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Moll M, Sordillo JE, Ghosh AJ, Hayden LP, McDermott G, McGeachie MJ, Dahlin A, Tiwari A, Manmadkar MG, Abston ED, Pavuluri C, Saferali A, Begum S, Ziniti JP, Gulsvik A, Bakke PS, Aschard H, Iribarren C, Hersh CP, Sparks JA, Hobbs BD, Lasky-Su JA, Silverman EK, Weiss ST, Wu AC, Cho MH. Polygenic risk scores identify heterogeneity in asthma and chronic obstructive pulmonary disease. J Allergy Clin Immunol 2023; 152:1423-1432. [PMID: 37595761 PMCID: PMC10841234 DOI: 10.1016/j.jaci.2023.08.002] [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: 01/11/2023] [Revised: 07/27/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Asthma and chronic obstructive pulmonary disease (COPD) have distinct and overlapping genetic and clinical features. OBJECTIVE We sought to test the hypothesis that polygenic risk scores (PRSs) for asthma (PRSAsthma) and spirometry (FEV1 and FEV1/forced vital capacity; PRSspiro) would demonstrate differential associations with asthma, COPD, and asthma-COPD overlap (ACO). METHODS We developed and tested 2 asthma PRSs and applied the higher performing PRSAsthma and a previously published PRSspiro to research (Genetic Epidemiology of COPD study and Childhood Asthma Management Program, with spirometry) and electronic health record-based (Mass General Brigham Biobank and Genetic Epidemiology Research on Adult Health and Aging [GERA]) studies. We assessed the association of PRSs with COPD and asthma using modified random-effects and binary-effects meta-analyses, and ACO and asthma exacerbations in specific cohorts. Models were adjusted for confounders and genetic ancestry. RESULTS In meta-analyses of 102,477 participants, the PRSAsthma (odds ratio [OR] per SD, 1.16 [95% CI, 1.14-1.19]) and PRSspiro (OR per SD, 1.19 [95% CI, 1.17-1.22]) both predicted asthma, whereas the PRSspiro predicted COPD (OR per SD, 1.25 [95% CI, 1.21-1.30]). However, results differed by cohort. The PRSspiro was not associated with COPD in GERA and Mass General Brigham Biobank. In the Genetic Epidemiology of COPD study, the PRSAsthma (OR per SD: Whites, 1.3; African Americans, 1.2) and PRSspiro (OR per SD: Whites, 2.2; African Americans, 1.6) were both associated with ACO. In GERA, the PRSAsthma was associated with asthma exacerbations (OR, 1.18) in Whites; the PRSspiro was associated with asthma exacerbations in White, LatinX, and East Asian participants. CONCLUSIONS PRSs for asthma and spirometry are both associated with ACO and asthma exacerbations. Genetic prediction performance differs in research versus electronic health record-based cohorts.
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Affiliation(s)
- Matthew Moll
- Department of Medicine, Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Harvard Medical School, Boston, Mass; Harvard Medical School, Brigham and Women's Hospital, Boston, Mass
| | - Joanne E Sordillo
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care, Boston, Mass
| | - Auyon J Ghosh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, SUNY Upstate Medical Center, Syracuse, NY
| | - Lystra P Hayden
- Department of Pediatrics, Division of Pulmonary Medicine, Boston Children's Hospital, Harvard Medical School, Massachusetts General Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Gregory McDermott
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, Mass
| | - Michael J McGeachie
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Amber Dahlin
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Anshul Tiwari
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Monica G Manmadkar
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Eric D Abston
- Department of Thoracic Surgery, Massachusetts General Hospital, Boston, Mass
| | - Chandan Pavuluri
- Department of Medicine, Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Harvard Medical School, Boston, Mass; Harvard Medical School, Brigham and Women's Hospital, Boston, Mass
| | - Aabida Saferali
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Sofina Begum
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - John P Ziniti
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Hugues Aschard
- Department of Computational Biology, Institut Pasteur, Universit de Paris, Paris, France
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, Calif
| | - Craig P Hersh
- Department of Medicine, Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Harvard Medical School, Boston, Mass; Harvard Medical School, Brigham and Women's Hospital, Boston, Mass
| | - Jeffrey A Sparks
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, Mass
| | - Brian D Hobbs
- Department of Medicine, Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Harvard Medical School, Boston, Mass; Harvard Medical School, Brigham and Women's Hospital, Boston, Mass
| | - Jessica A Lasky-Su
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Edwin K Silverman
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Scott T Weiss
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Ann Chen Wu
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care, Boston, Mass
| | - Michael H Cho
- Department of Medicine, Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Harvard Medical School, Boston, Mass; Harvard Medical School, Brigham and Women's Hospital, Boston, Mass.
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Chen Q, Dwaraka VB, Carreras-Gallo N, Mendez K, Chen Y, Begum S, Kachroo P, Prince N, Went H, Mendez T, Lin A, Turner L, Moqri M, Chu SH, Kelly RS, Weiss ST, Rattray NJ, Gladyshev VN, Karlson E, Wheelock C, Mathé EA, Dahlin A, McGeachie MJ, Smith R, Lasky-Su JA. OMICmAge: An integrative multi-omics approach to quantify biological age with electronic medical records. bioRxiv 2023:2023.10.16.562114. [PMID: 37904959 PMCID: PMC10614756 DOI: 10.1101/2023.10.16.562114] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Biological aging is a multifactorial process involving complex interactions of cellular and biochemical processes that is reflected in omic profiles. Using common clinical laboratory measures in ~30,000 individuals from the MGB-Biobank, we developed a robust, predictive biological aging phenotype, EMRAge, that balances clinical biomarkers with overall mortality risk and can be broadly recapitulated across EMRs. We then applied elastic-net regression to model EMRAge with DNA-methylation (DNAm) and multiple omics, generating DNAmEMRAge and OMICmAge, respectively. Both biomarkers demonstrated strong associations with chronic diseases and mortality that outperform current biomarkers across our discovery (MGB-ABC, n=3,451) and validation (TruDiagnostic, n=12,666) cohorts. Through the use of epigenetic biomarker proxies, OMICmAge has the unique advantage of expanding the predictive search space to include epigenomic, proteomic, metabolomic, and clinical data while distilling this in a measure with DNAm alone, providing opportunities to identify clinically-relevant interconnections central to the aging process.
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Affiliation(s)
- Qingwen Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Kevin Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Yulu Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Sofina Begum
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicole Prince
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Aaron Lin
- TruDiagnostic, Inc., Lexington, KY USA
| | | | - Mahdi Moqri
- Division of Genetics, Dept. of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Su H. Chu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Rachel S. Kelly
- 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
| | - Nicholas J.W Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde, Glasgow, UK
| | - Vadim N. Gladyshev
- Division of Genetics, Dept. of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Karlson
- Department of Personalized Medicine, Mass General Brigham and Harvard Medical School, Boston, MA, USA
| | - Craig Wheelock
- Division of Physiological Chemistry 2, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Ewy A. Mathé
- Division of Preclinical Innovation, National Center for Advancing Translational Science, National Institutes of Health, Rockville, MD, USA
| | - Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Michae J. McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Jessica A. Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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3
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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 2023; 78:432-441. [PMID: 35501119 PMCID: PMC9810110 DOI: 10.1136/thoraxjnl-2021-217674] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 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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4
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Wu W, Dahlin A, Andersson U, Wibom C, Jonsson S, Melin B. P10.18.A Replication of previous GWAS identifies TERT and near EGFR SNVs as risk factors in EPIC glioma patients: a nested case-control study. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac174.183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Gliomas, the most common malignant primary brain tumors in adults, typically have a poor prognosis irrespective of medical care. Previous large genome-wide association studies (GWAS) have identified 27 single-nucleotide variants (SNVs) that are significantly associated with glioma. However, most of the GWAS are conducted by case-control study designs, it is therefore prone to bias when rapidly lethal cases don’t have chance to be included in the study. This study aims to replicate the previous GWAS findings using prospective study design.
Material and Methods
We conducted a nested case-control study within the European Prospective Investigation into Cancer (EPIC) cohort from 7 European countries. GSA-MD Infinium global screening array was used for genotyping. Some subjects were genotyped by other platforms previously. In total, 468 glioma patients and 481 controls were included. The genotypes of 27 SNVs were extracted and for ungenotyped SNVs, datasets were imputed using SHAPEIT v4.1.3 and IMPUTE5 v1.1.5 based on the Haplotype Reference Consortium (Release 1.1) reference panel. Conditional logistic regression model was used to investigate the additive effect of SNVs on the risk of glioma.
Results
21 SNVs showed a consistent direction of effect with previous studies, whereas 6 SNVs did not (ORs between 0.72-0.99 and not significant). After adjusting for multiple testing, two SNVs, rs10069690 (TERT), and rs75061358 (near EGFR) were significantly associated with glioma risk. We observed that prominent OR (2.23, 95%CI=1.49-3.33) of rs75061358 in our study compared to the result from previous GWAS, which implied rs75061358 might be not only a risk factor but also affect survival. Different risk direction was observed for rs77633900 in ETFA gene (OR=0.72, 95%CI=0.51-1.01).
Conclusion
Our findings further confirmed the genetic role on the etiology of glioma in the European population. The potential biases from the previous GWAS are required to be elucidated.
