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Fraser SD, Thackray-Nocera S, Wright C, Flockton R, James SR, Crooks MG, Kaye PM, Hart SP. Effects of Azithromycin on Blood Inflammatory Gene Expression and Cytokine Production in Sarcoidosis. Lung 2024; 202:683-693. [PMID: 39284999 PMCID: PMC11427505 DOI: 10.1007/s00408-024-00743-w] [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: 07/01/2024] [Accepted: 08/26/2024] [Indexed: 09/27/2024]
Abstract
INTRODUCTION In sarcoidosis granulomas, monocyte-derived macrophages are activated by pro-inflammatory cytokines including TNF and IL-6. Current drug treatment for sarcoidosis aims to suppress inflammation but disabling side effects can ensue. The macrolide azithromycin may be anti-inflammatory. We aimed to determine whether treatment with azithromycin affects blood inflammatory gene expression and monocyte functions in sarcoidosis. METHODS Blood samples were collected from patients with chronic pulmonary sarcoidosis enrolled in a single arm, open label clinical trial who received oral azithromycin 250 mg once daily for 3 months. Whole blood inflammatory gene expression with or without LPS stimulation was measured using a 770-mRNA panel. Phenotypic analysis and cytokine production were conducted by flow cytometry and ELISA after 24h stimulation with growth factors and TLR ligands. mTOR activity was assessed by measuring phosphorylated S6RP. RESULTS Differential gene expression analysis indicated a state of heightened myeloid cell activation in sarcoidosis. Compared with controls, sarcoidosis patients showed increased LPS responses for several cytokines and chemokines. Treatment with azithromycin had minimal effect on blood gene expression overall, but supervised clustering analysis identified several chemokine genes that were upregulated. At the protein level, azithromycin treatment increased LPS-stimulated TNF and unstimulated IL-8 production. No other cytokines showed significant changes following azithromycin. Blood neutrophil counts fell during azithromycin treatment whereas mononuclear cells remained stable. Azithromycin had no detectable effects on mTOR activity or activation markers. CONCLUSION Blood myeloid cells are activated in sarcoidosis, but azithromycin therapy did not suppress inflammatory gene expression or cytokine production in blood. TRIAL REGISTRATION EudraCT 2019-000580-24 (17 May 2019).
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Affiliation(s)
- Simon D Fraser
- Respiratory Research Group, Hull York Medical School, Castle Hill Hospital, Cottingham, HU16 5JQ, UK
| | - Susannah Thackray-Nocera
- Respiratory Clinical Trials Unit, Hull University Teaching Hospitals NHS Trust, Castle Hill Hospital, Cottingham, HU16 5JQ, UK
| | - Caroline Wright
- Respiratory Clinical Trials Unit, Hull University Teaching Hospitals NHS Trust, Castle Hill Hospital, Cottingham, HU16 5JQ, UK
| | - Rachel Flockton
- Respiratory Clinical Trials Unit, Hull University Teaching Hospitals NHS Trust, Castle Hill Hospital, Cottingham, HU16 5JQ, UK
| | - Sally R James
- Biosciences Technology Facility, Dept. of Biology, University of York, York, UK
| | - Michael G Crooks
- Respiratory Research Group, Hull York Medical School, Castle Hill Hospital, Cottingham, HU16 5JQ, UK
| | - Paul M Kaye
- York Biomedical Research Institute, University of York, York, YO10 5DD, UK
| | - Simon P Hart
- Respiratory Research Group, Hull York Medical School, Castle Hill Hospital, Cottingham, HU16 5JQ, UK.
