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Li B, Zheng L, Yuan A, Ren Y, Xu Z, Liu Y, Tian J, Yu B, Shi X, Qiao L, Zhang Y. Mechanism analysis of essential oil from Radix Bupleuri for the treatment of asthma through regulation of ectopic olfactory receptor. JOURNAL OF ETHNOPHARMACOLOGY 2024; 334:118592. [PMID: 39025162 DOI: 10.1016/j.jep.2024.118592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/03/2024] [Accepted: 07/16/2024] [Indexed: 07/20/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Radix Bupleuri is the root of Bupleurum chinense DC. (BC) and a classic aromatic traditional Chinese medicine. The traditional pharmacological effects of Radix Bupleuri are alleviating bronchial spasms, dilating airways, and promoting the resolution of respiratory inflammation, thereby reducing asthma symptoms. AIM OF THE STUDY Studies have demonstrated the efficacy of water extracts from BC in asthma treatment. However, the potential role of volatile oil, another active constituent in BC, remains unexplored with asthma. Notably, volatile oil is renowned for its ease of absorption and direct targeting of affected areas, offering distinct advantages in alleviating airway inflammation. This study aims to explain the anti-asthmatic mechanism of BC-oil through in vivo and in vitro pharmacological experiments. MATERIALS AND METHODS Firstly, the OVA-induced SD rat asthma model was utilized to evaluate the pharmacological effect of BC-oil by lung function monitoring, HE staining, flow cytometry, ELISA, and RT-qPCR. The anti-asthmatic mechanism was further analyzed by combining transcriptomic analysis of lung tissue from rat model and airway smooth muscle tissue from public database. Initially, GC-MS was used to analyze the components of BC-oil. The anti-asthmatic activity was evaluated in 16-HBE, RBL-2H3, and ASMC cells using CAMKII inhibitors to explore of the critical signal transduction regulated by BC-oil. Furthermore, molecular docking and calcium flow assay were utilized to screen and identify the active components from BC-oil. RESULTS Oral administration of BC-oil significantly enhanced pulmonary function in asthmatic SD rats by reducing airway resistance and elastic resistance. Additionally, BC-oil inhibited inflammatory cytokines, including serum IL-2, pulmonary Il1b, Tnf, and Cxcl13, demonstrating potent anti-inflammatory and immunomodulatory effects. In this study, we analyzed the significant role of OR2W3 in asthma using public transcriptomic data. Furthermore, we indicated that BC-oil regulated the expression of Olr1433 and GNAL in rat lung tissue. BC-oil reduced degranulation and inhibited gene expression of Il3 and Tnf in RBL-2H3 cells and suppressed gene expression of IL8 and TNF in 16-HBE cells. BC-oil also attenuated airway smooth muscle cell proliferation and expression of Acta2 and Ccnd1. Furthermore, BC-oil regulates asthma-related cellular processes by activating CAMKII. GC-MS analysis identified 11 components of BC-oil, and n-hexadecanoic acid, linoleic acid and oleic acid from BC-oil were identified to interact with OR2W3 by molecular docking. The calcium flow assay revealed linoleic acid as a significant activator of OR2W3 and indicated that BC-oil alleviated asthma through the ectopic olfactory signaling pathway. CONCLUSIONS The mechanism of BC-oil in treating asthma through signal transduction of OR2W3 is revealed at the molecular and cellular levels.
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Affiliation(s)
- Beiyan Li
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Lulu Zheng
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Anlei Yuan
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Yue Ren
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Zhenzhen Xu
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Yanxia Liu
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Jiaye Tian
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Bin Yu
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Xiaojie Shi
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Liansheng Qiao
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China.
| | - Yanling Zhang
- Key Laboratory of TCM-information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China.
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Olszewska AM, Zmijewski MA. Genomic and non-genomic action of vitamin D on ion channels - Targeting mitochondria. Mitochondrion 2024; 77:101891. [PMID: 38692383 DOI: 10.1016/j.mito.2024.101891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
Recent studies revealed that mitochondria are not only a place of vitamin D3 metabolism but also direct or indirect targets of its activities. This review summarizes current knowledge on the regulation of ion channels from plasma and mitochondrial membranes by the active form of vitamin D3 (1,25(OH)2D3). 1,25(OH)2D3, is a naturally occurring hormone with pleiotropic activities; implicated in the modulation of cell differentiation, and proliferation and in the prevention of various diseases, including cancer. Many experimental data indicate that 1,25(OH)2D3 deficiency induces ionic remodeling and 1,25(OH)2D3 regulates the activity of multiple ion channels. There are two main theories on how 1,25(OH)2D3 can modify the function of ion channels. First, describes the involvement of genomic pathways of response to 1,25(OH)2D3 in the regulation of the expression of the genes encoding channels, their auxiliary subunits, or additional regulators. Interestingly, intracellular ion channels, like mitochondrial, are encoded by the same genes as plasma membrane channels. Therefore, the comprehensive genomic regulation of the channels from these two different cellular compartments we analyzed using a bioinformatic approach. The second theory explores non-genomic pathways of vitamin D3 activities. It was shown, that 1,25(OH)2D3 indirectly regulates enzymes that impact ion channels, change membrane physical properties, or directly bind to channel proteins. In this article, the involvement of genomic and non-genomic pathways regulated by 1,25(OH)2D3 in the modulation of the levels and activity of plasma membrane and mitochondrial ion channels was investigated by an extensive review of the literature and analysis of the transcriptomic data using bioinformatics.
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Affiliation(s)
- A M Olszewska
- Department of Histology, Medical University of Gdansk, 1a Debinki, 80-211 Gdansk, Poland
| | - M A Zmijewski
- Department of Histology, Medical University of Gdansk, 1a Debinki, 80-211 Gdansk, Poland.
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3
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Gibb M, Liu JY, Sayes CM. The transcriptomic signature of respiratory sensitizers using an alveolar model. Cell Biol Toxicol 2024; 40:21. [PMID: 38584208 PMCID: PMC10999393 DOI: 10.1007/s10565-024-09860-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/25/2024] [Indexed: 04/09/2024]
Abstract
Environmental contaminants are ubiquitous in the air we breathe and can potentially cause adverse immunological outcomes such as respiratory sensitization, a type of immune-driven allergic response in the lungs. Wood dust, latex, pet dander, oils, fragrances, paints, and glues have all been implicated as possible respiratory sensitizers. With the increased incidence of exposure to chemical mixtures and the rapid production of novel materials, it is paramount that testing regimes accounting for sensitization are incorporated into development cycles. However, no validated assay exists that is universally accepted to measure a substance's respiratory sensitizing potential. The lungs comprise various cell types and regions where sensitization can occur, with the gas-exchange interface being especially important due to implications for overall lung function. As such, an assay that can mimic the alveolar compartment and assess sensitization would be an important advance for inhalation toxicology. Some such models are under development, but in-depth transcriptomic analyses have yet to be reported. Understanding the transcriptome after sensitizer exposure would greatly advance hazard assessment and sustainability. We tested two known sensitizers (i.e., isophorone diisocyanate and ethylenediamine) and two known non-sensitizers (i.e., chlorobenzene and dimethylformamide). RNA sequencing was performed in our in vitro alveolar model, consisting of a 3D co-culture of epithelial, macrophage, and dendritic cells. Sensitizers were readily distinguishable from non-sensitizers by principal component analysis. However, few differentially regulated genes were common across all pair-wise comparisons (i.e., upregulation of genes SOX9, UACA, CCDC88A, FOSL1, KIF20B). While the model utilized in this study can differentiate the sensitizers from the non-sensitizers tested, further studies will be required to robustly identify critical pathways inducing respiratory sensitization.
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Affiliation(s)
- Matthew Gibb
- Institute of Biomedical Studies (BMS), Baylor University, Waco, TX, 76798-7266, USA
| | - James Y Liu
- Department of Environmental Science (ENV), Baylor University, One Bear Place #97266, Waco, TX, 76798-7266, USA
| | - Christie M Sayes
- Institute of Biomedical Studies (BMS), Baylor University, Waco, TX, 76798-7266, USA.
- Department of Environmental Science (ENV), Baylor University, One Bear Place #97266, Waco, TX, 76798-7266, USA.