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Affiliation(s)
- W Wu
- Umeå University , Umeå , Sweden
| | | | | | - C Wibom
- Umeå University , Umeå , Sweden
| | | | - B Melin
- Umeå University , Umeå , Sweden
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5
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Kachroo P, Stewart ID, Kelly RS, Stav M, Mendez K, Dahlin A, Soeteman DI, Chu SH, Huang M, Cote M, Knihtilä HM, Lee-Sarwar K, McGeachie M, Wang A, Wu AC, Virkud Y, Zhang P, Wareham NJ, Karlson EW, Wheelock CE, Clish C, Weiss ST, Langenberg C, Lasky-Su JA. Metabolomic profiling reveals extensive adrenal suppression due to inhaled corticosteroid therapy in asthma. Nat Med 2022; 28:814-822. [PMID: 35314841 PMCID: PMC9350737 DOI: 10.1038/s41591-022-01714-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [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: 02/22/2021] [Accepted: 01/24/2022] [Indexed: 02/02/2023]
Abstract
The application of large-scale metabolomic profiling provides new opportunities for realizing the potential of omics-based precision medicine for asthma. By leveraging data from over 14,000 individuals in four distinct cohorts, this study identifies and independently replicates 17 steroid metabolites whose levels were significantly reduced in individuals with prevalent asthma. Although steroid levels were reduced among all asthma cases regardless of medication use, the largest reductions were associated with inhaled corticosteroid (ICS) treatment, as confirmed in a 4-year low-dose ICS clinical trial. Effects of ICS treatment on steroid levels were dose dependent; however, significant reductions also occurred with low-dose ICS treatment. Using information from electronic medical records, we found that cortisol levels were substantially reduced throughout the entire 24-hour daily period in patients with asthma who were treated with ICS compared to those who were untreated and to patients without asthma. Moreover, patients with asthma who were treated with ICS showed significant increases in fatigue and anemia as compared to those without ICS treatment. Adrenal suppression in patients with asthma treated with ICS might, therefore, represent a larger public health problem than previously recognized. Regular cortisol monitoring of patients with asthma treated with ICS is needed to provide the optimal balance between minimizing adverse effects of adrenal suppression while capitalizing on the established benefits of ICS treatment.
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Affiliation(s)
- Priyadarshini Kachroo
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Rachel S Kelly
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Meryl Stav
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin Mendez
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Amber Dahlin
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Djøra I Soeteman
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Health Decision Science, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Su H Chu
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Mengna Huang
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Margaret Cote
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hanna M Knihtilä
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathleen Lee-Sarwar
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael McGeachie
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alberta Wang
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ann Chen Wu
- Harvard Pilgrim Health Care Institute and Department of Population Medicine, Harvard Medical School, Boston, MA, USA
| | - Yamini Virkud
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Pei Zhang
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry 2, Karolinska Institute, Stockholm, Sweden
| | | | - Elizabeth W Karlson
- Department of Medicine, Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Craig E Wheelock
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry 2, Karolinska Institute, Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm, Sweden
| | | | - Scott T Weiss
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jessica A Lasky-Su
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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Sordillo JE, Lutz SM, Jorgenson E, Iribarren C, McGeachie M, Dahlin A, Tantisira K, Kelly R, Lasky-Su J, Sakornsakolpat P, Moll M, Cho MH, Wu AC. A polygenic risk score for asthma in a large racially diverse population. Clin Exp Allergy 2021; 51:1410-1420. [PMID: 34459047 DOI: 10.1111/cea.14007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/02/2021] [Accepted: 08/27/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND Polygenic risk scores (PRSs) will have important utility for asthma and other chronic diseases as a tool for predicting disease incidence and subphenotypes. OBJECTIVE We utilized findings from a large multiancestry GWAS of asthma to compute a PRS for asthma with relevance for racially diverse populations. METHODS We derived two PRSs for asthma using a standard approach (based on genome-wide significant variants) and a lasso sum regression approach (allowing all genetic variants to potentially contribute). We used data from the racially diverse Kaiser Permanente GERA cohort (68 638 non-Hispanic Whites, 5874 Hispanics, 6870 Asians and 2760 Blacks). Race was self-reported by questionnaire. RESULTS For the standard PRS, non-Hispanic Whites showed the highest odds ratio for a standard deviation increase in PRS for asthma (OR = 1.16 (95% CI 1.14-1.18)). The standard PRS was also associated with asthma in Hispanic (OR = 1.12 (95% CI 1.05-1.19)) and Asian (OR = 1.10 (95% CI 1.04-1.17)) subjects, with a trend towards increased risk in Blacks (OR = 1.05 (95% CI 0.97-1.15)). We detected an interaction by sex, with men showing a higher risk of asthma with an increase in PRS as compared to women. The lasso sum regression-derived PRS showed stronger associations with asthma in non-Hispanic White subjects (OR = 1.20 (95% CI 1.18-1.23)), Hispanics (OR = 1.17 (95% 1.10-1.26)), Asians (OR = 1.18 (95% CI 1.10-1.27)) and Blacks (OR = 1.10 (95% CI 0.99-1.22)). CONCLUSION Polygenic risk scores across multiple racial/ethnic groups were associated with increased asthma risk, suggesting that PRSs have potential as a tool for predicting disease development.
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Affiliation(s)
- Joanne E Sordillo
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, Massachusetts, USA
| | - Sharon M Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, Massachusetts, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Michael McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Rachel Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew Moll
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ann Chen Wu
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, Massachusetts, USA
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Wu AC, Dahlin A, Wang AL. The Role of Environmental Risk Factors on the Development of Childhood Allergic Rhinitis. Children 2021; 8:children8080708. [PMID: 34438599 PMCID: PMC8391414 DOI: 10.3390/children8080708] [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] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/15/2021] [Accepted: 08/16/2021] [Indexed: 01/20/2023]
Abstract
Environmental factors play an important role in the development and exacerbation of allergic rhinitis (AR) in childhood. Indoor air pollution, such as house dust mites and secondhand smoke, can significantly increase the onset of AR, while pet dander may affect the exacerbation of AR symptoms in children. Furthermore, traffic related air pollution and pollen are outdoor air pollutants that can affect immune competency and airway responsiveness, increasing the risk of AR in children. Climate change has increased AR in children, as growth patterns of allergenic species have changed, resulting in longer pollen seasons. More extreme and frequent weather events also contribute to the deterioration of indoor air quality due to climate change. Additionally, viruses provoke respiratory tract infections, worsening the symptoms of AR, while viral infections alter the immune system. Although viruses and pollution influence development and exacerbation of AR, a variety of treatment and prevention options are available for AR patients. The protective influence of vegetation (greenness) is heavily associated with air pollution mitigation, relieving AR exacerbations, while the use of air filters can reduce allergic triggers. Oral antihistamines and intranasal corticosteroids are common pharmacotherapy for AR symptoms. In this review, we discuss the environmental risk factors for AR and summarize treatment strategies for preventing and managing AR in children.
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Voorhies K, Sordillo JE, McGeachie M, Ampleford E, Wang AL, Lasky-Su J, Tantisira K, Dahlin A, Kelly RS, Ortega VE, Lutz SM, Wu AC. Age by Single Nucleotide Polymorphism Interactions on Bronchodilator Response in Asthmatics. J Pers Med 2021; 11:jpm11010059. [PMID: 33477890 PMCID: PMC7833432 DOI: 10.3390/jpm11010059] [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] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 12/15/2022] Open
Abstract
An unaddressed and important issue is the role age plays in modulating response to short acting β2-agonists in individuals with asthma. The objective of this study was to identify whether age modifies genetic associations of single nucleotide polymorphisms (SNPs) with bronchodilator response (BDR) to β2-agonists. Using three cohorts with a total of 892 subjects, we ran a genome wide interaction study (GWIS) for each cohort to examine SNP by age interactions with BDR. A fixed effect meta-analysis was used to combine the results. In order to determine if previously identified BDR SNPs had an age interaction, we also examined 16 polymorphisms in candidate genes from two published genome wide association studies (GWAS) of BDR. There were no significant SNP by age interactions on BDR using the genome wide significance level of 5 × 10−8. Using a suggestive significance level of 5 × 10−6, three interactions, including one for a SNP within PRAG1 (rs4840337), were significant and replicated at the significance level of 0.05. Considering candidate genes from two previous GWAS of BDR, three SNPs (rs10476900 (near ADRB2) [p-value = 0.009], rs10827492 (CREM) [p-value = 0.02], and rs72646209 (NCOA3) [p-value = 0.02]) had a marginally significant interaction with age on BDR (p < 0.05). Our results suggest age may be an important modifier of genetic associations for BDR in asthma.
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Affiliation(s)
- Kirsten Voorhies
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02215, USA; (K.V.); (J.E.S.); (S.M.L.)
| | - Joanne E. Sordillo
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02215, USA; (K.V.); (J.E.S.); (S.M.L.)
| | - Michael McGeachie
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.M.); (A.L.W.); (J.L.-S.); (K.T.); (A.D.); (R.S.K.)
| | - Elizabeth Ampleford
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA; (E.A.); (V.E.O.)
| | - Alberta L. Wang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.M.); (A.L.W.); (J.L.-S.); (K.T.); (A.D.); (R.S.K.)
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.M.); (A.L.W.); (J.L.-S.); (K.T.); (A.D.); (R.S.K.)
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.M.); (A.L.W.); (J.L.-S.); (K.T.); (A.D.); (R.S.K.)