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Schrijver B, Göpfert J, La Distia Nora R, Putera I, Nagtzaam NM, Smits te Nijenhuis MA, van Rijswijk AL, ten Berge JC, van Laar JA, van Hagen PM, Dik WA. Increased serum interferon activity in sarcoidosis compared to that in tuberculosis: Implication for diagnosis? Heliyon 2024; 10:e37103. [PMID: 39309852 PMCID: PMC11416298 DOI: 10.1016/j.heliyon.2024.e37103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 08/23/2024] [Accepted: 08/27/2024] [Indexed: 09/25/2024] Open
Abstract
Objectives In this study, we measured serum interferon (IFN) levels and activity in patients with sarcoidosis and tuberculosis (TB) with and without uveitis. We aimed to understand the role of IFN in the pathophysiology of both conditions and explore its potential as a discriminating marker for these clinically similar diseases. Methods Sera from an Indonesian TB and a Dutch sarcoidosis cohort were used in the analysis. IFNα2 and IFNγ concentrations were measured using Simoa® and Luminex assays, respectively. Serum IFN activity was assessed by incubating THP-1 cells with patient serum and measuring IFN-stimulated gene transcription using qPCR. Anti-IFNα2 and IFNγ autoantibodies were detected via Luminex assay and tested for neutralizing capacity using a flow cytometry-based signal transducer and activator of transcription (STAT) 1 phosphorylation inhibition assay. Results IFNα2 was detected in 74 % and 64 % of patients with sarcoidosis and pulmonary TB, respectively, while IFNγ was found in 78 % and 23 % of patients with sarcoidosis and TB, respectively. For uveitis cases specifically, IFNα2 was detected in 85 % of sarcoid uveitis (SU) and 33 % of tubercular uveitis (TBU) cases. Similarly, IFNγ was detected in 69 % of SU and 17 % of TBU cases. IFNγ serum concentrations were higher in sarcoidosis than that in TB patients (p < 0.0001). Focusing on patients with uveitis, SU showed increased IFNα2 (p = 0.004) and IFNγ (p < 0.002) serum concentrations compared to that in TBU. Notably, TBU displayed significantly reduced IFNα2 concentrations compared to that in healthy controls (p = 0.006). These results align with the increased interferon stimulated gene (ISG) transcriptional upregulation observed in THP-1 cells stimulated with serum from patients with sarcoidosis. Elevated levels of non-neutralizing anti-IFN autoantibodies were observed in patients with TB; however, these levels were similar to those observed in geographically matched healthy Indonesian controls. Conclusion Our results suggest decreased serum levels and activity of type I and II IFN in TB compared to those in sarcoidosis. This is indicative of distinct pathophysiological processes in these highly clinically similar diseases. We propose that the assessment of serum IFN levels and IFN activity has the potential to distinguish between sarcoidosis/SU and TB/TBU.
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Affiliation(s)
- Benjamin Schrijver
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center Rotterdam, the Netherlands
| | - Jens Göpfert
- Department of Applied Biomarkers and Immunoassays, NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Rina La Distia Nora
- Department of Ophthalmology, Faculty of Medicine, Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Ikhwanuliman Putera
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center Rotterdam, the Netherlands
- Department of Ophthalmology, Faculty of Medicine, Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
- Department of Internal Medicine, section Allergy & Clinical Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Nicole M.A.N. Nagtzaam
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center Rotterdam, the Netherlands
| | - Marja A.W. Smits te Nijenhuis
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center Rotterdam, the Netherlands
| | - Angelique L.C.T. van Rijswijk
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center Rotterdam, the Netherlands
| | | | - Jan A.M. van Laar
- Department of Internal Medicine, section Allergy & Clinical Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - P. Martin van Hagen
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center Rotterdam, the Netherlands
- Department of Internal Medicine, section Allergy & Clinical Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Willem A. Dik
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center Rotterdam, the Netherlands
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Putera I, Schrijver B, Kolijn PM, van Stigt AC, Ten Berge JCEM, IJspeert H, Nagtzaam NMA, Swagemakers SMA, van Laar JAM, Agrawal R, Rombach SM, van Hagen PM, La Distia Nora R, Dik WA. A serum B-lymphocyte activation signature is a key distinguishing feature of the immune response in sarcoidosis compared to tuberculosis. Commun Biol 2024; 7:1114. [PMID: 39256610 PMCID: PMC11387424 DOI: 10.1038/s42003-024-06822-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 09/02/2024] [Indexed: 09/12/2024] Open
Abstract
