI: 10.1016/j.jaci.2023.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/14/2023] [Accepted: 10/25/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Piwi-interacting RNAs (piRNAs), comprising the largest noncoding RNA group, regulate transcriptional processes. Whether piRNAs are associated with type 2 (T2)-high asthma is unknown. OBJECTIVE We sought to investigate the association between piRNAs and T2-high asthma in childhood asthma. METHODS We sequenced plasma samples from 462 subjects in the Childhood Asthma Management Program (CAMP) as the discovery cohort and 1165 subjects in the Genetics of Asthma in Costa Rica Study (GACRS) as a replication cohort. Sequencing reads were filtered first, and piRNA reads were annotated and normalized. Linear regression was used for the association analysis of piRNAs and peripheral blood eosinophil count, total serum IgE level, and long-term asthma exacerbation in children with asthma. Mediation analysis was performed to investigate the effect direction. We then ascertained if the circulating piRNAs were present in asthmatic airway epithelial cells in a Gene Expression Omnibus (GEO; www.ncbi.nlm.nih.gov/geo) public data set. RESULTS Fifteen piRNAs were significantly associated with eosinophil count in CAMP (P ≤ .05), and 3 were successfully replicated in GACRS. Eleven piRNAs were associated with total IgE in CAMP, and one of these was replicated in GACRS. All 22 significant piRNAs were identified in epithelial cells in vitro, and 6 of these were differentially expressed between subjects with asthma and healthy controls. Fourteen piRNAs were associated with long-term asthma exacerbation, and effect of piRNAs on long-term asthma exacerbation are mediated through eosinophil count and serum IgE level. CONCLUSION piRNAs are associated with peripheral blood eosinophils and total serum IgE in childhood asthma and may play important roles in T2-high asthma.
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Affiliation(s)
- Jiang Li
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Shenzhen Key Laboratory of Chinese Medicine Active Substance Screening and Translational Research, Shenzhen, China
| | - Xiaoning Hong
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Mingye Jiang
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Alvin T Kho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Computational Health Informatics Program, Boston Children's Hospital, Boston, Mass
| | - Anshul Tiwari
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Alberta L Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Robert P Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Juan C Celedón
- Division of Pulmonary Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pa
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Partners Personalized Medicine, Partners Healthcare, Boston, Mass
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Department of Pediatrics, Division of Respiratory Medicine, University of California-San Diego, La Jolla, Calif.
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Sharma R, Tiwari A, Kho AT, Wang AL, Srivastava U, Piparia S, Desai B, Wong R, Celedón JC, Peters SP, Smith LJ, Irvin CG, Castro M, Weiss ST, Tantisira KG, McGeachie MJ. Circulating MicroRNAs associated with Bronchodilator Response in Childhood Asthma. Res Sq 2023:rs.3.rs-3101724. [PMID: 37461659 PMCID: PMC10350209 DOI: 10.21203/rs.3.rs-3101724/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Rationale Bronchodilator response (BDR) is a measure of improvement in airway smooth muscle tone, inhibition of liquid accumulation and mucus section into the lumen in response to short-acting beta-2 agonists that varies among asthmatic patients. MicroRNAs (miRNAs) are well-known post-translational regulators. Identifying miRNAs associated with BDR could lead to a better understanding of the underlying complex pathophysiology. Objective The purpose of this study is to identify circulating miRNAs associated with bronchodilator response in asthma and decipher possible mechanism of bronchodilator response variation. Methods We used available small RNA sequencing on blood serum from 1,134 asthmatic children aged 6 to 14 years who participated in the Genetics of Asthma in Costa Rica Study (GACRS). We filtered the participants into high and low bronchodilator response (BDR) quartiles and used DeSeq2 to identify miRNAs with differential expression (DE) in high (N= 277) vs low (N= 278) BDR group. Replication was carried out in the Leukotriene modifier Or Corticosteroids or Corticosteroid-Salmeterol trial (LOCCS), an adult asthma cohort. The putative target genes of DE miRNAs were identified, and pathway enrichment analysis was performed. Results We identified 10 down-regulated miRNAs having odds ratios (OR) between 0.37 and 0.76 for a doubling of miRNA counts and one up-regulated miRNA (OR=2.26) between high and low BDR group. These were assessed for replication in the LOCCS cohort, where two miRNAs (miR-200b-3p and miR-1246) were associated. Further, functional annotation of 11 DE miRNAs were performed as well as of two replicated miRs. Target genes of these miRs were enriched in regulation of cholesterol biosynthesis by SREBPs, ESR-mediated signaling, G1/S transition, RHO GTPase cycle, and signaling by TGFB family pathways. Conclusion MiRNAs miR-1246 and miR-200b-3p are associated with both childhood and adult asthma BDR. Our findings add to the growing body of evidence that miRNAs play a significant role in the difference of asthma treatment response among patients as it points to genomic regulatory machinery underlying difference in bronchodilator response among patients. Trial registration LOCCS cohort [ClinicalTrials.gov number: NCT00156819], GACRS cohort [ClinicalTrials.gov number: NCT00021840].
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Affiliation(s)
- Rinku Sharma
- Brigham and Women's Hospital and Harvard Medical School
| | | | - Alvin T Kho
- Brigham and Women's Hospital and Harvard Medical School
| | | | | | | | - Brinda Desai
- University of California San Diego and Rady Children's Hospital
| | - Richard Wong
- University of California San Diego and Rady Children's Hospital
| | - Juan C Celedón
- University of Pittsburgh, UPMC Children's Hospital of Pittsburgh
| | | | | | | | | | - Scott T Weiss
- Brigham and Women's Hospital and Harvard Medical School
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Tsai CH, Lai ACY, Lin YC, Chi PY, Chen YC, Yang YH, Chen CH, Shen SY, Hwang TL, Su MW, Hsu IL, Huang YC, Maitland-van der Zee AH, McGeachie MJ, Tantisira KG, Chang YJ, Lee YL. Neutrophil extracellular trap production and CCL4L2 expression influence corticosteroid response in asthma. Sci Transl Med 2023; 15:eadf3843. [PMID: 37285400 DOI: 10.1126/scitranslmed.adf3843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/04/2023] [Indexed: 06/09/2023]
Abstract
The association between neutrophil extracellular traps (NETs) and response to inhaled corticosteroids (ICS) in asthma is unclear. To better understand this relationship, we analyzed the blood transcriptomes from children with controlled and uncontrolled asthma in the Taiwanese Consortium of Childhood Asthma Study using weighted gene coexpression network analysis and pathway enrichment methods. We identified 298 uncontrolled asthma-specific differentially expressed genes and one gene module associated with neutrophil-mediated immunity, highlighting a potential role for neutrophils in uncontrolled asthma. We also found that NET abundance was associated with nonresponse to ICS in patients. In a neutrophilic airway inflammation murine model, steroid treatment could not suppress neutrophilic inflammation and airway hyperreactivity. However, NET disruption with deoxyribonuclease I (DNase I) efficiently inhibited airway hyperreactivity and inflammation. Using neutrophil-specific transcriptomic profiles, we found that CCL4L2 was associated with ICS nonresponse in asthma, which was validated in human and murine lung tissue. CCL4L2 expression was also negatively correlated with pulmonary function change after ICS treatment. In summary, steroids fail to suppress neutrophilic airway inflammation, highlighting the potential need to use alternative therapies such as leukotriene receptor antagonists or DNase I that target the neutrophil-associated phenotype. Furthermore, these results highlight CCL4L2 as a potential therapeutic target for individuals with asthma refractory to ICS.
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Affiliation(s)
- Ching-Hui Tsai
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | | | - Yu-Cheng Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Po-Yu Chi
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yun-Chi Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yao-Hsu Yang
- Department of Pediatrics, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Chien-Han Chen
- Department of Pediatrics, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City 243, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
| | - Sheng-Yeh Shen
- Department of Chest Medicine, MacKay Memorial Hospital, Taipei 104, Taiwan
| | - Tsong-Long Hwang
- Graduate Institute of Natural Products, School of Traditional Chinese Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Anesthesiology, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Ming-Wei Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - I-Ling Hsu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chi Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Anke H Maitland-van der Zee
- Department of Pulmonary Medicine, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Department of Pediatric Respiratory Medicine, Emma's Children Hospital, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, 1105 AZ Amsterdam, Netherlands
- Amsterdam Public Health, 1105 AZ Amsterdam, Netherlands
| | - Michael J McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kelan G Tantisira
- Division of Respiratory Medicine, Department of Pediatrics, University of California San Diego, San Diego, CA 92123, USA
| | - Ya-Jen Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Institute of Translational Medicine and New Drug Development, China Medical University, Taichung 404, Taiwan
| | - Yungling L Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- College of Public Health, China Medical University, Taichung 404, Taiwan
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei 115, Taiwan
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Bhattacharjee EB, Sun X, Malhotra A, Tantisira KG, Landeo‐Gutierrez JS, Jain S, Bhattacharjee R. Association of body anthropometry and obstructive sleep apnea in children: Variations observed in Hispanic children. Obes Sci Pract 2023; 9:210-217. [PMID: 37287517 PMCID: PMC10242256 DOI: 10.1002/osp4.641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/06/2022] [Accepted: 09/13/2022] [Indexed: 06/09/2023] Open
Abstract
Objectives Obesity is a risk factor for obstructive sleep apnea (OSA) in children. Childhood obesity rates vary amongst different ethnic groups. Here the interaction of Hispanic ethnicity and obesity on OSA risk was evaluated. Methods Retrospective cross-sectional analysis of consecutive children undergoing polysomnography and anthropometry using bioelectrical impedance from 2017 to 2020. Demographics obtained from the medical chart. Children who had also undergone cardiometabolic testing were identified and the relationship of cardiometabolic markers with OSA and anthropometry was assessed. Results Data from 1217 children revealed Hispanic children were more likely to have moderate-severe OSA (36.0%) compared to Non-Hispanic children (26.5%), p < 0.001. Hispanic children had greater Body mass index (BMI), BMI percentile and percent body fat, p < 0.0001. In children that underwent cardiometabolic testing, Hispanic children had significantly greater serum alanine aminotransferase levels (ALT) levels. Following adjustment of age and sex, Hispanic ethnicity was not found to moderate the association of anthropometry with OSA, anthropometry with cardiometabolic markers, and OSA with cardiometabolic markers. Conclusions OSA was more likely in Hispanic children; this relationship was likely driven by obesity status rather than ethnicity. Among children undergoing cardiometabolic testing, Hispanic children were observed to have greater ALT concentrations however ethnicity did not impact the association of anthropometry and ALT or other cardiometabolic markers.
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Affiliation(s)
| | - Xiaoying Sun
- Biostatistics Research CenterHerbert Wertheim School of Public Health and Human Longevity ScienceUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Atul Malhotra
- Division of Pulmonary, Critical Care, and Sleep MedicineDepartment of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kelan G. Tantisira
- Division of Respiratory MedicineDepartment of PediatricsUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Jeremy S. Landeo‐Gutierrez
- Division of Respiratory MedicineDepartment of PediatricsUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Sonia Jain
- Biostatistics Research CenterHerbert Wertheim School of Public Health and Human Longevity ScienceUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Rakesh Bhattacharjee
- Division of Respiratory MedicineDepartment of PediatricsUniversity of California San DiegoLa JollaCaliforniaUSA
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Sharma R, Tiwari A, Kho AT, Celedón JC, Weiss ST, Tantisira KG, McGeachie MJ. Systems Genomics Reveals microRNA Regulation of ICS Response in Childhood Asthma. Cells 2023; 12:1505. [PMID: 37296627 PMCID: PMC10309175 DOI: 10.3390/cells12111505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/29/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Asthmatic patients' responses to inhaled corticosteroids (ICS) are variable and difficult to quantify. We have previously defined a Cross-sectional Asthma STEroid Response (CASTER) measure of ICS response. MicroRNAs (miRNAs) have shown strong effects on asthma and inflammatory processes. OBJECTIVE The purpose of this study was to identify key associations between circulating miRNAs and ICS response in childhood asthma. METHODS Small RNA sequencing in peripheral blood serum from 580 children with asthma on ICS treatment from The Genetics of Asthma in Costa Rica Study (GACRS) was used to identify miRNAs associated with ICS response using generalized linear models. Replication was conducted in children on ICS from the Childhood Asthma Management Program (CAMP) cohort. The association between replicated miRNAs and the transcriptome of lymphoblastoid cell lines in response to a glucocorticoid was assessed. RESULTS The association study on the GACRS cohort identified 36 miRNAs associated with ICS response at 10% false discovery rate (FDR), three of which (miR-28-5p, miR-339-3p, and miR-432-5p) were in the same direction of effect and significant in the CAMP replication cohort. In addition, in vitro steroid response lymphoblastoid gene expression analysis revealed 22 dexamethasone responsive genes were significantly associated with three replicated miRNAs. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) revealed a significant association between miR-339-3p and two modules (black and magenta) of genes associated with immune response and inflammation pathways. CONCLUSION This study highlighted significant association between circulating miRNAs miR-28-5p, miR-339-3p, and miR-432-5p and ICS response. miR-339-3p may be involved in immune dysregulation, which leads to a poor response to ICS treatment.
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Affiliation(s)
- Rinku Sharma
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anshul Tiwari
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA
| | - Alvin T. Kho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Juan C. Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kelan G. Tantisira
- Division of Pediatric Respiratory Medicine, University of California San Diego, Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Michael J. McGeachie
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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Khare M, Piparia S, Tantisira KG. Pharmacogenetics of childhood uncontrolled asthma. Expert Rev Clin Immunol 2023:1-14. [PMID: 37190963 PMCID: PMC10657335 DOI: 10.1080/1744666x.2023.2214363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/11/2023] [Indexed: 05/17/2023]
Abstract
INTRODUCTION Asthma is a heterogeneous, multifactorial disease with multiple genetic and environmental risk factors playing a role in pathogenesis and therapeutic response. Understanding of pharmacogenetics can help with matching individualized treatments to specific genotypes of asthma to improve therapeutic outcomes especially in uncontrolled or severe asthma. AREAS COVERED In this review, we outline novel information about biology, pathways, and mechanisms related to interindividual variability in drug response (corticosteroids, bronchodilators, leukotriene modifiers, and biologics) for childhood asthma. We discuss candidate gene, genome-wide association studies and newer omics studies including epigenomics, transcriptomics, proteomics, and metabolomics as well as integrative genomics and systems biology methods related to childhood asthma. The articles were obtained after a series of searches, last updated November 2022, using database PubMed/CINAHL DB. EXPERT OPINION Implementation of pharmacogenetic algorithms can improve therapeutic targeting in children with asthma, particularly with severe or uncontrolled asthma who typically have challenges in clinical management and carry considerable financial burden. Future studies focusing on potential biomarkers both clinical and pharmacogenetic can help formulate a prognostic test for asthma treatment response that would represent true bench to bedside clinical implementation.
