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Konigsberg IR, Lin NW, Liao SY, Liu C, MacPhail K, Mroz MM, Davidson E, Restrepo CI, Sharma S, Li L, Maier LA, Yang IV. Multi-omic signatures of sarcoidosis and progression in bronchoalveolar lavage cells. Respir Res 2024; 25:289. [PMID: 39080656 PMCID: PMC11290275 DOI: 10.1186/s12931-024-02919-7] [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: 04/16/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Sarcoidosis is a heterogeneous granulomatous disease with no accurate biomarkers of disease progression. Therefore, we profiled and integrated the DNA methylome, mRNAs, and microRNAs to identify molecular changes associated with sarcoidosis and disease progression that might illuminate underlying mechanisms of disease and potential biomarkers. METHODS Bronchoalveolar lavage cells from 64 sarcoidosis subjects and 16 healthy controls were used. DNA methylation was profiled on Illumina HumanMethylationEPIC arrays, mRNA by RNA-sequencing, and miRNAs by small RNA-sequencing. Linear models were fit to test for effect of sarcoidosis diagnosis and progression phenotype, adjusting for age, sex, smoking, and principal components of the data. We built a supervised multi-omics model using a subset of features from each dataset. RESULTS We identified 1,459 CpGs, 64 mRNAs, and five miRNAs associated with sarcoidosis versus controls and four mRNAs associated with disease progression. Our integrated model emphasized the prominence of the PI3K/AKT1 pathway, which is important in T cell and mTOR function. Novel immune related genes and miRNAs including LYST, RGS14, SLFN12L, and hsa-miR-199b-5p, distinguished sarcoidosis from controls. Our integrated model also demonstrated differential expression/methylation of IL20RB, ABCC11, SFSWAP, AGBL4, miR-146a-3p, and miR-378b between non-progressive and progressive sarcoidosis. CONCLUSIONS Leveraging the DNA methylome, transcriptome, and miRNA-sequencing in sarcoidosis BAL cells, we detected widespread molecular changes associated with disease, many which are involved in immune response. These molecules may serve as diagnostic/prognostic biomarkers and/or drug targets, although future testing is required for confirmation.
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Affiliation(s)
- Iain R Konigsberg
- Department of Biomedical Informatics, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA.
| | - Nancy W Lin
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA.
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA.
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Shu-Yi Liao
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
- Department of Environmental and Occupational Health, Colorado School of Public Health, Aurora, CO, USA
| | - Cuining Liu
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Kristyn MacPhail
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Margaret M Mroz
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Elizabeth Davidson
- Department of Biomedical Informatics, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
| | - Clara I Restrepo
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Sunita Sharma
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
| | - Li Li
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
| | - Lisa A Maier
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
- Department of Environmental and Occupational Health, Colorado School of Public Health, Aurora, CO, USA
| | - Ivana V Yang
- Department of Biomedical Informatics, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
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Konigsberg IR, Lin NW, Liao SY, Liu C, MacPhail K, Mroz MM, Davidson E, Restrepo CI, Sharma S, Li L, Maier LA, Yang IV. Multi-Omic Signatures of Sarcoidosis and Progression in Bronchoalveolar Lavage Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525601. [PMID: 36747844 PMCID: PMC9901011 DOI: 10.1101/2023.01.26.525601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Introduction Sarcoidosis is a heterogeneous, granulomatous disease that can prove difficult to diagnose, with no accurate biomarkers of disease progression. Therefore, we profiled and integrated the DNA methylome, mRNAs, and microRNAs to identify molecular changes associated with sarcoidosis and disease progression that might illuminate underlying mechanisms of disease and potential genomic biomarkers. Methods Bronchoalveolar lavage cells from 64 sarcoidosis subjects and 16 healthy controls were used. DNA methylation was profiled on Illumina HumanMethylationEPIC arrays, mRNA by RNA-sequencing, and miRNAs by small RNA-sequencing. Linear models were fit to test for effect of diagnosis and phenotype, adjusting for age, sex, and smoking. We built a supervised multi-omics model using a subset of features from each dataset. Results We identified 46,812 CpGs, 1,842 mRNAs, and 5 miRNAs associated with sarcoidosis versus controls and 1 mRNA, SEPP1 - a protein that supplies selenium to cells, associated with disease progression. Our integrated model emphasized the prominence of the PI3K/AKT1 pathway in sarcoidosis, which is important in T cell and mTOR function. Novel immune related genes and miRNAs including LYST, RGS14, SLFN12L, and hsa-miR-199b-5p, distinguished sarcoidosis from controls. Our integrated model also demonstrated differential expression/methylation of IL20RB, ABCC11, SFSWAP, AGBL4, miR-146a-3p, and miR-378b between non-progressive and progressive sarcoidosis. Conclusions Leveraging the DNA methylome, transcriptome, and miRNA-sequencing in sarcoidosis BAL cells, we detected widespread molecular changes associated with disease, many which are involved in immune response. These molecules may serve as diagnostic/prognostic biomarkers and/or drug targets, although future testing will be required for confirmation.