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Weiss ST, Mirzakhani H, Carey VJ, O'Connor GT, Zeiger RS, Bacharier LB, Stokes J, Litonjua AA. Prenatal vitamin D supplementation to prevent childhood asthma: 15-year results from the Vitamin D Antenatal Asthma Reduction Trial (VDAART). J Allergy Clin Immunol 2024; 153:378-388. [PMID: 37852328 DOI: 10.1016/j.jaci.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/13/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023]
Abstract
This article provides an overview of the findings obtained from the Vitamin D Antenatal Asthma Reduction Trial (VDAART) spanning a period of 15 years. The review covers various aspects, including the trial's rationale, study design, and initial intent-to-treat analyses, as well as an explanation of why those analyses did not achieve statistical significance. Additionally, the article delves into the post hoc results obtained from stratified intent-to-treat analyses based on maternal vitamin D baseline levels and genotype-stratified analyses. These results demonstrate a statistically significant reduction in asthma among offspring aged 3 and 6 years when comparing vitamin D supplementation (4400 IU/d) to the standard prenatal multivitamin with vitamin D (400 IU/d). Furthermore, these post hoc analyses found that vitamin D supplementation led to a decrease in total serum IgE levels and improved lung function in children compared to those whose mothers received a placebo alongside the standard prenatal multivitamin with vitamin D. Last, the article concludes with recommendations regarding the optimal dosing of vitamin D for pregnant women to prevent childhood asthma as well as suggestions for future trials in this field.
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Affiliation(s)
- Scott T Weiss
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass.
| | - Hooman Mirzakhani
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Vincent J Carey
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - George T O'Connor
- Department of Medicine, Pulmonary Centre, Boston Medical Centre, Boston University, Boston, Mass
| | - Robert S Zeiger
- Department of Clinical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, Calif
| | - Leonard B Bacharier
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Pulmonary Medicine, Monroe Carell Jr Children's Hospital at Vanderbilt, Nashville, Tenn
| | - Jeffrey Stokes
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Pulmonary Medicine, Washington University, St Louis, Mo
| | - Augusto A Litonjua
- Department of Pediatrics Golisano Children's Hospital, Pediatric Pulmonary Division, University of Rochester Medical School, Rochester, NY
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Nguyen TM, Craig DB, Tran D, Nguyen T, Draghici S. A novel approach for predicting upstream regulators (PURE) that affect gene expression. Sci Rep 2023; 13:18571. [PMID: 37903768 PMCID: PMC10616115 DOI: 10.1038/s41598-023-41374-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 08/25/2023] [Indexed: 11/01/2023] Open
Abstract
External factors such as exposure to a chemical, drug, or toxicant (CDT), or conversely, the lack of certain chemicals can cause many diseases. The ability to identify such causal CDTs based on changes in the gene expression profile is extremely important in many studies. Furthermore, the ability to correctly infer CDTs that can revert the gene expression changes induced by a given disease phenotype is a crucial step in drug repurposing. We present an approach for Predicting Upstream REgulators (PURE) designed to tackle this challenge. PURE can correctly infer a CDT from the measured expression changes in a given phenotype, as well as correctly identify drugs that could revert disease-induced gene expression changes. We compared the proposed approach with four classical approaches as well as with the causal analysis used in Ingenuity Pathway Analysis (IPA) on 16 data sets (1 rat, 5 mouse, and 10 human data sets), involving 8 chemicals or drugs. We assessed the results based on the ability to correctly identify the CDT as indicated by its rank. We also considered the number of false positives, i.e. CDTs other than the correct CDT that were reported to be significant by each method. The proposed approach performed best in 11 out of the 16 experiments, reporting the correct CDT at the very top 7 times. IPA was the second best, reporting the correct CDT at the top 5 times, but was unable to identify the correct CDT at all in 5 out of the 16 experiments. The validation results showed that our approach, PURE, outperformed some of the most popular methods in the field. PURE could effectively infer the true CDTs responsible for the observed gene expression changes and could also be useful in drug repurposing applications.
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Affiliation(s)
- Tuan-Minh Nguyen
- Department of Computer Science, Wayne State University, Detroit, 48202, USA
| | - Douglas B Craig
- Department of Computer Science, Wayne State University, Detroit, 48202, USA
- Department of Oncology, School of Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - Duc Tran
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tin Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, 36849, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, 48202, USA.
- Advaita Bioinformatics, Ann Arbor, MI, 48105, USA.
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Miki H, Kiosses WB, Manresa MC, Gupta RK, Sethi GS, Herro R, Da Silva Antunes R, Dutta P, Miller M, Fung K, Chawla A, Dobaczewska K, Ay F, Broide DH, Tumanov AV, Croft M. Lymphotoxin beta receptor signaling directly controls airway smooth muscle deregulation and asthmatic lung dysfunction. J Allergy Clin Immunol 2023; 151:976-990.e5. [PMID: 36473503 PMCID: PMC10081945 DOI: 10.1016/j.jaci.2022.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/25/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Dysregulation of airway smooth muscle cells (ASM) is central to the severity of asthma. Which molecules dominantly control ASM in asthma is unclear. High levels of the cytokine LIGHT (aka TNFSF14) have been linked to asthma severity and lower baseline predicted FEV1 percentage, implying that signals through its receptors might directly control ASM dysfunction. OBJECTIVE Our study sought to determine whether signaling via lymphotoxin beta receptor (LTβR) or herpesvirus entry mediator from LIGHT dominantly drives ASM hyperreactivity induced by allergen. METHODS Conditional knockout mice deficient for LTβR or herpesvirus entry mediator in smooth muscle cells were used to determine their role in ASM deregulation and airway hyperresponsiveness (AHR) in vivo. Human ASM were used to study signals induced by LTβR. RESULTS LTβR was strongly expressed in ASM from normal and asthmatic subjects compared to several other receptors implicated in smooth muscle deregulation. Correspondingly, conditional deletion of LTβR only in smooth muscle cells in smMHCCreLTβRfl/fl mice minimized changes in their numbers and mass as well as AHR induced by house dust mite allergen in a model of severe asthma. Intratracheal LIGHT administration independently induced ASM hypertrophy and AHR in vivo dependent on direct LTβR signals to ASM. LIGHT promoted contractility, hypertrophy, and hyperplasia of human ASM in vitro. Distinguishing LTβR from the receptors for IL-13, TNF, and IL-17, which have also been implicated in smooth muscle dysregulation, LIGHT promoted NF-κB-inducing kinase-dependent noncanonical nuclear factor kappa-light-chain enhancer of activated B cells in ASM in vitro, leading to sustained accumulation of F-actin, phosphorylation of myosin light chain kinase, and contractile activity. CONCLUSIONS LTβR signals directly and dominantly drive airway smooth muscle hyperresponsiveness relevant for pathogenesis of airway remodeling in severe asthma.
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Affiliation(s)
- Haruka Miki
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, Calif
| | | | - Mario C Manresa
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, Calif
| | - Rinkesh K Gupta
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, Calif
| | - Gurupreet S Sethi
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, Calif
| | - Rana Herro
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, Calif
| | | | - Paramita Dutta
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, Calif
| | - Marina Miller
- Department of Medicine, University of California-San Diego, San Diego, Calif
| | - Kai Fung
- Bioinformatics Core, La Jolla Institute for Immunology, La Jolla, Calif
| | - Ashu Chawla
- Bioinformatics Core, La Jolla Institute for Immunology, La Jolla, Calif
| | | | - Ferhat Ay
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, Calif
| | - David H Broide
- Department of Medicine, University of California-San Diego, San Diego, Calif
| | - Alexei V Tumanov
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, Tex
| | - Michael Croft
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, Calif; Department of Medicine, University of California-San Diego, San Diego, Calif.
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Sokolowski DJ, Ahn J, Erdman L, Hou H, Ellis K, Wang L, Goldenberg A, Wilson M. Differential Expression Enrichment Tool (DEET): an interactive atlas of human differential gene expression. NAR Genom Bioinform 2023; 5:lqad003. [PMID: 36694664 PMCID: PMC9869326 DOI: 10.1093/nargab/lqad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/14/2022] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Differential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share similar genes, pathways, and TF targets to their own gene lists. DEET identifies relevant studies based on shared results with the user's gene lists, aiding in hypothesis generation and data-driven literature review.