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Affiliation(s)
- Manaswitha Khare
- Division of Pediatric Hospital Medicine, Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Division of Pediatric Hospital Medicine, Department of Pediatrics, Rady Children's Hospital of San Diego, San Diego, CA, USA
| | - Shraddha Piparia
- Division of Pediatric Respiratory Medicine, Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Kelan G Tantisira
- Division of Pediatric Respiratory Medicine, Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Division of Pediatric Respiratory Medicine, Department of Pediatrics, Rady Children's Hospital of San Diego, San Diego, CA, USA
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8
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Gross R, Thaweethai T, Rosenzweig EB, Chan J, Chibnik LB, Cicek MS, Elliott AJ, Flaherman VJ, Foulkes AS, Witvliet MG, Gallagher R, Gennaro ML, Jernigan TL, Karlson EW, Katz SD, Kinser PA, Kleinman LC, Lamendola-Essel MF, Milner JD, Mohandas S, Mudumbi PC, Newburger JW, Rhee KE, Salisbury AL, Snowden JN, Stein CR, Stockwell MS, Tantisira KG, Thomason ME, Truong DT, Warburton D, Wood JC, Ahmed S, Akerlundh A, Alshawabkeh AN, Anderson BR, Aschner JL, Atz AM, Aupperle RL, Baker FC, Balaraman V, Banerjee D, Barch DM, Baskin-Sommers A, Bhuiyan S, Bind MAC, Bogie AL, Buchbinder NC, Bueler E, Bükülmez H, Casey B, Chang L, Clark DB, Clifton RG, Clouser KN, Cottrell L, Cowan K, D’Sa V, Dapretto M, Dasgupta S, Dehority W, Dummer KB, Elias MD, Esquenazi-Karonika S, Evans DN, Faustino EVS, Fiks AG, Forsha D, Foxe JJ, Friedman NP, Fry G, Gaur S, Gee DG, Gray KM, Harahsheh AS, Heath AC, Heitzeg MM, Hester CM, Hill S, Hobart-Porter L, Hong TK, Horowitz CR, Hsia DS, Huentelman M, Hummel KD, Iacono WG, Irby K, Jacobus J, Jacoby VL, Jone PN, Kaelber DC, Kasmarcak TJ, Kluko MJ, Kosut JS, Laird AR, Landeo-Gutierrez J, Lang SM, Larson CL, Lim PPC, Lisdahl KM, McCrindle BW, McCulloh RJ, Mendelsohn AL, Metz TD, Morgan LM, Müller-Oehring EM, Nahin ER, Neale MC, Ness-Cochinwala M, Nolan SM, Oliveira CR, Oster ME, Payne RM, Raissy H, Randall IG, Rao S, Reeder HT, Rosas JM, Russell MW, Sabati AA, Sanil Y, Sato AI, Schechter MS, Selvarangan R, Shakti D, Sharma K, Squeglia LM, Stevenson MD, Szmuszkovicz J, Talavera-Barber MM, Teufel RJ, Thacker D, Udosen MM, Warner MR, Watson SE, Werzberger A, Weyer JC, Wood MJ, Yin HS, Zempsky WT, Zimmerman E, Dreyer BP. Researching COVID to enhance recovery (RECOVER) pediatric study protocol: Rationale, objectives and design. medRxiv 2023:2023.04.27.23289228. [PMID: 37214806 PMCID: PMC10197716 DOI: 10.1101/2023.04.27.23289228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Importance The prevalence, pathophysiology, and long-term outcomes of COVID-19 (post-acute sequelae of SARS-CoV-2 [PASC] or "Long COVID") in children and young adults remain unknown. Studies must address the urgent need to define PASC, its mechanisms, and potential treatment targets in children and young adults. Observations We describe the protocol for the Pediatric Observational Cohort Study of the NIH's RE searching COV ID to E nhance R ecovery (RECOVER) Initiative. RECOVER-Pediatrics is an observational meta-cohort study of caregiver-child pairs (birth through 17 years) and young adults (18 through 25 years), recruited from more than 100 sites across the US. This report focuses on two of five cohorts that comprise RECOVER-Pediatrics: 1) a de novo RECOVER prospective cohort of children and young adults with and without previous or current infection; and 2) an extant cohort derived from the Adolescent Brain Cognitive Development (ABCD) study ( n =10,000). The de novo cohort incorporates three tiers of data collection: 1) remote baseline assessments (Tier 1, n=6000); 2) longitudinal follow-up for up to 4 years (Tier 2, n=6000); and 3) a subset of participants, primarily the most severely affected by PASC, who will undergo deep phenotyping to explore PASC pathophysiology (Tier 3, n=600). Youth enrolled in the ABCD study participate in Tier 1. The pediatric protocol was developed as a collaborative partnership of investigators, patients, researchers, clinicians, community partners, and federal partners, intentionally promoting inclusivity and diversity. The protocol is adaptive to facilitate responses to emerging science. Conclusions and Relevance RECOVER-Pediatrics seeks to characterize the clinical course, underlying mechanisms, and long-term effects of PASC from birth through 25 years old. RECOVER-Pediatrics is designed to elucidate the epidemiology, four-year clinical course, and sociodemographic correlates of pediatric PASC. The data and biosamples will allow examination of mechanistic hypotheses and biomarkers, thus providing insights into potential therapeutic interventions. Clinical Trialsgov Identifier Clinical Trial Registration: http://www.clinicaltrials.gov . Unique identifier: NCT05172011.
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Affiliation(s)
- Rachel Gross
- Department of Pediatrics, New York University Grossman School of Medicine, New York, NY, USA
| | - Tanayott Thaweethai
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA
| | - Erika B. Rosenzweig
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - James Chan
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA
| | - Lori B. Chibnik
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA
| | - Mine S. Cicek
- Department of Laboratory Medicine and Pathology, Mayo Clinic Hospital, Rochester, MN, USA
| | - Amy J. Elliott
- Avera Research Institute, Avera Health, Sioux Falls, SD, USA
| | - Valerie J. Flaherman
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Andrea S. Foulkes
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA
| | | | - Richard Gallagher
- Department of Child and Adolescent Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Maria Laura Gennaro
- Public Health Research Institute and Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Terry L. Jernigan
- Center for Human Development, Cognitive Science, Psychiatry, Radiology, University of California San Diego, La Jolla, CA, USA
| | | | - Stuart D. Katz
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Patricia A. Kinser
- Department of Physical Medicine and Rehabilitation, Virginia Commonwealth University School of Nursing, Richmond, VA, USA
| | - Lawrence C. Kleinman
- Department of Pediatrics, Division of Population Health, Quality, and Implementation Sciences (POPQuIS), Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | | | - Joshua D. Milner
- Department of Pediatrics, Columbia University Medical Center: Columbia University Irving Medical Center, New York, NY, USA
| | - Sindhu Mohandas
- Department of Infectious Diseases, Children’s Hospital Los Angeles and the Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Praveen C. Mudumbi
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, USA
| | - Jane W. Newburger
- Department of Cardiology, Boston Children’s Hospital, Boston, MA, USA
| | - Kyung E. Rhee
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Amy L. Salisbury
- School of Nursing, Virginia Commonwealth University, Richmond, VA, USA
| | - Jessica N. Snowden
- Departments of Pediatrics and Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Cheryl R. Stein
- Department of Child and Adolescent Psychiatry, Hassenfeld Children’s Hospital at NYU Langone, New York, NY, USA
| | - Melissa S. Stockwell
- Department of Pediatrics, Division of Child and Adolescent Health, Columbia University Vagelos College of Physicians and Surgeons and NewYork-Presbyterian, New York, NY, USA
| | - Kelan G. Tantisira
- Division of Pediatric Respiratory Medicine, University of California San Diego, San Diego, CA, USA
| | - Moriah E. Thomason
- Department of Child and Adolescent Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Dongngan T. Truong
- Division of Pediatric Cardiology, University of Utah and Primary Children’s Hospital, Salt Lake City, UT, USA
| | - David Warburton
- Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - John C. Wood
- Department of Pediatrics and Radiology, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Shifa Ahmed
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA
| | - Almary Akerlundh
- Department of Pulmonary Research, Rady Children’s Hospital-San Diego, San Diego, CA, USA
| | | | - Brett R. Anderson
- Division of Pediatric Cardiology, NewYork-Presbyterian/Columbia University Irving Medical Center, New York, NY, USA
| | - Judy L. Aschner
- Department of Pediatrics, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Andrew M. Atz
- Department of Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Robin L. Aupperle
- Oxley College of Health Sciences, Laureate Institute for Brain Research, Tulsa, OK, USA
| | - Fiona C. Baker
- Center for Health Sciences, SRI International, Menlo Park, CA, USA
| | - Venkataraman Balaraman
- Department of Pediatrics, Kapiolani Medical Center for Women and Children, Honolulu, HI, USA
| | - Dithi Banerjee
- Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, MO, USA
| | - Deanna M. Barch
- Department of Psychological & Brain Sciences, Psychiatry, and Radiology, Washington University in St. Louis, Saint Louis, MO, USA
| | | | - Sultana Bhuiyan
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Marie-Abele C. Bind
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA
| | - Amanda L. Bogie
- Department of Pediatrics, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Natalie C. Buchbinder
- Center for Human Development, University of California San Diego, San Diego, CA, USA
| | - Elliott Bueler
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Hülya Bükülmez
- Department of Pediatrics, Division of Rheumatology, The MetroHealth System, Case Western Reserve University, Cleveland, OH, USA
| | - B.J. Casey
- Department of Neuroscience and Behavior, Barnard College - Columbia University, New York, NY, USA
| | - Linda Chang
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Duncan B. Clark
- Departments of Psychiatry and Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Katharine N. Clouser
- Department of Pediatrics, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Lesley Cottrell
- Department of Pediatrics, West Virginia University, Morgantown, WV, USA
| | - Kelly Cowan
- Department of Pediatrics, Robert Larner M.D. College of Medicine at the University of Vermont, Burlington, VT, USA
| | - Viren D’Sa
- Department of Pediatrics, Rhode Island Hospital, Providence, RI, USA
| | - Mirella Dapretto
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA, USA
| | - Soham Dasgupta
- Department of Pediatrics, Norton Children’s Hospital, University of Louisville, Louisville, KY, USA
| | - Walter Dehority
- Department of Pediatrics, Division of Infectious Diseases, University of New Mexico, Albuquerque, NM, USA
| | - Kirsten B. Dummer
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Matthew D. Elias
- Division of Cardiology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shari Esquenazi-Karonika
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, USA
| | - Danielle N. Evans
- Arkansas Children’s Research Institute, Arkansas Children’s Hospital, Little Rock, AR, USA
| | | | - Alexander G. Fiks
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daniel Forsha
- Department of Cardiology, Children’s Mercy Kansas City, Ward Family Heart Center, Kansas City, MO, USA, Kansas City, MO, USA
| | - John J. Foxe
- Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Naomi P. Friedman
- Institute for Behavioral Genetics and Department of Psychology and Neuroscience, University of Colorado Boulder, Bolder, CO, USA
| | - Greta Fry
- Pennington Biomedical Research Center Clinic, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Sunanda Gaur
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Dylan G. Gee
- Department of Psychology, Yale University, New Haven, CT, USA
| | - Kevin M. Gray
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Ashraf S. Harahsheh
- Department of Pediatrics, Division of Cardiology, George Washington University School of Medicine & Health Sciences, Washington, DC, USA
| | - Andrew C. Heath
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Mary M. Heitzeg
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Christina M. Hester
- Division of Practice-Based Research, Innovation, & Evaluation, American Academy of Family Physicians, Leawood, KS, USA
| | - Sophia Hill
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Laura Hobart-Porter
- Departments of Pediatrics and Physical Medicine & Rehabilitation, Section of Pediatric Rehabilitation, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Travis K.F. Hong
- Department of Pediatrics, Kapiolani Medical Center for Women and Children, Honolulu, HI, USA
| | - Carol R. Horowitz
- Center for Health Equity and Community Engaged Research and Department of Population Health Science and Policy, New York, NY, USA
| | - Daniel S. Hsia
- Clinical Trials Unit, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Matthew Huentelman
- Division of Neurogenomics, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Kathy D. Hummel
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - William G. Iacono
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Katherine Irby
- Department of Pediatrics, Arkansas Children’s Hospital, University of Arkansas Medical School, Little Rock, AR, USA
| | - Joanna Jacobus
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Vanessa L. Jacoby
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Pei-Ni Jone
- Department of Pediatrics, Pediatric Cardiology, Lurie Children’s Hospital, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David C. Kaelber
- Departments of Pediatrics, Internal Medicine, and Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Tyler J. Kasmarcak
- Department of Pediatric Clinical Research, Medical University of South Carolina, Charleston, SC, USA
| | - Matthew J. Kluko
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Jessica S. Kosut
- Department of Pediatrics, Kapiolani Medical Center for Women and Children, Honolulu, HI, USA
| | - Angela R. Laird
- Department of Physics, Florida International University, Miami, FL, USA
| | - Jeremy Landeo-Gutierrez
- Department of Pediatrics, Respiratory Medicine Division, University of California San Diego, San Diego, CA, USA
| | - Sean M. Lang
- Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Christine L. Larson
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Peter Paul C. Lim
- Department of Pediatric Infectious Disease, Avera McKennan University Health Center, University of South Dakota, Sioux Falls, SD, USA
| | - Krista M. Lisdahl
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Brian W. McCrindle
- Department of Pediatrics, University of Toronto, Labatt Family Heart Center, The Hospital for Sick Children, Toronto, ON, Canada
| | - Russell J. McCulloh
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Alan L. Mendelsohn
- Department of Pediatrics, Division of Developmental-Behavioral Pediatrics, New York University Grossman School of Medicine, New York, NY, USA
| | - Torri D. Metz
- Department of Obstetrics and Gynecology, University of Utah Health, Salt Lake City, UT, USA
| | - Lerraughn M. Morgan
- Department of Pediatrics, Valley Children’s Healthcare, Department of Pediatrics, Madera, CA, Madera, CA, USA
| | | | - Erica R. Nahin
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Michael C. Neale
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Manette Ness-Cochinwala
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Sheila M. Nolan
- Department of Pediatrics, New York Medical College, Valhalla, NY, USA
| | - Carlos R. Oliveira
- Department of Pediatrics, Section of Infectious Diseases and Global Health, Yale University School of Medicine, New Haven, CT, USA
| | - Matthew E. Oster
- Department of Pediatric Cardiology, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - R. Mark Payne
- Department of Pediatrics, Division of Pediatric Cardiology, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hengameh Raissy
- Department of Pediatrics, University of New Mexico, Health Sciences Center, Albuquerque, NM, USA
| | - Isabelle G. Randall
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Suchitra Rao
- Department of Pediatrics, Division of Infectious Diseases, Epidemiology and Hospital Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Harrison T. Reeder
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA
| | - Johana M. Rosas
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Mark W. Russell
- Department of Pediatrics, University of Michigan Health System, Ann Arbor, MI, USA
| | - Arash A. Sabati
- Department of Pediatric Cardiology, Phoenix Children’s Hospital, Phoenix, AZ, USA
| | - Yamuna Sanil
- Division of Pediatric Cardiology, Children’s Hospital of Michigan, Detroit, MI, USA
| | - Alice I. Sato
- Department of Pediatric Infectious Disease, University of Nebraska Medical Center, Omaha, NE, USA
| | - Michael S. Schechter
- Department of Pediatrics, Children’s Hospital of Richmond at Virginia Commonwealth University, Richmond, VA, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, MO, USA
| | - Divya Shakti
- Department of Pediatrics, Pediatric Cardiology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Kavita Sharma
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lindsay M. Squeglia
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Michelle D. Stevenson
- Department of Pediatrics, University of Louisville School of Medicine, Louisville, KY, USA
| | | | - Maria M. Talavera-Barber
- Department of Pediatrics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD, USA
| | - Ronald J. Teufel
- Department of Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Deepika Thacker
- Nemours Cardiac Center, Nemours Childrens Health, Delaware, Wilmington, DE, USA
| | - Mmekom M. Udosen
- RECOVER Neurocognitive and Wellbeing/Mental Health Team, NYU Grossman School of Medicine, New York, NY, USA
| | - Megan R. Warner
- Department of Pulmonary Research, Rady Children’s Hospital-San Diego, San Diego, CA, USA
| | - Sara E. Watson
- Department of Pediatrics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Alan Werzberger
- Department of Pediatrics, Columbia University Medical Center: Columbia University Irving Medical Center, New York, NY, USA
| | - Jordan C. Weyer
- Center for Individualized Medicine, Mayo Clinic Hospital, Rochester, MN, USA
| | - Marion J. Wood
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, USA
| | - H. Shonna Yin
- Departments of Pediatrics and Population Health, New York University Grossman School of Medicine, New York, NY, USA
| | - William T. Zempsky
- Department of Pediatrics, Connecticut Children’s Medical Center, Hartford, CT, USA
| | - Emily Zimmerman
- Department of Communication Sciences & Disorders, Northeastern University, Boston, MA, USA
| | - Benard P. Dreyer
- Department of Pediatrics, New York University Grossman School of Medicine, New York, NY, USA
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9
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Rosenberg L, Liu C, Sharma R, Wood C, Vyhlidal CA, Gaedigk R, Kho AT, Ziniti JP, Celedón JC, Tantisira KG, Weiss ST, McGeachie MJ, Kechris K, Sharma S. Intrauterine Smoke Exposure, microRNA Expression during Human Lung Development, and Childhood Asthma. Int J Mol Sci 2023; 24:ijms24097727. [PMID: 37175432 PMCID: PMC10178351 DOI: 10.3390/ijms24097727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Intrauterine smoke (IUS) exposure during early childhood has been associated with a number of negative health consequences, including reduced lung function and asthma susceptibility. The biological mechanisms underlying these associations have not been established. MicroRNAs regulate the expression of numerous genes involved in lung development. Thus, investigation of the impact of IUS on miRNA expression during human lung development may elucidate the impact of IUS on post-natal respiratory outcomes. We sought to investigate the effect of IUS exposure on miRNA expression during early lung development. We hypothesized that miRNA-mRNA networks are dysregulated by IUS during human lung development and that these miRNAs may be associated with future risk of asthma and allergy. Human fetal lung samples from a prenatal tissue retrieval program were tested for differential miRNA expression with IUS exposure (measured using placental cotinine concentration). RNA was extracted and miRNA-sequencing was performed. We performed differential expression using IUS exposure, with covariate adjustment. We also considered the above model with an additional sex-by-IUS interaction term, allowing IUS effects to differ by male and female samples. Using paired gene expression profiles, we created sex-stratified miRNA-mRNA correlation networks predictive of IUS using DIABLO. We additionally evaluated whether miRNAs were associated with asthma and allergy outcomes in a cohort of childhood asthma. We profiled pseudoglandular lung miRNA in n = 298 samples, 139 (47%) of which had evidence of IUS exposure. Of 515 miRNAs, 25 were significantly associated with intrauterine smoke exposure (q-value < 0.10). The IUS associated miRNAs were correlated with well-known asthma genes (e.g., ORM1-Like Protein 3, ORDML3) and enriched in disease-relevant pathways (oxidative stress). Eleven IUS-miRNAs were also correlated with clinical measures (e.g., Immunoglobulin E andlungfunction) in children with asthma, further supporting their likely disease relevance. Lastly, we found substantial differences in IUS effects by sex, finding 95 significant IUS-miRNAs in male samples, but only four miRNAs in female samples. The miRNA-mRNA correlation networks were predictive of IUS (AUC = 0.78 in males and 0.86 in females) and suggested that IUS-miRNAs are involved in regulation of disease-relevant genes (e.g., A disintegrin and metalloproteinase domain 19 (ADAM19), LBH regulator of WNT signaling (LBH)) and sex hormone signaling (Coactivator associated methyltransferase 1(CARM1)). Our study demonstrated differential expression of miRNAs by IUS during early prenatal human lung development, which may be modified by sex. Based on their gene targets and correlation to clinical asthma and atopy outcomes, these IUS-miRNAs may be relevant for subsequent allergy and asthma risk. Our study provides insight into the impact of IUS in human fetal lung transcriptional networks and on the developmental origins of asthma and allergic disorders.