- Division of Pediatric Respiratory Medicine, Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.M.); (A.L.W.); (J.L.-S.); (K.T.); (A.D.); (R.S.K.)
| | - Rachel S. Kelly
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (M.M.); (A.L.W.); (J.L.-S.); (K.T.); (A.D.); (R.S.K.)
| | - Victor E. Ortega
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA; (E.A.); (V.E.O.)
| | - Sharon M. Lutz
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02215, USA; (K.V.); (J.E.S.); (S.M.L.)
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Ann C. Wu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02215, USA; (K.V.); (J.E.S.); (S.M.L.)
- Division of General Pediatrics, Department of Pediatrics, Children’s Hospital, Boston, MA 02215, USA
- Correspondence: ; Tel.: +1-(617)-867-4823; Fax: +1-(617)-867-4276
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Tian L, Wang XW, Wu AK, Fan Y, Friedman J, Dahlin A, Waldor MK, Weinstock GM, Weiss ST, Liu YY. Deciphering functional redundancy in the human microbiome. Nat Commun 2020; 11:6217. [PMID: 33277504 PMCID: PMC7719190 DOI: 10.1038/s41467-020-19940-1] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [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: 12/19/2019] [Accepted: 11/04/2020] [Indexed: 02/07/2023] Open
Abstract
Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved - implying an ecological property known as functional redundancy. Such functional redundancy has been hypothesized to underlie the stability and resilience of the human microbiome, but this hypothesis has never been quantitatively tested. The origin of functional redundancy is still elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network - a bipartite graph that links microbes to the genes in their genomes. We find that this network exhibits several topological features that favor high functional redundancy. Furthermore, we develop a simple genome evolution model to generate genomic content network, finding that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with key topological features that favor high functional redundancy. Finally, we analyze data from two published studies of fecal microbiota transplantation (FMT), finding that high functional redundancy of the recipient's pre-FMT microbiota raises barriers to donor microbiota engraftment. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience.
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Affiliation(s)
- Liang Tian
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Physics, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Hong Kong SAR, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China
| | - Xu-Wen Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Ang-Kun Wu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, 08854, USA
| | - Yuhang Fan
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Jonathan Friedman
- Faculty of Agriculture, Food and Environment, Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | | | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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10
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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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11
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Sordillo JE, Lutz SM, Kelly RS, McGeachie MJ, Dahlin A, Tantisira K, Clish C, Lasky-Su J, Wu AC. Plasmalogens Mediate the Effect of Age on Bronchodilator Response in Individuals With Asthma. Front Med (Lausanne) 2020; 7:38. [PMID: 32118022 PMCID: PMC7034309 DOI: 10.3389/fmed.2020.00038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 09/11/2019] [Accepted: 01/27/2020] [Indexed: 12/17/2022] Open
Abstract
Background: Asthma is known to display different phenotypes across the life-course, suggesting that age related changes are particularly relevant to understanding asthma pathogenesis and remission. We have previously demonstrated that a lung function phenotype associated with asthma, bronchodilator response, is reduced with age, at rate of 0.24 percent per year. Methods: In this study, we interrogated the serum metabolome, to determine whether circulating metabolites mediate age-related changes in bronchodilator response (BDR) for individuals with asthma. We used data on 295 participants from the follow-up phase of the CAMP clinical trial (age 12.2-25.9 years; mean BDR of 8%, standard deviation 7%). Using a counterfactual framework, we analyzed over 500 pareto-scaled metabolites using mediation analysis to identify indirect effects of age through potential metabolite mediators. Results: There was a significant indirect effect of age on BDR through 4 plasmalogens (C36:1 PC and related metabolites) (Indirect Effect Beta = -0.001, p = 0.006). Conclusions: Our findings suggest that plasmalogens may contribute to age-related asthma phenotypes, and may also serve as potential pharmacologic targets for enhancement of lung function in individuals with asthma. Trial Registration: This work uses data from the previous clinical trial of asthma, the Childhood Asthma Management Program (CAMP), registered at ClinicalTrials.gov, # NCT00000575.
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Affiliation(s)
- Joanne E. Sordillo
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, United States
| | - Sharon M. Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, United States
| | - Rachel S. Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Michael J. McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Clary Clish
- The Broad Institute, Cambridge, MA, United States
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Ann Chen Wu
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, United States,*Correspondence: Ann Chen Wu
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12
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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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13
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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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14
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Sordillo JE, McGeachie M, Lutz SM, Lasky-Su J, Tantisira K, Tsai CH, Dahlin A, Kelly R, Wu AC. Longitudinal analysis of bronchodilator response in asthmatics and effect modification of age-related trends by genotype. Pediatr Pulmonol 2019; 54:158-164. [PMID: 30585438 PMCID: PMC6818258 DOI: 10.1002/ppul.24219] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/03/2018] [Indexed: 01/26/2023]
Abstract
BACKGROUND AND OBJECTIVES Genome Wide Association Studies (GWAS) have identified genetic polymorphisms associated with bronchodilator response (BDR), but it is unknown how these associations change across life stages. We examined the impact of genetic variants on BDR from childhood to adulthood in asthmatics to uncover potential effect modification by age. METHODS We searched the National Human Genome Research Institute (NHGRI) catalog of published GWAS to obtain a list of genetic associations with BDR, and tested them for effect modification by age in 604 subjects from the Childhood Asthma Management Program (CAMP), a clinical trial with longitudinal measures of BDR (age range 5-30 years). We performed longitudinal analyses using linear mixed models and visualized longitudinal changes in BDR using generalized additive models with repeated measures, adjusting for treatment group, sex, and main effects of age and additive genotype. RESULTS Increasing age was associated with decreased BDR (-0.24% per year). Polymorphisms rs295137 (T allele) near SPATS2L and rs2626393 (C allele) near ASB3 demonstrated their strongest associations with BDR in early childhood through adolescence, with a large decrease in their magnitude of effect from adolescence onward. The effect estimate for % BDR associated with rs295137 genotype (Beta = 1.3; 95%CI 0.6-2.1) was diminished by age (interaction term = -0.06, P = 0.004). The effect estimate for rs2626393 (Beta = -0.92 (95%CI -1.7 to -0.2) was also modified by age (interaction term = 0.05, P = 0.0004). CONCLUSIONS Polymorphisms associated with BDR in childhood may not be relevant for predicting adolescent and adult BDR, which could reflect age-related changes in asthma phenotypes.
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Affiliation(s)
- Joanne E Sordillo
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA
| | - Michael McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA
| | - Sharon M Lutz
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA
| | - Ching Hui Tsai
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA
| | - Rachel Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA
| | - Ann Chen Wu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA.,Division of General Pediatrics, Department of Pediatrics, Children's Hospital, Boston, MA
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15
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Virkud YV, Kelly RS, Croteau-Chonka DC, Celedón JC, Dahlin A, Avila L, Raby BA, Weiss ST, Lasky-Su JA. Novel eosinophilic gene expression networks associated with IgE in two distinct asthma populations. Clin Exp Allergy 2018; 48:1654-1664. [PMID: 30107053 PMCID: PMC6659730 DOI: 10.1111/cea.13249] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Asthma represents a significant public health burden; however, novel biological therapies targeting immunoglobulin E (IgE)-mediated pathways have widened clinical treatment options for the disease. OBJECTIVE In this study, we sought to identify gene transcripts and gene networks involved in the determination of serum IgE levels in people with asthma that can help inform the development of novel therapeutic agents. METHODS We analysed gene expression data from a cross-sectional study of 326 Costa Rican children with asthma, aged 6 to 12 years, from the Genetics of Asthma in Costa Rica Study and 610 young adults with asthma, aged 16 to 25 years, from the Childhood Asthma Management Program trial. We utilized differential gene expression analysis and performed weighted gene coexpression network analysis on 25 060 genes, to identify gene transcripts and network modules associated with total IgE, adjusting for age and gender. We used pathway enrichment analyses to identify key biological pathways underlying significant modules. We compared findings that replicated between both populations. RESULTS We identified 31 transcripts associated with total IgE that replicated between the two study cohorts. These results were notable for increased eosinophil-related transcripts (including IL5RA, CLC, SMPD3, CCL23 and CEBPE). Pathway enrichment identified the regulation of T cell tolerance as important in the determination of total IgE levels, supporting a key role for IDO1. CONCLUSIONS AND CLINICAL RELEVANCE These results provide robust evidence that biologically meaningful gene expression profiles (relating to eosinophilic and regulatory T cell pathways in particular) associated with total IgE levels can be identified in individuals diagnosed with asthma during childhood. These profiles and their constituent genes may represent novel therapeutic targets.