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Affiliation(s)
| | - Jedid Ahn
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Lauren Erdman
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Huayun Hou
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Kai Ellis
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Liangxi Wang
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Anna Goldenberg
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Computer Science, University of Toronto, Toronto, ON, Canada,Vector Institute, Toronto, ON, Canada,CIFAR, Toronto, ON, Canada
| | - Michael D Wilson
- To whom correspondence should be addressed. Tel: +1 416 813 7654 (Ext 328699); Fax: +1 416 813 4931;
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Severity of COVID-19 patients with coexistence of asthma and vitamin D deficiency. INFORMATICS IN MEDICINE UNLOCKED 2022; 34:101116. [PMID: 36338941 PMCID: PMC9616486 DOI: 10.1016/j.imu.2022.101116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 11/06/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19)-driven global pandemic triggered innumerable health complications, imposing great challenges in managing other respiratory diseases like asthma. Furthermore, increases in the underlying inflammation involved in the fatality of COVID-19 have been linked with lack of vitamin D. In this research work, we intend to investigate the possible genetic linkage of asthma and vitamin D deficiency with the severity and fatality of COVID-19 using a network-based approach. We identified and analysed 41 and 14 differentially expressed genes (DEGs) of COVID-19 being common with asthma and vitamin D deficiency, respectively, through the comparative differential gene expression analysis and their footprints on signalling pathways. Gene set enrichment analysis for GO terms and signalling pathways reveals key biological activities, including inflammatory response-related pathways (e.g., cytokine- and chemokine-mediated signalling pathways, IL-17, and TNF signalling pathways). Besides, the Protein–Protein Interaction network analysis of those DEGs reveals hub proteins, some of which are reported as inflammatory antiviral interferon-stimulated biomarkers that potentially drive the cytokine storm leading to COVID-19 severity and fatality, and contributes in the early stage of viral replication, respectively. Moreover, the regulatory network analysis found these DEGs associated with antiviral and tumour inhibitory transcription factors and micro-RNAs. Finally, drug–target enrichment analysis yields tetradioxin, estradiol, arsenenous acid, and zinc, which have been reported to be effective in suppressing the pro-inflammatory cytokines production, and other respiratory tract infections. Our results yield shared biomarker-driven key hypotheses followed by network-based analytics, demystifying the mechanistic details of COVID-19 comorbidity of asthma and vitamin D deficiency with their potential therapeutic implications.
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Blackmur JP, Vaughan-Shaw PG, Donnelly K, Harris BT, Svinti V, Ochocka-Fox AM, Freile P, Walker M, Gurran T, Reid S, Semple CA, Din FVN, Timofeeva M, Dunlop MG, Farrington SM. Gene Co-Expression Network Analysis Identifies Vitamin D-Associated Gene Modules in Adult Normal Rectal Epithelium Following Supplementation. Front Genet 2022; 12:783970. [PMID: 35096006 PMCID: PMC8790603 DOI: 10.3389/fgene.2021.783970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is a common, multifactorial disease. While observational studies have identified an association between lower vitamin D and higher CRC risk, supplementation trials have been inconclusive and the mechanisms by which vitamin D may modulate CRC risk are not well understood. We sought to perform a weighted gene co-expression network analysis (WGCNA) to identify modules present after vitamin D supplementation (when plasma vitamin D level was sufficient) which were absent before supplementation, and then to identify influential genes in those modules. The transcriptome from normal rectal mucosa biopsies of 49 individuals free from CRC were assessed before and after 12 weeks of 3200IU/day vitamin D (Fultium-D3) supplementation using paired-end total RNAseq. While the effects on expression patterns following vitamin D supplementation were subtle, WGCNA identified highly correlated genes forming gene modules. Four of the 17 modules identified in the post-vitamin D network were not preserved in the pre-vitamin D network, shedding new light on the biochemical impact of supplementation. These modules were enriched for GO terms related to the immune system, hormone metabolism, cell growth and RNA metabolism. Across the four treatment-associated modules, 51 hub genes were identified, with enrichment of 40 different transcription factor motifs in promoter regions of those genes, including VDR:RXR. Six of the hub genes were nominally differentially expressed in studies of vitamin D effects on adult normal mucosa organoids: LCN2, HLA-C, AIF1L, PTPRU, PDE4B and IFI6. By taking a gene-correlation network approach, we have described vitamin D induced changes to gene modules in normal human rectal epithelium in vivo, the target tissue from which CRC develops.
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Affiliation(s)
- James P. Blackmur
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter G. Vaughan-Shaw
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Kevin Donnelly
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Bradley T. Harris
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Victoria Svinti
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Anna-Maria Ochocka-Fox
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Paz Freile
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Marion Walker
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Toby Gurran
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Stuart Reid
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Colin A. Semple
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Farhat V. N. Din
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Maria Timofeeva
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Department of Public Health, Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Malcolm G. Dunlop
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Susan M. Farrington
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
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10
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Li YK, Zhang XX, Yang Y, Gao J, Shi Q, Liu SD, Fu WP, Sun C. Convergent Evidence Supports TH2LCRR as a Novel Asthma Susceptibility Gene. Am J Respir Cell Mol Biol 2021; 66:283-292. [PMID: 34851809 DOI: 10.1165/rcmb.2020-0481oc] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Asthma is a common complex disease with apparent genetic predispositions, and previous genome-wide association studies suggest that rs1295686 within the IL13 (interleukin 13) gene is significantly associated with asthma. Analysis of the data provided by the 1000 Genomes Project indicated that there are additional four SNPs in nearly complete linkage disequilibrium with rs1295686 in Caucasians. However, the causal SNPs and the associated mechanism remain unclear. To investigate this issue, functional genomics approaches were utilized to analyze the functions of these SNPs. Dual-luciferase assays indicated that the functional SNP is not rs1295686 but a haplotype consisting of other three SNPs, rs1295685, rs848 and rs847. Through chromosome conformation capture, it was found that the enhancer containing the three functional SNPs interacts with the promoter of TH2LCRR (T helper type 2 locus control region associated RNA), a recently identified long non-coding RNA. RNA-seq data analysis indicated that TH2LCRR expression is significantly increased in asthma patients and is dependent on the genotype at this locus, indicating that TH2LCRR is a novel susceptibility gene for asthma and that these SNPs confer asthma risk by regulating TH2LCRR expression. By chromatin immunoprecipitation, the related transcription factors that bind in the region surrounding these three SNPs were identified, and their interactions were investigated by functional genomics approaches. Our effort identified a novel mechanism through which genetic variations at this locus could influence asthma susceptibility.
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Affiliation(s)
- Yi-Kun Li
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China
| | - Xin-Xin Zhang
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China
| | - Yuan Yang
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China
| | - Jing Gao
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China
| | - Qiang Shi
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China
| | - Shao-Dong Liu
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China
| | - Wei-Ping Fu
- Kunming Medical University First Affilliated Hospital, 36657, Kunming, China
| | - Chang Sun
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China;
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11
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Metabolomics in asthma: A platform for discovery. Mol Aspects Med 2021; 85:100990. [PMID: 34281719 DOI: 10.1016/j.mam.2021.100990] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 06/21/2021] [Accepted: 07/06/2021] [Indexed: 12/28/2022]
Abstract
Asthma, characterized by airway hyperresponsiveness, inflammation and remodeling, is a chronic airway disease with complex etiology. Severe asthma is characterized by frequent exacerbations and poor therapeutic response to conventional asthma therapy. A clear understanding of cellular and molecular mechanisms of asthma is critical for the discovery of novel targets for optimal therapeutic control of asthma. Metabolomics is emerging as a powerful tool to elucidate novel disease mechanisms in a variety of diseases. In this review, we summarize the current status of knowledge in asthma metabolomics at systemic and cellular levels. The findings demonstrate that various metabolic pathways, related to energy metabolism, macromolecular biosynthesis and redox signaling, are differentially modulated in asthma. Airway smooth muscle cell plays pivotal roles in asthma by contributing to airway hyperreactivity, inflammatory mediator release and remodeling. We posit that metabolomic profiling of airway structural cells, including airway smooth muscle cells, will shed light on molecular mechanisms of asthma and airway hyperresponsiveness and help identify novel therapeutic targets.