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Affiliation(s)
- Lynne Rosenberg
- Department of Pediatrics and Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Cuining Liu
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado-Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Rinku Sharma
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Cheyret Wood
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado-Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Roger Gaedigk
- Children's Mercy Hospital and Clinics, Kansas City, MO 64108, USA
| | - Alvin T Kho
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - John P Ziniti
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Kelan G Tantisira
- Division of Pediatric Respiratory Medicine, Rady Children's Hospital, University of California, San Diego, CA 92123, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado-Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sunita Sharma
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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10
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Panganiban RAM, Yang Z, Sun M, Park CY, Kasahara DI, Schaible N, Krishnan R, Kho AT, Israel E, Hershenson MB, Weiss ST, Himes BE, Fredberg JJ, Tantisira KG, Shore SA, Lu Q. Antagonizing cholecystokinin A receptor in the lung attenuates obesity-induced airway hyperresponsiveness. Nat Commun 2023; 14:47. [PMID: 36599824 PMCID: PMC9813361 DOI: 10.1038/s41467-022-35739-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
Obesity increases asthma prevalence and severity. However, the underlying mechanisms are poorly understood, and consequently, therapeutic options for asthma patients with obesity remain limited. Here we report that cholecystokinin-a metabolic hormone best known for its role in signaling satiation and fat metabolism-is increased in the lungs of obese mice and that pharmacological blockade of cholecystokinin A receptor signaling reduces obesity-associated airway hyperresponsiveness. Activation of cholecystokinin A receptor by the hormone induces contraction of airway smooth muscle cells. In vivo, cholecystokinin level is elevated in the lungs of both genetically and diet-induced obese mice. Importantly, intranasal administration of cholecystokinin A receptor antagonists (proglumide and devazepide) suppresses the airway hyperresponsiveness in the obese mice. Together, our results reveal an unexpected role for cholecystokinin in the lung and support the repurposing of cholecystokinin A receptor antagonists as a potential therapy for asthma patients with obesity.
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Affiliation(s)
- Ronald Allan M Panganiban
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Zhiping Yang
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Maoyun Sun
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Chan Young Park
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - David I Kasahara
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Niccole Schaible
- Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Ramaswamy Krishnan
- Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Alvin T Kho
- Computational Health informatics Program, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Elliot Israel
- Asthma Research Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marc B Hershenson
- Department of Pediatrics and Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Blanca E Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jeffrey J Fredberg
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Kelan G Tantisira
- Division of Pediatric Respiratory Medicine, University of California San Diego and Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Stephanie A Shore
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Quan Lu
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
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11
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Wang AL, Lahousse L, Dahlin A, Edris A, McGeachie M, Lutz SM, Sordillo JE, Brusselle G, Lasky-Su J, Weiss ST, Iribarren C, Lu MX, Tantisira KG, Wu AC. Novel genetic variants associated with inhaled corticosteroid treatment response in older adults with asthma. Thorax 2022; 78:432-441. [PMID: 35501119 PMCID: PMC9810110 DOI: 10.1136/thoraxjnl-2021-217674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 04/01/2022] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Older adults have the greatest burden of asthma and poorest outcomes. The pharmacogenetics of inhaled corticosteroid (ICS) treatment response is not well studied in older adults. METHODS A genome-wide association study of ICS response was performed in asthmatics of European ancestry in Genetic Epidemiology Research on Adult Health and Aging (GERA) by fitting Cox proportional hazards regression models, followed by validation in the Mass General Brigham (MGB) Biobank and Rotterdam Study. ICS response was measured using two definitions in asthmatics on ICS treatment: (1) absence of oral corticosteroid (OCS) bursts using prescription records and (2) absence of asthma-related exacerbations using diagnosis codes. A fixed-effect meta-analysis was performed for each outcome. The validated single-nucleotide polymorphisms (SNPs) were functionally annotated to standard databases. RESULTS In 5710 subjects in GERA, 676 subjects in MGB Biobank, and 465 subjects in the Rotterdam Study, four novel SNPs on chromosome six near PTCHD4 validated across all cohorts and met genome-wide significance on meta-analysis for the OCS burst outcome. In 4541 subjects in GERA and 505 subjects in MGB Biobank, 152 SNPs with p<5 × 10-5 were validated across these two cohorts for the asthma-related exacerbation outcome. The validated SNPs included methylation and expression quantitative trait loci for CPED1, CRADD and DST for the OCS burst outcome and GM2A, SNW1, CACNA1C, DPH1, and RPS10 for the asthma-related exacerbation outcome. CONCLUSIONS Multiple novel SNPs associated with ICS response were identified in older adult asthmatics. Several SNPs annotated to genes previously associated with asthma and other airway or allergic diseases, including PTCHD4.
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Affiliation(s)
- Alberta L Wang
- Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ahmed Edris
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Michael McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Sharon M Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Joanne E Sordillo
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Guy Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Carlos Iribarren
- Kaiser Permanente Division of Research, Kaiser Permanente, Oakland, California, USA
| | - Meng X Lu
- Kaiser Permanente Division of Research, Kaiser Permanente, Oakland, California, USA
| | - Kelan G Tantisira
- Division of Pediatric Respiratory Medicine, Rady's Children's Hospital-San Diego, University of California San Diego School of Medicine, San Diego, California, USA
| | - Ann C Wu
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
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Kho AT, McGeachie MJ, Li J, Chase RP, Amr SS, Hastie AT, Hawkins GA, Li X, Chupp GL, Meyers DA, Bleecker ER, Weiss ST, Tantisira KG. Lung function, airway and peripheral basophils and eosinophils are associated with molecular pharmacogenomic endotypes of steroid response in severe asthma. Thorax 2022; 77:452-460. [PMID: 34580195 PMCID: PMC9016241 DOI: 10.1136/thoraxjnl-2020-215523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/26/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Asthma is a complex disease with heterogeneous expression/severity. There is growing interest in defining asthma endotypes consistently associated with different responses to therapy, focusing on type 2 inflammation (Th2) as a key pathological mechanism. Current asthma endotypes are defined primarily by clinical/laboratory criteria. Each endotype is likely characterised by distinct molecular mechanisms that identify optimal therapies. METHODS We applied unsupervised (without a priori clinical criteria) principal component analysis on sputum airway cells RNA-sequencing transcriptomic data from 19 asthmatics from the Severe Asthma Research Program at baseline and 6-8 weeks follow-up after a 40 mg dose of intramuscular corticosteroids. We investigated principal components PC1, PC3 for association with 55 clinical variables. RESULTS PC3 was associated with baseline Th2 clinical features including blood (rank-sum p=0.0082) and airway (rank-sum p=0.0024) eosinophilia, FEV1 change (Kendall tau-b R=-0.333 (-0.592 to -0.012)) and follow-up FEV1 albuterol response (Kendall tau-b R=0.392 (0.079 to 0.634)). PC1 with blood basophlia (rank-sum p=0.0191). The top 5% genes contributing to PC1, PC3 were enriched for distinct immune system/inflammation ontologies suggesting distinct subject-specific clusters of transcriptomic response to corticosteroids. PC3 association with FEV1 change was reproduced in silico in a comparable independent 14-subject (baseline, 8 weeks after daily inhaled corticosteroids (ICS)) airway epithelial cells microRNAome dataset. CONCLUSIONS Transcriptomic PCs from this unsupervised methodology define molecular pharmacogenomic endotypes that may yield novel biology underlying different subject-specific responses to corticosteroid therapy in asthma, and optimal personalised asthma care. Top contributing genes to these PCs may suggest new therapeutic targets.
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Affiliation(s)
- Alvin T Kho
- Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jiang Li
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Scientific Research Centre, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, People's Republic of China
| | - Robert P Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Sami S Amr
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Partners Personalized Medicine, Partners Healthcare, Boston, Massachusetts, USA
| | - Annette T Hastie
- Center for Genomics and Personalized Medicine Research, Wake Forest Health Sciences, Winston Salem, North Carolina, USA
| | - Gregory A Hawkins
- Center for Genomics and Personalized Medicine Research, Wake Forest Health Sciences, Winston Salem, North Carolina, USA
| | - Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, University of Arizona Health Sciences, Tucson, Arizona, USA
| | - Geoffrey L Chupp
- Pulmonary & Critical Care Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, University of Arizona Health Sciences, Tucson, Arizona, USA
| | - Eugene R Bleecker
- Division of Genetics, Genomics and Precision Medicine, University of Arizona Health Sciences, Tucson, Arizona, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Partners Personalized Medicine, Partners Healthcare, Boston, Massachusetts, USA
| | - Kelan G Tantisira
- Department of Pediatrics, Division of Respiratory Medicine, University of California San Diego, La Jolla, California, USA
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13
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Tiwari A, Hobbs BD, Li J, Kho AT, Amr S, Celedón JC, Weiss ST, Hersh CP, Tantisira KG, McGeachie MJ. Blood miRNAs Are Linked to Frequent Asthma Exacerbations in Childhood Asthma and Adult COPD. Noncoding RNA 2022; 8:ncrna8020027. [PMID: 35447890 PMCID: PMC9030787 DOI: 10.3390/ncrna8020027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/23/2022] [Accepted: 03/30/2022] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs have been independently associated with asthma and COPD; however, it is unclear if microRNA associations will overlap when evaluating retrospective acute exacerbations. Objective: We hypothesized that peripheral blood microRNAs would be associated with retrospective acute asthma exacerbations in a pediatric asthma cohort and that such associations may also be relevant to acute COPD exacerbations. Methods: We conducted small-RNA sequencing on 374 whole-blood samples from children with asthma ages 6-14 years who participated in the Genetics of Asthma in Costa Rica Study (GACRS) and 450 current and former adult smokers with and without COPD who participated in the COPDGene study. Measurements and Main Results: After QC, we had 351 samples and 649 microRNAs for Differential Expression (DE) analysis between the frequent (n = 183) and no or infrequent exacerbation (n = 168) groups in GACRS. Fifteen upregulated miRs had odds ratios (OR) between 1.22 and 1.59 for a doubling of miR counts, while five downregulated miRs had ORs between 0.57 and 0.8. These were assessed for generalization in COPDGene, where three of the upregulated miRs (miR-532-3p, miR-296-5p, and miR-766-3p) and two of the downregulated miRs (miR-7-5p and miR-451b) replicated. Pathway enrichment analysis showed MAPK and PI3K-Akt signaling pathways were strongly enriched for target genes of DE miRNAs and miRNAs generalizing to COPD exacerbations, as well as infection response pathways to various pathogens. Conclusion: miRs (451b; 7-5p; 532-3p; 296-5p and 766-3p) associated with both childhood asthma and adult COPD exacerbations may play a vital role in airflow obstruction and exacerbations and point to shared genomic regulatory machinery underlying exacerbations in both diseases.
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Affiliation(s)
- Anshul Tiwari
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (A.T.); (B.D.H.); (J.L.); (A.T.K.); (S.T.W.); (C.P.H.)
| | - Brian D. Hobbs
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (A.T.); (B.D.H.); (J.L.); (A.T.K.); (S.T.W.); (C.P.H.)
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jiang Li
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (A.T.); (B.D.H.); (J.L.); (A.T.K.); (S.T.W.); (C.P.H.)
| | - Alvin T. Kho
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (A.T.); (B.D.H.); (J.L.); (A.T.K.); (S.T.W.); (C.P.H.)
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Samir Amr
- Translational Genomics Core, Mass General Brigham Personalized Medicine, Cambridge, MA 02139, USA;
| | - Juan C. Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA;
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (A.T.); (B.D.H.); (J.L.); (A.T.K.); (S.T.W.); (C.P.H.)
| | - Craig P. Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (A.T.); (B.D.H.); (J.L.); (A.T.K.); (S.T.W.); (C.P.H.)
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kelan G. Tantisira
- Division of Pediatric Respiratory Medicine, Rady Children’s Hospital, University of California, San Diego, CA 92123, USA;
| | - Michael J. McGeachie
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (A.T.); (B.D.H.); (J.L.); (A.T.K.); (S.T.W.); (C.P.H.)
- Correspondence: ; Tel.: +617-525-2272; Fax: 617-731-1541
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Hernandez-Pacheco N, Gorenjak M, Li J, Repnik K, Vijverberg SJ, Berce V, Jorgensen A, Karimi L, Schieck M, Samedy-Bates LA, Tavendale R, Villar J, Mukhopadhyay S, Pirmohamed M, Verhamme KMC, Kabesch M, Hawcutt DB, Turner S, Palmer CN, Tantisira KG, Burchard EG, Maitland-van der Zee AH, Flores C, Potočnik U, Pino-Yanes M. Identification of ROBO2 as a Potential Locus Associated with Inhaled Corticosteroid Response in Childhood Asthma. J Pers Med 2021; 11:jpm11080733. [PMID: 34442380 PMCID: PMC8399629 DOI: 10.3390/jpm11080733] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
Inhaled corticosteroids (ICS) are the most common asthma controller medication. An important contribution of genetic factors in ICS response has been evidenced. Here, we aimed to identify novel genetic markers involved in ICS response in asthma. A genome-wide association study (GWAS) of the change in lung function after 6 weeks of ICS treatment was performed in 166 asthma patients from the SLOVENIA study. Patients with an improvement in lung function ≥8% were considered as ICS responders. Suggestively associated variants (p-value ≤ 5 × 10−6) were evaluated in an independent study (n = 175). Validation of the association with asthma exacerbations despite ICS use was attempted in European (n = 2681) and admixed (n = 1347) populations. Variants previously associated with ICS response were also assessed for replication. As a result, the SNP rs1166980 from the ROBO2 gene was suggestively associated with the change in lung function (OR for G allele: 7.01, 95% CI: 3.29–14.93, p = 4.61 × 10−7), although this was not validated in CAMP. ROBO2 showed gene-level evidence of replication with asthma exacerbations despite ICS use in Europeans (minimum p-value = 1.44 × 10−5), but not in admixed individuals. The association of PDE10A-T with ICS response described by a previous study was validated. This study suggests that ROBO2 could be a potential novel locus for ICS response in Europeans.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Carretera General del Rosario 145, 38010 Santa Cruz de Tenerife, Spain;
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez s/n, Faculty of Science, Apartado 456, 38200 San Cristóbal de La Laguna, Spain;
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Avenida de Monforte de Lemos, 5, 28029 Madrid, Spain;
- Correspondence: (N.H.-P.); (U.P.); Tel.: +46-0702983315 (N.H.-P.); +386-22345854 (U.P.)
| | - Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (M.G.); (K.R.); (V.B.)
| | - Jiang Li
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, 75 Francis St, Boston, MA 02115, USA; (J.L.); (K.G.T.)
| | - Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (M.G.); (K.R.); (V.B.)
- Laboratory for Biochemistry, Molecular Biology, and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia
| | - Susanne J. Vijverberg
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (S.J.V.); (A.H.M.-v.d.Z.)
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
- Department of Pediatric Respiratory Medicine and Allergy, Emma’s Children Hospital, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Vojko Berce
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (M.G.); (K.R.); (V.B.)
- Department of Pediatrics, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia
| | - Andrea Jorgensen
- Department of Biostatistics, University of Liverpool, Crown Street, Liverpool L69 3BX, UK;
| | - Leila Karimi
- Department of Medical Informatics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (L.K.); (K.M.C.V.)
| | - Maximilian Schieck
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO), Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany; (M.S.); (M.K.)
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Lesly-Anne Samedy-Bates
- Department of Medicine, University of California, San Francisco, CA 94143, USA; (L.-A.S.-B.); (E.G.B.)
- Department of Bioengineering and Therapeutic Sciences, University of California, 533 Parnassus Ave, San Francisco, CA 94143, USA
| | - Roger Tavendale
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital, and Medical School, University of Dundee, Dundee DD1 9SY, UK; (R.T.); (S.M.); (C.N.P.)
| | - Jesús Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Avenida de Monforte de Lemos, 5, 28029 Madrid, Spain;
- Multidisciplinary Organ Dysfunction Evaluation Research Network, Research Unit, Hospital Universitario Dr. Negrín, Calle Barranco de la Ballena s/n, 35019 Las Palmas de Gran Canaria, Spain
- Keenan Research Center for Biomedical Science, Li Ka Shing Knowledge Institute, St Michael’s Hospital, 30 Bond St, Toronto, ON M5B 1W8, Canada
| | - Somnath Mukhopadhyay
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital, and Medical School, University of Dundee, Dundee DD1 9SY, UK; (R.T.); (S.M.); (C.N.P.)
- Academic Department of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children’s Hospital, 94 N-S Rd, Falmer, Brighton BN2 5BE, UK
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, 200 London Rd, Liverpool L3 9TA, UK;
| | - Katia M. C. Verhamme
- Department of Medical Informatics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (L.K.); (K.M.C.V.)
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO), Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany; (M.S.); (M.K.)
| | - Daniel B. Hawcutt
- Department of Women’s and Children’s Health, University of Liverpool, Liverpool L69 3BX, UK;
- Alder Hey Children’s Hospital, E Prescot Rd, Liverpool L14 5AB, UK
| | - Steve Turner
- Child Health, University of Aberdeen, King’s College, Aberdeen AB24 3FX, UK;
| | - Colin N. Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital, and Medical School, University of Dundee, Dundee DD1 9SY, UK; (R.T.); (S.M.); (C.N.P.)
| | - Kelan G. Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, 75 Francis St, Boston, MA 02115, USA; (J.L.); (K.G.T.)