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Affiliation(s)
- Iain R. Konigsberg
- Department of Biomedical Informatics, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO
| | - Nancy W. Lin
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver CO
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora CO
| | - Shu-Yi Liao
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver CO
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora CO
- Department of Environmental and Occupational Health, Colorado School of Public Health, Aurora, CO
| | - Cuining Liu
- Department of Biostatistics and Bioinformatics, Colorado School of Public Health, Aurora CO
| | - Kristyn MacPhail
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver CO
| | - Margaret M. Mroz
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver CO
| | - Elizabeth Davidson
- Department of Biomedical Informatics, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO
| | - Clara I. Restrepo
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver CO
| | - Sunita Sharma
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora CO
| | - Li Li
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver CO
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora CO
| | - Lisa A. Maier
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver CO
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora CO
- Department of Environmental and Occupational Health, Colorado School of Public Health, Aurora, CO
| | - Ivana V. Yang
- Department of Biomedical Informatics, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora CO
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Non-Coding RNAs in Pulmonary Diseases: Comparison of Different Airway-Derived Biosamples. Int J Mol Sci 2023; 24:ijms24032006. [PMID: 36768329 PMCID: PMC9916756 DOI: 10.3390/ijms24032006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Due to their structural conservation and functional role in critical signalling pathways, non-coding RNA (ncRNA) is a promising biomarker and modulator of pathological conditions. Most research has focussed on the role of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). These molecules have been investigated both in a cellular and an extracellular context. Sources of ncRNAs may include organ-specific body fluids. Therefore, studies on ncRNAs in respiratory diseases include those on sputum, bronchoalveolar lavage fluid (BALF) and exhaled breath condensate (EBC). It is worth identifying the limitations of these biosamples in terms of ncRNA abundance, processing and diagnostic potential. This review describes the progress in the literature on the role of ncRNAs in the pathogenesis and progression of severe respiratory diseases, including cystic fibrosis, asthma and interstitial lung disease. We showed that there is a deficit of information on lncRNAs and circRNAs in selected diseases, despite attempts to functionally bind them to miRNAs. miRNAs remain the most well-studied, but only a few investigations have been conducted on the least invasive biosample material, i.e., EBC. To summarise the studies conducted to date, we also performed a preliminary in silico analysis of the reported miRNAs, demonstrating the complexity of their role and interactions in selected respiratory diseases.
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Duo M, Liu Z, Li P, Wang Y, Zhang Y, Weng S, Zheng Y, Fan M, Wu R, Xu H, Ren Y, Cheng Z. Integrative bioinformatics analysis to explore a robust diagnostic signature and landscape of immune cell infiltration in sarcoidosis. Front Med (Lausanne) 2022; 9:942177. [DOI: 10.3389/fmed.2022.942177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
BackgroundThe unknown etiology of sarcoidosis with variable clinical features leads to delayed diagnosis and limited therapeutic strategies. Hence, exploring the latent mechanisms and constructing an accessible and reliable diagnostic model of sarcoidosis is vital for innovative therapeutic approaches to improve prognosis.MethodsThis retrospective study analyzed transcriptomes from 11 independent sarcoidosis cohorts, comprising 313 patients and 400 healthy controls. The weighted gene co-expression network analysis (WGCNA) and differentially expressed gene (DEG) analysis were performed to identify molecular biomarkers. Machine learning was employed to fit a diagnostic model. The potential pathogenesis and immune landscape were detected by bioinformatics tools.ResultsA 10-gene signature SARDS consisting of GBP1, LEF1, IFIT3, LRRN3, IFI44, LHFPL2, RTP4, CD27, EPHX2, and CXCL10 was further constructed in the training cohorts by the LASSO algorithm, which performed well in the four independent cohorts with the splendid AUCs ranging from 0.938 to 1.000. The findings were validated in seven independent publicly available gene expression datasets retrieved from whole blood, PBMC, alveolar lavage fluid cells, and lung tissue samples from patients with outstanding AUCs ranging from 0.728 to 0.972. Transcriptional signatures associated with sarcoidosis revealed a potential role of immune response in the development of the disease through bioinformatics analysis.ConclusionsOur study identified and validated molecular biomarkers for the diagnosis of sarcoidosis and constructed the diagnostic model SARDS to improve the accuracy of early diagnosis of the disease.
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Olgun G, Gopalan V, Hannenhalli S. miRSCAPE - inferring miRNA expression from scRNA-seq data. iScience 2022; 25:104962. [PMID: 36060076 PMCID: PMC9437856 DOI: 10.1016/j.isci.2022.104962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/09/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022] Open
Abstract
Our understanding of miRNA activity at cellular resolution is thwarted by the inability of standard scRNA-seq protocols to capture miRNAs. We introduce a novel tool, miRSCAPE, to infer miRNA expression in a sample from its RNA-seq profile. We establish miRSCAPE's accuracy in 10 tumor and normal cohorts demonstrating its superiority over alternatives. miRSCAPE accurately infers cell type-specific miRNA activities (predicted versus observed fold-difference correlation ∼0.81) in two independent scRNA-seq datasets. We apply miRSCAPE to infer miRNA activities in scRNA clusters in pancreatic and lung adenocarcinomas, as well as in 56 cell types in the human cell landscape (HCL). In pancreatic and breast cancer scRNA-seq data, miRSCAPE recapitulates miRNAs associated with stemness and epithelial-mesenchymal transition (EMT) cell states, respectively. Overall, miRSCAPE recapitulates and refines miRNA biology at cellular resolution. miRSCAPE is freely available and is easily applicable to scRNA-seq data to infer miRNA activities at cellular resolution.