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Affiliation(s)
- Yamini V Virkud
- Division of Allergy and Immunology, Department of Pediatrics, Harvard Medical School, Massachusetts General Hospital for Children, Boston, Massachusetts.,Channing Division of Network Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts
| | - Rachel S Kelly
- Channing Division of Network Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts
| | - Damien C Croteau-Chonka
- Channing Division of Network Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lydiana Avila
- Department of Pediatrics, Hospital Nacional de Niños, San Jose, Costa Rica
| | - Benjamin A Raby
- Channing Division of Network Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts
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16
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Panganiban RA, Sun M, Dahlin A, Park HR, Kan M, Himes BE, Mitchel JA, Iribarren C, Jorgenson E, Randell SH, Israel E, Tantisira K, Shore S, Park JA, Weiss ST, Wu AC, Lu Q. A functional splice variant associated with decreased asthma risk abolishes the ability of gasdermin B to induce epithelial cell pyroptosis. J Allergy Clin Immunol 2018; 142:1469-1478.e2. [PMID: 29330013 PMCID: PMC6037620 DOI: 10.1016/j.jaci.2017.11.040] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [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: 05/20/2017] [Revised: 11/12/2017] [Accepted: 11/22/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Genetic variants in the chromosomal region 17q21 are consistently associated with asthma. However, mechanistic studies have not yet linked any of the associated variants to a function that could influence asthma, and as a result, the identity of the asthma gene(s) remains elusive. OBJECTIVES We sought to identify and characterize functional variants in the 17q21 locus. METHODS We used the Exome Aggregation Consortium browser to identify coding (amino acid-changing) variants in the 17q21 locus. We obtained asthma association measures for these variants in both the Genetic Epidemiology Research in Adult Health and Aging (GERA) cohort (16,274 cases and 38,269 matched controls) and the EVE Consortium study (5,303 asthma cases and 12,560 individuals). Gene expression and protein localization were determined by quantitative RT-PCR and fluorescence immunostaining, respectively. Molecular and cellular studies were performed to determine the functional effects of coding variants. RESULTS Two coding variants (rs2305480 and rs11078928) of the gasdermin B (GSDMB) gene in the 17q21 locus were associated with lower asthma risk in both GERA (odds ratio, 0.92; P = 1.01 × 10-6) and EVE (odds ratio, 0.85; joint PEVE = 1.31 × 10-13). In GERA, rs11078928 had a minor allele frequency (MAF) of 0.45 in unaffected (nonasthmatic) controls and 0.43 in asthma cases. For European Americans in EVE, the MAF of rs2305480 was 0.45 for controls and 0.39 for cases; for all EVE subjects, the MAF was 0.32 for controls and 0.27 for cases. GSDMB is highly expressed in differentiated airway epithelial cells, including the ciliated cells. We found that, when the GSDMB protein is cleaved by inflammatory caspase-1 to release its N-terminal fragment, potent pyroptotic cell death is induced. The splice variant rs11078928 deletes the entire exon 6, which encodes 13 amino acids in the critical N-terminus, and abolishes the pyroptotic activity of the GSDMB protein. CONCLUSIONS Our study identified a functional asthma variant in the GSDMB gene of the 17q21 locus and implicates GSDMB-mediated epithelial cell pyroptosis in pathogenesis.
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Affiliation(s)
- Ronald A 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, Mass
| | - Maoyun Sun
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Hae-Ryung Park
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Mengyuan Kan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Blanca E Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer A Mitchel
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, Calif
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, Calif
| | - Scott H Randell
- Marsico Lung Institute/Cystic Fibrosis Center, University of North Carolina, Chapel Hill, NC
| | - Elliot Israel
- Asthma Research Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Stephanie Shore
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Jin-Ah Park
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, 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
| | - Ann Chen Wu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Precision Medicine Translational Research Center, Department of Population Medicine, Harvard Medical School, Boston, Mass
| | - 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, Mass.
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17
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Romlin B, Dahlin A, Wåhlander H, Hallhagen S. Pediatric mechanical circulatory support and coagulation complications; a single-center experience. J Cardiothorac Vasc Anesth 2018. [DOI: 10.1053/j.jvca.2018.08.067] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Kelly RS, Sordillo JE, Lasky-Su J, Dahlin A, Perng W, Rifas-Shiman SL, Weiss ST, Gold DR, Litonjua AA, Hivert MF, Oken E, Wu AC. Plasma metabolite profiles in children with current asthma. Clin Exp Allergy 2018; 48:1297-1304. [PMID: 29808611 DOI: 10.1111/cea.13183] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/13/2018] [Accepted: 04/19/2018] [Indexed: 01/09/2023]
Abstract
BACKGROUND Identifying metabolomic profiles of children with asthma has the potential to increase understanding of asthma pathophysiology. OBJECTIVE To identify differences in plasma metabolites between children with and without current asthma at mid-childhood. METHODS We used untargeted mass spectrometry to measure plasma metabolites in 237 children (46 current asthma cases and 191 controls) in Project Viva, a birth cohort from eastern Massachusetts, USA. Current asthma was assessed at mid-childhood (mean age 8.0 years). The ability of a broad spectrum metabolic profile to distinguish between cases and controls was assessed using partial least squares discriminant analysis. We used logistic regression models to identify individual metabolites that were differentially abundant by case-control status. We tested significant metabolites for replication in 411 children from the VDAART clinical trial. RESULTS There was no evidence of a systematic difference in the metabolome of children reporting current asthma vs. healthy controls according to partial least squares discriminant analysis. However, several metabolites were associated with odds of current asthma at a nominally significant threshold (P < .05), including a metabolite of nicotinamide (N1-Methyl-2-pyridone-5-carboxamide (Odds Ratio (OR) = 2.8 (95% CI 1.1-8.0)), a pyrimidine metabolite (5,6-dihydrothymine (OR = 0.4 (95% CI 0.2-0.9)), bile constituents (biliverdin (OR = 0.4 (95%CI 0.1-0.9), taurocholate (OR = 2.0 (95% CI 1.2-3.4)), two peptides likely derived from fibrinopeptide A (ORs from 1.6 to 1.7), and a gut microbiome metabolite (p-cresol sulphate OR = 0.5 (95% CI 0.2-0.9)). The associations for N1-Methyl-2-pyridone-5-carboxamide and p-cresol sulphate replicated in the independent VDAART population (one-sided P values = .03-.04). CONCLUSIONS AND CLINICAL RELEVANCE Current asthma is nominally associated with altered levels of several metabolites, including metabolites in the nicotinamide pathway, and a bacterial metabolite derived from the gut microbiome.
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Affiliation(s)
- R S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - J E Sordillo
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA
| | - J Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - A Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - W Perng
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - S L Rifas-Shiman
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA
| | - S T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - D R Gold
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - A A Litonjua
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - M-F Hivert
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA.,Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - E Oken
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - A C Wu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA.,Division of General Pediatrics, Department of Pediatrics, Children's Hospital, Boston, MA, USA
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19
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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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20
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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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21
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Abstract
Aspirin-exacerbated respiratory disease (AERD) severity and its clinical phenotypes are characterized by genetic variation within pathways for arachidonic acid metabolism, inflammation, and immune responses. Epigenetic effects, including DNA methylation and histone protein modification, contribute to regulation of many genes that contribute to inflammatory states in AERD. The development of noninvasive, predictive clinical tests using data from genetic, epigenetic, pharmacogenetic, and biomarker studies will improve precision medicine efforts for AERD and asthma treatment.
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Affiliation(s)
- Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA.
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22
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Lasky-Su J, Dahlin A, Litonjua AA, Rogers AJ, McGeachie MJ, Baron RM, Gazourian L, Barragan-Bradford D, Fredenburgh LE, Choi AMK, Mogensen KM, Quraishi SA, Amrein K, Christopher KB. Metabolome alterations in severe critical illness and vitamin D status. Crit Care 2017; 21:193. [PMID: 28750641 PMCID: PMC5532782 DOI: 10.1186/s13054-017-1794-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/12/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND Metabolic homeostasis is substantially disrupted in critical illness. Given the pleiotropic effects of vitamin D, we hypothesized that metabolic profiles differ between critically ill patients relative to their vitamin D status. METHODS We performed a metabolomics study on biorepository samples collected from a single academic medical center on 65 adults with systemic inflammatory response syndrome or sepsis treated in a 20-bed medical ICU between 2008 and 2010. To identify key metabolites and metabolic pathways related to vitamin D status in critical illness, we first generated metabolomic data using gas and liquid chromatography mass spectroscopy. We followed this by partial least squares-discriminant analysis to identify individual metabolites that were significant. We then interrogated the entire metabolomics profile using metabolite set enrichment analysis to identify groups of metabolites and pathways that were differentiates of vitamin D status. Finally we performed logistic regression to construct a network model of chemical-protein target interactions important in vitamin D status. RESULTS Metabolomic profiles significantly differed in critically ill patients with 25(OH)D ≤ 15 ng/ml relative to those with levels >15 ng/ml. In particular, increased 1,5-anhydroglucitol, tryptophan betaine, and 3-hydroxyoctanoate as well as decreased 2-arachidonoyl-glycerophosphocholine and N-6-trimethyllysine were strong predictors of 25(OH)D >15 ng/ml. The combination of these five metabolites led to an area under the curve for discrimination for 25(OH)D > 15 ng/ml of 0.82 (95% CI 0.71-0.93). The metabolite pathways related to glutathione metabolism and glutamate metabolism are significantly enriched with regard to vitamin D status. CONCLUSION Vitamin D status is associated with differential metabolic profiles during critical illness. Glutathione and glutamate pathway metabolism, which play principal roles in redox regulation and immunomodulation, respectively, were significantly altered with vitamin D status.
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Affiliation(s)
- Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Augusto A Litonjua
- Pulmonary and Critical Care Division, Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Angela J Rogers
- Pulmonary & Critical Care Medicine, Stanford University Medical Center, Stanford, CA, USA
| | - Michael J McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rebecca M Baron
- Pulmonary and Critical Care Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Lee Gazourian
- Pulmonary and Critical Care Medicine, Lahey Hospital & Medical Center, Burlington, MA, USA
| | - Diana Barragan-Bradford
- Pulmonary and Critical Care Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Laura E Fredenburgh
- Pulmonary and Critical Care Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Augustine M K Choi
- Department of Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | - Kris M Mogensen
- Department of Nutrition, Brigham and Women's Hospital, Boston, MA, USA
| | - Sadeq A Quraishi
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Karin Amrein
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Kenneth B Christopher
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA. .,Renal Division, Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 75 Francis Street, MRB 418, Boston, MA, 02115, USA.