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, and Harvard Medical School, 75 Francis St, Boston, MA 02115, USA
| | - Esteban G. Burchard
- Department of Medicine, University of California, San Francisco, CA 94143, USA; (L.-A.S.-B.); (E.G.B.)
- Department of Bioengineering and Therapeutic Sciences, University of California, 533 Parnassus Ave, San Francisco, CA 94143, USA
| | - Anke H. Maitland-van der Zee
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (S.J.V.); (A.H.M.-v.d.Z.)
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
- Department of Pediatric Respiratory Medicine and Allergy, Emma’s Children Hospital, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Carretera General del Rosario 145, 38010 Santa Cruz de Tenerife, Spain;
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Avenida de Monforte de Lemos, 5, 28029 Madrid, Spain;
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Polígono Industrial de Granadilla, 38600 Granadilla, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Faculty of Health Sciences, Apartado 456, 38200 San Cristóbal de La Laguna, Spain
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (M.G.); (K.R.); (V.B.)
- Laboratory for Biochemistry, Molecular Biology, and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia
- Correspondence: (N.H.-P.); (U.P.); Tel.: +46-0702983315 (N.H.-P.); +386-22345854 (U.P.)
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez s/n, Faculty of Science, Apartado 456, 38200 San Cristóbal de La Laguna, Spain;
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Avenida de Monforte de Lemos, 5, 28029 Madrid, Spain;
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Faculty of Health Sciences, Apartado 456, 38200 San Cristóbal de La Laguna, Spain
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Tiwari A, Wang AL, Li J, Lutz SM, Kho AT, Weiss ST, Tantisira KG, McGeachie MJ. Seasonal Variation in miR-328-3p and let-7d-3p Are Associated With Seasonal Allergies and Asthma Symptoms in Children. Allergy Asthma Immunol Res 2021; 13:576-588. [PMID: 34212545 PMCID: PMC8255344 DOI: 10.4168/aair.2021.13.4.576] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/26/2020] [Accepted: 10/08/2020] [Indexed: 12/26/2022]
Abstract
OBJECTIVE MicroRNAs (miRs) are small non-coding RNA molecules of around 18-22 nucleotides that are key regulators of many biologic processes, particularly inflammation. The purpose of this study was to determine the association of circulating miRs from asthmatic children with seasonal variation in allergic inflammation and asthma symptoms. METHODS We used available small RNA sequencing on blood serum from 398 children with mild-to-moderate asthma from the Childhood Asthma Management Program. We used seasonal asthma symptom data at the study baseline and allergen affection status from baseline skin prick tests as primary outcomes. We identified differentially expressed (DE) miRs between pairs of seasons using DESeq2. Regression analysis was used to identify associations between allergy status to specific seasonal allergens and DE miRs in 4 seasons and between seasonal asthma symptom data and DE miRs. We performed pathway enrichment analysis for target genes of the DE miRs using DAVID. RESULTS After quality control, 398 samples underwent differential analysis between the 4 seasons. We found 52 unique miRs from a total of 81 DE miRs across seasons. Further investigation of the association between these miRs and sensitization to seasonal allergens using skin prick tests revealed that 26 unique miRs from a total of 38 miRs were significantly associated with a same-season allergen. Comparison between seasonal asthma symptom data revealed that 2 of these 26 miRs also had significant associations with asthma symptoms in the same seasons: miR-328-3p (P < 0.03) and let-7d-3p (P < 0.05). Enrichment analysis showed that the most enriched pathway clusters were Rap1, Ras, and MAPK signaling pathways. CONCLUSION Our results show seasonal variation in miR-328-3p and let-7d-3p are significantly associated with seasonal asthma symptoms and seasonal allergies. These indicate a potentially protective role for let-7d-3p and a deleterious role for miR-328-3p in asthmatics sensitized to mulberry. Further work will determine whether these miRs are drivers or results of the allergic response.
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Affiliation(s)
- Anshul Tiwari
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alberta L Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jiang Li
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sharon M Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA
| | - Alvin T Kho
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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Tiwari A, Li J, Kho AT, Sun M, Lu Q, Weiss ST, Tantisira KG, McGeachie MJ. COPD-associated miR-145-5p is downregulated in early-decline FEV 1 trajectories in childhood asthma. J Allergy Clin Immunol 2021; 147:2181-2190. [PMID: 33385444 PMCID: PMC8184594 DOI: 10.1016/j.jaci.2020.11.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Many microRNAs (miRNAs) have been associated with asthma and chronic obstructive pulmonary disease (COPD). Longitudinal lung function growth trajectories of children with asthma-normal growth, reduced growth (RG), early decline (ED), and RG with an ED (RGED)-have been observed, with RG and RGED associated with adverse outcomes, including COPD. OBJECTIVE Our aim was to determine whether circulating miRNAs from an early age in children with asthma would be prognostic of reduced lung function growth patterns over the next 16 years. METHODS We performed small RNA sequencing on sera from 492 children aged 5 to 12 years with mild-to-moderate asthma from the CAMP clinical trial, who were subsequently followed for 12 to 16 years. miRNAs were assessed for differential expression between previously assigned lung function growth patterns. RESULTS We had 448 samples and 259 miRNAs for differential analysis. In a comparison of the normal and the most severe group (ie, normal growth compared with RGED), we found 1 strongly dysregulated miRNA, hsa-miR-145-5p (P < 8.01E-05). This miR was downregulated in both ED groups (ie, ED and RGED). We verified that miR-145-5p was strongly associated with airway smooth muscle cell growth in vitro. CONCLUSION Our results showed that miR-145-5p is associated with the ED patterns of lung function growth leading to COPD in children with asthma and additionally increases airway smooth muscle cell proliferation. This represents a significant extension of our understanding of the role of miR-145-5p in COPD and suggests that reduced expression of miR-145-5p is a risk factor for ED of long-term lung function.
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Affiliation(s)
- Anshul Tiwari
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Jiang Li
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Alvin T Kho
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Computational Health Informatics Program, Boston Children's Hospital, Boston, Mass
| | - Maoyun Sun
- Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Quan Lu
- Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
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Hernandez-Pacheco N, Vijverberg SJ, Herrera-Luis E, Li J, Sio YY, Granell R, Corrales A, Maroteau C, Lethem R, Perez-Garcia J, Farzan N, Repnik K, Gorenjak M, Soares P, Karimi L, Schieck M, Pérez-Méndez L, Berce V, Tavendale R, Eng C, Sardon O, Kull I, Mukhopadhyay S, Pirmohamed M, Verhamme KMC, Burchard EG, Kabesch M, Hawcutt DB, Melén E, Potočnik U, Chew FT, Tantisira KG, Turner S, Palmer CN, Flores C, Pino-Yanes M, Maitland-van der Zee AH. Genome-wide association study of asthma exacerbations despite inhaled corticosteroid use. Eur Respir J 2021; 57:2003388. [PMID: 33303529 PMCID: PMC8122045 DOI: 10.1183/13993003.03388-2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
RATIONALE Substantial variability in response to asthma treatment with inhaled corticosteroids (ICS) has been described among individuals and populations, suggesting the contribution of genetic factors. Nonetheless, only a few genes have been identified to date. We aimed to identify genetic variants associated with asthma exacerbations despite ICS use in European children and young adults and to validate the findings in non-Europeans. Moreover, we explored whether a gene-set enrichment analysis could suggest potential novel asthma therapies. METHODS A genome-wide association study (GWAS) of asthma exacerbations was tested in 2681 children of European descent treated with ICS from eight studies. Suggestive association signals were followed up for replication in 538 European asthma patients. Further evaluation was performed in 1773 non-Europeans. Variants revealed by published GWAS were assessed for replication. Additionally, gene-set enrichment analysis focused on drugs was performed. RESULTS 10 independent variants were associated with asthma exacerbations despite ICS treatment in the discovery phase (p≤5×10-6). Of those, one variant at the CACNA2D3-WNT5A locus was nominally replicated in Europeans (rs67026078; p=0.010), but this was not validated in non-European populations. Five other genes associated with ICS response in previous studies were replicated. Additionally, an enrichment of associations in genes regulated by trichostatin A treatment was found. CONCLUSIONS The intergenic region of CACNA2D3 and WNT5A was revealed as a novel locus for asthma exacerbations despite ICS treatment in European populations. Genes associated were related to trichostatin A, suggesting that this drug could regulate the molecular mechanisms involved in treatment response.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Genomics and Health Group, Dept of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Susanne J Vijverberg
- Dept of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Dept of Paediatric Respiratory Medicine and Allergy, Emma's Children Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Esther Herrera-Luis
- Genomics and Health Group, Dept of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Jiang Li
- The Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yang Yie Sio
- Dept of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Raquel Granell
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Almudena Corrales
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Cyrielle Maroteau
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Ryan Lethem
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Javier Perez-Garcia
- Genomics and Health Group, Dept of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Niloufar Farzan
- Dept of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Breathomix B.V., El Reeuwijk, The Netherlands
| | - Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Patricia Soares
- Academic Dept of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
- Escola Nacional de Saúde Pública, Lisboa, Portugal
| | - Leila Karimi
- Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maximilian Schieck
- Dept of Paediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
- Dept of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Lina Pérez-Méndez
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Dept of Clinic Epidemiology and Biostatistics, Research Unit, Hospital Universitario N.S. de Candelaria, Gerencia de Atención Primaria, Santa Cruz de Tenerife, Spain
| | - Vojko Berce
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Dept of Paediatrics, University Medical Centre Maribor, Maribor, Slovenia
| | - Roger Tavendale
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Celeste Eng
- Dept of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Olaia Sardon
- Division of Paediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain
- Dept of Paediatrics, University of the Basque Country (UPV/EHU), San Sebastián, Spain
| | - Inger Kull
- Dept of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet and Sachs' Children's Hospital, Stockholm, Sweden
| | - Somnath Mukhopadhyay
- Academic Dept of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Munir Pirmohamed
- Dept of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Katia M C Verhamme
- Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Esteban G Burchard
- Dept of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Dept of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Michael Kabesch
- Dept of Paediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Daniel B Hawcutt
- Dept of Women's and Children's Health, University of Liverpool, Liverpool, UK
- Alder Hey Children's Hospital, Liverpool, UK
| | - Erik Melén
- Dept of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet and Sachs' Children's Hospital, Stockholm, Sweden
- Institute of Environmental Medicine, Karolinska Institutet, Solna, Sweden
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Fook Tim Chew
- Dept of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Steve Turner
- Child Health, University of Aberdeen, Aberdeen, UK
| | - Colin N Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Genomics and Health Group, Dept of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- These authors contributed equally to this work
| | - Anke H Maitland-van der Zee
- Dept of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Dept of Paediatric Respiratory Medicine and Allergy, Emma's Children Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- These authors contributed equally to this work
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18
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Li J, Tiwari A, Mirzakhani H, Wang AL, Kho AT, McGeachie MJ, Litonjua AA, Weiss ST, Tantisira KG. Circulating MicroRNA: Incident Asthma Prediction and Vitamin D Effect Modification. J Pers Med 2021; 11:jpm11040307. [PMID: 33923455 PMCID: PMC8073146 DOI: 10.3390/jpm11040307] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 12/23/2022] Open
Abstract
Of children with recurrent wheezing in early childhood, approximately half go on to develop asthma. MicroRNAs have been described as excellent non-invasive biomarkers due to their prognostic utility. We hypothesized that circulating microRNAs can predict incident asthma and that that prediction might be modified by vitamin D. We selected 75 participants with recurrent wheezing at 3 years old from the Vitamin D Antenatal Asthma Reduction Trial (VDAART). Plasma samples were collected at age 3 and sequenced for small RNA-Seq. The read counts were normalized and filtered by depth and coverage. Logistic regression was employed to associate miRNAs at age 3 with asthma status at age 5. While the overall effect of miRNA on asthma occurrence was weak, we identified 38 miRNAs with a significant interaction effect with vitamin D and 32 miRNAs with a significant main effect in the high vitamin D treatment group in VDAART. We validated the VDAART results in Project Viva for both the main effect and interaction effect. Meta-analysis was performed on both cohorts to obtain the combined effect and a logistic regression model was used to predict incident asthma at age 7 in Project Viva. Of the 23 overlapped miRNAs in the stratified and interaction analysis above, 9 miRNAs were replicated in Project Viva with strong effect size and remained in the meta-analysis of the two populations. The target genes of the 9 miRNAs were enriched for asthma-related Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways. Using logistic regression, microRNA hsa-miR-574-5p had a good prognostic ability for incident asthma prognosis with an area under the receiver operating characteristic (AUROC) of 0.83. In conclusion, miRNAs appear to be good biomarkers of incident asthma, but only when vitamin D level is considered.
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Affiliation(s)
- Jiang Li
- Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen 518107, China;
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.T.); (H.M.); (A.L.W.); (A.T.K.); (M.J.M.); (S.T.W.)
| | - Anshul Tiwari
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.T.); (H.M.); (A.L.W.); (A.T.K.); (M.J.M.); (S.T.W.)
| | - Hooman Mirzakhani
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.T.); (H.M.); (A.L.W.); (A.T.K.); (M.J.M.); (S.T.W.)
| | - Alberta L. Wang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.T.); (H.M.); (A.L.W.); (A.T.K.); (M.J.M.); (S.T.W.)
| | - Alvin T. Kho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.T.); (H.M.); (A.L.W.); (A.T.K.); (M.J.M.); (S.T.W.)
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Michael J. McGeachie
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.T.); (H.M.); (A.L.W.); (A.T.K.); (M.J.M.); (S.T.W.)
| | - Augusto A. Litonjua
- Division of Pediatric Pulmonary Medicine, Golisano Children’s Hospital at Strong, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.T.); (H.M.); (A.L.W.); (A.T.K.); (M.J.M.); (S.T.W.)
| | - Kelan G. Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.T.); (H.M.); (A.L.W.); (A.T.K.); (M.J.M.); (S.T.W.)
- Division of Pediatric Respiratory Medicine, Rady Children’s Hospital San Diego, University of California, San Diego, CA 92123, USA
- Correspondence: ; Tel.: +1-(858)-966-5846; Fax: +1-(858)-966-8457
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19
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Wang AL, Li J, Kho AT, McGeachie MJ, Tantisira KG. Enhancing the prediction of childhood asthma remission: Integrating clinical factors with microRNAs. J Allergy Clin Immunol 2021; 147:1093-1095.e1. [PMID: 32888944 PMCID: PMC8515417 DOI: 10.1016/j.jaci.2020.08.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/06/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022]
Abstract
The novel integration of baseline clinical and microRNA variables significantly improves the long-term individualized prediction of childhood asthma remission by early adulthood compared to using clinical variables alone.
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Affiliation(s)
- Alberta L Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Mass; Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass.
| | - Jiang Li
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Mass
| | - Alvin T Kho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Mass
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Mass
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Mass; Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston, Mass
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20
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Edris A, de Roos EW, McGeachie MJ, Verhamme KMC, Brusselle GG, Tantisira KG, Iribarren C, Lu M, Wu AC, Stricker BH, Lahousse L. Pharmacogenetics of inhaled corticosteroids and exacerbation risk in adults with asthma. Clin Exp Allergy 2021; 52:33-45. [PMID: 33428814 DOI: 10.1111/cea.13829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Inhaled corticosteroids (ICS) are a cornerstone of asthma treatment. However, their efficacy is characterized by wide variability in individual responses. OBJECTIVE We investigated the association between genetic variants and risk of exacerbations in adults with asthma and how this association is affected by ICS treatment. METHODS We investigated the pharmacogenetic effect of 10 single nucleotide polymorphisms (SNPs) selected from the literature, including SNPs previously associated with response to ICS (assessed by change in lung function or exacerbations) and novel asthma risk alleles involved in inflammatory pathways, within all adults with asthma from the Dutch population-based Rotterdam study with replication in the American GERA cohort. The interaction effects of the SNPs with ICS on the incidence of asthma exacerbations were assessed using hurdle models adjusting for age, sex, BMI, smoking and treatment step according to the GINA guidelines. Haplotype analyses were also conducted for the SNPs located on the same chromosome. RESULTS rs242941 (CRHR1) homozygotes for the minor allele (A) showed a significant, replicated increased risk for frequent exacerbations (RR = 6.11, P < 0.005). In contrast, rs1134481 T allele within TBXT (chromosome 6, member of a family associated with embryonic lung development) showed better response with ICS. rs37973 G allele (GLCCI1) showed a significantly poorer response on ICS within the discovery cohort, which was also significant but in the opposite direction in the replication cohort. CONCLUSION rs242941 in CRHR1 was associated with poor ICS response. Conversely, TBXT variants were associated with improved ICS response. These associations may reveal specific endotypes, potentially allowing prediction of exacerbation risk and ICS response.