Sarcoidosis and tuberculosis (TB) are two granulomatous diseases that often share overlapping clinical features, including uveitis. We measured 368 inflammation-related proteins in serum in both diseases, with and without uveitis from two distinct geographically separated cohorts: sarcoidosis from the Netherlands and TB from Indonesia. A total of 192 and 102 differentially expressed proteins were found in sarcoidosis and active pulmonary TB compared to their geographical healthy controls, respectively. While substantial overlap exists in the immune-related pathways involved in both diseases, activation of B cell activating factor (BAFF) signaling and proliferation-inducing ligand (APRIL) mediated signaling pathways was specifically associated with sarcoidosis. We identified a B-lymphocyte activation signature consisting of BAFF, TNFRSF13B/TACI, TRAF2, IKBKG, MAPK9, NFATC1, and DAPP1 that was associated with sarcoidosis, regardless of the presence of uveitis. In summary, a difference in B-lymphocyte activation is a key discriminative immunological feature between sarcoidosis/ocular sarcoidosis (OS) and TB/ocular TB (OTB).
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Affiliation(s)
- Ikhwanuliman Putera
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine Section Allergy & Clinical Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Ophthalmology, Faculty of Medicine, Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Benjamin Schrijver
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - P Martijn Kolijn
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Astrid C van Stigt
- Department of Internal Medicine Section Allergy & Clinical Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center), Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Hanna IJspeert
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center), Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Nicole M A Nagtzaam
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sigrid M A Swagemakers
- Department of Bioinformatics, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Jan A M van Laar
- Department of Internal Medicine Section Allergy & Clinical Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Rupesh Agrawal
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Duke NUS University, Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
- Moorfields Eye Hospital, London, United Kingdom
| | - Saskia M Rombach
- Department of Internal Medicine Section Allergy & Clinical Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - P Martin van Hagen
- Department of Internal Medicine Section Allergy & Clinical Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Rina La Distia Nora
- Department of Ophthalmology, Faculty of Medicine, Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Willem A Dik
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands.
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van Wijck RTA, Sharma HS, Swagemakers SMA, Dik WA, IJspeert H, Dalm VASH, van Daele PLA, van Hagen PM, van der Spek PJ. Bioinformatic meta-analysis reveals novel differentially expressed genes and pathways in sarcoidosis. Front Med (Lausanne) 2024; 11:1381031. [PMID: 38938383 PMCID: PMC11208482 DOI: 10.3389/fmed.2024.1381031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/23/2024] [Indexed: 06/29/2024] Open
Abstract
Introduction Sarcoidosis is a multi-system inflammatory disease of unknown origin with heterogeneous clinical manifestations varying from a single organ non-caseating granuloma site to chronic systemic inflammation and fibrosis. Gene expression studies have suggested several genes and pathways implicated in the pathogenesis of sarcoidosis, however, due to differences in study design and variable statistical approaches, results were frequently not reproducible or concordant. Therefore, meta-analysis of sarcoidosis gene-expression datasets is of great importance to robustly establish differentially expressed genes and signalling pathways. Methods We performed meta-analysis on 22 published gene-expression studies on sarcoidosis. Datasets were analysed systematically using same statistical cut-offs. Differentially expressed genes were identified by pooling of p-values using Edgington's method and analysed for pathways using Ingenuity Pathway Analysis software. Results A consistent and significant signature of novel and well-known genes was identified, those collectively implicated both type I and type II interferon mediated signalling pathways in sarcoidosis. In silico functional analysis showed consistent downregulation of eukaryotic initiation factor 2 signalling, whereas cytokines like interferons and transcription factor STAT1 were upregulated. Furthermore, we analysed affected tissues to detect differentially expressed genes likely to be involved in granuloma biology. This revealed that matrix metallopeptidase 12 was exclusively upregulated in affected tissues, suggesting a crucial role in disease pathogenesis. Discussion Our analysis provides a concise gene signature in sarcoidosis and expands our knowledge about the pathogenesis. Our results are of importance to improve current diagnostic approaches and monitoring strategies as well as in the development of targeted therapeutics.