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Affiliation(s)
- Gulden Olgun
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vishaka Gopalan
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Abstract
Epigenetic modifications are emerging as important regulatory mechanisms of gene expression in lung disease, given that they are influenced by environmental exposures and genetic variants, and that they regulate immune and fibrotic processes. In this review, we introduce these concepts with a focus on the study of DNA methylation and histone modifications and discuss how they have been applied to lung disease, and how they can be applied to sarcoidosis. This information has implications for other exposure and immunologically mediated lung diseases, such as chronic beryllium disease, hypersensitivity pneumonitis, and asbestosis.
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Affiliation(s)
- Iain R Konigsberg
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lisa A Maier
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Medicine, National Jewish Health, Denver, CO, USA
- Dept of Environmental and Occupational Health, Colorado School of Public Health, Aurora, CO, USA
| | - Ivana V Yang
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
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Cao Y, Zhang H, Zheng L, Li Q. Identification of the Core MicroRNAs and Potential Molecular Mechanismsin Sarcoidosis Using Bioinformatics Analysis. Front Mol Biosci 2021; 8:644232. [PMID: 34055877 PMCID: PMC8155597 DOI: 10.3389/fmolb.2021.644232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 04/19/2021] [Indexed: 11/18/2022] Open
Abstract
Sarcoidosis is a systemic heterogeneous inflammatory disease; however, the etiology and pathogenesis of sarcoidosis are still unknown. Herein, we investigated the core microRNAs and potential molecular mechanisms in sarcoidosis. The DE-miRNAs were diagnosed using the LIMMA software package. DIANA-mirPath was employed to perform pathway and GO enrichment analysis of the DE-miRNAs. PPI networks and miRNA-target gene regulatory networks were used to obtain insight into the actions of DE-miRNAs. Expression of the hub genes along with miRNAs was validated in clinical specimens. Overall, 266 DE-miRNAs were screened. Among these DE-miRNAs, hsa-miR-144, hsa-miR-126, as well as hsa-miR-106a were the upmost upregulated miRNAs; hsa-miR-151-3p, hsa-miR-320d, and hsa-miR-324-3p were the top downregulated miRNAs. NR3C1, ZBTB7A, NUFIP2, BZW1, ERGIC2, and VEGFA were mapped as the most targeted hub genes in the upregulation of miRNAs, and MCL1 and SAE1 were the most targeted hub genes in the downregulation of miRNA. VEGFA and NR3C1 were selected and potentially modulated by hsa-miR-20b, hsa-miR-126, and hsa-miR-106a. In sarcoidosis pathological tissue, hsa-miR-126 was highly expressed, and VEGFA and NR3C1 were overexpressed. In conclusion, our results revealed the dysregulation of hsa-miR-126 and a potential regulatory mechanism for pathogenesis in sarcoidosis.
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Affiliation(s)
- Yuan Cao
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University (Xibei Hospital), Xi'an, China
| | - Hua Zhang
- Department of Respiratory Medicine, Zhangjiakou First Hospital, Zhangjiakou, China
| | - Lulu Zheng
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University (Xibei Hospital), Xi'an, China
| | - Qiao Li
- Clinical Laboratory, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, China
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Mousapasandi A, Herbert C, Thomas P. Potential use of biomarkers for the clinical evaluation of sarcoidosis. J Investig Med 2021; 69:jim-2020-001659. [PMID: 33452128 DOI: 10.1136/jim-2020-001659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2020] [Indexed: 12/20/2022]
Abstract
Sarcoidosis is a systemic granulomatous disease of unknown etiology and pathogenesis with a heterogeneous clinical presentation. In the appropriate clinical and radiological context and with the exclusion of other diagnoses, the disease is characterized by the pathological presence of non-caseating epithelioid cell granulomas. Sarcoidosis is postulated to be a multifactorial disease caused by chronic antigenic stimulation. The immunopathogenesis of sarcoidosis encompasses a complex interaction between the host, genetic factors and postulated environmental and infectious triggers, which result in granuloma development.The exact pathogenesis of the disease has yet to be elucidated, but some of the inflammatory pathways that play a key role in disease progression and outcomes are becoming apparent, and these may form the logical basis for selecting potential biomarkers.Biomarkers are biological molecules that are altered pathologically. To date, there exists no single reliable biomarker for the evaluation of sarcoidosis, either diagnostically or prognostically but new candidates are emerging. A diagnosis of sarcoidosis ideally requires a biopsy confirming non-caseating granulomas, but the likelihood of progression that requires intervention remains unpredictable. These challenging aspects could be potentially resolved by incorporating biomarkers into clinical practice for both diagnosis and monitoring disease activity.This review outlines the current knowledge on sarcoidosis with an emphasis on pulmonary sarcoidosis, and delineates the understanding surrounding the implication of biomarkers for the clinical evaluation of sarcoidosis.