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Kelly RS, Croteau-Chonka DC, Dahlin A, Mirzakhani H, Wu AC, Wan ES, McGeachie MJ, Qiu W, Sordillo JE, Al-Garawi A, Gray KJ, McElrath TF, Carey VJ, Clish CB, Litonjua AA, Weiss ST, Lasky-Su JA. Integration of metabolomic and transcriptomic networks in pregnant women reveals biological pathways and predictive signatures associated with preeclampsia. Metabolomics 2017; 13:7. [PMID: 28596717 PMCID: PMC5458629 DOI: 10.1007/s11306-016-1149-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Preeclampsia is a leading cause of maternal and fetal mortality worldwide, yet its exact pathogenesis remains elusive. OBJECTIVES This study, nested within the Vitamin D Antenatal Asthma Reduction Trial (VDAART), aimed to develop integrated omics models of preeclampsia that have utility in both prediction and in the elucidation of underlying biological mechanisms. METHODS Metabolomic profiling was performed on first trimester plasma samples of 47 pregnant women from VDAART who subsequently developed preeclampsia and 62 controls with healthy pregnancies, using liquid-chromatography tandem mass-spectrometry. Metabolomic profiles were generated based on logistic regression models and assessed using Received Operator Characteristic Curve analysis. These profiles were compared to profiles from generated using third trimester samples. The first trimester metabolite profile was then integrated with a pre-existing transcriptomic profile using network methods. RESULTS In total, 72 (0.9%) metabolite features were associated (p<0.01) with preeclampsia after adjustment for maternal age, race, and gestational age. These features had moderate to good discriminatory ability; in ROC curve analyses a summary score based on these features displayed an area under the curve (AUC) of 0.794 (95%CI 0.700, 0.888). This profile retained the ability to distinguish preeclamptic from healthy pregnancies in the third trimester (AUC:0.762 (95% CI 0.663, 0.860)). Additionally, metabolite set enrichment analysis identified common pathways, including glycerophospholipid metabolism, at the two time-points. Integration with the transcriptomic signature refined these results suggesting a particular role for lipid imbalance, immune function and the circulatory system. CONCLUSIONS These findings suggest it is possible to develop a predictive metabolomic profile of preeclampsia. This profile is characterized by changes in lipid and amino acid metabolism and dysregulation of immune response and can be refined through interaction with transcriptomic data. However validation in larger and more diverse populations is required.
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Affiliation(s)
- Rachel S. Kelly
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Damien C. Croteau-Chonka
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Amber Dahlin
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hooman Mirzakhani
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ann C. Wu
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Emily S. Wan
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Michael J. McGeachie
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Weiliang Qiu
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Joanne E. Sordillo
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Amal Al-Garawi
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kathryn J. Gray
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Thomas F. McElrath
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Vincent J. Carey
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Clary B. Clish
- Metabolomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02141, USA
| | - Augusto A. Litonjua
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Scott T. Weiss
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jessica A. Lasky-Su
- Channing Department of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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Kelly RS, Dahlin A, McGeachie MJ, Qiu W, Sordillo J, Wan ES, Wu AC, Lasky-Su J. Asthma Metabolomics and the Potential for Integrative Omics in Research and the Clinic. Chest 2016; 151:262-277. [PMID: 27776981 DOI: 10.1016/j.chest.2016.10.008] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/26/2016] [Accepted: 10/07/2016] [Indexed: 12/11/2022] Open
Abstract
Asthma is a complex disease well-suited to metabolomic profiling, both for the development of novel biomarkers and for the improved understanding of pathophysiology. In this review, we summarize the 21 existing metabolomic studies of asthma in humans, all of which reported significant findings and concluded that individual metabolites and metabolomic profiles measured in exhaled breath condensate, urine, plasma, and serum could identify people with asthma and asthma phenotypes with high discriminatory ability. There was considerable consistency across the studies in terms of the reported biomarkers, regardless of biospecimen, profiling technology, and population age. In particular, acetate, adenosine, alanine, hippurate, succinate, threonine, and trans-aconitate, and pathways relating to hypoxia response, oxidative stress, immunity, inflammation, lipid metabolism and the tricarboxylic acid cycle were all identified as significant in at least two studies. There were also a number of nonreplicated results; however, the literature is not yet sufficiently developed to determine whether these represent spurious findings or reflect the substantial heterogeneity and limited statistical power in the studies and their methods to date. This review highlights the need for additional asthma metabolomic studies to explore these issues, and, further, the need for standardized methods in the way these studies are conducted. We conclude by discussing the potential of translation of these metabolomic findings into clinically useful biomarkers and the crucial role that integrated omics is likely to play in this endeavor.
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Affiliation(s)
- Rachel S Kelly
- Channing Division of Network Medicine, Brigham Women's Hospital and Harvard Medical School, Boston, MA
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham Women's Hospital and Harvard Medical School, Boston, MA
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham Women's Hospital and Harvard Medical School, Boston, MA
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham Women's Hospital and Harvard Medical School, Boston, MA
| | - Joanne Sordillo
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA
| | - Emily S Wan
- Channing Division of Network Medicine, Brigham Women's Hospital and Harvard Medical School, Boston, MA; VA Boston Healthcare System, Department of Veterans Affairs, Boston, MA
| | - Ann Chen Wu
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham Women's Hospital and Harvard Medical School, Boston, MA.
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Dahlin A, Denny J, Roden DM, Brilliant MH, Ingram C, Kitchner TE, Linneman JG, Shaffer CM, Weeke P, Xu H, Kubo M, Tamari M, Clemmer GL, Ziniti J, McGeachie MJ, Tantisira KG, Weiss ST, Wu AC. CMTR1 is associated with increased asthma exacerbations in patients taking inhaled corticosteroids. Immun Inflamm Dis 2015; 3:350-9. [PMID: 26734457 PMCID: PMC4693729 DOI: 10.1002/iid3.73] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 06/03/2015] [Accepted: 06/13/2015] [Indexed: 12/25/2022]
Abstract
Inhaled corticosteroids (ICS) are the most effective controller medications for asthma, and variability in ICS response is associated with genetic variation. Despite ICS treatment, some patients with poor asthma control experience severe asthma exacerbations, defined as a hospitalization or emergency room visit. We hypothesized that some individuals may be at increased risk of asthma exacerbations, despite ICS use, due to genetic factors. A GWAS of 237,726 common, independent markers was conducted in 806 Caucasian asthmatic patients from two population-based biobanks: BioVU, at Vanderbilt University Medical Center (VUMC) in Tennessee (369 patients), and Personalized Medicine Research Project (PMRP) at the Marshfield Clinic in Wisconsin (437 patients). Using a case-control study design, the association of each SNP locus with the outcome of asthma exacerbations (defined as asthma-related emergency department visits or hospitalizations concurrent with oral corticosteroid use), was evaluated for each population by logistic regression analysis, adjusting for age, gender and the first four principal components. A meta-analysis of the results was conducted. Validation of expression of selected candidate genes was determined by evaluating an independent microarray expression data set. Our study identified six novel SNPs associated with differential risk of asthma exacerbations (P < 10(-05)). The top GWAS result, rs2395672 in CMTR1, was associated with an increased risk of exacerbations in both populations (OR = 1.07, 95% CI 1.03-1.11; joint P = 2.3 × 10(-06)). Two SNPs (rs2395672 and rs279728) were associated with increased risk of exacerbations, while the remaining four SNPs (rs4271056, rs6467778, rs2691529, and rs9303988) were associated with decreased risk. Three SNPs (rs2395672, rs6467778, and rs2691529) were present in three genes: CMTR1, TRIM24 and MAGI2. The CMTR1 mRNA transcript was significantly differentially expressed in nasal lavage samples from asthmatics during acute exacerbations, suggesting potential involvement of this gene in the development of this phenotype. We show that genetic variability may contribute to asthma exacerbations in patients taking ICS. Furthermore, our studies implicate CMTR1 as a novel candidate gene with potential roles in the pathogenesis of asthma exacerbations.