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Affiliation(s)
- Rogier T. A. van Wijck
- Department of Pathology & Clinical Bioinformatics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Hari S. Sharma
- Department of Pathology & Clinical Bioinformatics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Sigrid M. A. Swagemakers
- Department of Pathology & Clinical Bioinformatics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Willem A. Dik
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Hanna IJspeert
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Virgil A. S. H. Dalm
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, Division of Allergy & Clinical Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Paul L. A. van Daele
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, Division of Allergy & Clinical Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - P. Martin van Hagen
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, Division of Allergy & Clinical Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Peter J. van der Spek
- Department of Pathology & Clinical Bioinformatics, Erasmus MC University Medical Center, Rotterdam, Netherlands
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Choudhury P, Dasgupta S, Kar A, Sarkar S, Chakraborty P, Bhattacharyya P, Roychowdhury S, Chaudhury K. Bioinformatics analysis of hypoxia associated genes and inflammatory cytokine profiling in COPD-PH. Respir Med 2024; 227:107658. [PMID: 38704051 DOI: 10.1016/j.rmed.2024.107658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/08/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Pulmonary hypertension (PH) in chronic obstructive pulmonary disease (COPD) is associated with worse clinical outcomes and decreased survival rates. In absence of disease specific diagnostic/therapeutic targets and unclear pathophysiology, there is an urgent need for the identification of potential genetic/molecular markers and disease associated pathways. The present study aims to use a bioinformatics approach to identify and validate hypoxia-associated gene signatures in COPD-PH patients. Additionally, hypoxia-related inflammatory profile is also explored in these patients. Microarray dataset obtained from the Gene Expression Omnibus repository was used to identify differentially expressed genes (DEGs) in a hypoxic PH mice model. The top three hub genes identified were further validated in COPD-PH patients, with chemokine (C-X-C motif) ligand 9 (CXCL9) and CXCL12 showing significant changes in comparison to healthy controls. Furthermore, multiplexed analysis of 10 inflammatory cytokines, tumor necrosis factor alpha (TNF-α), transforming growth factor β (TGF-β), interleukin 1-beta (IL-1β), IL-4, IL-5, IL-6, IL-13, IL-17, IL-18 and IL-21 was also performed. These markers showed significant changes in COPD-PH patients as compared to controls. They also exhibited the ability to differentially diagnose COPD-PH patients in comparison to COPD. Additionally, IL-6 and IL-17 showed significant positive correlation with systolic pulmonary artery pressure (sPAP). This study is the first report to assess the levels of CXCL9 and CXCL12 in COPD-PH patients and also explores their link with the inflammatory profile of these patients. Our findings could be extended to better understand the underlying disease mechanism and possibly used for tailoring therapies exclusive for the disease.
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Affiliation(s)
- Priyanka Choudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Sanjukta Dasgupta
- Department of Biotechnology, Brainware University, Barasat, West Bengal, India
| | - Abhik Kar
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Sagartirtha Sarkar
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | | | | | | | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India.
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Bhargava M, Crouser ED. Application of laboratory models for sarcoidosis research. J Autoimmun 2024:103184. [PMID: 38443221 DOI: 10.1016/j.jaut.2024.103184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/07/2024]
Abstract
This manuscript will review the implications and applications of sarcoidosis models towards advancing our understanding of sarcoidosis disease mechanisms, identification of biomarkers, and preclinical testing of novel therapies. Emerging disease models and innovative research tools will also be considered.
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Affiliation(s)
- Maneesh Bhargava
- University of Minnesota Medical Center, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, 420 Delaware Street SE, MMC 276. Minneapolis, MN 55455, USA
| | - Elliott D Crouser
- Ohio State University Wexner Medicine Center, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, 241 W. 11th Street, Suite 5000, Columbus, OH 43201, USA.