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Affiliation(s)
- Amir Mousapasandi
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Cristan Herbert
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Paul Thomas
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Department of Respiratory Medicine, Prince of Wales' Hospital and Prince of Wales' Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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Yi S, Liu YP, Li XY, Yuan XY, Wang Y, Cai Y, Lei YD, Huang L, Zhang ZH. The expression profile and bioinformatics analysis of microRNAs in human bronchial epithelial cells treated by beryllium sulfate. J Appl Toxicol 2020; 41:1275-1285. [PMID: 33197057 DOI: 10.1002/jat.4116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/17/2020] [Accepted: 11/02/2020] [Indexed: 11/08/2022]
Abstract
Beryllium and its compounds are systemic toxicants that mainly accumulate in the lungs. As a regulator of gene expression, microRNAs (miRNAs) were involved in some lung diseases. This study aimed to analyze the levels of some inflammatory cytokine and the differential expressions of miRNAs in human bronchial epithelial cells (16HBE) induced by beryllium sulfate (BeSO4 ) and to further explore the biological functions of differentially expressed miRNAs. The profile of miRNAs in 16HBE cells was detected using the high-throughput sequencing between the control groups (n = 3) and the 150 μmol/L of BeSO4 -treated groups (n = 3). Bioinformatics analysis of differentially expressed miRNAs was performed, including the prediction of target genes, Gene Ontology (GO) analysis, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Quantitative real-time polymerase chain reaction (qRT-PCR) was applied to verify some damage-related miRNAs. We found that BeSO4 can increase the levels of some inflammatory cytokine such as interleukin-10 (IL-10), tumor necrosis factor-alpha (TNF-α), interferon-γ (IFN-γ), inducible nitric oxide synthase (iNOS), and cyclooxygenase-2 (COX-2). And BeSO4 altered miRNAs expression of 16HBE cells and a total of 179 differentially expressed miRNAs were identified, including 88 upregulated miRNAs and 91 downregulated miRNAs. The target genes predicted by 28 dysregulated miRNAs were mainly involved in the transcription regulation, signal transduction, MAPK, and VEGF signaling pathway. The qRT-PCR verification results were consistent with the sequencing results. miRNA expression profiling in 16HBE cells exposed to BeSO4 provides new insights into the toxicity mechanism of beryllium exposure.
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Affiliation(s)
- Shan Yi
- School of Public Health, University of South China, Hengyang, China
| | - Yan-Ping Liu
- School of Public Health, University of South China, Hengyang, China
| | - Xun-Ya Li
- School of Public Health, University of South China, Hengyang, China
| | - Xiao-Yan Yuan
- School of Public Health, University of South China, Hengyang, China
| | - Ye Wang
- School of Public Health, University of South China, Hengyang, China
| | - Ying Cai
- School of Public Health, University of South China, Hengyang, China
| | - Yuan-di Lei
- School of Public Health, University of South China, Hengyang, China
| | - Lian Huang
- School of Public Health, University of South China, Hengyang, China
| | - Zhao-Hui Zhang
- School of Public Health, University of South China, Hengyang, China
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Zhao YB, Li W, Zhang Q, Yin Y, Yang CJ, Xu WX, Kang J, Qi RQ, Hou G. Distinct miRNA Gene Expression Profiles Among the Nodule Tissues of Lung Sarcoidosis, Tuberculous Lymphadenitis and Normal Healthy Control Individuals. Front Med (Lausanne) 2020; 7:527433. [PMID: 33178707 PMCID: PMC7596360 DOI: 10.3389/fmed.2020.527433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 09/08/2020] [Indexed: 12/28/2022] Open
Abstract
Background: Sarcoidosis and tuberculosis share similarities in clinical manifestations and histopathological features. We aimed to identify the microRNA (miRNA) profiles of the lymph nodes of individuals with sarcoidosis and of those with tuberculous lymphadenitis to investigate the value of miRNAs in the differential diagnosis of sarcoidosis and tuberculous lymphadenitis. Methods: The miRNA profiles of the lymph nodes of individuals with sarcoidosis, those with tuberculous lymphadenitis (TBLN) and controls were detected by miRNA microarray analysis in the age- and sex-matched development group of the controls (n = 3), patients with TBLN (n = 3) and patients with sarcoidosis (n = 3), and the results were validated by quantitative real-time polymerase chain reaction in the validation group of the controls (n = 30), TBLN (n = 30) and patients with sarcoidosis (n = 31). The relationship between miRNA expression and the clinical parameters of sarcoidosis was analyzed. Results: miR-145, miR-185-5p, miR-301, miR-425-5P, miR-449b and miR-885-5P were differentially expressed between individuals with sarcoidosis and controls (P < 0.0001, P < 0.0001, P = 0.0008, P = 0.0002, P = 0.0018, and P < 0.0001, respectively), and the same six miRNAs were differentially expressed between individuals with tuberculous lymphadenitis and controls (P = 0.0002, P = 0.0004, P = 0.0238, P = 0.0006, P = 0.0149, and P = 0.0045, respectively). miR-185-5p was differentially expressed between individuals with tuberculous lymphadenitis and those with sarcoidosis (P = 0.0101). The area under the receiver operating characteristic curve calculated for miR-185-5p was 0.6860, and the sensitivity and specificity of miR-185-5p for the differential diagnosis of sarcoidosis from TBLN were 61 and 80%, respectively. The levels of miR-145, miR-301, miR-425-5P, and miR-885-5P were positively correlated with CD4+/CD8+ T lymphocytes in bronchoalveolar lavage fluid. Conclusions: miRNAs in lymph nodes show similar expression patterns between individuals with sarcoidosis and those with tuberculous lymphadenitis, which were experimentally selected. miR-185-5p in the lymph nodes can be used as an auxiliary marker for the differential diagnosis of sarcoidosis and tuberculous lymphadenitis.