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Affiliation(s)
- Ahmed Edris
- Department of Bioanalysis, Ghent University, Ghent, Belgium.,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Emmely W de Roos
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium.,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Katia M C Verhamme
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Guy G Brusselle
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium.,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Respiratory Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,University of California San Diego, CA, USA
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Meng Lu
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Ann Chen Wu
- Department of Population Medicine, Precision Medicine Translational Research (PROMoTeR) Center, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA
| | - Bruno H Stricker
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, Ghent, Belgium.,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
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21
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Kachroo P, Morrow JD, Kho AT, Vyhlidal CA, Silverman EK, Weiss ST, Tantisira KG, DeMeo DL. Co-methylation analysis in lung tissue identifies pathways for fetal origins of COPD. Eur Respir J 2020; 56:13993003.02347-2019. [PMID: 32482784 DOI: 10.1183/13993003.02347-2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/21/2020] [Indexed: 12/21/2022]
Abstract
COPD likely has developmental origins; however, the underlying molecular mechanisms are not fully identified. Investigation of lung tissue-specific epigenetic modifications such as DNA methylation using network approaches might facilitate insights linking in utero smoke (IUS) exposure and risk for COPD in adulthood.We performed genome-wide methylation profiling for adult lung DNA from 160 surgical samples and 78 fetal lung DNA samples isolated from discarded tissue at 8-18 weeks of gestation. Co-methylation networks were constructed to identify preserved modules that shared methylation patterns in fetal and adult lung tissues and associations with fetal IUS exposure, gestational age and COPD.Weighted correlation networks highlighted preserved and co-methylated modules for both fetal and adult lung data associated with fetal IUS exposure, COPD and lower adult lung function. These modules were significantly enriched for genes involved in embryonic organ development and specific inflammation-related pathways, including Hippo, phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT), Wnt, mitogen-activated protein kinase and transforming growth factor-β signalling. Gestational age-associated modules were remarkably preserved for COPD and lung function, and were also annotated to genes enriched for the Wnt and PI3K/AKT pathways.Epigenetic network perturbations in fetal lung tissue exposed to IUS and of early lung development recapitulated in adult lung tissue from ex-smokers with COPD. Overlapping fetal and adult lung tissue network modules highlighted putative disease pathways supportive of exposure-related and age-associated developmental origins of COPD.
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Affiliation(s)
- Priyadarshini Kachroo
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jarrett D Morrow
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alvin T Kho
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Edwin K Silverman
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA .,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
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22
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King C, McKenna A, Farzan N, Vijverberg SJ, van der Schee MP, Maitland-van der Zee AH, Arianto L, Bisgaard H, BØnnelykke K, Berce V, PotoČnik U, Repnik K, Carleton B, Daley D, Chew FT, Chiang WC, Sio YY, Cloutier MM, Den Dekker HT, Duijts L, de Jongste JC, Dijk FN, Flores C, Hernandez-Pacheco N, Mukhopadhyay S, Basu K, Tantisira KG, Verhamme KM, Celedón JC, Forno E, Canino G, Francis B, Pirmohamed M, Sinha I, Hawcutt DB. Pharmacogenomic associations of adverse drug reactions in asthma: systematic review and research prioritisation. Pharmacogenomics J 2020; 20:621-628. [PMID: 31949291 PMCID: PMC7502355 DOI: 10.1038/s41397-019-0140-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 11/22/2019] [Accepted: 12/16/2019] [Indexed: 11/16/2022]
Abstract
A systematic review of pharmacogenomic studies capturing adverse drug reactions (ADRs) related to asthma medications was undertaken, and a survey of Pharmacogenomics in Childhood Asthma (PiCA) consortia members was conducted. Studies were eligible if genetic polymorphisms were compared with suspected ADR(s) in a patient with asthma, as either a primary or secondary outcome. Five studies met the inclusion criteria. The ADRs and polymorphisms identified were change in lung function tests (rs1042713), adrenal suppression (rs591118), and decreased bone mineral density (rs6461639) and accretion (rs9896933, rs2074439). Two of these polymorphisms were replicated within the paper, but none had external replication. Priorities from PiCA consortia members (representing 15 institution in eight countries) for future studies were tachycardia (SABA/LABA), adrenal suppression/crisis and growth suppression (corticosteroids), sleep/behaviour disturbances (leukotriene receptor antagonists), and nausea and vomiting (theophylline). Future pharmacogenomic studies in asthma should collect relevant ADR data as well as markers of efficacy.
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Affiliation(s)
- Charlotte King
- Department of Women and Child's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Amanda McKenna
- Department of Women and Child's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Niloufar Farzan
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne J Vijverberg
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Marc P van der Schee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Lambang Arianto
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus BØnnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Vojko Berce
- Department of Pediatrics, University Medical Centre Maribor, Maribor, Slovenia
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Uros PotoČnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Katja Repnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Bruce Carleton
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, BC Children's Hospital and Research Institute, Vancouver, Canada
| | - Denise Daley
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, BC Children's Hospital and Research Institute, Vancouver, Canada
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore, Singapore
| | - Wen Chin Chiang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore, Singapore
| | - Yang Yie Sio
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore, Singapore
| | - Michelle M Cloutier
- Asthma Center, Connecticut Children's Medical Center, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Herman T Den Dekker
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Liesbeth Duijts
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan C de Jongste
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands
| | - F Nicole Dijk
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands
- Groningen Research Institute for Asthma & COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Somnath Mukhopadhyay
- Academic Department of Paediatrics, Brighton & Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
| | - Kaninika Basu
- Academic Department of Paediatrics, Brighton & Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Boston, MA, 02115, USA
- Division of Pulmonary & Critical Care Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA, 02115, USA
| | - Katia M Verhamme
- Department of Medical Informatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Glorisa Canino
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Ben Francis
- Department of Biostatistics, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Munir Pirmohamed
- Department of Molecular & Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Ian Sinha
- Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, England
| | - Daniel B Hawcutt
- Department of Women and Child's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, England.
- NIHR Alder Hey Clinical Research Facility, Alder Hey Children's Hospital, Liverpool, England.
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23
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Kho AT, Sordillo J, Wu AC, Cho MH, Sharma S, Tiwari A, Lasky-Su J, Weiss ST, Tantisira KG, McGeachie MJ. CASTER: Cross-Sectional Asthma STEroid Response Measurement. J Pers Med 2020; 10:jpm10030095. [PMID: 32825299 PMCID: PMC7564544 DOI: 10.3390/jpm10030095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 11/16/2022] Open
Abstract
Asthma patient response to inhaled corticosteroids (ICS) is variable and difficult to quantify. We aimed to define a measure of steroid response suitable for pharmacogenetic research in longitudinal and cross-sectional cohorts. Using longitudinal data from the Childhood Asthma Management Program (CAMP) asthma cohort, we defined the Cross-sectional Asthma STEroid Response (CASTER) measure in cross-sectional data. We then applied this to cross-sectional slices of four independent asthma cohorts: The Improving Asthma Control Trial (IMPACT), the Salmeterol or Corticosteroids Study (SOCS), the Pediatric Asthma Controller Trial (PACT), and the Genetics of Asthma in Costa Rica Study (GACRS). CASTER achieved high accuracy on the childhood asthma cohorts: GACRS, PACT, and also on cross-sectional data from CAMP (AUCs 82%, 71%, 63%, respectively). This demonstrates that select cross-sectional clinical information is sufficient to identify good and poor responders to ICS treatment in childhood asthma. Thus, CASTER represents a major improvement in the usability and applicability of steroid response measures in asthma research.
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Affiliation(s)
- Alvin T. Kho
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02215, USA;
| | - Joanne Sordillo
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02215, USA; (J.S.); (A.C.W.)
| | - Ann Chen Wu
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02215, USA; (J.S.); (A.C.W.)
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA; (M.H.C.); (A.T.); (J.L.-S.); (S.T.W.); (K.G.T.)
| | - Sunita Sharma
- Department of Medicine—Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora, CO 80010, USA;
| | - Anshul Tiwari
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA; (M.H.C.); (A.T.); (J.L.-S.); (S.T.W.); (K.G.T.)
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA; (M.H.C.); (A.T.); (J.L.-S.); (S.T.W.); (K.G.T.)
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA; (M.H.C.); (A.T.); (J.L.-S.); (S.T.W.); (K.G.T.)
| | - Kelan G. Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA; (M.H.C.); (A.T.); (J.L.-S.); (S.T.W.); (K.G.T.)
| | - Michael J. McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA; (M.H.C.); (A.T.); (J.L.-S.); (S.T.W.); (K.G.T.)
- Correspondence: ; Tel.: +1-617-525-2272
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24
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King C, McKenna A, Farzan N, Vijverberg SJ, van der Schee MP, Maitland-van der Zee AH, Arianto L, Bisgaard H, BØnnelykke K, Berce V, PotoČnik U, Repnik K, Carleton B, Daley D, Chew FT, Chiang WC, Sio YY, Cloutier MM, Den Dekker HT, Duijts L, de Jongste JC, Dijk FN, Flores C, Hernandez-Pacheco N, Mukhopadhyay S, Basu K, Tantisira KG, Verhamme KM, Celedón JC, Forno E, Canino G, Francis B, Pirmohamed M, Sinha I, Hawcutt DB. Correction: Pharmacogenomic associations of adverse drug reactions in asthma: systematic review and research prioritization. Pharmacogenomics J 2020; 20:746. [PMID: 32704026 PMCID: PMC7502354 DOI: 10.1038/s41397-020-0178-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Charlotte King
- Department of Women and Child's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Amanda McKenna
- Department of Women and Child's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Niloufar Farzan
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne J Vijverberg
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Marc P van der Schee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Lambang Arianto
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus BØnnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Vojko Berce
- Department of Pediatrics, University Medical Centre Maribor, Maribor, Slovenia.,Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Uros PotoČnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Katja Repnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Bruce Carleton
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, BC Children's Hospital and Research Institute, Vancouver, Canada
| | - Denise Daley
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, BC Children's Hospital and Research Institute, Vancouver, Canada
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore, Singapore
| | - Wen Chin Chiang
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore, Singapore
| | - Yang Yie Sio
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore, Singapore
| | - Michelle M Cloutier
- Asthma Center, Connecticut Children's Medical Center, University of Connecticut Health Center, Connecticut, USA
| | - Herman T Den Dekker
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Liesbeth Duijts
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan C de Jongste
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands
| | - F Nicole Dijk
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands.,Groningen Research Institute for Asthma & COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Somnath Mukhopadhyay
- Academic Department of Paediatrics, Brighton & Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
| | - Kaninika Basu
- Academic Department of Paediatrics, Brighton & Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA, 02115, USA.,Division of Pulmonary & Critical Care Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA, 02115, USA
| | - Katia M Verhamme
- Department of Medical Informatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Glorisa Canino
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Ben Francis
- Department of Biostatistics, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Munir Pirmohamed
- Department of Molecular & Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Ian Sinha
- Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, England
| | - Daniel B Hawcutt
- Department of Women and Child's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, England. .,NIHR Alder Hey Clinical Research Facility, Alder Hey Children's Hospital, Liverpool, England.
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25
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Li J, Panganiban R, Kho AT, McGeachie MJ, Farnam L, Chase RP, Weiss ST, Lu Q, Tantisira KG. Circulating MicroRNAs and Treatment Response in Childhood Asthma. Am J Respir Crit Care Med 2020; 202:65-72. [PMID: 32272022 PMCID: PMC7328325 DOI: 10.1164/rccm.201907-1454oc] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 04/09/2020] [Indexed: 12/16/2022] Open
Abstract
Rationale: Inhaled corticosteroids (ICS) are key treatments for controlling asthma and preventing asthma attacks. However, the responsiveness to ICS varies among individuals. MicroRNAs (miRNAs) have been lauded for their prognostic utility.Objectives: We hypothesized that circulating miRNAs obtained at baseline/prerandomization in the Childhood Asthma Management Program (CAMP) could serve as biomarkers and biologic mediators of ICS clinical response over the 4-year clinical trial period.Methods: We selected baseline serum samples from 462 CAMP subjects subsequently randomized to either ICS (budesonide) or placebo. Samples underwent small RNA sequencing, and read counts were normalized and filtered by depth and coverage. Linear regression was used to associate miRNAs with change in FEV1% (prebronchodilator FEV1 as a percent predicted) over the 4-year treatment period in both main effects and interaction models. We validated the function of the top associated miRNAs by luciferase reporter assays of glucocorticoid-mediated transrepression and predicted response to ICS through logistic regression models.Measurements and Main Results: We identified 7 miRNAs significantly associated with FEV1% change (P ≤ 0.05) and 15 miRNAs with significant interaction (P ≤ 0.05) to ICS versus placebo treatments. We selected three miRNAs for functional validation, of which hsa-miR-155-5p and hsa-miR-532-5p were significantly associated with changes in dexamethasone-induced transrepression of NF-κB. Combined, these two miRNAs were predictive of ICS response over the course of the clinical trial, with an area under the receiver operating characteristic curve of 0.86.Conclusions: We identified two functional circulating miRNAs predictive of asthma ICS treatment response over time.
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Affiliation(s)
- Jiang Li
- Channing Division of Network Medicine and
| | - Ronald Panganiban
- Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; and
| | - Alvin T. Kho
- Boston Children’s Hospital, Boston, Massachusetts
| | | | | | | | | | - Quan Lu
- Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; and
| | - Kelan G. Tantisira
- Channing Division of Network Medicine and
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
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26
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McGeachie MJ, Wang AL, Lutz SM, Sordillo JE, Weiss ST, Tantisira KG, Iribarren C, Lu MX, Wu AC. Real-Life Patterns of Exacerbations While on Inhaled Corticosteroids and Long-Acting Beta Agonists for Asthma over 15 Years. J Clin Med 2020; 9:jcm9030819. [PMID: 32197337 PMCID: PMC7141292 DOI: 10.3390/jcm9030819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/10/2020] [Accepted: 03/16/2020] [Indexed: 12/14/2022] Open
Abstract
Asthma affects more than 300 million people in the world, costs over $80 billion annually in the United States, and is efficaciously treated with inhaled corticosteroids (ICS). To our knowledge, no studies have examined the real-world effectiveness of ICS, including the combination therapy consisting of ICS and long-acting beta agonists (LABAs), and patterns of use over a 15-year time period. We used data from the Kaiser Permanente Northern California multi-ethnic Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort which comprises longitudinal electronic health record data of over 100,000 people. Data included longitudinal asthma-related events, such as ambulatory office visits, hospitalizations, emergency department (ED) visits, and fills of ICS and ICS-LABA combination. Asthma exacerbations were defined as an asthma-related ED visit, hospitalization, or oral corticosteroid (OCS) burst. We used an expected-value approach to determine ICS and ICS-LABA coverage over exacerbation events. We compared rates of exacerbation of subjects on ICS or ICS-LABAs to their own rates of exacerbation when off controller medications. We found ICS-LABA therapy had significant effects, reducing all types of exacerbations per day by a factor of 1.76 (95% CI (1.06, 2.93), p = 0.03) and, specifically, bursts per day by a factor of 1.91 (95% CI (1.04, 3.53), p = 0.037). In conclusion, ICS-LABA therapy was significantly associated with fewer asthma-related exacerbations in a large population of individuals with asthma who were followed for 15 years.
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Affiliation(s)
- Michael J. McGeachie
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.J.M.)
| | - Alberta L. Wang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.J.M.)
| | - Sharon M. Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02115, USA
| | - Joanne E. Sordillo
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02115, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.J.M.)
| | - Kelan G. Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.J.M.)
| | - Carlos Iribarren
- Kaiser Permanente Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Meng X. Lu
- Kaiser Permanente Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Ann Chen Wu
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02115, USA
- Correspondence: ; Tel.: +1-617-867-4823
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27
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Li J, Kho AT, Chase RP, Pantano L, Farnam L, Amr SS, Tantisira KG. COMPSRA: a COMprehensive Platform for Small RNA-Seq data Analysis. Sci Rep 2020; 10:4552. [PMID: 32165660 PMCID: PMC7067867 DOI: 10.1038/s41598-020-61495-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/20/2020] [Indexed: 11/09/2022] Open
Abstract
Small RNA-Seq is a common means to interrogate the small RNA’ome or the full spectrum of small RNAs (<200 nucleotide length) of a biological system. A pivotal problem in NGS based small RNA analysis is identifying and quantifying the small RNA’ome constituent components. For example, small RNAs in the circulatory system (circulating RNAs) are potential disease biomarkers and their function is being actively investigated. Most existing NGS data analysis tools focus on the microRNA component and a few other small RNA types like piRNA, snRNA and snoRNA. A comprehensive platform is needed to interrogate the full small RNA’ome, a prerequisite for down-stream data analysis. We present COMPSRA, a comprehensive modular stand-alone platform for identifying and quantifying small RNAs from small RNA sequencing data. COMPSRA contains prebuilt customizable standard RNA databases and sequence processing tools to enable turnkey basic small RNA analysis. We evaluated COMPSRA against comparable existing tools on small RNA sequencing data set from serum samples of 12 healthy human controls, and COMPSRA identified a greater diversity and abundance of small RNA molecules. COMPSRA is modular, stand-alone and integrates multiple customizable RNA databases and sequence processing tool and is distributed under the GNU General Public License free to non-commercial registered users at https://github.com/cougarlj/COMPSRA.
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Affiliation(s)
- Jiang Li
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | | | - Robert P Chase
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lorena Pantano
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Leanna Farnam
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sami S Amr
- Partners Personalized Medicine, Boston, MA, USA
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA. .,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.