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12
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Guo H, Zhao Q, Li SY, Xu X, Xu N, Lv C, Shen ZS, Li JG. Successful treatment of fatal asthma combined with a silent chest: A case report. J Int Med Res 2021; 48:300060520925683. [PMID: 32466702 PMCID: PMC7263110 DOI: 10.1177/0300060520925683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Fatal asthma is a rare and potentially fatal disease. This disease requires suitable treatment to achieve rehabilitation, especially when accompanied by other complications, such as a silent chest and severe bronchial spasm. A 36-year-old man presented with a 10-year history of asthma that broke out into persistent asthma attacks and cardiac arrest, and was accompanied by a silent chest for 18 hours. He recovered and was discharged without any sequelae after being treated by a ventilator, hormones, epinephrine, analgesics, sedation, and muscle relaxants. Comprehensive treatment with a ventilator, hormones, epinephrine, analgesics, sedation, and muscle relaxants has a good effect on fatal asthma combined with a silent chest.
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Affiliation(s)
- Hui Guo
- HeBei General Hospital, Hebei, China
| | - Qian Zhao
- HeBei General Hospital, Hebei, China
| | - Su-Yan Li
- HeBei General Hospital, Hebei, China
| | - Xin Xu
- HeBei General Hospital, Hebei, China
| | - Ning Xu
- HeBei General Hospital, Hebei, China
| | - Chang Lv
- HeBei General Hospital, Hebei, China
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13
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Kan M, Koziol-White C, Shumyatcher M, Johnson M, Jester W, Panettieri RA, Himes BE. Airway Smooth Muscle-Specific Transcriptomic Signatures of Glucocorticoid Exposure. Am J Respir Cell Mol Biol 2020; 61:110-120. [PMID: 30694689 PMCID: PMC6604213 DOI: 10.1165/rcmb.2018-0385oc] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Glucocorticoids, commonly used asthma controller medications, decrease symptoms in most patients, but some remain symptomatic despite high-dose treatment. The physiological basis underlying the glucocorticoid response, especially in asthma patients with severe, refractory disease, is not fully understood. We sought to identify differences between the transcriptomic response of airway smooth muscle (ASM) cells derived from donors with fatal asthma and donors without asthma to glucocorticoid exposure and to compare ASM-specific changes with those observed in other cell types. In cells derived from nine donors with fatal asthma and eight donors without asthma, RNA sequencing was used to measure ASM transcriptome changes after exposure to budesonide (100 nM 24 h) or control vehicle (DMSO). Differential expression results were obtained for this dataset, as well as 13 publicly available glucocorticoid-response transcriptomic datasets corresponding to seven cell types. Specific genes were differentially expressed in response to glucocorticoid exposure (7,835 and 6,957 in ASM cells derived from donors with fatal asthma and donors without asthma, respectively; adjusted P value < 0.05). Transcriptomic changes in response to glucocorticoid exposure were similar in ASM derived from donors with fatal asthma and donors without asthma, with enriched ontological pathways that included cytokine- and chemokine-related categories. A comparison of glucocorticoid-induced changes in the nonasthma ASM transcriptome with those observed in six other cell types showed that ASM has a distinct glucocorticoid-response signature that is also present in ASM cells from donors with fatal asthma.
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Affiliation(s)
- Mengyuan Kan
- 1 Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania; and
| | - Cynthia Koziol-White
- 2 Rutgers Institute for Translational Medicine and Science, Rutgers University, New Brunswick, New Jersey
| | - Maya Shumyatcher
- 1 Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania; and
| | - Martin Johnson
- 2 Rutgers Institute for Translational Medicine and Science, Rutgers University, New Brunswick, New Jersey
| | - William Jester
- 2 Rutgers Institute for Translational Medicine and Science, Rutgers University, New Brunswick, New Jersey
| | - Reynold A Panettieri
- 2 Rutgers Institute for Translational Medicine and Science, Rutgers University, New Brunswick, New Jersey
| | - Blanca E Himes
- 1 Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania; and
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14
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Tang HHF, Sly PD, Holt PG, Holt KE, Inouye M. Systems biology and big data in asthma and allergy: recent discoveries and emerging challenges. Eur Respir J 2020; 55:13993003.00844-2019. [PMID: 31619470 DOI: 10.1183/13993003.00844-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/12/2019] [Indexed: 12/15/2022]
Abstract
Asthma is a common condition caused by immune and respiratory dysfunction, and it is often linked to allergy. A systems perspective may prove helpful in unravelling the complexity of asthma and allergy. Our aim is to give an overview of systems biology approaches used in allergy and asthma research. Specifically, we describe recent "omic"-level findings, and examine how these findings have been systematically integrated to generate further insight.Current research suggests that allergy is driven by genetic and epigenetic factors, in concert with environmental factors such as microbiome and diet, leading to early-life disturbance in immunological development and disruption of balance within key immuno-inflammatory pathways. Variation in inherited susceptibility and exposures causes heterogeneity in manifestations of asthma and other allergic diseases. Machine learning approaches are being used to explore this heterogeneity, and to probe the pathophysiological patterns or "endotypes" that correlate with subphenotypes of asthma and allergy. Mathematical models are being built based on genomic, transcriptomic and proteomic data to predict or discriminate disease phenotypes, and to describe the biomolecular networks behind asthma.The use of systems biology in allergy and asthma research is rapidly growing, and has so far yielded fruitful results. However, the scale and multidisciplinary nature of this research means that it is accompanied by new challenges. Ultimately, it is hoped that systems medicine, with its integration of omics data into clinical practice, can pave the way to more precise, personalised and effective management of asthma.
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Affiliation(s)
- Howard H F Tang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia .,Cambridge Baker Systems Genomics Initiative, Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Peter D Sly
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Patrick G Holt
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Kathryn E Holt
- Dept of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia.,Cambridge Baker Systems Genomics Initiative, Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,School of BioSciences, The University of Melbourne, Parkville, Australia.,The Alan Turing Institute, London, UK
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15
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Adler KB. Does Transforming Growth Factor-β Induce Persistent Airway Obstruction after Asthma Exacerbations? Am J Respir Cell Mol Biol 2019; 58:543-544. [PMID: 29714630 DOI: 10.1165/rcmb.2017-0339ed] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Kenneth B Adler
- 1 College of Veterinary Medicine North Carolina State University Raleigh, North Carolina
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16
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High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report. Ann Am Thorac Soc 2019; 16:1-16. [PMID: 30592451 PMCID: PMC6812157 DOI: 10.1513/annalsats.201810-716ws] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
High-throughput, "next-generation" sequencing methods are now being broadly applied across all fields of biomedical research, including respiratory disease, critical care, and sleep medicine. Although there are numerous review articles and best practice guidelines related to sequencing methods and data analysis, there are fewer resources summarizing issues related to study design and interpretation, especially as applied to common, complex, nonmalignant diseases. To address these gaps, a single-day workshop was held at the American Thoracic Society meeting in May 2017, led by the American Thoracic Society Section on Genetics and Genomics. The aim of this workshop was to review the design, analysis, interpretation, and functional follow-up of high-throughput sequencing studies in respiratory, critical care, and sleep medicine research. This workshop brought together experts in multiple fields, including genetic epidemiology, biobanking, bioinformatics, and research ethics, along with physician-scientists with expertise in a range of relevant diseases. The workshop focused on application of DNA and RNA sequencing research in common chronic diseases and did not cover sequencing studies in lung cancer, monogenic diseases (e.g., cystic fibrosis), or microbiome sequencing. Participants reviewed and discussed study design, data analysis and presentation, interpretation, functional follow-up, and reporting of results. This report summarizes the main conclusions of the workshop, specifically addressing the application of these methods in respiratory, critical care, and sleep medicine research. This workshop report may serve as a resource for our research community as well as for journal editors and reviewers of sequencing-based manuscript submissions in our research field.
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17
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Koziol-White CJ, Panettieri RA. Modulation of Bronchomotor Tone Pathways in Airway Smooth Muscle Function and Bronchomotor Tone in Asthma. Clin Chest Med 2018; 40:51-57. [PMID: 30691716 DOI: 10.1016/j.ccm.2018.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Airway smooth muscle is the primary cell mediating bronchomotor tone. The milieu created in the asthmatic lung modulates airway smooth muscle contractility and relaxation. Experimental findings suggest intrinsic abnormalities in airway smooth muscle derived from patients with asthma in comparison with airway smooth muscle from those without asthma. These changes to excitation-contraction pathways may underlie airway hyperresponsiveness and increased airway resistance associated with asthma.
