title: RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.
abstract: Asthma is a chronic inflammatory respiratory disease that affects over 300 million people worldwide. Glucocorticoids are a mainstay therapy for asthma because they exert anti-inflammatory effects in multiple lung tissues, including the airway smooth muscle (ASM). However, the mechanism by which glucocorticoids suppress inflammation in ASM remains poorly understood. Using RNA-Seq, a high-throughput sequencing method, we characterized transcriptomic changes in four primary human ASM cell lines that were treated with dexamethasone--a potent synthetic glucocorticoid (1 µM for 18 hours). Based on a Benjamini-Hochberg corrected p-value <0.05, we identified 316 differentially expressed genes, including both well known (DUSP1, KLF15, PER1, TSC22D3) and less investigated (C7, CCDC69, CRISPLD2) glucocorticoid-responsive genes. CRISPLD2, which encodes a secreted protein previously implicated in lung development and endotoxin regulation, was found to have SNPs that were moderately associated with inhaled corticosteroid resistance and bronchodilator response among asthma patients in two previously conducted genome-wide association studies. Quantitative RT-PCR and Western blotting showed that dexamethasone treatment significantly increased CRISPLD2 mRNA and protein expression in ASM cells. CRISPLD2 expression was also induced by the inflammatory cytokine IL1β, and small interfering RNA-mediated knockdown of CRISPLD2 further increased IL1β-induced expression of IL6 and IL8. Our findings offer a comprehensive view of the effect of a glucocorticoid on the ASM transcriptome and identify CRISPLD2 as an asthma pharmacogenetics candidate gene that regulates anti-inflammatory effects of glucocorticoids in the ASM.
authors.affiliation: Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America; Partners HealthCare Personalized Medicine, Boston, Massachusetts, United States of America; Children's Hospital Informatics Program, Boston, Massachusetts, United States of America.
authors.forename: Blanca E
authors.initials: BE
authors.lastname: Himes
authors.affiliation: Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health, and Genetics and Complex Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Jiang
authors.affiliation: Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health, and Genetics and Complex Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Peter
authors.initials: P
authors.lastname: Wagner
authors.affiliation: Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health, and Genetics and Complex Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Ruoxi
authors.initials: R
authors.lastname: Hu
authors.affiliation: Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health, and Genetics and Complex Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Qiyu
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Partners HealthCare Personalized Medicine, Boston, Massachusetts, United States of America.
authors.forename: Barbara
authors.initials: B
authors.lastname: Klanderman
authors.affiliation: Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Reid M
authors.initials: RM
authors.lastname: Whitaker
authors.affiliation: Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Qingling
authors.initials: Q
authors.lastname: Duan
authors.affiliation: Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Jessica
authors.initials: J
authors.lastname: Lasky-Su
authors.affiliation: Pulmonary, Allergy and Critical Care Division, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors.forename: Christina
authors.initials: C
authors.lastname: Nikolos
authors.affiliation: Pulmonary, Allergy and Critical Care Division, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors.forename: William
authors.initials: W
authors.lastname: Jester
authors.affiliation: Pulmonary, Allergy and Critical Care Division, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors.forename: Martin
authors.initials: M
authors.lastname: Johnson
authors.affiliation: Pulmonary, Allergy and Critical Care Division, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors.forename: Reynold A
authors.initials: RA
authors.lastname: Panettieri
authors.affiliation: Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Kelan G
authors.initials: KG
authors.lastname: Tantisira
authors.affiliation: Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America; Partners HealthCare Personalized Medicine, Boston, Massachusetts, United States of America.
authors.forename: Scott T
authors.initials: ST
authors.lastname: Weiss
authors.affiliation: Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health, and Genetics and Complex Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Quan
authors.initials: Q
authors.lastname: Lu
mesh_terms: D000280:Administration, Inhalation; D000893:Anti-Inflammatory Agents / Q000008:administration & dosage / Q000494:pharmacology*; D001249:Asthma / Q000188:drug therapy* / Q000235:genetics / Q000378:metabolism; D015815:Cell Adhesion Molecules / Q000235:genetics* / Q000378:metabolism; D002460:Cell Line; D003907:Dexamethasone / Q000008:administration & dosage / Q000494:pharmacology*; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation / Q000187:drug effects; D006801:Humans; D050835:Interferon Regulatory Factors / Q000235:genetics* / Q000378:metabolism; D008168:Lung / Q000166:cytology* / Q000473:pathology; D009130:Muscle, Smooth / Q000187:drug effects; D020641:Polymorphism, Single Nucleotide; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D000893:Anti-Inflammatory Agents; C525599:CRISPLD2 protein, human; D015815:Cell Adhesion Molecules; D050835:Interferon Regulatory Factors; D003907:Dexamethasone