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Affiliation(s)
- Ya-Bin Zhao
- Department of Respiratory Medicine, First Hospital of China Medical University, Shenyang, China
| | - Wei Li
- Department of Respiratory Medicine, The Third People's Hospital of Hubei Province, Wuhan, China
| | - Qin Zhang
- Department of Respiratory Medicine, First Hospital of China Medical University, Shenyang, China
| | - Yan Yin
- Department of Respiratory Medicine, First Hospital of China Medical University, Shenyang, China
| | - Chuan-Jia Yang
- Department of Thyroid Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Wen-Xiang Xu
- Department of Pathology, Shenyang Thoracic Hospital, Shenyang, China
| | - Jian Kang
- Department of Respiratory Medicine, First Hospital of China Medical University, Shenyang, China
| | - Rui-Qun Qi
- Department of Dermatology, First Hospital of China Medical University, Shenyang, China
| | - Gang Hou
- Department of Respiratory Medicine, First Hospital of China Medical University, Shenyang, China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
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Abstract
PURPOSE OF REVIEW Sarcoidosis is a systemic disease characterized by granulomatous inflammation of unknown cause. There is extensive heterogeneity between patients with respect to the number and types of organs involved, disease course, and response to therapy. Recent research in the field has leveraged 'omics' techniques such as transcriptomics to identify important 'molecular profiles' in the disease. These tools may help in identifying clinically useful biomarkers and targets for therapy. RECENT FINDINGS Several studies have used gene expression profiling of predesignated lists or the entire genome to find genes and markers that differentiate sarcoidosis from healthy controls, but only a few have compared sarcoidosis patients based on disease phenotypes and organ involvement. The common gene pathways that have been repeatedly identified include those related to the interferon response, T-cell receptor signaling, and the major histocompatibility complex. SUMMARY While the molecular profiling studies to date offer the ability to compare sarcoidosis and health as well as across tissues, further longitudinal studies that include sarcoidosis patients with varying outcomes with respect to organ involvement and response to treatment are needed to identify clinically important phenotypes in the disease that can then be differentiated based on molecular features.
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Affiliation(s)
- Nicholas K. Arger
- University of California, San Francisco, Division of Pulmonary and Critical Care, 505 Parnassus Ave, San Francisco, CA 94143, USA
| | - Brian O’Connor
- National Jewish Health, Center for Genes, Environment, & Health, 1400 Jackson St, Denver, CO 80206, USA
| | - Laura L. Koth
- University of California, San Francisco, Division of Pulmonary and Critical Care, 505 Parnassus Ave, San Francisco, CA 94143, USA
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Hoefel GA, Tay HL, Foster PS. Response. Chest 2020; 158:828-829. [PMID: 32768068 DOI: 10.1016/j.chest.2020.03.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 10/23/2022] Open
Affiliation(s)
- Gabriela A Hoefel
- Priority Research Centre for Healthy Lungs, Department of Microbiology and Immunology, School of Biomedical Sciences and Medicine, Faculty of Health and Medicine, Hunter Medical Research Institute and the University of Newcastle, Newcastle, NSW, Australia
| | - Hock L Tay
- Priority Research Centre for Healthy Lungs, Department of Microbiology and Immunology, School of Biomedical Sciences and Medicine, Faculty of Health and Medicine, Hunter Medical Research Institute and the University of Newcastle, Newcastle, NSW, Australia
| | - Paul S Foster
- Priority Research Centre for Healthy Lungs, Department of Microbiology and Immunology, School of Biomedical Sciences and Medicine, Faculty of Health and Medicine, Hunter Medical Research Institute and the University of Newcastle, Newcastle, NSW, Australia.