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Weeratunga P, Moller DR, Ho LP. Immune mechanisms of granuloma formation in sarcoidosis and tuberculosis. J Clin Invest 2024; 134:e175264. [PMID: 38165044 PMCID: PMC10760966 DOI: 10.1172/jci175264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Abstract
Sarcoidosis is a complex immune-mediated disease characterized by clusters of immune cells called granulomas. Despite major steps in understanding the cause of this disease, many questions remain. In this Review, we perform a mechanistic interrogation of the immune activities that contribute to granuloma formation in sarcoidosis and compare these processes with its closest mimic, tuberculosis, highlighting shared and divergent immune activities. We examine how Mycobacterium tuberculosis is sensed by the immune system; how the granuloma is initiated, formed, and perpetuated in tuberculosis compared with sarcoidosis; and the role of major innate and adaptive immune cells in shaping these processes. Finally, we draw these findings together around several recent high-resolution studies of the granuloma in situ that utilized the latest advances in single-cell technology combined with spatial methods to analyze plausible disease mechanisms. We conclude with an overall view of granuloma formation in sarcoidosis.
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Affiliation(s)
- Praveen Weeratunga
- MRC Translational Immunology Discovery Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Ling-Pei Ho
- MRC Translational Immunology Discovery Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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8
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Casanova NG, Camp SM, Gonzalez-Garay ML, Batai K, Garman L, Montgomery CG, Ellis N, Kittles R, Bime C, Hsu AP, Holland S, Lussier YA, Karnes J, Sweiss N, Maier LA, Koth L, Moller DR, Kaminski N, Garcia JGN. Examination of eQTL Polymorphisms Associated with Increased Risk of Progressive Complicated Sarcoidosis in European and African Descent Subjects. EUROPEAN JOURNAL OF RESPIRATORY MEDICINE 2023; 5:359-371. [PMID: 38390497 PMCID: PMC10883688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Background A limited pool of SNPs are linked to the development and severity of sarcoidosis, a systemic granulomatous inflammatory disease. By integrating genome-wide association studies (GWAS) data and expression quantitative trait loci (eQTL) single nuclear polymorphisms (SNPs), we aimed to identify novel sarcoidosis SNPs potentially influencing the development of complicated sarcoidosis. Methods A GWAS (Affymetrix 6.0) involving 209 African-American (AA) and 193 European-American (EA, 75 and 51 complicated cases respectively) and publicly-available GWAS controls (GAIN) was utilized. Annotation of multi-tissue eQTL SNPs present on the GWAS created a pool of ~46,000 eQTL SNPs examined for association with sarcoidosis risk and severity (Logistic Model, Plink). The most significant EA/AA eQTL SNPs were genotyped in a sarcoidosis validation cohort (n=1034) and cross-validated in two independent GWAS cohorts. Results No single GWAS SNP achieved significance (p<1x10-8), however, analysis of the eQTL/GWAS SNP pool yielded 621 eQTL SNPs (p<10-4) associated with 730 genes that highlighted innate immunity, MHC Class II, and allograft rejection pathways with multiple SNPs validated in an independent sarcoidosis cohort (105 SNPs analyzed) (NOTCH4, IL27RA, BTNL2, ANXA11, HLA-DRB1). These studies confirm significant association of eQTL/GWAS SNPs in EAs and AAs with sarcoidosis risk and severity (complicated sarcoidosis) involving HLA region and innate immunity. Conclusion Despite the challenge of deciphering the genetic basis for sarcoidosis risk/severity, these results suggest that integrated eQTL/GWAS approaches may identify novel variants/genes and support the contribution of dysregulated innate immune responses to sarcoidosis severity.