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Affiliation(s)
- Cynthia J Koziol-White
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers Institute for Translational Medicine and Science, Rutgers University, State University of New Jersey, 89 French Street, Suite 4268, New Brunswick, NJ 08901, USA.
| | - Reynold A Panettieri
- Department of Medicine, Rutgers Institute for Translational Medicine and Science, Rutgers University, State University of New Jersey, 89 French Street, Room 4210, New Brunswick, NJ 08901, USA
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18
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Kan M, Shumyatcher M, Diwadkar A, Soliman G, Himes BE. Integration of Transcriptomic Data Identifies Global and Cell-Specific Asthma-Related Gene Expression Signatures. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2018; 2018:1338-1347. [PMID: 30815178 PMCID: PMC6371257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Over 140,000 transcriptomic studies performed in healthy and diseased cell and tissue types, at baseline and after exposure to various agents, are available in public repositories. Integrating results of transcriptomic datasets has been an attractive approach to identify gene expression signatures that are more robust than those obtained for individual datasets, especially datasets with small sample size. We developed Reproducible Analysis and Validation of Expression Data (RAVED), a pipeline that facilitates the creation of R Markdown reports detailing reproducible analysis of publicly available transcriptomic data, and used it to analyze asthma and glucocorticoid response microarray and RNA-Seq datasets. Subsequently, we used three approaches to integrate summary statistics of these studies and identify cell/tissue-specific and global asthma and glucocorticoid-induced gene expression changes. Transcriptomic integration methods were incorporated into an online app called REALGAR, where end-users can specify datasets to integrate and quickly obtain results that may facilitate design of experimental studies.
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Affiliation(s)
- Mengyuan Kan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Maya Shumyatcher
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Avantika Diwadkar
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabriel Soliman
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Blanca E Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
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19
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Choi S, Liu X, Pan Z. Zinc deficiency and cellular oxidative stress: prognostic implications in cardiovascular diseases. Acta Pharmacol Sin 2018; 39:1120-1132. [PMID: 29926844 PMCID: PMC6289396 DOI: 10.1038/aps.2018.25] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/28/2018] [Indexed: 12/11/2022] Open
Abstract
Zinc is an essential nutrient for human health and has anti-oxidative stress and anti-inflammatory functions. The association between zinc deficiency and the development of cardiovascular diseases (CVDs) has been supported by numerous studies. Supplementing zinc can reduce the risk of atherosclerosis and protect against myocardial infarction and ischemia/reperfusion injury. In this review we summarize the evidence in the literature, to consolidate the current knowledge on the dysregulation of zinc homeostasis in CVDs, and to explore the significant roles of the zinc homeostasis-regulatory proteins in cardiac physiology and pathophysiology. Moreover, this review also deliberates on the potential diagnostic and prognostic implications of zinc/zinc homeostasis-associated molecules (ZIP, ZnT, and MTs) in CVDs.
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20
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Ojiaku CA, Cao G, Zhu W, Yoo EJ, Shumyatcher M, Himes BE, An SS, Panettieri RA. TGF-β1 Evokes Human Airway Smooth Muscle Cell Shortening and Hyperresponsiveness via Smad3. Am J Respir Cell Mol Biol 2018; 58:575-584. [PMID: 28984468 PMCID: PMC5946330 DOI: 10.1165/rcmb.2017-0247oc] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/05/2017] [Indexed: 01/10/2023] Open
Abstract
Transforming growth factor β1 (TGF-β1), a cytokine whose levels are elevated in the airways of patients with asthma, perpetuates airway inflammation and modulates airway structural cell remodeling. However, the role of TGF-β1 in excessive airway narrowing in asthma, or airway hyperresponsiveness (AHR), remains unclear. In this study, we set out to investigate the direct effects of TGF-β1 on human airway smooth muscle (HASM) cell shortening and hyperresponsiveness. The dynamics of AHR and single-cell excitation-contraction coupling were measured in human precision-cut lung slices and in isolated HASM cells using supravital microscopy and magnetic twisting cytometry, respectively. In human precision-cut lung slices, overnight treatment with TGF-β1 significantly augmented basal and carbachol-induced bronchoconstriction. In isolated HASM cells, TGF-β1 increased basal and methacholine-induced cytoskeletal stiffness in a dose- and time-dependent manner. TGF-β1-induced single-cell contraction was corroborated by concomitant increases in myosin light chain and myosin phosphatase target subunit 1 phosphorylation levels, which were attenuated by small interfering RNA-mediated knockdown of Smad3 and pharmacological inhibition of Rho kinase. Strikingly, these physiological effects of TGF-β1 occurred through a RhoA-independent mechanism, with little effect on HASM cell [Ca2+]i levels. Together, our data suggest that TGF-β1 enhances HASM excitation-contraction coupling pathways to induce HASM cell shortening and hyperresponsiveness. These findings reveal a potential link between airway injury-repair responses and bronchial hyperreactivity in asthma, and define TGF-β1 signaling as a potential target to reduce AHR in asthma.
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Affiliation(s)
- Christie A. Ojiaku
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, and
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, New Jersey; and
| | - Gaoyuan Cao
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, New Jersey; and
| | - Wanqu Zhu
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, and
| | - Edwin J. Yoo
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, and
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, New Jersey; and
| | - Maya Shumyatcher
- 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
| | - Steven S. An
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, and
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Reynold A. Panettieri
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, New Jersey; and
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21
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Shumyatcher M, Hong R, Levin J, Himes BE. Disease-Specific Integration of Omics Data to Guide Functional Validation of Genetic Associations. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2018; 2017:1589-1596. [PMID: 29854229 PMCID: PMC5977601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Unbiased genetic association studies, including genome-wide association and whole-genome sequencing studies, have uncovered many novel disease-associated variants. Relatively few of these associated regions, however, have led to insights that are biologically mechanistic or clinically actionable due in part to the difficulty in designing appropriate functional validation studies to understand how variants contribute to disease. Asthma is a complex inflammatory lung disease for which many genetic associations have been identified. Using asthma as a disease model, we designed Reducing Associations by Linking Genes And transcriptomic Results (REALGAR), an app that facilitates the design of functional validation studies by integrating cell- and tissue-specific results of diseaserelevant gene expression and other omics studies. Via specific examples, we demonstrate how integrated gene- centric and disease-specific information leads to asthma insights, and more broadly, can help understand complex diseases.
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Affiliation(s)
- Maya Shumyatcher
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Rui Hong
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jessica Levin
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Blanca E Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
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22
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Johnstone TB, Smith KH, Koziol-White CJ, Li F, Kazarian AG, Corpuz ML, Shumyatcher M, Ehlert FJ, Himes BE, Panettieri RA, Ostrom RS. PDE8 Is Expressed in Human Airway Smooth Muscle and Selectively Regulates cAMP Signaling by β 2-Adrenergic Receptors and Adenylyl Cyclase 6. Am J Respir Cell Mol Biol 2018; 58:530-541. [PMID: 29262264 PMCID: PMC5894499 DOI: 10.1165/rcmb.2017-0294oc] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 12/20/2017] [Indexed: 12/15/2022] Open
Abstract
Two cAMP signaling compartments centered on adenylyl cyclase (AC) exist in human airway smooth muscle (HASM) cells, one containing β2-adrenergic receptor AC6 and another containing E prostanoid receptor AC2. We hypothesized that different PDE isozymes selectively regulate cAMP signaling in each compartment. According to RNA-sequencing data, 18 of 24 PDE genes were expressed in primary HASM cells derived from age- and sex-matched donors with and without asthma. PDE8A was the third most abundant of the cAMP-degrading PDE genes, after PDE4A and PDE1A. Knockdown of PDE8A using shRNA evoked twofold greater cAMP responses to 1 μM forskolin in the presence of 3-isobutyl-1-methylxanthine. Overexpression of AC2 did not alter this response, but overexpression of AC6 increased cAMP responses an additional 80%. We examined cAMP dynamics in live HASM cells using a fluorescence sensor. PF-04957325, a PDE8-selective inhibitor, increased basal cAMP concentrations by itself, indicating a significant basal level of cAMP synthesis. In the presence of an AC inhibitor to reduce basal signaling, PF-04957325 accelerated cAMP production and increased the inhibition of cell proliferation induced by isoproterenol, but it had no effect on cAMP concentrations or cell proliferation regulated by prostaglandin E2. Lipid raft fractionation of HASM cells revealed PDE8A immunoreactivity in buoyant fractions containing caveolin-1 and AC5/6 immunoreactivity. Thus, PDE8 is expressed in lipid rafts of HASM cells, where it specifically regulates β2-adrenergic receptor AC6 signaling without effects on signaling by the E prostanoid receptors 2/4-AC2 complex. In airway diseases such as asthma and chronic obstructive pulmonary disease, PDE8 may represent a novel therapeutic target to modulate HASM responsiveness and airway remodeling.