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13
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Pattnaik B, Sryma PB, Mittal S, Agrawal A, Guleria R, Madan K. MicroRNAs in pulmonary sarcoidosis: A systematic review. Respir Investig 2020; 58:232-238. [PMID: 32305227 DOI: 10.1016/j.resinv.2020.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 02/11/2020] [Accepted: 02/20/2020] [Indexed: 01/05/2023]
Abstract
Sarcoidosis is a multisystemic granulomatous disorder of unknown etiology. Diagnosis of sarcoidosis is made by correlating clinical and radiological features along with the histopathological demonstration of non-necrotizing granulomas in tissue samples. Diagnosis is often challenging as the clinical profile may mimic other granulomatous disorders, including infections, inflammatory diseases, and lymphoid malignancies. Differentiation from tuberculosis is especially crucial in endemic regions where exclusion of mediastinal tuberculosis is necessary before any immunosuppressant treatment can be initiated for symptomatic sarcoidosis. Identification of biomarkers, which can aid in diagnosis as well as prognosis, can be helpful in clinical decision making. MicroRNAs are small non-coding regulatory RNAs that serve as post-transcriptional regulators of gene expression and have been studied as emerging biomarkers in many other respiratory diseases, including lung cancer, asthma, idiopathic pulmonary fibrosis, and chronic obstructive pulmonary disease. In the context of sarcoidosis, miRNA expression has been studied in the lungs, lymph nodes, bronchoalveolar lavage fluid, and peripheral blood mononuclear cells. A comprehensive search of the PubMed database was performed by two authors independently, and relevant studies were retrieved for review. This systematic review summarizes the current information on miRNAs in sarcoidosis, the biological mechanisms involved in CD4+ T-helper 1 and macrophage polarization, and the use of exhaled breath condensate as an alternative, noninvasive and potential source of miRNAs.
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Affiliation(s)
- Bijay Pattnaik
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - P B Sryma
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Saurabh Mittal
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Anurag Agrawal
- Centre of Excellence in Asthma and Lung Disease, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Karan Madan
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India.
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14
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Sarcoidosis: Causes, Diagnosis, Clinical Features, and Treatments. J Clin Med 2020; 9:jcm9041081. [PMID: 32290254 PMCID: PMC7230978 DOI: 10.3390/jcm9041081] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/04/2020] [Accepted: 04/08/2020] [Indexed: 12/19/2022] Open
Abstract
Sarcoidosis is a multisystem granulomatous disease with nonspecific clinical manifestations that commonly affects the pulmonary system and other organs including the eyes, skin, liver, spleen, and lymph nodes. Sarcoidosis usually presents with persistent dry cough, eye and skin manifestations, weight loss, fatigue, night sweats, and erythema nodosum. Sarcoidosis is not influenced by sex or age, although it is more common in adults (< 50 years) of African-American or Scandinavians decent. Diagnosis can be difficult because of nonspecific symptoms and can only be verified following histopathological examination. Various factors, including infection, genetic predisposition, and environmental factors, are involved in the pathology of sarcoidosis. Exposures to insecticides, herbicides, bioaerosols, and agricultural employment are also associated with an increased risk for sarcoidosis. Due to its unknown etiology, early diagnosis and detection are difficult; however, the advent of advanced technologies, such as endobronchial ultrasound-guided biopsy, high-resolution computed tomography, magnetic resonance imaging, and 18F-fluorodeoxyglucose positron emission tomography has improved our ability to reliably diagnose this condition and accurately forecast its prognosis. This review discusses the causes and clinical features of sarcoidosis, and the improvements made in its prognosis, therapeutic management, and the recent discovery of potential biomarkers associated with the diagnostic assay used for sarcoidosis confirmation.
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15
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Molecular profiling of regulatory T cells in pulmonary sarcoidosis. J Autoimmun 2018; 94:56-69. [DOI: 10.1016/j.jaut.2018.07.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/11/2018] [Accepted: 07/15/2018] [Indexed: 11/23/2022]
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16
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Kishore A, Navratilova Z, Kolek V, Novosadova E, Čépe K, du Bois RM, Petrek M. Expression analysis of extracellular microRNA in bronchoalveolar lavage fluid from patients with pulmonary sarcoidosis. Respirology 2018; 23:1166-1172. [PMID: 29956871 DOI: 10.1111/resp.13364] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 01/20/2023]
Abstract
BACKGROUND AND OBJECTIVE MicroRNA (miRNA) are transcriptional regulators implicated in pulmonary sarcoidosis and packaged in extracellular vesicles (EV) during cellular communication. We characterized EV and investigated miRNA expression in bronchoalveolar lavage (BAL) fluid from sarcoidosis patients. METHODS EV were characterized for size(s) using dynamic light scattering and transmission electron microscopy (TEM) analysis and protein markers by immunoblotting. Twelve extracellular and 5 cellular miRNA were investigated in BAL from 16 chest X-ray stage-I (CXR-I) and 17 CXR stage-II (CXR-II) sarcoidosis patients. Associations between miRNA and disease characteristics (extrapulmonary involvement, pulmonary function and BAL cell profile) were statistically analysed. RESULTS BAL from sarcoidosis patients contained exosomes and microvesicles (MV) as EV. In these EV, expression of miR-146a (P = 0.007), miR-150 (P = 0.003) and BAL cellular miR-21 (P = 0.01) was increased in CXR-II compared with CXR-I. Other detected EV (miR-21 and miR-26a) and cellular (miR-31, miR-129-3p, miR-146a and miR-452) miRNA were not differentially expressed. The investigated miRNA did not reflect extrapulmonary involvement, but EV miR-146a and miR-150 were negatively correlated with pulmonary function (miR-146a with vital capacity (VC; Spearman's correlation coefficient (rs ), P = -0.657, 0.007), percent predicted forced expiratory volume in 1 s (FEV1 ; -0.662, 0.006) and FEV1 /forced vital capacity (FVC) ratio (-0.649, 0.008); miR-150 correlated negatively with VC (-0.584, 0.019) and FEV1 /FVC ratio (-0.746, 0.001) in CXR-II cases). CONCLUSION Our data provide evidence that exosomes and microvesicles as extracellular vesicles are present in the bronchoalveolar space of sarcoidosis patients and they differentially express EV miRNA (miR-146a and miR-150), the expression of which correlates negatively with pulmonary function indices. The significance of these findings for disease pathophysiology and clinical course require further investigation.