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28
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Wang AL, Qiu W, DeMeo DL, Raby BA, Weiss ST, Tantisira KG. DNA methylation is associated with improvement in lung function on inhaled corticosteroids in pediatric asthmatics. Pharmacogenet Genomics 2020; 29:65-68. [PMID: 30640894 DOI: 10.1097/fpc.0000000000000366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Asthma is the most common chronic disease in children. Inhaled corticosteroids (ICS) are the first-line treatment for asthma control, but up to one-third of children have a poor treatment response. The mechanism of ICS resistance is poorly understood, and the role of DNA methylation in ICS treatment response is not known. We examined the association between peripheral blood DNA methylation and ICS treatment response in 152 pediatric persistent asthmatics from the Childhood Asthma Management Program. Response to ICS was measured by the percentage change in forced expiratory volume in 1 s (FEV1) 8 weeks after treatment initiation. The top CpG sites with a nominal P value less than 0.001 were correlated with gene expression using Pearson's and partial correlations. In 152 participants, mean±SD age was 9.8±2.0 years and median change in FEV1 after ICS initiation was 4.6% (interquartile range: 10.4%). A total of 545 CpG sites were differentially methylated (nominal P<0.05), and seven CpG sites had a nominal P value less than 0.001. Relative hypermethylation of cg20434811, cg02822723, cg14066280, cg27254601, and cg23913400 and relative hypomethylation of cg24937126 and cg24711626 were associated with an increase in FEV1 on ICS treatment. One CpG site was associated with gene expression. Relative hypermethylation of cg27254601 was associated with both an increase in FEV1 and BOLA2 expression (ρ=0.25, P=0.02). We identified a novel association between BOLA2 methylation, gene expression, and ICS response as measured by lung function. Pharmacoepigenetics has the potential to detect treatment sensitivity in persistent childhood asthma.
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Affiliation(s)
- Alberta L Wang
- Channing Division of Network Medicine.,Division of Rheumatology, Immunology and Allergy
| | | | - Dawn L DeMeo
- Channing Division of Network Medicine.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital
| | - Benjamin A Raby
- Channing Division of Network Medicine.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital.,Division of Pulmonary Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Kelan G Tantisira
- Channing Division of Network Medicine.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital
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29
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Dahlin A, Sordillo JE, McGeachie M, Kelly RS, Tantisira KG, Lutz SM, Lasky-Su J, Wu AC. Genome-wide interaction study reveals age-dependent determinants of responsiveness to inhaled corticosteroids in individuals with asthma. PLoS One 2020; 15:e0229241. [PMID: 32119686 PMCID: PMC7051058 DOI: 10.1371/journal.pone.0229241] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/01/2020] [Indexed: 11/19/2022] Open
Abstract
While genome-wide association studies have identified genes involved in differential treatment responses to inhaled corticosteroids (ICS) in asthma, few studies have evaluated the potential effects of age in this context. A significant proportion of asthmatics experience exacerbations (hospitalizations and emergency department visits) during ICS treatment. We evaluated the interaction of genetic variation and age on ICS response (measured by the occurrence of exacerbations) through a genome-wide interaction study (GWIS) of 1,321 adult and child asthmatic patients of European ancestry. We identified 107 genome-wide suggestive (P<10-05) age-by-genotype interactions, two of which also met genome-wide significance (P<5x10-08) (rs34631960 [OR 2.3±1.6-3.3] in thrombospondin type 1 domain-containing protein 4 (THSD4) and rs2328386 [OR 0.5±0.3-0.7] in human immunodeficiency virus type I enhancer binding protein 2 (HIVEP2)) by joint analysis of GWIS results from discovery and replication populations. In addition to THSD4 and HIVEP2, age-by-genotype interactions also prioritized genes previously identified as asthma candidate genes, including DPP10, HDAC9, TBXAS1, FBXL7, and GSDMB/ORMDL3, as pharmacogenomic loci as well. This study is the first to link these genes to a pharmacogenetic trait for asthma.
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Affiliation(s)
- Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joanne E. Sordillo
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States of America
| | - Michael McGeachie
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rachel S. Kelly
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kelan G. Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Sharon M. Lutz
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States of America
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ann Chen Wu
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States of America
- * E-mail:
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30
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Merid SK, Novoloaca A, Sharp GC, Küpers LK, Kho AT, Roy R, Gao L, Annesi-Maesano I, Jain P, Plusquin M, Kogevinas M, Allard C, Vehmeijer FO, Kazmi N, Salas LA, Rezwan FI, Zhang H, Sebert S, Czamara D, Rifas-Shiman SL, Melton PE, Lawlor DA, Pershagen G, Breton CV, Huen K, Baiz N, Gagliardi L, Nawrot TS, Corpeleijn E, Perron P, Duijts L, Nohr EA, Bustamante M, Ewart SL, Karmaus W, Zhao S, Page CM, Herceg Z, Jarvelin MR, Lahti J, Baccarelli AA, Anderson D, Kachroo P, Relton CL, Bergström A, Eskenazi B, Soomro MH, Vineis P, Snieder H, Bouchard L, Jaddoe VW, Sørensen TIA, Vrijheid M, Arshad SH, Holloway JW, Håberg SE, Magnus P, Dwyer T, Binder EB, DeMeo DL, Vonk JM, Newnham J, Tantisira KG, Kull I, Wiemels JL, Heude B, Sunyer J, Nystad W, Munthe-Kaas MC, Räikkönen K, Oken E, Huang RC, Weiss ST, Antó JM, Bousquet J, Kumar A, Söderhäll C, Almqvist C, Cardenas A, Gruzieva O, Xu CJ, Reese SE, Kere J, Brodin P, Solomon O, Wielscher M, Holland N, Ghantous A, Hivert MF, Felix JF, Koppelman GH, London SJ, Melén E. Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age. Genome Med 2020; 12:25. [PMID: 32114984 PMCID: PMC7050134 DOI: 10.1186/s13073-020-0716-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. METHODS We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: fetal brain and lung. RESULTS We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10- 7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. CONCLUSIONS We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.
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Affiliation(s)
- Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Leanne K Küpers
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alvin T Kho
- Computational Health Informatics Program, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ritu Roy
- Computational Biology And Informatics, University of California, San Francisco, San Francisco, CA, USA
- HDF Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Isabella Annesi-Maesano
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Pooja Jain
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK
| | - Michelle Plusquin
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
| | - Florianne O Vehmeijer
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Nabila Kazmi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, USA
| | - Faisal I Rezwan
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Genomic of Complex diseases, School of Public Health, Imperial College London, London, UK
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Phillip E Melton
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Australia
- Curtin/UWA Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Carrie V Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Nour Baiz
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Luigi Gagliardi
- Division of Neonatology and Pediatrics, Ospedale Versilia, Viareggio, AUSL Toscana Nord Ovest, Pisa, Italy
| | - Tim S Nawrot
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Department of Public Health & Primary Care, Leuven University, Leuven, Belgium
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Department of Medicine, Université de Sherbrooke, Sherbrooke, Canada
| | - Liesbeth Duijts
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ellen Aagaard Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Susan L Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Shanshan Zhao
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | | | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Marjo-Riitta Jarvelin
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Turku Institute for Advanced Studies, University of Turku, Turku, Finland
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY, USA
| | - Denise Anderson
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), University of California, Berkeley, Berkeley, CA, USA
| | - Munawar Hussain Soomro
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Luigi Bouchard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of medical biology, CIUSSS-SLSJ, Saguenay, QC, Canada
| | - Vincent W Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martine Vrijheid
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - S Hasan Arshad
- Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- The David Hide Asthma and Allergy Research Centre, Newport, Isle of Wight, UK
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Per Magnus
- Norwegian Institute of Public Health, Oslo, Norway
| | - Terence Dwyer
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
- Murdoch Children's Research Institute, Australia Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - John Newnham
- Faculty of Health and Medical Sciences, UWA Medical School, University of Western Australia, Perth, Australia
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Inger Kull
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children's Hospital, Södersjukhuset, 118 83, Stockholm, Sweden
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, USA
| | - Barbara Heude
- INSERM, UMR1153 Epidemiology and Biostatistics Sorbonne Paris Cité Center (CRESS), Research Team on Early life Origins of Health (EarOH), Paris Descartes University, Paris, France
| | - Jordi Sunyer
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | | | - Monica C Munthe-Kaas
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Pediatric Oncology and Hematology, Oslo University Hospital, Oslo, Norway
| | | | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Josep Maria Antó
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Jean Bousquet
- University Hospital, Montpellier, France
- Department of Dermatology, Charité, Berlin, Germany
| | - Ashish Kumar
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, The Netherlands
| | - Sarah E Reese
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Folkhälsa Research Institute, Helsinki, and Stem Cells and Metabolism Research Program, University of Helsinki Finland, Helsinki, Finland
| | - Petter Brodin
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Department of Newborn Medicine, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Olivia Solomon
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Nina Holland
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Marie-France Hivert
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, The Netherlands
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.
- Sachs' Children's Hospital, South General Hospital, Stockholm, Sweden.
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Barrios J, Kho AT, Aven L, Mitchel JA, Park JA, Randell SH, Miller LA, Tantisira KG, Ai X. Pulmonary Neuroendocrine Cells Secrete γ-Aminobutyric Acid to Induce Goblet Cell Hyperplasia in Primate Models. Am J Respir Cell Mol Biol 2020; 60:687-694. [PMID: 30571139 DOI: 10.1165/rcmb.2018-0179oc] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mucus overproduction is a major contributor to morbidity and mortality in asthma. Mucus overproduction is induced by orchestrated actions of multiple factors that include inflammatory cytokines and γ-aminobutyric acid (GABA). GABA is produced only by pulmonary neuroendocrine cells (PNECs) in the mouse lung. Recent studies in a neonatal mouse model of allergic inflammation have shown that PNECs play an essential role in mucus overproduction by GABA hypersecretion. Whether PNECs mediate dysregulated GABA signaling for mucus overproduction in asthma is unknown. In this study, we characterized the cellular source of GABA in the lungs of nonhuman primates and humans and assessed GABA secretion and signaling in primate disease models. We found that like in mice, PNECs were the major source of GABA in primate lungs. In addition, an infant nonhuman primate model of asthma exhibited an increase in GABA secretion. Furthermore, subjects with asthma had elevated levels of expression of a subset of GABA type α (GABAα) and type β (GABAβ) receptors in airway epithelium compared with those of healthy control subjects. Last, employing a normal human bronchial epithelial cell model of preinduced mucus overproduction, we showed pharmaceutical blockade of GABAα and GABAβ receptor signaling reversed the effect of IL-13 on MUC5AC gene expression and goblet cell proliferation. Together, our data demonstrate an evolutionarily conserved intraepithelial GABA signaling that, in concert with IL-13, plays an essential role in mucus overproduction. Our findings may offer new strategies to ameliorate mucus overproduction in patients with asthma by targeting PNEC secretion and GABA signaling.
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Affiliation(s)
- Juliana Barrios
- 1 The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Alvin T Kho
- 2 The Channing Division of Network Medicine, and
| | - Linh Aven
- 1 The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Jennifer A Mitchel
- 3 Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Jin-Ah Park
- 3 Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Scott H Randell
- 4 Department of Cell Biology and Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; and
| | - Lisa A Miller
- 5 Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, California
| | | | - Xingbin Ai
- 6 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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32
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McGeachie MJ, Sordillo JE, Dahlin A, Wang AL, Lutz SM, Tantisira KG, Panganiban R, Lu Q, Sajuthi S, Urbanek C, Kelly R, Saef B, Eng C, Oh SS, Kho AT, Croteau-Chonka DC, Weiss ST, Raby BA, Mak ACY, Rodriguez-Santana JR, Burchard EG, Seibold MA, Wu AC. Expression of SMARCD1 interacts with age in association with asthma control on inhaled corticosteroid therapy. Respir Res 2020; 21:31. [PMID: 31992292 PMCID: PMC6988322 DOI: 10.1186/s12931-020-1295-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/14/2020] [Indexed: 01/13/2023] Open
Abstract
Background Global gene expression levels are known to be highly dependent upon gross demographic features including age, yet identification of age-related genomic indicators has yet to be comprehensively undertaken in a disease and treatment-specific context. Methods We used gene expression data from CD4+ lymphocytes in the Asthma BioRepository for Integrative Genomic Exploration (Asthma BRIDGE), an open-access collection of subjects participating in genetic studies of asthma with available gene expression data. Replication population participants were Puerto Rico islanders recruited as part of the ongoing Genes environments & Admixture in Latino Americans (GALA II), who provided nasal brushings for transcript sequencing. The main outcome measure was chronic asthma control as derived by questionnaires. Genomic associations were performed using regression of chronic asthma control score on gene expression with age in years as a covariate, including a multiplicative interaction term for gene expression times age. Results The SMARCD1 gene (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1) interacted with age to influence chronic asthma control on inhaled corticosteroids, with a doubling of expression leading to an increase of 1.3 units of chronic asthma control per year (95% CI [0.86, 1.74], p = 6 × 10− 9), suggesting worsening asthma control with increasing age. This result replicated in GALA II (p = 3.8 × 10− 8). Cellular assays confirmed the role of SMARCD1 in glucocorticoid response in airway epithelial cells. Conclusion Focusing on age-dependent factors may help identify novel indicators of asthma medication response. Age appears to modulate the effect of SMARCD1 on asthma control with inhaled corticosteroids.
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Affiliation(s)
- Michael J McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joanne E Sordillo
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, 401 Park Drive, Suite 401, Boston, MA, 02215-5301, USA
| | - Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alberta L Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sharon M Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, 401 Park Drive, Suite 401, Boston, MA, 02215-5301, USA
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ronald Panganiban
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Quan Lu
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Satria Sajuthi
- Center for Genes, Environment and Health, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Cydney Urbanek
- Center for Genes, Environment and Health, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Rachel Kelly
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Benjamin Saef
- Center for Genes, Environment and Health, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sam S Oh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alvin T Kho
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Damien C Croteau-Chonka
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Benjamin A Raby
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Respiratory Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Angel C Y Mak
- Center for Genes, Environment and Health, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | | | - Esteban G Burchard
- Center for Genes, Environment and Health, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Max A Seibold
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ann Chen Wu
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, 401 Park Drive, Suite 401, Boston, MA, 02215-5301, USA.
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Kang MG, Lee HS, Tantisira KG, Park HW. Genetic Signatures of Acute Asthma Exacerbation Related With Ineffective Response to Corticosteroid. Allergy Asthma Immunol Res 2020; 12:626-640. [PMID: 32400129 PMCID: PMC7224997 DOI: 10.4168/aair.2020.12.4.626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/18/2022]
Abstract
Purpose Acute exacerbation (AE) is an important domain of asthma management and may be related with ineffective response to corticosteroid. This study aimed to find mechanisms of AE using genome-wide gene expression profiles of blood cells from asthmatics and its perturbation by in vitro dexamethasone (Dex)-treatment. Methods We utilized lymphoblastoid B cells from 107 childhood asthmatics and peripheral blood mononuclear cells from 29 adult asthmatics who were treated with inhaled corticosteroids. We searched for a preserved co-expression gene module significantly associated with the AE rate in both cohorts and measured expression changes of genes belong to this module after Dex-treatment. Results We identified a preserved module composed of 77 genes. Among them, expressions of 2 genes (EIF2AK2 and NOL11) decreased significantly after Dex-treatment in both cohorts. EIF2AK2, a key gene acting antiviral defense mechanism, showed significantly higher expressions in asthmatics with AE. The protein repair pathway was enriched significantly in 64 genes which belong to the preserved module but showed no expression differences after Dex-treatment in both cohorts. Among them, MSRA and MSRB2 may play key roles by controlling oxidative stress. Conclusions Many genes belong to the AE rate-associated and preserved module identified in blood cells from childhood and adults asthmatics showed no expression changes after in vitro Dex-treatment. These findings suggest that we may need alternative treatment options to corticosteroids to prevent AE. EIF2AK2, MSRA and MSRB2 expressions on blood cells may help us select AE-susceptible asthmatics and adjust treatments to prevent AE.
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Affiliation(s)
- Min Gyu Kang
- Department of Internal Medicine, Chungbuk National University Hospital, Cheongju, Korea
| | - Hyun Seung Lee
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul, Korea
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Heung Woo Park
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul, Korea.,The Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
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Leong KW, Yu F, Adalsteinsson VA, Reed S, Gydush G, Ladas I, Li J, Tantisira KG, Makrigiorgos GM. A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment. Nucleic Acids Res 2019; 47:e147. [PMID: 31598677 PMCID: PMC6902007 DOI: 10.1093/nar/gkz870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 09/06/2019] [Accepted: 10/01/2019] [Indexed: 11/13/2022] Open
Abstract
DNA target enrichment via hybridization capture is a commonly adopted approach which remains expensive due in-part to using biotinylated-probe panels. Here we provide a novel isothermal amplification reaction to amplify rapidly existing probe panels without knowledge of the sequences involved, thereby decreasing a major portion of the overall sample preparation cost. The reaction employs two thermostable enzymes, BST-polymerase and duplex-specific nuclease DSN. DSN initiates random ‘nicks’ on double-stranded-DNA which enable BST to polymerize DNA by displacing the nicked-strand. Displaced strands re-hybridize and the process leads to an exponential chain-reaction generating biotinylated DNA fragments within minutes. When starting from single-stranded-DNA, DNA is first converted to double-stranded-DNA via terminal-deoxynucleotidyl-transferase (TdT) prior to initiation of BST–DSN reaction. Biotinylated probes generated by TdT–BST–DSN (TBD) reactions using panels of 33, 190 or 7186 DNA targets are used for hybrid-capture-based target enrichment from amplified circulating-DNA, followed by targeted re-sequencing. Polymerase-nuclease isothermal-chain-reactions generate random amplified probes with no apparent sequence dependence. One round of target-capture using TBD probes generates a modest on-target sequencing ratio, while two successive rounds of capture generate >80% on-target reads with good sequencing uniformity. TBD-reactions generate enough capture-probes to increase by approximately two to three orders-of-magnitude the target-enrichment experiments possible from an initial set of probes.