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MESH Headings
- 3',5'-Cyclic-AMP Phosphodiesterases/genetics
- 3',5'-Cyclic-AMP Phosphodiesterases/metabolism
- Adenylyl Cyclases/genetics
- Adenylyl Cyclases/metabolism
- Airway Remodeling
- Asthma/enzymology
- Asthma/genetics
- Asthma/pathology
- Asthma/physiopathology
- Case-Control Studies
- Cell Proliferation
- Cells, Cultured
- Cyclic AMP/metabolism
- Humans
- Membrane Microdomains/enzymology
- Membrane Microdomains/pathology
- Muscle, Smooth/enzymology
- Muscle, Smooth/pathology
- Muscle, Smooth/physiopathology
- Myocytes, Smooth Muscle/enzymology
- Myocytes, Smooth Muscle/pathology
- Receptors, Adrenergic, beta-2/genetics
- Receptors, Adrenergic, beta-2/metabolism
- Respiratory System/enzymology
- Respiratory System/pathology
- Respiratory System/physiopathology
- Second Messenger Systems
- Time Factors
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Affiliation(s)
- Timothy B. Johnstone
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California
| | - Kaitlyn H. Smith
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Cynthia J. Koziol-White
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, New Jersey
| | - Fengying Li
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Austin G. Kazarian
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California
| | - Maia L. Corpuz
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California
| | - Maya Shumyatcher
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania; and
| | - Frederick J. Ehlert
- Department of Pharmacology, School of Medicine, University of California, Irvine, Irvine, California
| | - Blanca E. Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania; and
| | - Reynold A. Panettieri
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, New Jersey
| | - Rennolds S. Ostrom
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California
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23
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Abstract
Airway inflammation is key to the severity and persistence of asthma. Recent studies have revealed novel immune mechanisms that target dendritic cells, T helper 2 cytokines, regulatory T cells, and type 2 innate lymphoid cells in allergic inflammation, as well as novel approaches that target airway smooth muscle in asthma. These advances inform the development of new targeted treatments for allergic inflammation and asthma with the potential to provide therapeutic benefit.
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Affiliation(s)
- Scott T Weiss
- Harvard Medical School and Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
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24
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Yoo EJ, Cao G, Koziol‐White CJ, Ojiaku CA, Sunder K, Jude JA, Michael JV, Lam H, Pushkarsky I, Damoiseaux R, Di Carlo D, Ahn K, An SS, Penn RB, Panettieri RA. Gα 12 facilitates shortening in human airway smooth muscle by modulating phosphoinositide 3-kinase-mediated activation in a RhoA-dependent manner. Br J Pharmacol 2017; 174:4383-4395. [PMID: 28921504 PMCID: PMC5715591 DOI: 10.1111/bph.14040] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND AND PURPOSE PI3K-dependent activation of Rho kinase (ROCK) is necessary for agonist-induced human airway smooth muscle cell (HASMC) contraction, and inhibition of PI3K promotes bronchodilation of human small airways. The mechanisms driving agonist-mediated PI3K/ROCK axis activation, however, remain unclear. Given that G12 family proteins activate ROCK pathways in other cell types, their role in M3 muscarinic acetylcholine receptor-stimulated PI3K/ROCK activation and contraction was examined. EXPERIMENTAL APPROACH Gα12 coupling was evaluated using co-immunoprecipitation and serum response element (SRE)-luciferase reporter assays. siRNA and pharmacological approaches, as well as overexpression of a regulator of G-protein signaling (RGS) proteins were applied in HASMCs. Phosphorylation levels of Akt, myosin phosphatase targeting subunit-1 (MYPT1), and myosin light chain-20 (MLC) were measured. Contraction and shortening were evaluated using magnetic twisting cytometry (MTC) and micro-pattern deformation, respectively. Human precision-cut lung slices (hPCLS) were utilized to evaluate bronchoconstriction. KEY RESULTS Knockdown of M3 receptors or Gα12 attenuated activation of Akt, MYPT1, and MLC phosphorylation. Gα12 coimmunoprecipitated with M3 receptors, and p115RhoGEF-RGS overexpression inhibited carbachol-mediated induction of SRE-luciferase reporter. p115RhoGEF-RGS overexpression inhibited carbachol-induced activation of Akt, HASMC contraction, and shortening. Moreover, inhibition of RhoA blunted activation of PI3K. Lastly, RhoA inhibitors induced dilation of hPCLS. CONCLUSIONS AND IMPLICATIONS Gα12 plays a crucial role in HASMC contraction via RhoA-dependent activation of the PI3K/ROCK axis. Inhibition of RhoA activation induces bronchodilation in hPCLS, and targeting Gα12 signaling may elucidate novel therapeutic targets in asthma. These findings provide alternative approaches to the clinical management of airway obstruction in asthma.
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Affiliation(s)
- Edwin J Yoo
- Rutgers Institute for Translational Medicine and Science, Child Health InstituteRutgers UniversityNew BrunswickNJUSA
| | - Gaoyuan Cao
- Rutgers Institute for Translational Medicine and Science, Child Health InstituteRutgers UniversityNew BrunswickNJUSA
| | - Cynthia J Koziol‐White
- Rutgers Institute for Translational Medicine and Science, Child Health InstituteRutgers UniversityNew BrunswickNJUSA
| | - Christie A Ojiaku
- Rutgers Institute for Translational Medicine and Science, Child Health InstituteRutgers UniversityNew BrunswickNJUSA
| | - Krishna Sunder
- Rutgers Institute for Translational Medicine and Science, Child Health InstituteRutgers UniversityNew BrunswickNJUSA
| | - Joseph A Jude
- Rutgers Institute for Translational Medicine and Science, Child Health InstituteRutgers UniversityNew BrunswickNJUSA
| | - James V Michael
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Center for Translational Medicine, Jane and Leonard Korman Lung CenterThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Hong Lam
- Department of Environmental Health and EngineeringJohns Hopkins Bloomberg School of Public HealthBaltimoreMDUSA
| | - Ivan Pushkarsky
- Department of BioengineeringUniversity of CaliforniaLos AngelesCAUSA
| | - Robert Damoiseaux
- Department of Molecular and Medicinal PharmacologyUniversity of CaliforniaLos AngelesCAUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCAUSA
| | - Dino Di Carlo
- Department of BioengineeringUniversity of CaliforniaLos AngelesCAUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCAUSA
- Department of Mechanical EngineeringUniversity of CaliforniaLos AngelesCAUSA
| | - Kwangmi Ahn
- National Institute of Mental HealthBethesdaMDUSA
| | - Steven S An
- Department of Environmental Health and EngineeringJohns Hopkins Bloomberg School of Public HealthBaltimoreMDUSA
- Department of Chemical and Biomolecular EngineeringJohns Hopkins UniversityBaltimoreMDUSA
| | - Raymond B Penn
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Center for Translational Medicine, Jane and Leonard Korman Lung CenterThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Reynold A Panettieri
- Rutgers Institute for Translational Medicine and Science, Child Health InstituteRutgers UniversityNew BrunswickNJUSA
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Sasse SK, Kadiyala V, Danhorn T, Panettieri RA, Phang TL, Gerber AN. Glucocorticoid Receptor ChIP-Seq Identifies PLCD1 as a KLF15 Target that Represses Airway Smooth Muscle Hypertrophy. Am J Respir Cell Mol Biol 2017; 57:226-237. [PMID: 28375666 DOI: 10.1165/rcmb.2016-0357oc] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Glucocorticoids exert important therapeutic effects on airway smooth muscle (ASM), yet few direct targets of glucocorticoid signaling in ASM have been definitively identified. Here, we show that the transcription factor, Krüppel-like factor 15 (KLF15), is directly induced by glucocorticoids in primary human ASM, and that KLF15 represses ASM hypertrophy. We integrated transcriptome data from KLF15 overexpression with genome-wide analysis of RNA polymerase (RNAP) II and glucocorticoid receptor (GR) occupancy to identify phospholipase C delta 1 as both a KLF15-regulated gene and a novel repressor of ASM hypertrophy. Our chromatin immunoprecipitation sequencing data also allowed us to establish numerous direct transcriptional targets of GR in ASM. Genes with inducible GR occupancy and putative antiinflammatory properties included IRS2, APPL2, RAMP1, and MFGE8. Surprisingly, we also observed GR occupancy in the absence of supplemental ligand, including robust GR binding peaks within the IL11 and LIF loci. Detection of antibody-GR complexes at these areas was abrogated by dexamethasone treatment in association with reduced RNA polymerase II occupancy, suggesting that noncanonical pathways contribute to cytokine repression by glucocorticoids in ASM. Through defining GR interactions with chromatin on a genome-wide basis in ASM, our data also provide an important resource for future studies of GR in this therapeutically relevant cell type.