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Affiliation(s)
- Amit Kishore
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Zdenka Navratilova
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Vitezslav Kolek
- Department of Respiratory Medicine and Tuberculosis, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Eva Novosadova
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Klára Čépe
- Faculty of Science, Palacky University, Olomouc, Czech Republic
| | | | - Martin Petrek
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
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17
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Malysheva IE, Balan OV, Tikhonovich EL, Volkova TO. Expression of DROSHA and DICER genes in peripheral blood leukocytes in lung sarcoidosis. TERAPEVT ARKH 2018; 90:21-24. [PMID: 30701851 DOI: 10.26442/terarkh201890321-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
AIM To study the expression level of the genes DROSHA and DICER in peripheral blood leukocytes (PBL) of patients with sarcoidosis of the lungs. MATERIALS AND METHODS The study included 32 patients diagnosed with persistent lung sarcoidosis (mean age 41.56±1.27 years) and 36 healthy donors (control; mean age 42.79±1.95 years). The level of expression of messenger RNA (mRNA) of the genes DROSHA and DICER were determined in PBL of healthy donors and patients with sarcoidosis of the lung by polymerase chain reaction in real time. RESULTS As a result of the conducted researches it is established that the level of drosha gene expression in PBL patients with sarcoidosis of lungs is significantly reduced in comparison with the control (p<0.01). We also found a significant decrease in the number of Dicker gene transcripts in the PBL of the study group of patients (p<0.01). CONCLUSION According to the results of the conducted studies, a significant decrease in the number of DROSHA and DICER transcripts in PBL patients with the development of lung sarcoidosis has been found, which can contribute to the pathogenesis of this disease.
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Affiliation(s)
- I E Malysheva
- IB KarRC RAS, laboratory of genetics, Petrozavodsk, Russia
| | - O V Balan
- IB KarRC RAS, laboratory of genetics, Petrozavodsk, Russia
| | - E L Tikhonovich
- Republican Hospital named after. V.A. Baranov, Petrozavodsk, Russia
| | - T O Volkova
- Petrozavodsk state University, Department of Hospital Therapy, Petrozavodsk, Russia
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18
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Affiliation(s)
- Catherine A Bonham
- 1 Section of Pulmonary and Critical Care Medicine University of Chicago Chicago, Illinois
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19
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Salamo O, Mortaz E, Mirsaeidi M. Noncoding RNAs: New Players in Pulmonary Medicine and Sarcoidosis. Am J Respir Cell Mol Biol 2018; 58:147-156. [DOI: 10.1165/rcmb.2017-0196tr] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Oriana Salamo
- Division of Pulmonary and Critical Care, University of Miami, Miami, Florida
| | - Esmaeil Mortaz
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands; and
| | - Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, University of Miami, Miami, Florida
- Section of Pulmonary Medicine, Miami Veterans Affairs Healthcare System, Miami, Florida
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20
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Ascoli C, Huang Y, Schott C, Turturice BA, Metwally A, Perkins DL, Finn PW. A Circulating MicroRNA Signature Serves as a Diagnostic and Prognostic Indicator in Sarcoidosis. Am J Respir Cell Mol Biol 2018; 58:40-54. [PMID: 28812922 DOI: 10.1165/rcmb.2017-0207oc] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) act as post-transcriptional regulators of gene expression. In sarcoidosis, aberrant miRNA expression may enhance immune responses mounted against an unknown antigenic agent. We tested whether a distinct miRNA signature functions as a diagnostic biomarker and explored its role as an immune modulator in sarcoidosis. The expression of miRNAs in peripheral blood mononuclear cells from subjects who met clinical and histopathologic criteria for sarcoidosis was compared with that observed in matched controls in the ACCESS (A Case Controlled Etiologic Study of Sarcoidosis) study. Signature miRNAs were determined by miRNA microarray analysis and validated by quantitative RT-PCR. Microarray analysis identified 54 mature, human feature miRNAs that were differentially expressed between the groups. Significant feature miRNAs that distinguished subjects with sarcoidosis from controls were selected by means of probabilistic models adjusted for clinical variables. Eight signature miRNAs were chosen to verify the diagnosis of sarcoidosis in a validation cohort, and distinguished subjects with sarcoidosis from controls with a positive predictive value of 88%. We identified both novel and previously described genes and molecular pathways associated with sarcoidosis as targets of these signature miRNAs. Additionally, we demonstrate that signature miRNAs (hsa-miR-150-3p and hsa-miR-342-5p) are significantly associated with reduced lymphocytes and airflow limitations, both of which are known markers of a poor prognosis. Together, these findings suggest that a circulating miRNA signature serves as a noninvasive biomarker that supports the diagnosis of sarcoidosis. Future studies will test the miRNA signature as a prognostication tool to identify unfavorable changes associated with poor clinical outcomes in sarcoidosis.