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Affiliation(s)
- Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Sarah Reed
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gregory Gydush
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jiang Li
- The Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medicine School, Boston, MA 02142, USA
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medicine School, Boston, MA 02142, USA
| | - Gerassimos Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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35
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Wang AL, Gruzieva O, Qiu W, Kebede Merid S, Celedón JC, Raby BA, Söderhäll C, DeMeo DL, Weiss ST, Melén E, Tantisira KG. DNA methylation is associated with inhaled corticosteroid response in persistent childhood asthmatics. Clin Exp Allergy 2019; 49:1225-1234. [PMID: 31187518 DOI: 10.1111/cea.13447] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/19/2019] [Accepted: 05/18/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Response to inhaled corticosteroids is highly variable, and the association between DNA methylation and treatment response is not known. OBJECTIVE To examine the association between peripheral blood DNA methylation and inhaled corticosteroid response in children with persistent asthma. METHODS Epigenome-wide DNA methylation was analysed in individuals on inhaled corticosteroids in three independent and ethnically diverse cohorts-Childhood Asthma Management Program (CAMP); Children, Allergy, Milieu, Stockholm, Epidemiology (BAMSE); and Genetic Epidemiology of Asthma in Costa Rica Study (GACRS). Treatment response was evaluated using two definitions, the absence of emergency department visits and/or hospitalizations and the absence oral corticosteroid use while on inhaled corticosteroid therapy. CpG sites meeting nominal significance (P < 0.05) for each outcome were combined in a three-cohort meta-analysis with adjustment for multiple testing. DNA methylation was correlated with gene expression using Pearson and partial correlations. RESULTS In 154 subjects from CAMP, 72 from BAMSE, and 168 from GACRS, relative hypomethylation of cg00066816 (171 bases upstream of IL12B) was associated with the absence of emergency department visits and/or hospitalizations (Q = 0.03) in all cohorts and lower IL12B expression (ρ = 0.34, P = 0.01) in BAMSE. Relative hypermethylation of cg04256470 (688 bases upstream of CORT) was associated with the absence of oral corticosteroid use (Q = 0.04) in all cohorts and higher CORT expression (ρ = 0.20, P = 0.045) in CAMP. CONCLUSION AND CLINICAL RELEVANCE Differential DNA methylation of IL12B and CORT are associated with inhaled corticosteroid treatment response in persistent childhood asthmatics. Pharmaco-methylation can identify novel markers of treatment sensitivity in asthma.
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Affiliation(s)
- Alberta L Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Benjamin A Raby
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Pulmonary Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden.,Sachs' Children's Hospital, Stockholm, Sweden
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Hobbs BD, Tantisira KG. MicroRNAs in COPD: small molecules with big potential. Eur Respir J 2019; 53:53/4/1900515. [DOI: 10.1183/13993003.00515-2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 12/22/2022]
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Choi J, Tantisira KG, Duan QL. Whole genome sequencing identifies high-impact variants in well-known pharmacogenomic genes. Pharmacogenomics J 2019; 19:127-135. [PMID: 30214008 PMCID: PMC6417988 DOI: 10.1038/s41397-018-0048-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 07/10/2018] [Accepted: 08/10/2018] [Indexed: 01/21/2023]
Abstract
More than 1100 genetic loci have been correlated with drug response outcomes but disproportionately few have been translated into clinical practice. One explanation for the low rate of clinical implementation is that the majority of associated variants may be in linkage disequilibrium (LD) with the causal variants, which are often elusive. This study aims to identify and characterize likely causal variants within well-established pharmacogenomic genes using next-generation sequencing data from the 1000 Genomes Project. We identified 69,319 genetic variations within 160 pharmacogenomic genes, of which 8207 variants are in strong LD (r2>0.8) with known pharmacogenomic variants. Of the latter, eight are coding or structural variants predicted to have high impact, with 19 additional missense variants that are predicted to have moderate impact. In conclusion, we identified putatively functional variants within known pharmacogenomics loci that could account for the association signals and represent the missing causative variants underlying drug response phenotypes.
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Affiliation(s)
- Jihoon Choi
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
- School of Computing, Queen's University, Kingston, ON, Canada
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Qing Ling Duan
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.
- School of Computing, Queen's University, Kingston, ON, Canada.
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Dahlin A, Sordillo JE, Ziniti J, Iribarren C, Lu M, Weiss ST, Tantisira KG, Lu Q, Kan M, Himes BE, Jorgenson E, Wu AC. Large-scale, multiethnic genome-wide association study identifies novel loci contributing to asthma susceptibility in adults. J Allergy Clin Immunol 2019; 143:1633-1635. [PMID: 30578877 PMCID: PMC6451881 DOI: 10.1016/j.jaci.2018.11.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/06/2018] [Accepted: 11/16/2018] [Indexed: 11/16/2022]
Abstract
In this large, multi-ethnic GWAS of asthma, we identified novel associations with potential functional relevance for asthma susceptibility in older adults of diverse racial backgrounds.
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Affiliation(s)
- Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Joanne E Sordillo
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Mass
| | - John Ziniti
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, Calif
| | - Meng Lu
- Division of Research, Kaiser Permanente Northern California, Oakland, Calif
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Partners Center for Personalized Medicine, Partners Health Care, Boston, Mass
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Partners Center for Personalized Medicine, Partners Health Care, Boston, Mass
| | - Quan Lu
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Mass; Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Mengyuan Kan
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pa
| | - Blanca E Himes
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pa
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, Calif
| | - Ann Chen Wu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Mass.
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Wang AL, Tantisira KG. Reply. J Allergy Clin Immunol 2019; 143:1975. [PMID: 30876727 DOI: 10.1016/j.jaci.2019.01.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Alberta L Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass.
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
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Wang AL, Datta S, Weiss ST, Tantisira KG. Remission of persistent childhood asthma: Early predictors of adult outcomes. J Allergy Clin Immunol 2018; 143:1752-1759.e6. [PMID: 30445065 DOI: 10.1016/j.jaci.2018.09.038] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/20/2018] [Accepted: 09/21/2018] [Indexed: 11/18/2022]
Abstract
BACKGROUND Few data exist on the predictors of asthma remission by early adulthood in North America. OBJECTIVE The predictors of adult asthma remission were determined in a multiethnic population of patients with mild-to-moderate persistent childhood asthma. METHODS Asthma remission in early adulthood was measured by using 2 definitions: a clinical and a strict definition. Both included normal lung function and the absence of symptoms, exacerbations, and medication use. The strict definition also included normal airways responsiveness. Predictors were identified from 23 baseline measures by using multivariate logistic regression. The probability of remission was modeled by using decision tree analysis. RESULTS In 879 subjects the mean ± SD baseline age was 8.8 ± 2.1 years, 59.4% were male, and 68.7% were white. By adulthood, 229 (26.0%) of 879 participants were in clinical remission, and 111 (15.0%) of 741 participants were in strict remission. The degree of FEV1/forced vital capacity (FVC) ratio impairment was the largest predictor of asthma remission. More than half of boys and two thirds of girls with baseline FEV1/FVC ratios of 90% or greater were in remission at adulthood. Decreased airways responsiveness was also a predictor for both remission definitions (clinical remission odds ratio, 1.23 [95% CI, 1.09-1.39]; strict remission odds ratio, 1.52 [95% CI, 1.26-1.84]). The combination of normal FEV1/FVC ratio, airways responsiveness, and serum eosinophil count at baseline yielded greater than 80% probability of remission by adulthood. CONCLUSION A considerable minority of patients with persistent childhood asthma will have disease remission by adulthood. Clinical prognostic indicators of asthma remission, including baseline lung function, can be seen from an early age.
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Affiliation(s)
- Alberta L Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Soma Datta
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass.
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Kho AT, McGeachie MJ, Moore KG, Sylvia JM, Weiss ST, Tantisira KG. Circulating microRNAs and prediction of asthma exacerbation in childhood asthma. Respir Res 2018; 19:128. [PMID: 29940952 PMCID: PMC6020199 DOI: 10.1186/s12931-018-0828-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/12/2018] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Circulating microRNAs have shown promise as non-invasive biomarkers and predictors of disease activity. Prior asthma studies using clinical, biochemical and genomic data have not shown excellent prediction of exacerbation. We hypothesized that a panel of circulating microRNAs in a pediatric asthma cohort combined with an exacerbation clinical score might predict exacerbation better than the latter alone. METHODS Serum samples from 153 children at randomization in the Childhood Asthma Management Program were profiled for 754 microRNAs. Data dichotomized for asthma exacerbation one year after randomization to inhaled corticosteroid treatment were used for binary logistic regression with miRNA expressions and exacerbation clinical score. RESULTS 12 of 125 well-detected circulating microRNAs had significant odd ratios for exacerbation with miR-206 being most significant. Each doubling of expression of the 12 microRNA corresponded to a 25-67% increase in exacerbation risk. Stepwise logistic regression yielded a 3-microRNA model (miR-146b, miR-206 and miR-720) that, combined with the exacerbation clinical score, had excellent predictive power with a 0.81 AUROC. These 3 microRNAs were involved in NF-kβ and GSK3/AKT pathways. CONCLUSIONS This combined circulating microRNA-clinical score model predicted exacerbation in asthmatic subjects on inhaled corticosteroids better than each constituent feature alone. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT00000575 .
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Affiliation(s)
- Alvin T. Kho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- Harvard Medical School, 25 Shattuck Street, Boston, MA 02115 USA
- Computational Health Informatics Program, Boston Children’s Hospital, 320 Longwood Avenue, Boston, MA 02115 USA
| | - Michael J. McGeachie
- Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- Harvard Medical School, 25 Shattuck Street, Boston, MA 02115 USA
| | - Kip G. Moore
- Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
| | - Jody M. Sylvia
- Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- Harvard Medical School, 25 Shattuck Street, Boston, MA 02115 USA
| | - Kelan G. Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- Harvard Medical School, 25 Shattuck Street, Boston, MA 02115 USA
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Mak ACY, White MJ, Eckalbar WL, Szpiech ZA, Oh SS, Pino-Yanes M, Hu D, Goddard P, Huntsman S, Galanter J, Wu AC, Himes BE, Germer S, Vogel JM, Bunting KL, Eng C, Salazar S, Keys KL, Liberto J, Nuckton TJ, Nguyen TA, Torgerson DG, Kwok PY, Levin AM, Celedón JC, Forno E, Hakonarson H, Sleiman PM, Dahlin A, Tantisira KG, Weiss ST, Serebrisky D, Brigino-Buenaventura E, Farber HJ, Meade K, Lenoir MA, Avila PC, Sen S, Thyne SM, Rodriguez-Cintron W, Winkler CA, Moreno-Estrada A, Sandoval K, Rodriguez-Santana JR, Kumar R, Williams LK, Ahituv N, Ziv E, Seibold MA, Darnell RB, Zaitlen N, Hernandez RD. Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma. Am J Respir Crit Care Med 2018; 197:1552-1564. [PMID: 29509491 PMCID: PMC6006403 DOI: 10.1164/rccm.201712-2529oc] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/05/2018] [Indexed: 12/25/2022] Open
Abstract
RATIONALE Albuterol, a bronchodilator medication, is the first-line therapy for asthma worldwide. There are significant racial/ethnic differences in albuterol drug response. OBJECTIVES To identify genetic variants important for bronchodilator drug response (BDR) in racially diverse children. METHODS We performed the first whole-genome sequencing pharmacogenetics study from 1,441 children with asthma from the tails of the BDR distribution to identify genetic association with BDR. MEASUREMENTS AND MAIN RESULTS We identified population-specific and shared genetic variants associated with BDR, including genome-wide significant (P < 3.53 × 10-7) and suggestive (P < 7.06 × 10-6) loci near genes previously associated with lung capacity (DNAH5), immunity (NFKB1 and PLCB1), and β-adrenergic signaling (ADAMTS3 and COX18). Functional analyses of the BDR-associated SNP in NFKB1 revealed potential regulatory function in bronchial smooth muscle cells. The SNP is also an expression quantitative trait locus for a neighboring gene, SLC39A8. The lack of other asthma study populations with BDR and whole-genome sequencing data on minority children makes it impossible to perform replication of our rare variant associations. Minority underrepresentation also poses significant challenges to identify age-matched and population-matched cohorts of sufficient sample size for replication of our common variant findings. CONCLUSIONS The lack of minority data, despite a collaboration of eight universities and 13 individual laboratories, highlights the urgent need for a dedicated national effort to prioritize diversity in research. Our study expands the understanding of pharmacogenetic analyses in racially/ethnically diverse populations and advances the foundation for precision medicine in at-risk and understudied minority populations.
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Affiliation(s)
| | | | | | | | | | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N. S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | | | | | - Ann Chen Wu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Precision Medicine Translational Research (PRoMoTeR) Center, Department of Population Medicine, Harvard Medical School and Pilgrim Health Care Institute, Boston, Massachusetts
| | - Blanca E. Himes
- Department of Biostatistics, Epidemiology and Informatics and
| | | | | | | | | | | | | | | | | | | | | | - Pui-Yan Kwok
- Cardiovascular Research Institute
- Institute for Human Genetics, and
| | | | - Juan C. Celedón
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Hakon Hakonarson
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Center for Applied Genomics, The Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania
| | - Patrick M. Sleiman
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Center for Applied Genomics, The Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania
| | - Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kelan G. Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Denise Serebrisky
- Pediatric Pulmonary Division, Jacobi Medical Center, Bronx, New York
| | | | - Harold J. Farber
- Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas
| | - Kelley Meade
- Children’s Hospital and Research Center, Oakland, California
| | | | - Pedro C. Avila
- Department of Medicine, Northwestern University, Chicago, Illinois
| | | | - Shannon M. Thyne
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | | | - Cheryl A. Winkler
- Basic Science Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Frederick National Laboratory, Frederick, Maryland
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Rajesh Kumar
- Division of Allergy and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - L. Keoki Williams
- Department of Internal Medicine, and
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Michigan
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences
- Institute for Human Genetics, and
| | | | - Max A. Seibold
- Center for Genes, Environment and Health, Department of Pediatrics, National Jewish Health, Denver, Colorado; and
| | - Robert B. Darnell
- New York Genome Center, New York, New York
- Laboratory of Molecular Neuro-Oncology and
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York
| | | | - Ryan D. Hernandez
- Department of Bioengineering and Therapeutic Sciences
- Cardiovascular Research Institute
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, California
| | - on behalf of the NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
- Department of Medicine
- Department of Bioengineering and Therapeutic Sciences
- Department of Pediatrics
- Cardiovascular Research Institute
- Institute for Human Genetics, and
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, California
- Research Unit, Hospital Universitario N. S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Precision Medicine Translational Research (PRoMoTeR) Center, Department of Population Medicine, Harvard Medical School and Pilgrim Health Care Institute, Boston, Massachusetts
- Department of Biostatistics, Epidemiology and Informatics and
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- New York Genome Center, New York, New York
- Department of Public Health Sciences
- Department of Internal Medicine, and
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Michigan
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Center for Applied Genomics, The Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania
- Pediatric Pulmonary Division, Jacobi Medical Center, Bronx, New York
- Department of Allergy and Immunology, Kaiser Permanente Vallejo Medical Center, Vallejo, California
- Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas
- Children’s Hospital and Research Center, Oakland, California
- Bay Area Pediatrics, Oakland, California
- Department of Medicine, Northwestern University, Chicago, Illinois
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Veterans Caribbean Health Care System, San Juan, Puerto Rico
- Basic Science Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Frederick National Laboratory, Frederick, Maryland
- National Laboratory of Genomics for Biodiversity (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
- Centro de Neumologia Pediatrica, San Juan, Puerto Rico
- Division of Allergy and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
- Center for Genes, Environment and Health, Department of Pediatrics, National Jewish Health, Denver, Colorado; and
- Laboratory of Molecular Neuro-Oncology and
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York
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Cho MH, Tantisira KG. Adrenal insufficiency and ICS: genetics takes a breath. Lancet Respir Med 2018; 6:407-408. [PMID: 29551625 DOI: 10.1016/s2213-2600(18)30101-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Michael H Cho
- Brigham and Women's Hospital, Department of Medicine, Channing Division of Network Medicine, Boston, MA 02115, USA.
| | - Kelan G Tantisira
- Brigham and Women's Hospital, Department of Medicine, Channing Division of Network Medicine, Boston, MA 02115, USA
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Dahlin A, Qiu W, Litonjua AA, Lima JJ, Tamari M, Kubo M, Irvin CG, Peters SP, Wu AC, Weiss ST, Tantisira KG. The phosphatidylinositide 3-kinase (PI3K) signaling pathway is a determinant of zileuton response in adults with asthma. Pharmacogenomics J 2018; 18:665-677. [PMID: 29298996 PMCID: PMC6150906 DOI: 10.1038/s41397-017-0006-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 09/18/2017] [Indexed: 12/31/2022]
Abstract
Variable responsiveness to zileuton, a leukotriene antagonist used to treat asthma, may be due in part to genetic variation. While individual SNPs were previously associated with zileuton-related lung function changes, specific quantitative trait loci (QTLs) and biological pathways that may contribute have not been identified. In this study, we investigated the hypothesis that genetic variation within biological pathways is associated with zileuton response. We performed an integrative QTL mapping and pathway enrichment study to investigate data from a GWAS of zileuton response, in addition to mRNA expression profiles and leukotriene production data from lymphoblastoid cell lines (LCLs) (derived from asthmatics) that were treated with zileuton or ethanol (control). We identified 1060 QTLs jointly associated with zileuton-related differential LTB4 production in LCLs and lung function change in patients taking zileuton, of which eight QTLs were also significantly associated with persistent LTB4 production in LCLs following zileuton treatment (i.e., ‘poor’ responders). Four nominally significant trans-eQTLs were predicted to regulate three candidate genes (SELL, MTF2, and GAL), the expression of which was significantly reduced in LCLs following zileuton treatment. Gene and pathway enrichment analyses of QTL associations identified multiple genes and pathways, predominantly related to phosphatidyl inositol signaling via PI3K. We validated the PI3K pathway activation status in a subset of LCLs demonstrating variable zileuton-related LTB4 production, and show that in contrast to LCLs that responded to zileuton, the PI3K pathway was activated in poor responder LCLs. Collectively, these findings demonstrate a role for the PIK3 pathway and its targets as important determinants of differential responsiveness to zileuton.