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Affiliation(s)
| | | | - Thomas Danhorn
- 2 Center for Genes, Health, and the Environment, National Jewish Health, Denver, Colorado
| | - Reynold A Panettieri
- 3 Rutgers Institute for Translational Medicine and Science, Rutgers University, New Brunswick, New Jersey; and
| | - Tzu L Phang
- 4 Department of Medicine, University of Colorado, Denver, Colorado
| | - Anthony N Gerber
- 1 Department of Medicine and.,4 Department of Medicine, University of Colorado, Denver, Colorado
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26
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Kan M, Shumyatcher M, Himes BE. Using omics approaches to understand pulmonary diseases. Respir Res 2017; 18:149. [PMID: 28774304 PMCID: PMC5543452 DOI: 10.1186/s12931-017-0631-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/26/2017] [Indexed: 12/24/2022] Open
Abstract
Omics approaches are high-throughput unbiased technologies that provide snapshots of various aspects of biological systems and include: 1) genomics, the measure of DNA variation; 2) transcriptomics, the measure of RNA expression; 3) epigenomics, the measure of DNA alterations not involving sequence variation that influence RNA expression; 4) proteomics, the measure of protein expression or its chemical modifications; and 5) metabolomics, the measure of metabolite levels. Our understanding of pulmonary diseases has increased as a result of applying these omics approaches to characterize patients, uncover mechanisms underlying drug responsiveness, and identify effects of environmental exposures and interventions. As more tissue- and cell-specific omics data is analyzed and integrated for diverse patients under various conditions, there will be increased identification of key mechanisms that underlie pulmonary biological processes, disease endotypes, and novel therapeutics that are efficacious in select individuals. We provide a synopsis of how omics approaches have advanced our understanding of asthma, chronic obstructive pulmonary disease (COPD), acute respiratory distress syndrome (ARDS), idiopathic pulmonary fibrosis (IPF), and pulmonary arterial hypertension (PAH), and we highlight ongoing work that will facilitate pulmonary disease precision medicine.
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Affiliation(s)
- Mengyuan Kan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
| | - Maya Shumyatcher
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
| | - Blanca E. Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
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27
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Vitamin D and Bronchial Asthma: An Overview of Data From the Past 5 Years. Clin Ther 2017; 39:917-929. [PMID: 28449868 DOI: 10.1016/j.clinthera.2017.04.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 11/23/2022]
Abstract
PURPOSE Vitamin D is a potent immunomodulator capable of dampening inflammatory signals in several cell types involved in the asthmatic response. Its deficiency has been associated with increased inflammation, exacerbations, and overall poor outcomes in patients with asthma. Given the increase in the prevalence of asthma over the past few decades, there has been enormous interest in the use of vitamin D supplementation as a potential therapeutic option. Here, we critically reviewed the most recent findings from in vitro studies, animal models, and clinical trials regarding the role of vitamin D in treating bronchial asthma. METHODS Using the key terms [Vitamin D, asthma, clinical trials, in vivo and in vitro studies], the [PubMed, Google Scholar] databases were searched for [clinical trials, original research articles, meta-analyses, and reviews], English-language articles published from [2012] to the present. Articles that were [Articles that did not meet these criteria were excluded] excluded from the analysis. FINDINGS Several studies have found that low serum levels of vitamin D (< 20 ng/mL) are associated with increased exacerbations, increased airway inflammation, decreased lung function, and poor prognosis in asthmatic patients. Results from in vitro and in vivo studies in animals and humans have suggested that supplementation with vitamin D may ameliorate several hallmark features of asthma. However, the findings obtained from clinical trials are controversial and do not unequivocally support a beneficial role of vitamin D in asthma. Largely, interventional studies in children, pregnant women, and adults have primarily found little to no effect of vitamin D supplementation on improved asthma symptoms, onset, or progression of the disease. This could be related to the severity of the disease process and other confounding factors. IMPLICATIONS Despite the conflicting data obtained from clinical trials, vitamin D deficiency may influence the inflammatory response in the airways. Further studies are needed to determine the exact mechanisms by which vitamin D supplementation may induce antiinflammatory effects.
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Koziol-White CJ, Jia Y, Baltus GA, Cooper PR, Zaller DM, Crackower MA, Sirkowski EE, Smock S, Northrup AB, Himes BE, Alves SE, Panettieri RA. Inhibition of spleen tyrosine kinase attenuates IgE-mediated airway contraction and mediator release in human precision cut lung slices. Br J Pharmacol 2016; 173:3080-3087. [PMID: 27417329 DOI: 10.1111/bph.13550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 06/30/2016] [Accepted: 07/02/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND AND PURPOSE Asthma presents as a heterogeneous syndrome characterized by airway obstruction, inflammation and hyper-reactivity (AHR). Spleen tyrosine kinase (Syk) mediates allergen-induced mast cell degranulation, a central component of allergen-induced inflammation and AHR. However, the role of Syk in IgE-mediated constriction of human small airways remains unknown. In this study, we addressed whether selective inhibition of Syk attenuates IgE-mediated constriction and mast cell mediator release in human small airways. EXPERIMENTAL APPROACH Human precision cut lung slices (hPCLS) ex vivo derived from non-asthmatic donors were incubated overnight with human IgE, dexamethasone, montelukast, antihistamines or a selective Syk inhibitor (SYKi). High-affinity IgE receptor (FcεRI) activation by anti-IgE cross-linking was performed, and constriction and mediator release measured. Airway constriction was normalized to that induced by maximal carbachol stimulation. Syk expression (determined by qPCR and immunoblot) was also evaluated in human primary airway smooth muscle (HASM) cells to determine whether Syk directly modulates HASM function. KEY RESULTS While dexamethasone had little effect on FcεR-mediated contraction, montelukast or antihistamines partially attenuated the response. SYKi abolished anti-IgE-mediated contraction and suppressed the release of mast cell or basophil mediators from the IgE-treated hPCLS. In contrast, SYKi had little effect on the non-allergic contraction induced by carbachol. Syk mRNA and protein were undetectable in HASM cells. CONCLUSIONS AND IMPLICATIONS A selective Syk inhibitor, but not corticosteroids, abolished FcεR-mediated contraction in human small airways ex vivo. The mechanism involved FcεRI receptor activation on mast cells or basophils that degranulate causing airway constriction, rather than direct actions on HASM.
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Affiliation(s)
- Cynthia J Koziol-White
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, NJ, Canada
| | - Yanlin Jia
- Merck Research Laboratories, Boston, MA, USA
| | | | - Philip R Cooper
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, NJ, Canada
| | | | | | | | | | | | - Blanca E Himes
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Reynold A Panettieri
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, NJ, Canada.