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Affiliation(s)
- Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts 02115
| | - Joshua Denny
- Department of Medical BioinformaticsVanderbilt University School of MedicineNashvilleTennessee37235; Department of MedicineVanderbilt UniversityNashvilleTennessee37235
| | - Dan M Roden
- Division of Clinical Pharmacology, Department of Medicine Vanderbilt University School of Medicine Nashville Tennessee 37235
| | - Murray H Brilliant
- Center for Human Genetics Marshfield Clinic Research Foundation Marshfield Wisconsin 54449
| | - Christie Ingram
- Department of Medicine Vanderbilt University Nashville Tennessee 37235
| | - Terrie E Kitchner
- Center for Human Genetics Marshfield Clinic Research Foundation Marshfield Wisconsin 54449
| | - James G Linneman
- Biomedical Informatics Research Center Marshfield Clinic Research Foundation Marshfield Wisconsin 54449
| | | | - Peter Weeke
- Department of MedicineVanderbilt UniversityNashvilleTennessee37235; Department of CardiologyCopenhagen, University HospitalGentofteDenmark
| | - Hua Xu
- School of Biomedical Informatics The University of Texas Health Science Center at Houston Houston Texas 77030
| | | | | | - George L Clemmer
- Channing Division of Network Medicine, Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts 02115
| | - John Ziniti
- Channing Division of Network Medicine, Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts 02115
| | - Michael J McGeachie
- Channing Division of Network Medicine, Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts 02115
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts 02115
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts 02115
| | - Ann Chen Wu
- Channing Division of Network Medicine, Department of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusetts02115; Center for Child Health Care Studies, Department of Population MedicineHarvard Pilgrim Health Care Institute and Harvard Medical SchoolBostonMassachusetts02115
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McGeachie MJ, Dahlin A, Qiu W, Croteau-Chonka DC, Savage J, Wu AC, Wan ES, Sordillo JE, Al-Garawi A, Martinez FD, Strunk RC, Lemanske RF, Liu AH, Raby BA, Weiss S, Clish CB, Lasky-Su JA. The metabolomics of asthma control: a promising link between genetics and disease. Immun Inflamm Dis 2015; 3:224-38. [PMID: 26421150 PMCID: PMC4578522 DOI: 10.1002/iid3.61] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 03/26/2015] [Accepted: 03/27/2015] [Indexed: 12/12/2022]
Abstract
Short-acting β agonists (e.g., albuterol) are the most commonly used medications for asthma, a disease that affects over 300 million people in the world. Metabolomic profiling of asthmatics taking β agonists presents a new and promising resource for identifying the molecular determinants of asthma control. The objective is to identify novel genetic and biochemical predictors of asthma control using an integrative "omics" approach. We generated lipidomic data by liquid chromatography tandem mass spectrometry (LC-MS), - using plasma samples from 20 individuals with asthma. The outcome of interest was a binary indicator of asthma control defined by the use of albuterol inhalers in the preceding week. We integrated metabolomic data with genome-wide genotype, gene expression, and methylation data of this cohort to identify genomic and molecular indicators of asthma control. A Conditional Gaussian Bayesian Network (CGBN) was generated using the strongest predictors from each of these analyses. Integrative and metabolic pathway over-representation analyses (ORA) identified enrichment of known biological pathways within the strongest molecular determinants. Of the 64 metabolites measured, 32 had known identities. The CGBN model based on four SNPs (rs9522789, rs7147228, rs2701423, rs759582) and two metabolites-monoHETE_0863 and sphingosine-1-phosphate (S1P) could predict asthma control with an AUC of 95%. Integrative ORA identified 17 significantly enriched pathways related to cellular immune response, interferon signaling, and cytokine-related signaling, for which arachidonic acid, PGE2 and S1P, in addition to six genes (CHN1, PRKCE, GNA12, OASL, OAS1, and IFIT3) appeared to drive the pathway results. Of these predictors, S1P, GNA12, and PRKCE were enriched in the results from integrative and metabolic ORAs. Through an integrative analysis of metabolomic, genomic, and methylation data from a small cohort of asthmatics, we implicate altered metabolic pathways, related to sphingolipid metabolism, in asthma control. These results provide insight into the pathophysiology of asthma control.
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Affiliation(s)
- Michael J McGeachie
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts, USA
| | - Amber Dahlin
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts, USA
| | - Weiliang Qiu
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts, USA
| | - Damien C Croteau-Chonka
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts, USA
| | - Jessica Savage
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts, USA
| | - Ann Chen Wu
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts, USA ; Children's Hospital and Harvard Medical School Boston, Massachusetts, USA ; Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute Boston, Massachusetts, USA
| | - Emily S Wan
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts, USA
| | - Joanne E Sordillo
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts, USA
| | - Amal Al-Garawi
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts, USA
| | - Fernando D Martinez
- Arizona Respiratory Center and BIO5 Institute, University of Arizona Tucson, Arizona, USA
| | - Robert C Strunk
- Department of Pediatrics, Division of Allergy, Immunology and Pulmonary Medicine, Washington University School of Medicine St. Louis, Missouri, USA
| | - Robert F Lemanske
- University of Wisconsin School of Medicine and Public Health Madison, Wisconsin, USA
| | - Andrew H Liu
- Department of Pediatrics, Division of Allergy and Clinical Immunology, National Jewish Health and University of Colorado School of Medicine Denver, Colorado, USA
| | - Benjamin A Raby
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts, USA
| | - Scott Weiss
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts, USA
| | | | - Jessica A Lasky-Su
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts, USA
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McGeachie MJ, Clemmer GL, Lasky-Su J, Dahlin A, Raby BA, Weiss ST. Joint GWAS Analysis: Comparing similar GWAS at different genomic resolutions identifies novel pathway associations with six complex diseases. Genom Data 2014; 2:202-211. [PMID: 25838990 PMCID: PMC4378545 DOI: 10.1016/j.gdata.2014.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We show here that combining two existing genome wide association studies (GWAS) yields additional biologically relevant information, beyond that obtained by either GWAS separately. We propose Joint GWAS Analysis, a method that compares a pair of GWAS for similarity among the top SNP associations, top genes identified, gene functional clusters, and top biological pathways. We show that Joint GWAS Analysis identifies additional enriched biological pathways that would be missed by traditional Single-GWAS analysis. Furthermore, we examine the similarities of six complex genetic disorders at the SNP-level, gene-level, gene-cluster-level, and pathway-level. We make concrete hypotheses regarding novel pathway associations for several complex disorders considered, based on the results of Joint GWAS Analysis. Together, these results demonstrate that common complex disorders share substantially more genomic architecture than has been previously realized and that the meta-analysis of GWAS needs not be limited to GWAS of the same phenotype to be informative.
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Affiliation(s)
- Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA ; Harvard Medical School, Boston, MA, USA
| | - George L Clemmer
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA ; Harvard Medical School, Boston, MA, USA
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA ; Harvard Medical School, Boston, MA, USA
| | - Benjamin A Raby
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA ; Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA ; Harvard Medical School, Boston, MA, USA
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Wibom C, Spaeth F, Dahlin A, Langseth H, Hovig E, Rajaraman P, Andersson U, Melin B. P17.94 * GLIOMA GWAS HITS - MARKERS FOR RISK OR FOR PROGNOSIS? Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou174.423] [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: 11/13/2022] Open
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Park HW, Dahlin A, Tse S, Duan QL, Schuemann B, Martinez FD, Peters SP, Szefler SJ, Lima JJ, Kubo M, Tamari M, Tantisira KG. Genetic predictors associated with improvement of asthma symptoms in response to inhaled corticosteroids. J Allergy Clin Immunol 2014; 133:664-9.e5. [PMID: 24486069 DOI: 10.1016/j.jaci.2013.12.1042] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 01/01/2023]
Abstract
BACKGROUND To date, genome-wide association studies (GWASs) of inhaled corticosteroid (ICS) response in asthmatic patients have focused primarily on lung function and exacerbations. OBJECTIVE We hypothesized that GWAS analysis could identify novel genetic markers predicting a symptomatic response to ICSs. METHODS We analyzed differences in asthma symptoms in response to ICSs in 124 white children from the Childhood Asthma Management Program (CAMP) trial using scores from diary cards. Of the 440,862 single nucleotide polymorphisms (SNPs) analyzed, the top 100 ranked SNPs were pursued for replication initially in subjects from the pediatric Childhood Asthma Research and Education trials (77 white children) and then in subjects from the adult Asthma Clinical Research Network (110 white adults) and Leukotriene Modifier or Corticosteroid or Corticosteroid-Salmeterol trials (110 white adults). RESULTS The lowest P value for GWAS analysis in the CAMP trial was 8.94 × 10(-8) (rs2388639). Of the 60 SNPs available in the Childhood Asthma Research and Education Network trials, rs1558726 (combined P = 1.02 × 10(-5)), rs2388639 (combined P = 8.56 × 10(-9)), and rs10044254 (combined P = 9.16 × 10(-8)) independently replicated. However, these 3 SNPs were not additionally replicated in the adult asthmatic patients of the remaining trials. rs10044254 lies in the intronic region of F-box and leucine-rich repeat protein 7 (FBXL7) and is associated with decreased expression in immortalized B cells derived from CAMP participants. CONCLUSIONS We have identified a novel SNP, rs10044254, associated with both decreased expression of FBXL7 and improved symptomatic response to ICSs in 2 independent pediatric cohorts. Our results suggest that there might be a specific genetic mechanism regulating symptomatic response to ICSs in children that does not carry over to adults.
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Affiliation(s)
- Heung-Woo Park
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Szeman Tse
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Qing Ling Duan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Brooke Schuemann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Fernando D Martinez
- Arizona Respiratory Center, University of Arizona, College of Medicine, Tucson, Ariz
| | - Stephen P Peters
- Center for Genomics and Personalized Medicine Research and the Section on Pulmonary, Critical Care, Allergy and Immunologic Diseases, Wake Forest School of Medicine, Winston-Salem, NC
| | - Stanley J Szefler
- Department of Pediatric and Pharmacology, National Jewish Health and University of Colorado, Denver School of Medicine, Denver, Colo
| | - John J Lima
- Center for Pharmacogenomics and Translational Research, Nemours Children's Clinic, Jacksonville, Fla
| | - Michiaki Kubo
- Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Mayumi Tamari
- Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Mass.
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Abstract
In order to improve therapeutic outcomes, there is a tremendous need to identify patients who are likely to respond to a given asthma treatment. Pharmacogenomic studies have explained a portion of the variability in drug response and provided an increasing list of candidate genes and SNPs. However, as phenotypic variation arises from a network of complex interactions among genetic and environmental factors, rather than individual genes or SNPs, a multidisciplinary, systems-level approach is required in order to understand the inter-relationships among these factors. Systems biology, which seeks to capture interactions between genetic factors and other variables, offers a promising approach to improved therapeutic outcomes in asthma. This aritcle will review and update progress in the pharmacogenomics of asthma and then discuss the application of systems biology approaches to asthma pharmacogenomics.