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Affiliation(s)
- Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Augusto A Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Stephen P Peters
- Wake Forest University Health Science Center, Winston-Salem, NC, USA
| | - Ann C Wu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Partners Center for Personalized Genetic Medicine, Partners Health Care, Boston, MA, USA
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,University of Vermont, Burlington, VT, USA
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45
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Davis JS, Sun M, Kho AT, Moore KG, Sylvia JM, Weiss ST, Lu Q, Tantisira KG. Circulating microRNAs and association with methacholine PC20 in the Childhood Asthma Management Program (CAMP) cohort. PLoS One 2017; 12:e0180329. [PMID: 28749975 PMCID: PMC5531511 DOI: 10.1371/journal.pone.0180329] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 06/08/2017] [Indexed: 11/18/2022] Open
Abstract
Introduction Circulating microRNAs (miRNA) are promising biomarkers for human diseases. Our study hypothesizes that circulating miRNA would reveal candidate biomarkers related to airway hyperresponsiveness (AHR) and provide biologic insights into asthma epigenetic influences. Methods Serum samples obtained at randomization for 160 children in the Childhood Asthma Management Program were profiled using a TaqMan miRNA array set. The association of the isolated miRNA with methacholine PC20 was assessed. Network and pathway analyses were performed. Functional validation of two significant miRNAs was performed in human airway smooth muscle cells (HASMs). Results Of 155 well-detected circulating miRNAs, eight were significantly associated with PC20 with the strongest association with miR-296-5p. Pathway analysis revealed miR-16-5p as a network hub, and involvement of multiple miRNAs interacting with genes in the FoxO and Hippo signaling pathways by KEGG analysis. Functional validation of two miRNA in HASM showed effects on cell growth and diameter. Conclusion Reduced circulatory miRNA expression at baseline is associated with an increase in PC20. These miRNA provide biologic insights into, and may serve as biomarkers of, asthma severity. miR-16-5p and -30d-5p regulate airway smooth muscle phenotypes critically involved in asthma pathogenesis, supporting a mechanistic link to these findings. Functional ASM phenotypes may be directly relevant to AHR.
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Affiliation(s)
- Joshua S. Davis
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Maoyun Sun
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Alvin T. Kho
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Kip G. Moore
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jody M. Sylvia
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Quan Lu
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Kelan G. Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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46
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Qiu W, Guo F, Glass K, Yuan GC, Quackenbush J, Zhou X, Tantisira KG. Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma. J Allergy Clin Immunol 2017; 141:1250-1258. [PMID: 28736268 DOI: 10.1016/j.jaci.2017.05.052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/02/2017] [Accepted: 05/03/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Variations in drug response between individuals have prevented us from achieving high drug efficacy in treating many complex diseases, including asthma. Genetics plays an important role in accounting for such interindividual variations in drug response. However, systematic approaches for addressing how genetic factors and their regulators determine variations in drug response in asthma treatment are lacking. OBJECTIVE We sought to identify key transcriptional regulators of corticosteroid response in asthma using a novel systems biology approach. METHODS We used Passing Attributes between Networks for Data Assimilations (PANDA) to construct the gene regulatory networks associated with good responders and poor responders to inhaled corticosteroids based on a subset of 145 white children with asthma who participated in the Childhood Asthma Management Cohort. PANDA uses gene expression profiles and published relationships among genes, transcription factors (TFs), and proteins to construct the directed networks of TFs and genes. We assessed the differential connectivity between the gene regulatory network of good responders versus that of poor responders. RESULTS When compared with poor responders, the network of good responders has differential connectivity and distinct ontologies (eg, proapoptosis enriched in network of good responders and antiapoptosis enriched in network of poor responders). Many of the key hubs identified in conjunction with clinical response are also cellular response hubs. Functional validation demonstrated abrogation of differences in corticosteroid-treated cell viability following siRNA knockdown of 2 TFs and differential downstream expression between good responders and poor responders. CONCLUSIONS We have identified and validated multiple TFs influencing asthma treatment response. Our results show that differential connectivity analysis can provide new insights into the heterogeneity of drug treatment effects.
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Affiliation(s)
- Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Feng Guo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Guo Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Mass; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Mass; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
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47
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McGeachie MJ, Yates KP, Zhou X, Guo F, Sternberg AL, Van Natta ML, Wise RA, Szefler SJ, Sharma S, Kho AT, Cho MH, Croteau-Chonka DC, Castaldi PJ, Jain G, Sanyal A, Zhan Y, Lajoie BR, Dekker J, Stamatoyannopoulos J, Covar RA, Zeiger RS, Adkinson NF, Williams PV, Kelly HW, Grasemann H, Vonk JM, Koppelman GH, Postma DS, Raby BA, Houston I, Lu Q, Fuhlbrigge AL, Tantisira KG, Silverman EK, Tonascia J, Strunk RC, Weiss ST. Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma. Am J Respir Crit Care Med 2017; 194:1465-1474. [PMID: 27367781 DOI: 10.1164/rccm.201602-0250oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Patterns of longitudinal lung function growth and decline in childhood asthma have been shown to be important in determining risk for future respiratory ailments including chronic airway obstruction and chronic obstructive pulmonary disease. OBJECTIVES To determine the genetic underpinnings of lung function patterns in subjects with childhood asthma. METHODS We performed a genome-wide association study of 581 non-Hispanic white individuals with asthma that were previously classified by patterns of lung function growth and decline (normal growth, normal growth with early decline, reduced growth, and reduced growth with early decline). The strongest association was also measured in two additional cohorts: a small asthma cohort and a large chronic obstructive pulmonary disease metaanalysis cohort. Interaction between the genomic region encompassing the most strongly associated single-nucleotide polymorphism and nearby genes was assessed by two chromosome conformation capture assays. MEASUREMENTS AND MAIN RESULTS An intergenic single-nucleotide polymorphism (rs4445257) on chromosome 8 was strongly associated with the normal growth with early decline pattern compared with all other pattern groups (P = 6.7 × 10-9; odds ratio, 2.8; 95% confidence interval, 2.0-4.0); replication analysis suggested this variant had opposite effects in normal growth with early decline and reduced growth with early decline pattern groups. Chromosome conformation capture experiments indicated a chromatin interaction between rs4445257 and the promoter of the distal CSMD3 gene. CONCLUSIONS Early decline in lung function after normal growth is associated with a genetic polymorphism that may also protect against early decline in reduced growth groups. Clinical trial registered with www.clinicaltrials.gov (NCT00000575).
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Affiliation(s)
- Michael J McGeachie
- 1 Channing Division of Network Medicine and.,2 Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Xiaobo Zhou
- 1 Channing Division of Network Medicine and.,2 Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Feng Guo
- 1 Channing Division of Network Medicine and.,2 Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | | | - Robert A Wise
- 4 School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Stanley J Szefler
- 5 National Jewish Health and Research Center, Denver, Colorado.,6 Children's Hospital Colorado and
| | - Sunita Sharma
- 7 Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Denver, Colorado
| | - Alvin T Kho
- 1 Channing Division of Network Medicine and.,2 Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,8 Boston Children's Hospital, Boston, Massachusetts
| | - Michael H Cho
- 1 Channing Division of Network Medicine and.,2 Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Damien C Croteau-Chonka
- 1 Channing Division of Network Medicine and.,2 Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Peter J Castaldi
- 1 Channing Division of Network Medicine and.,2 Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Gaurav Jain
- 9 Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, and
| | - Amartya Sanyal
- 9 Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, and.,10 School of Biological Sciences, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Ye Zhan
- 9 Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, and
| | - Bryan R Lajoie
- 9 Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, and
| | - Job Dekker
- 11 Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | | | - Ronina A Covar
- 5 National Jewish Health and Research Center, Denver, Colorado.,6 Children's Hospital Colorado and.,13 University of Colorado, Denver, Colorado
| | - Robert S Zeiger
- 14 Department of Pediatrics, University of California at San Diego, La Jolla, California.,15 Kaiser Permanente Southern California Region, San Diego, California
| | | | - Paul V Williams
- 16 ASTHMA, Inc., Clinical Research Center and Northwest Asthma & Allergy Center, Seattle, Washington
| | - H William Kelly
- 17 University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Hartmut Grasemann
- 18 Division of Respiratory Medicine, Department of Pediatrics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | | | - Gerard H Koppelman
- 20 Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, and
| | - Dirkje S Postma
- 21 Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - Benjamin A Raby
- 1 Channing Division of Network Medicine and.,2 Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Isaac Houston
- 1 Channing Division of Network Medicine and.,2 Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Quan Lu
- 22 Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; and
| | - Anne L Fuhlbrigge
- 1 Channing Division of Network Medicine and.,23 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,2 Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kelan G Tantisira
- 1 Channing Division of Network Medicine and.,2 Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Edwin K Silverman
- 1 Channing Division of Network Medicine and.,2 Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Robert C Strunk
- 24 Division of Allergy, Immunology, and Pulmonary Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Scott T Weiss
- 1 Channing Division of Network Medicine and.,2 Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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48
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Kho AT, Chhabra D, Sharma S, Qiu W, Carey VJ, Gaedigk R, Vyhlidal CA, Leeder JS, Tantisira KG, Weiss ST. Age, Sexual Dimorphism, and Disease Associations in the Developing Human Fetal Lung Transcriptome. Am J Respir Cell Mol Biol 2017; 54:814-21. [PMID: 26584061 DOI: 10.1165/rcmb.2015-0326oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The fetal origins of disease hypothesis suggests that variations in the course of prenatal lung development may affect life-long pulmonary function growth, decline, and pathobiology. Many studies support the existence of differences in the developing lung trajectory in males and females, and sex-specific differences in the prevalence of chronic lung diseases, such as asthma and bronchopulmonary dysplasia. The objectives of this study were to investigate the early developing fetal lung for transcriptomic correlates of postconception age (maturity) and sex, and their associations with chronic lung diseases. We analyzed whole-lung transcriptome profiles of 61 females and 78 males at 54-127 days postconception (dpc) from nonsmoking mothers using unsupervised principal component analysis and supervised linear regression models. We identified dominant transcriptomic correlates for postconception age and sex with corresponding gene sets that were enriched for developing lung structural and functional ontologies. We observed that the transcriptomic sex difference was not a uniform global time shift/lag, rather, lungs of males appear to be more mature than those of females before 96 dpc, and females appear to be more mature than males after 96 dpc. The age correlate gene set was consistently enriched for asthma and bronchopulmonary dysplasia genes, but the sex correlate gene sets were not. Despite sex differences in the developing fetal lung transcriptome, postconception age appears to be more dominant than sex in the effect of early fetal lung developments on disease risk during this early pseudoglandular phase of development.
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Affiliation(s)
- Alvin T Kho
- 1 Children's Hospital Informatics Program, Boston Children's Hospital, Boston, Massachusetts.,2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and
| | - Divya Chhabra
- 2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and
| | - Sunita Sharma
- 2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and.,4 Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Weiliang Qiu
- 2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and
| | - Vincent J Carey
- 2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and
| | - Roger Gaedigk
- 5 Division of Pediatric Clinical Pharmacology and Medical Toxicology, Children's Mercy Hospital and Clinics, Kansas City, Missouri; and
| | - Carrie A Vyhlidal
- 5 Division of Pediatric Clinical Pharmacology and Medical Toxicology, Children's Mercy Hospital and Clinics, Kansas City, Missouri; and
| | - J Steven Leeder
- 5 Division of Pediatric Clinical Pharmacology and Medical Toxicology, Children's Mercy Hospital and Clinics, Kansas City, Missouri; and
| | - Kelan G Tantisira
- 2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and
| | - Scott T Weiss
- 2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and
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Farzan N, Vijverberg SJ, Andiappan AK, Arianto L, Berce V, Blanca-López N, Bisgaard H, Bønnelykke K, Burchard EG, Campo P, Canino G, Carleton B, Celedón JC, Chew FT, Chiang WC, Cloutier MM, Daley D, Den Dekker HT, Dijk FN, Duijts L, Flores C, Forno E, Hawcutt DB, Hernandez-Pacheco N, de Jongste JC, Kabesch M, Koppelman GH, Manolopoulos VG, Melén E, Mukhopadhyay S, Nilsson S, Palmer CN, Pino-Yanes M, Pirmohamed M, Potočnik U, Raaijmakers JA, Repnik K, Schieck M, Sio YY, Smyth RL, Szalai C, Tantisira KG, Turner S, van der Schee MP, Verhamme KM, Maitland-van der Zee AH. Rationale and design of the multiethnic Pharmacogenomics in Childhood Asthma consortium. Pharmacogenomics 2017. [PMID: 28639505 DOI: 10.2217/pgs-2017-0035] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
AIM International collaboration is needed to enable large-scale pharmacogenomics studies in childhood asthma. Here, we describe the design of the Pharmacogenomics in Childhood Asthma (PiCA) consortium. MATERIALS & METHODS Investigators of each study participating in PiCA provided data on the study characteristics by answering an online questionnaire. RESULTS A total of 21 studies, including 14,227 children/young persons (58% male), from 12 different countries are currently enrolled in the PiCA consortium. Fifty six percent of the patients are Caucasians. In total, 7619 were inhaled corticosteroid users. Among patients from 13 studies with available data on asthma exacerbations, a third reported exacerbations despite inhaled corticosteroid use. In the future pharmacogenomics studies within the consortium, the pharmacogenomics analyses will be performed separately in each center and the results will be meta-analyzed. CONCLUSION PiCA is a valuable platform to perform pharmacogenetics studies within a multiethnic pediatric asthma population.
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Affiliation(s)
- Niloufar Farzan
- Division of Pharmacoepidemiology & Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.,Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne J Vijverberg
- Division of Pharmacoepidemiology & Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.,Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Anand K Andiappan
- Singapore Immunology Network, Agency for Science, Technology & Research, Singapore 138648, Singapore
| | - Lambang Arianto
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Vojko Berce
- Department of Pediatrics, University Medical Centre Maribor, Maribor, Slovenia.,Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | | | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Esteban G Burchard
- Departments of Medicine, Bioengineering & Therapeutic Sciences University of California, San Francisco, CA 94110, USA
| | - Paloma Campo
- Allergy Unit, IBIMA, Regional University Hospital of Malaga, Malaga, Spain
| | - Glorisa Canino
- Behavioral Sciences institute, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | - Bruce Carleton
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Juan C Celedón
- Division of Pulmonary Medicine, Allergy, & Immunology, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore
| | - Wen Chin Chiang
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore
| | - Michelle M Cloutier
- Asthma Center, Connecticut Children's Medical Center, University of Connecticut Health Center, CT 06106, USA
| | - Denis Daley
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Herman T Den Dekker
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - F Nicole Dijk
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands.,Groningen Research Institute for Asthma & COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Liesbeth Duijts
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pediatrics, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Carlos Flores
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Erick Forno
- Division of Pulmonary Medicine, Allergy, & Immunology, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Daniel B Hawcutt
- Alder Hey Children's Hospital, Liverpool, UK.,Department of Women's & Children's Health, University of Liverpool, Liverpool, UK
| | - Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Johan C de Jongste
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Michael Kabesch
- Department of Pediatric Pneumology & Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands.,Groningen Research Institute for Asthma & COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Vangelis G Manolopoulos
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre of Occupational & Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Somnath Mukhopadhyay
- Academic Department of Paediatrics, Brighton & Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK.,Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital & Medical School University of Dundee, Dundee, UK
| | - Sara Nilsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre of Occupational & Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Colin N Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital & Medical School University of Dundee, Dundee, UK
| | - Maria Pino-Yanes
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Munir Pirmohamed
- Department of Molecular & Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Uros Potočnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Faculty for Chemistry & Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Jan A Raaijmakers
- Division of Pharmacoepidemiology & Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Katja Repnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Faculty for Chemistry & Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Maximilian Schieck
- Department of Pediatric Pneumology & Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany.,Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Yang Yie Sio
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore
| | - Rosalind L Smyth
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Csaba Szalai
- Department of Genetics, Cell & Immuno-biology, Semmelweis University, Budapest, Hungary.,Central Laboratory, Heim Pal Children Hospital, Budapest, Hungary
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's hospital & Harvard Medical School, Boston, MA 02115, USA.,Division of Pulmonary & Critical Care Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Steve Turner
- Child Health, University of Aberdeen, Aberdeen, UK
| | - Marc P van der Schee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Katia M Verhamme
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anke H Maitland-van der Zee
- Division of Pharmacoepidemiology & Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.,Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
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Wang AL, Qiu W, Tantisira KG. DNA Methylation Status Predicts Response to Inhaled Corticosteroids in Pediatric Asthmatics. J Allergy Clin Immunol 2017. [DOI: 10.1016/j.jaci.2016.12.916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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