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Affiliation(s)
- Nancy G Casanova
- Department of Molecular Medicine, Univeristy of Florida, Scripps, Jupiter FL, USA
| | - Sara M Camp
- Center for Inflammation Science and Systems Medicine, University of Florida, Wertheim Scripps Research Institute, Jupiter FL, USA
| | - Manuel L Gonzalez-Garay
- Division of Health Equities, Department of Population Sciences, City of Hope, Duarte, California, USA
| | - Ken Batai
- Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Lori Garman
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | | - Nathan Ellis
- University of Arizona Cancer Center, Tucson, AZ, USA
| | - Rick Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope, Duarte, California, USA
| | - Christian Bime
- Department of Medicine University of Arizona, Tucson, AZ, USA
| | - Amy P Hsu
- National Institute of Allergy and Infectious Diseases. National Institutes of Health, USA
| | - Steven Holland
- National Institute of Allergy and Infectious Diseases. National Institutes of Health, USA
| | - Yves A Lussier
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | - Jason Karnes
- Department of Pharmacology, University of Arizona, College of Pharmacy, Tucson, AZ, USA
| | - Nadera Sweiss
- Department of Medicine University of Illinois, Chicago, IL, USA
| | - Lisa A Maier
- Department of Medicine National Jewish Health, University of Colorado, Denver, CO, USA
| | - Laura Koth
- Department of Medicine University of California San Francisco, San Francisco, CA, US, USA
| | - David R Moller
- Department of Medicine Johns Hopkins University School of Medicine, Baltimore Maryland, USA
| | - Naftali Kaminski
- Department of Medicine Yale University School of Medicine, New Haven, CT, USA
| | - Joe G N Garcia
- Center for Inflammation Science and Systems Medicine, University of Florida, Wertheim Scripps Research Institute, Jupiter FL, USA
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Sodsri T, Baughman RP, Sriprasart T. Diagnosis of pulmonary sarcoidosis in tuberculosis endemic area-a narrative review. J Thorac Dis 2023; 15:5760-5772. [PMID: 37969315 PMCID: PMC10636435 DOI: 10.21037/jtd-23-192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 08/18/2023] [Indexed: 11/17/2023]
Abstract
Background and Objective Pulmonary sarcoidosis and tuberculosis (TB) are the most frequent tissue-confirmed granulomatous diseases. Due to its unknown etiology, pulmonary sarcoidosis is diagnosed by ruling out other granulomatous diseases and necessitating clinical, radiological, and pathological evidence. There are many factors that contribute to the diagnostic dilemma between these two diseases. Even though some aspects of both diseases, such as their pathological evidence and abnormal X-ray findings, are quite similar, the treatment options for each are entirely different. The standard treatment for sarcoidosis is immunosuppressive agents such as glucocorticoids, which can exacerbate TB. Consequently, the overlap between clinical and radiological features constitutes a significant challenge for many physicians in selecting the optimal treatment for each patient. Therefore, the exclusion of pulmonary TB is a mandatory step for the diagnosis of pulmonary sarcoidosis. This article reviews and summarizes basic science and clinical research on distinguishing these two disorders. Methods A systematic search of the MEDLINE and PubMed databases focusing on studies published within the last 35 years was conducted. The last search date is February 4, 2023. The authors used the following combinations of terms: tuberculosis, sarcoidosis, diagnosis, bronchoscopy, biomarkers, and radiography. All studies were reviewed, and 69 references from 1990 to 2023 were found to be relevant. Key Content and Findings Innovative laboratory tests are essential for distinguishing between pulmonary sarcoidosis and TB. The Xpert MTB/RIF assay diagnoses TB with 98% sensitivity and 89% specificity. Loop-mediated isothermal amplification (LAMP) and simultaneous amplification and testing method for Mycobacterium tuberculosis rRNA (SAT-TB) are also highly sensitive and specific for TB diagnosis. Several novel tests, such as the difference of immune complexes for the ESAT-6/SFP-10 antigen in vitro with dynamic light scattering (DLS), lung tissue-based molecular markers, and the blood transcriptome, are promising for differentiating TB from sarcoidosis. Conclusions Recent advancements in laboratory investigations, non-invasive procedures, and invasive procedures play an important role in the diagnosis of sarcoidosis in TB-endemic areas. However, further study is needed to evaluate the diagnostic performance of all tests in terms of their competency in distinguishing between TB and sarcoidosis.