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Affiliation(s)
- Amber Dahlin
- Channing Laboratory, Brigham & Women's Hospital & Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
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Dahlin A, Geier E, Stocker SL, Cropp CD, Grigorenko E, Bloomer M, Siegenthaler J, Xu L, Basile AS, Tang-Liu DDS, Giacomini KM. Gene expression profiling of transporters in the solute carrier and ATP-binding cassette superfamilies in human eye substructures. Mol Pharm 2013; 10:650-63. [PMID: 23268600 DOI: 10.1021/mp300429e] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The barrier epithelia of the cornea and retina control drug and nutrient access to various compartments of the human eye. While ocular transporters are likely to play a critical role in homeostasis and drug delivery, little is known about their expression, localization and function. In this study, the mRNA expression levels of 445 transporters, metabolic enzymes, transcription factors and nuclear receptors were profiled in five regions of the human eye: cornea, iris, ciliary body, choroid and retina. Through RNA expression profiling and immunohistochemistry, several transporters were identified as putative targets for drug transport in ocular tissues. Our analysis identified SLC22A7 (OAT2), a carrier for the antiviral drug acyclovir, in the corneal epithelium, in addition to ABCG2 (BCRP), an important xenobiotic efflux pump, in retinal nerve fibers and the retinal pigment epithelium. Collectively, our results provide an understanding of the transporters that serve to maintain ocular homeostasis and which may be potential targets for drug delivery to deep compartments of the eye.
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Affiliation(s)
- Amber Dahlin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
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Stocker SL, Morrissey KM, Yee SW, Castro RA, Xu L, Dahlin A, Ramirez AH, Roden DM, Wilke RA, McCarty CA, Davis RL, Brett CM, Giacomini KM. The effect of novel promoter variants in MATE1 and MATE2 on the pharmacokinetics and pharmacodynamics of metformin. Clin Pharmacol Ther 2012; 93:186-94. [PMID: 23267855 DOI: 10.1038/clpt.2012.210] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Interindividual variation in response to metformin, first-line therapy for type 2 diabetes, is substantial. Given that transporters are determinants of metformin pharmacokinetics, we examined the effects of promoter variants in both multidrug and toxin extrusion protein 1 (MATE1) (g.-66T → C, rs2252281) and MATE2 (g.-130G → A, rs12943590) on variation in metformin disposition and response. The pharmacokinetics and glucose-lowering effects of metformin were assessed in healthy volunteers (n = 57) receiving metformin. The renal and secretory clearances of metformin were higher (22% and 26%, respectively) in carriers of variant MATE2 who were also MATE1 reference (P < 0.05). Both MATE genotypes were associated with altered post-metformin glucose tolerance, with variant carriers of MATE1 and MATE2 having an enhanced (P < 0.01) and reduced (P < 0.05) response, respectively. Consistent with these results, patients with diabetes (n = 145) carrying the MATE1 variant showed enhanced metformin response. These findings suggest that promoter variants of MATE1 and MATE2 are important determinants of metformin disposition and response in healthy volunteers and diabetic patients.
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Affiliation(s)
- S L Stocker
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
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Schlessinger A, Wittwer MB, Dahlin A, Khuri N, Bonomi M, Fan H, Giacomini KM, Sali A. High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach. J Biol Chem 2012; 287:37745-56. [PMID: 22932902 DOI: 10.1074/jbc.m112.388157] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The solute carrier 6 (SLC6) is a family of ion-dependent transporters that mediate uptake into the cell of osmolytes such as neurotransmitters and amino acids. Four SLC6 members transport GABA, a key neurotransmitter that triggers inhibitory signaling pathways via various receptors (e.g., GABA(A)). The GABA transporters (GATs) regulate the concentration of GABA available for signaling and are thus targeted by a variety of anticonvulsant and relaxant drugs. Here, we characterize GAT-2, a transporter that plays a role in peripheral GABAergic mechanisms, by constructing comparative structural models based on crystallographic structures of the leucine transporter LeuT. Models of GAT-2 in two different conformations were constructed and experimentally validated, using site-directed mutagenesis. Computational screening of 594,166 compounds including drugs, metabolites, and fragment-like molecules from the ZINC database revealed distinct ligands for the two GAT-2 models. 31 small molecules, including high scoring compounds and molecules chemically related to known and predicted GAT-2 ligands, were experimentally tested in inhibition assays. Twelve ligands were found, six of which were chemically novel (e.g., homotaurine). Our results suggest that GAT-2 is a high selectivity/low affinity transporter that is resistant to inhibition by typical GABAergic inhibitors. Finally, we compared the binding site of GAT-2 with those of other SLC6 members, including the norepinephrine transporter and other GATs, to identify ligand specificity determinants for this family. Our combined approach may be useful for characterizing interactions between small molecules and other membrane proteins, as well as for describing substrate specificities in other protein families.
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Affiliation(s)
- Avner Schlessinger
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA
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Abstract
The choroid plexus (CP) is a highly vascularized tissue in the brain ventricles and acts as the blood-cerebrospinal fluid (CSF) barrier (BCSFB). A main function of the CP is to secrete CSF, which is accomplished by active transport of small ions and water from the blood side to the CSF side. The CP also supplies the brain with certain nutrients, hormones, and metal ions, while removing metabolites and xenobiotics from the CSF. Numerous membrane transporters are expressed in the CP in order to facilitate the solute exchange between the blood and the CSF. The solute carrier (SLC) superfamily represents a major class of transporters in the CP that constitutes the molecular mechanisms for CP function. Recently, we systematically and quantitatively examined Slc gene expression in 20 anatomically comprehensive brain areas in the adult mouse brain using high-quality in situ hybridization data generated by the Allen Brain Atlas. Here we focus our analysis on Slc gene expression at the BCSFB using previously obtained data. Of the 252 Slc genes present in the mouse brain, 202 Slc genes were found at detectable levels in the CP. Unsupervised hierarchical cluster analysis showed that the CP Slc gene expression pattern is substantially different from the other 19 analyzed brain regions. The majority of the Slc genes in the CP are expressed at low to moderate levels, whereas 28 Slc genes are present in the CP at the highest levels. These highly expressed Slc genes encode transporters involved in CSF secretion, energy production, and transport of nutrients, hormones, neurotransmitters, sulfate, and metal ions. In this review, the functional characteristics and potential importance of these Slc transporters in the CP are discussed, with particular emphasis on their localization and physiological functions at the BCSFB.
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Affiliation(s)
- Horace T B Ho
- Department of Pharmaceutics, University of Washington Seattle, WA, USA
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Lilja H, Savage C, Gerdtsson A, Bjork T, Manjer J, Nilsson P, Dahlin A, Bjartell A, Scardino PT, Ulmert D, Vickers AJ. Toward a rational strategy for prostate cancer screening based on long-term risk of prostate cancer metastases and death: Data from a large, unscreened, population-based cohort followed for up to 30 years. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.4512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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36
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Vickers A, Cronin A, Bjork T, Manjer J, Nilsson P, Dahlin A, Biartell A, Scardino P, Ulmert D, Lilia H. 982 LIFETIME RISK OF DEATH FROM PROSTATE CANCER PREDICTED BY KALLIKREIN MARKERS IN BLOOD TAKEN AT AGE 60. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/s1569-9056(10)60961-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
The solute carrier (Slc) superfamily is a major group of membrane transport proteins present in mammalian cells. Although Slc transporters play essential and diverse roles in the central nervous system, the localization and function of the vast majority of Slc genes in the mammalian brain are largely unknown. Using high-throughput in situ hybridization data generated by the Allen Brain Atlas, we systematically and quantitatively analyzed the spatial and cellular distribution of 307 Slc genes, which represent nearly 90% of presently known mouse Slc genes, in the adult C57BL/6J mouse brain. Our analysis showed that 252 (82%) of the 307 Slc genes are present in the brain, and a large proportion of these genes were detected at low to moderate expression levels. Evaluation of 20 anatomical brain subdivisions demonstrated a comparable level of Slc gene complexity but significant difference in transcript enrichment. The distribution of the expressed Slc genes was diverse, ranging from near-ubiquitous to highly localized. Functional annotation in 20 brain regions, including the blood-brain and blood-cerebral spinal fluid (CSF) barriers, suggests major roles of Slc transporters in supporting brain energy utilization, neurotransmission, nutrient supply, and CSF production. Furthermore, hierarchical cluster analysis revealed intricate Slc expression patterns associated with neuroanatomical organization. Our studies also revealed Slc genes present within defined brain microstructures and described the putative cell types expressing individual Slc genes. These results provide a useful resource for investigators to explore the roles of Slc genes in neurophysiological and pathological processes.
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Affiliation(s)
- Amber Dahlin
- Department of Pharmaceutics, University of Washington, Seattle, WA 98195, USA
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Abstract
Any treatment of a pregnant woman with medication (drugs) de facto results in the treatment of her unborn child, even when her unborn child is not the target of drug therapy. This is because, in most instances, the placenta is not a complete barrier to the passage of drugs from the maternal to the fetal compartment. This barrier is in part due to the presence of various efflux transporters in the placenta. The placenta is also richly endowed with influx transporters. In this article, we will review the physiological characteristics of the placenta and how it functions as a barrier to passage of drugs into the fetal compartment. In addition, we will review placental transporters that are important in modulating the exposure of the fetus to drugs and, therefore, the efficacy and toxicity of such drugs towards the fetus.