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Affiliation(s)
- Christian Ascoli
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine
| | - Yue Huang
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine
| | - Cody Schott
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine.,Department of Microbiology and Immunology
| | - Benjamin A Turturice
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine.,Department of Microbiology and Immunology
| | | | - David L Perkins
- Department of Bioengineering.,Division of Nephrology, Department of Medicine, and.,Department of Surgery, University of Illinois at Chicago, Chicago, Illinois
| | - Patricia W Finn
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine.,Department of Microbiology and Immunology
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21
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Zhou T, Casanova N, Pouladi N, Wang T, Lussier Y, Knox KS, Garcia JGN. Identification of Jak-STAT signaling involvement in sarcoidosis severity via a novel microRNA-regulated peripheral blood mononuclear cell gene signature. Sci Rep 2017; 7:4237. [PMID: 28652588 PMCID: PMC5484682 DOI: 10.1038/s41598-017-04109-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 05/10/2017] [Indexed: 11/28/2022] Open
Abstract
Sarcoidosis is a granulomatous lung disorder of unknown cause. The majority of individuals with sarcoidosis spontaneously achieve full remission (uncomplicated sarcoidosis), however, ~20% of sarcoidosis-affected individuals experience progressive lung disease or cardiac and nervous system involvement (complicated sarcoidosis). We investigated peripheral blood mononuclear cell (PBMC) microRNA and protein-coding gene expression data from healthy controls and patients with uncomplicated or complicated sarcoidosis. We identified 46 microRNAs and 1,559 genes that were differentially expressed across a continuum of sarcoidosis severity (healthy control → uncomplicated sarcoidosis → complicated sarcoidosis). A total of 19 microRNA-mRNA regulatory pairs were identified within these deregulated microRNAs and mRNAs, which consisted of 17 unique protein-coding genes yielding a 17-gene signature. Pathway analysis of the 17-gene signature revealed Jak-STAT signaling pathway as the most significantly represented pathway. A severity score was assigned to each patient based on the expression of the 17-gene signature and a significant increasing trend in the severity score was observed from healthy control, to uncomplicated sarcoidosis, and finally to complicated sarcoidosis. In addition, this microRNA-regulated gene signature differentiates sarcoidosis patients from healthy controls in independent validation cohorts. Our study suggests that PBMC gene expression is useful in diagnosis of sarcoidosis.
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Affiliation(s)
- Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Nancy Casanova
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Nima Pouladi
- Center for Bioinformatics and Biostatistics, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Ting Wang
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Yves Lussier
- Center for Bioinformatics and Biostatistics, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Kenneth S Knox
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Joe G N Garcia
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA.
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22
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The Serum Expression of Selected miRNAs in Pulmonary Sarcoidosis with/without Löfgren's Syndrome. Mediators Inflamm 2016; 2016:1246129. [PMID: 28050119 PMCID: PMC5165170 DOI: 10.1155/2016/1246129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/10/2016] [Indexed: 12/12/2022] Open
Abstract
Purpose. Pulmonary sarcoidosis is associated with dysregulated expression of intracellular miRNAs. There is however only little information on extracellular miRNAs and their association with the disease course in sarcoidosis. We therefore assessed serum miRNAs in sarcoidosis classified according to the presence of Löfgren's syndrome (LS) as a hallmark of good prognosis in contrast to more advanced disease course. Methods. RT-PCR was used to assess 35 miRNAs in 13 healthy controls and 24 sarcoidosis patients (12 with X-ray (CXR) stage ≤ 1 and LS and 12 with insidious onset and CXR stage ≥ 3). Results. Compared to controls, we consistently observed dysregulated expressions of miR-146, miR-16, miR-425-5p, and miR-93-5p in both sarcoidosis groups irrespective of disease course. Specifically, patients without LS had dysregulated expressions of miR-150-5p, miR-1, and miR-212 compared to controls. Patients with LS had dysregulated expressions of miR-21-5p and miR-340-5p compared to controls. Bioinformatics predicted consistently "Pathways in cancer" to be modulated by both altered profiles in patients with/without LS. Three miRNAs (miR-21-5p, miR-340-5p, and miR-212-3p) differed between our patients with LS and those without LS; their cumulative effect may modulate "TGF-β signalling pathway." Conclusions. Further study should focus on possible applications of serum miRNAs for diagnostics follow-up and for prognosis.
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