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29
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Gupta J, Johansson E, Bernstein JA, Chakraborty R, Khurana Hershey GK, Rothenberg ME, Mersha TB. Resolving the etiology of atopic disorders by using genetic analysis of racial ancestry. J Allergy Clin Immunol 2016; 138:676-699. [PMID: 27297995 PMCID: PMC5014679 DOI: 10.1016/j.jaci.2016.02.045] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 02/09/2016] [Accepted: 02/25/2016] [Indexed: 12/23/2022]
Abstract
Atopic dermatitis (AD), food allergy, allergic rhinitis, and asthma are common atopic disorders of complex etiology. The frequently observed atopic march from early AD to asthma, allergic rhinitis, or both later in life and the extensive comorbidity of atopic disorders suggest common causal mechanisms in addition to distinct ones. Indeed, both disease-specific and shared genomic regions exist for atopic disorders. Their prevalence also varies among races; for example, AD and asthma have a higher prevalence in African Americans when compared with European Americans. Whether this disparity stems from true genetic or race-specific environmental risk factors or both is unknown. Thus far, the majority of the genetic studies on atopic diseases have used populations of European ancestry, limiting their generalizability. Large-cohort initiatives and new analytic methods, such as admixture mapping, are currently being used to address this knowledge gap. Here we discuss the unique and shared genetic risk factors for atopic disorders in the context of ancestry variations and the promise of high-throughput "-omics"-based systems biology approach in providing greater insight to deconstruct their genetic and nongenetic etiologies. Future research will also focus on deep phenotyping and genotyping of diverse racial ancestry, gene-environment, and gene-gene interactions.
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Affiliation(s)
- Jayanta Gupta
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Elisabet Johansson
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Jonathan A Bernstein
- Division of Immunology/Allergy Section, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Ranajit Chakraborty
- Center for Computational Genomics, Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Tex
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio.
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30
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Koziol-White CJ, Yoo EJ, Cao G, Zhang J, Papanikolaou E, Pushkarsky I, Andrews A, Himes BE, Damoiseaux RD, Liggett SB, Di Carlo D, Kurten RC, Panettieri RA. Inhibition of PI3K promotes dilation of human small airways in a rho kinase-dependent manner. Br J Pharmacol 2016; 173:2726-38. [PMID: 27352269 PMCID: PMC4995285 DOI: 10.1111/bph.13542] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 05/27/2016] [Accepted: 06/05/2016] [Indexed: 12/03/2022] Open
Abstract
Background and Purpose Asthma manifests as a heterogeneous syndrome characterized by airway obstruction, inflammation and hyperresponsiveness (AHR). Although the molecular mechanisms remain unclear, activation of specific PI3K isoforms mediate inflammation and AHR. We aimed to determine whether inhibition of PI3Kδ evokes dilation of airways and to elucidate potential mechanisms. Experimental Approach Human precision cut lung slices from non‐asthma donors and primary human airway smooth muscle (HASM) cells from both non‐asthma and asthma donors were utilized. Phosphorylation of Akt, myosin phosphatase target subunit 1 (MYPT1) and myosin light chain (MLC) were assessed in HASM cells following either PI3K inhibitor or siRNA treatment. HASM relaxation was assessed by micro‐pattern deformation. Reversal of constriction of airways was assessed following stimulation with PI3K or ROCK inhibitors. Key Results Soluble inhibitors or PI3Kδ knockdown reversed carbachol‐induced constriction of human airways, relaxed agonist‐contracted HASM and inhibited pAkt, pMYPT1 and pMLC in HASM. Similarly, inhibition of Rho kinase also dilated human PCLS airways and suppressed pMYPT1 and pMLC. Baseline pMYPT1 was significantly elevated in HASM cells derived from asthma donors in comparison with non‐asthma donors. After desensitization of the β2‐adrenoceptors, a PI3Kδ inhibitor remained an effective dilator. In the presence of IL‐13, dilation by a β agonist, but not PI3K inhibitor, was attenuated. Conclusion and Implications PI3Kδ inhibitors act as dilators of human small airways. Taken together, these findings provide alternative approaches to the clinical management of airway obstruction in asthma.
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Affiliation(s)
- Cynthia J Koziol-White
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, NJ, USA
| | - Edwin J Yoo
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, NJ, USA
| | - Gaoyuan Cao
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, NJ, USA
| | - Jie Zhang
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, NJ, USA
| | - Eleni Papanikolaou
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, NJ, USA
| | - Ivan Pushkarsky
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Adam Andrews
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Blanca E Himes
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert D Damoiseaux
- California NanoSystems Institute, University of California, Los Angeles, CA, USA.,Department of Molecular and Medicinal Pharmacology, University of California, Los Angeles, CA, USA
| | | | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, CA, USA.,California NanoSystems Institute, University of California, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
| | - Richard C Kurten
- Arkansas Children's Hospital Research Institute and Department of Physiology & Biophysics, University of Arkansas Medical Sciences, Little Rock, AR, USA
| | - Reynold A Panettieri
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, NJ, USA
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31
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Belanger KK, Ameredes BT, Boldogh I, Aguilera-Aguirre L. The Potential Role of 8-Oxoguanine DNA Glycosylase-Driven DNA Base Excision Repair in Exercise-Induced Asthma. Mediators Inflamm 2016; 2016:3762561. [PMID: 27524866 PMCID: PMC4976190 DOI: 10.1155/2016/3762561] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 06/13/2016] [Indexed: 12/20/2022] Open
Abstract
Asthma is characterized by reversible airway narrowing, shortness of breath, wheezing, coughing, and other symptoms driven by chronic inflammatory processes, commonly triggered by allergens. In 90% of asthmatics, most of these symptoms can also be triggered by intense physical activities and severely exacerbated by environmental factors. This condition is known as exercise-induced asthma (EIA). Current theories explaining EIA pathogenesis involve osmotic and/or thermal alterations in the airways caused by changes in respiratory airflow during exercise. These changes, along with existing airway inflammatory conditions, are associated with increased cellular levels of reactive oxygen species (ROS) affecting important biomolecules including DNA, although the underlying molecular mechanisms have not been completely elucidated. One of the most abundant oxidative DNA lesions is 8-oxoguanine (8-oxoG), which is repaired by 8-oxoguanine DNA glycosylase 1 (OGG1) during the base excision repair (BER) pathway. Whole-genome expression analyses suggest a cellular response to OGG1-BER, involving genes that may have a role in the pathophysiology of EIA leading to mast cell degranulation, airway hyperresponsiveness, and bronchoconstriction. Accordingly, this review discusses a potential new hypothesis in which OGG1-BER-induced gene expression is associated with EIA symptoms.
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Affiliation(s)
- KarryAnne K. Belanger
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Bill T. Ameredes
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Molecular Medicine, School of Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Environmental Health and Medicine, School of Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Istvan Boldogh
- Sealy Center for Molecular Medicine, School of Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Environmental Health and Medicine, School of Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Leopoldo Aguilera-Aguirre
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
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32
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Jung JW, Kang HR. Evaluation of vitamin D in patients with asthma. ALLERGY ASTHMA & RESPIRATORY DISEASE 2016. [DOI: 10.4168/aard.2016.4.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Jae-Woo Jung
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Hye-Ryun Kang
- Department of Internal Medicine, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
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33
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Hall SC, Fischer KD, Agrawal DK. The impact of vitamin D on asthmatic human airway smooth muscle. Expert Rev Respir Med 2015; 10:127-35. [PMID: 26634624 DOI: 10.1586/17476348.2016.1128326] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Asthma is a chronic heterogeneous disorder, which involves airway inflammation, airway hyperresponsiveness (AHR) and airway remodeling. The airway smooth muscle (ASM) bundle regulates the broncho-motor tone and plays a critical role in AHR as well as orchestrating inflammation. Vitamin D deficiency has been linked to increased severity and exacerbations of symptoms in asthmatic patients. It has been shown to modulate both immune and structural cells, including ASM cells, in inflammatory diseases. Given that current asthma therapies have not been successful in reversing airway remodeling, vitamin D supplementation as a potential therapeutic option has gained a great deal of attention. Here, we highlight the potential immunomodulatory properties of vitamin D in regulating ASM function and airway inflammation in bronchial asthma.
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Affiliation(s)
- Sannette C Hall
- a Department of Biomedical Science , Creighton University School of Medicine , Omaha , NE , USA
| | - Kimberly D Fischer
- b Department of Medical Microbiology and Immunology , Creighton University School of Medicine , Omaha , NE , USA
| | - Devendra K Agrawal
- a Department of Biomedical Science , Creighton University School of Medicine , Omaha , NE , USA.,b Department of Medical Microbiology and Immunology , Creighton University School of Medicine , Omaha , NE , USA.,c Department of Clinical and Translational Science , Creighton University School of Medicine , Omaha , NE , USA
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