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Affiliation(s)
- Jashvant D Unadkat
- Department of Pharmaceutics, University of Washington, Seattle WA 98195, USA.
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Disis ML, Scholler N, Dahlin A, Pullman J, Knutson KL, Hellström KE, Hellström I. Plasmid-based vaccines encoding rat neu and immune stimulatory molecules can elicit rat neu-specific immunity. Mol Cancer Ther 2003; 2:995-1002. [PMID: 14578464] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
DNA vaccines are ideally suited for immunizing against tumor antigens because constructs can be formulated that not only encode the tumor antigen but also encode molecules chosen to improve the ability to elicit an antitumor response. Ligands expressed on antigen-presenting cells associated with stimulating a robust T-cell response are excellent candidates for inclusion in a DNA vaccine. Mice transgenic for the HER-2/neu homologue, rat neu, were immunized with full-length rat neu cDNA given alone or in combination with plasmids encoding costimulatory molecules CD80 or CD86 and the ligand for CD137 (CD137L). Intradermal injection of the plasmid constructs resulted in both plasmid transcript and antigen protein expression being detected in lymph nodes draining the injection site. Immunization with plasmids encoding the neu antigen along with plasmids encoding CD137L and either CD80 or CD86 resulted in the generation of neu-specific antibodies that induced phopshorylation of the neu tyrosine kinase and inhibited the growth of cultured tumor cells overexpressing neu. Survival of animals was significantly prolonged after immunization with vaccines encoding neu together with the costimulatory molecules. Although tumors eventually occurred in the vaccinated animals, they were markedly infiltrated with CD4+ T cells. DNA vaccines encoding neu, when given in combination with both CD137L and either CD80 or CD86, can induce cellular and humoral immunity and result in an antitumor effect.
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Affiliation(s)
- Mary L Disis
- Tumor Vaccine Group, Division of Oncology, University of Washington, Seattle, WA 98195-6527, USA.
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Abstract
Monoclonal antibodies against the T-cell activation molecule 4-1BB have been effective in the treatment of established mouse tumors. To create a vaccine that stimulates the immune system similarly to the efficacious monoclonal anti-4-1BB antibody, 1D8, we constructed a vector encoding cell-bound single-chain Fv fragments from 1D8. We transfected the vector into cells from the K1735 melanoma, selected because of its low immunogenicity and very low expression of major histocompatibility complex class I. The transfected cells induced a strong type 1 T-helper cell response, for which CD4+ but not CD8+ T lymphocytes were necessary and that involved natural killer cells. Vaccinated mice rejected established wild-type K1735 tumors growing as subcutaneous nodules or in the lung. An analogous approach may be effective against micrometastases in human patients, including tumors whose expression of major histocompatibility complex class I is very low.
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Affiliation(s)
- Zhengmao Ye
- Pacific Northwest Research Institute, Seattle, Washington, USA
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41
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Scholler N, Hayden-Ledbetter M, Dahlin A, Hellström I, Hellström KE, Ledbetter JA. Cutting edge: CD83 regulates the development of cellular immunity. J Immunol 2002; 168:2599-602. [PMID: 11884422 DOI: 10.4049/jimmunol.168.6.2599] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We recently found that human CD83, a marker of mature dendritic cells, is an adhesion receptor that binds to resting monocytes and a subset of activated CD8(+) T cells. We injected CD83-Ig into mice transplanted with the immunogenic P815 mastocytoma and showed that it significantly enhanced the rate of tumor growth and inhibited the development of cytotoxic T cells. In contrast, mice immunized with CD83-transfected K1735 cells, a poorly immunogenic melanoma, could prevent the outgrowth of wild-type K1735 cells. Studies performed in vitro with human PBL showed that coimmobilized CD83-Ig and anti-CD3 enhanced T cell proliferation and increased the proportion of CD8(+) T cells. CD83-transfected B-lymphoblastoid T51 cells stimulated T cell proliferation more effectively than untransfected T51 cells in MLR cultures and increased the generation of cytolytic T cells. We conclude that CD83 is a functionally important receptor that can regulate the development of cellular immunity by interacting with its ligand(s).
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MESH Headings
- Animals
- Antibodies, Monoclonal/metabolism
- Antigens, CD
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- CD3 Complex/immunology
- CD8-Positive T-Lymphocytes/immunology
- Cell Division/genetics
- Cell Division/immunology
- Cell Line, Transformed
- Cytotoxicity, Immunologic/genetics
- Female
- Humans
- Immunity, Cellular/genetics
- Immunity, Cellular/immunology
- Immunoglobulins/administration & dosage
- Immunoglobulins/genetics
- Immunoglobulins/metabolism
- Immunoglobulins/physiology
- Immunosuppressive Agents/pharmacology
- Injections, Intraperitoneal
- K562 Cells
- Lymphocyte Activation/genetics
- Lymphocyte Activation/immunology
- Lymphocyte Culture Test, Mixed
- Membrane Glycoproteins/administration & dosage
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Membrane Glycoproteins/physiology
- Mice
- Mice, Inbred C3H
- Mice, Inbred DBA
- Neoplasm Transplantation
- Recombinant Fusion Proteins/administration & dosage
- Recombinant Fusion Proteins/genetics
- Solubility
- T-Lymphocytes/immunology
- Tumor Cells, Cultured
- CD83 Antigen
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Affiliation(s)
- Nathalie Scholler
- Laboratories of. Tumor Immunology, and Immunobiology, Pacific Northwest Research Institute, Seattle, WA 98122, USA.
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42
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Affiliation(s)
- A Dahlin
- Nordic Council on Medicines, Box 1983, SE-751 49 Uppsala, Sweden
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43
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Kjellman UW, Björk K, Dahlin A, Ekroth R, Kirnö K, Svensson G, Wernerman J. Insulin(GIK) improves myocardial metabolism in patients during blood cardioplegia. SCAND CARDIOVASC J 2000; 34:321-30. [PMID: 10935781 DOI: 10.1080/713783123] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The aim of this study was to test the hypothesis that abnormalities of myocardial substrate metabolism during blood cardioplegic aortic cross-clamping and early reperfusion are attenuated further by insulin(GIK) than by alpha-ketoglutarate enrichment of blood cardioplegia alone. Twenty-eight males (47 to 78 years) undergoing coronary artery bypass grafting (CABG) participated in a prospective, controlled, randomized study. All patients had alpha-ketoglutarate-enriched blood cardioplegia. Insulin(GIK) was infused in 13 patients during aortic cross-clamping. Insulin(GIK) prevented lactate release during cardioplegia (1.5+/-15 vs -44+/-14 micromol/min, p = 0.04), and a significant extraction of lactate was induced shortly after declamping the aorta (15+/-3 vs 2+/-1%, p = 0.001). Free fatty acid uptake was reduced after cardioplegic cross-clamping (5.7+/-1.6 vs 16.0+/-3.8 micromol/min, p = 0.02). More positive/less negative levels of alanine, aspartate, glutamine, glycine, ornithine, taurine and tyrosine were found in all the insulin-treated patients. We conclude that insulin(GIK) attenuates abnormalities of myocardial substrate metabolism during blood cardioplegic aortic cross-clamping and early reperfusion further than is obtained with alpha-ketoglutarate enrichment of blood cardioplegia alone.
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Affiliation(s)
- U W Kjellman
- Department of Cardiothoracic Surgery, Sahlgrenska University Hospital, Göteborg, Sweden
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44
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Abstract
This study examined the effects of life events, social support, personality traits, and siblings' birth-order on the health of women. 199 middle-class participants were included. 95 women, randomly assigned from four different patient groups, were compared with a control group of 96 randomly selected women without any special health problems. They completed a questionnaire which included questions regarding family background, health, different life events, social support, and signs of disease and a projective test, the Sivik Psychosomatism Test. Analysis indicated that report of negative life events was associated with more physical symptoms than positive life events and that the patient groups reported more negative life events and less social support than the control group.
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Affiliation(s)
- T Norlander
- Department of Psychology, Karlstad University, Sweden
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45
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Abstract
De-airing of the heart in open heart surgery is a necessary routine. Most of the air is evacuated from the heart before the aortic cross clamp is removed, but the de-airing may be continued even after declamping. One way to continue de-airing is to partially clamp the ascending aorta, proximally to the aortic cannula, in order to create a pocket for trapping residual air coming from the left ventricle. This paper describes a clamp specially designed and developed for this purpose. It has been used in our center since 1990 and our experience is reported. The clamp has been used on 250 patients and in 50% ultrasonography has been used to examine the heart being free from air bubbles within 20 min from releasing the aortic cross clamp.
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Affiliation(s)
- M Bugge
- Department of Cardiovascular Surgery, Sahlgrenska Hospital, Gothenburg University, Sweden
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46
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Abstract
A 90 degree bent two-stage venous cannula for cardiopulmonary bypass is presented and discussed. Its main advantages, compared to similar straight ones, are that it is out of the way of the surgeon, by being placed under the right sternum and also that the venous return seems uninfluenced by displacement of the heart when operating on the posterior side of the heart. No major drawbacks for the cannula have been noticed so far.
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Affiliation(s)
- M Bugge
- Department of Cardiovascular Surgery, Sahlgrenska Hospital, Gothenburg University, Sweden
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