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Affiliation(s)
- Tulaton Sodsri
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan, Thailand
| | - Robert P. Baughman
- Department of Internal Medicine, University of Cincinnati Medical Center, Cincinnati, OH, USA
| | - Thitiwat Sriprasart
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
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Shen Y, Liu C, Zheng L, Zhao Y. Sarcoidosis or Tuberculosis: Should Corticosteroids Be Used? Cureus 2023; 15:e47191. [PMID: 38022146 PMCID: PMC10652288 DOI: 10.7759/cureus.47191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Sarcoidosis shows high similarity with tuberculosis in clinical manifestations and imaging features. It is rarely reported whether sarcoidosis patients with suspected latent tuberculosis can be treated safely with immunosuppressive therapy. We reported on a 54-year-old man who presented with enlarged lymph nodes persisting for decades, accompanied by renal impairment and refractory hypercalcemia. The patient was diagnosed with sarcoidosis and suspected latent tuberculosis (as suggested by a positive tuberculin test and tuberculosis interferon-gamma release assays) and received prednisone under follow-up. The patient showed significant amelioration in hypercalcemia and shrinkage of lymph nodes, without evidence of developing active tuberculosis. For sarcoidosis patients with suspected latent tuberculosis, immunosuppressive agents can be utilized safely based on close monitoring. Further efforts are required to reveal whether sarcoidosis and tuberculosis can trigger similar immune responses and what the clinical implications are.
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Affiliation(s)
- Yuting Shen
- Department of Nephrology, Chengdu Seventh People's Hospital (Affiliated Cancer Hospital of Chengdu Medical College), Chengdu, CHN
- Department of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu, CHN
| | - Caihong Liu
- Department of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu, CHN
| | - Lan Zheng
- Department of Nephrology, Zhongjiang County People's Hospital, Deyang, CHN
| | - Yuliang Zhao
- Department of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu, CHN
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11
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Jain R, Kumari R, Chakraborty S, Mitra DK, Mohan A, Hadda V, Madan K, Guleria R. T-cell signature cytokines distinguish pulmonary sarcoidosis from pulmonary tuberculosis. Eur J Immunol 2023; 53:e2250255. [PMID: 37505436 DOI: 10.1002/eji.202250255] [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: 11/14/2022] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 07/29/2023]
Abstract
Sarcoidosis is a systemic inflammatory disorder characterized by tissue infiltration due to mononuclear phagocytes and lymphocytes and associated noncaseating granuloma formation. Pulmonary sarcoidosis (PS) shares a number of clinical, radiological, and histopathological characteristics with that of pulmonary tuberculosis (PTB). Due to this, clinicians face issues in differentiating between PS and PTB in a substantial number of cases. There is a lack of any specific biomarker that can diagnose PS distinctively from PTB. We compared T-cell-based signature cytokines in patients with PS and PTB. In this study, we proposed a serum biomarker panel consisting of cytokines from cells: T helper (Th) 1 [interferon-gamma (IFN-γ); tumor necrosis factor-alpha (TNF-α)], Th9 [interleukin (IL)-9], Th17 [IL-17], and T regulatory (Treg) [IL-10; transforming growth factor-beta (TGF-β)]. We performed the principal component analysis that demonstrated that our serum cytokine panel has a significant predictive ability to differentiate PS from PTB. Our results could aid clinicians to improve the diagnostic workflow for patients with PS in TB endemic settings where the diagnosis between PS and PTB is often ambiguous.
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Affiliation(s)
- Rashi Jain
- Department of Pulmonary Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Rinkee Kumari
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Sushmita Chakraborty
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Dipendra K Mitra
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Anant Mohan
- Department of Pulmonary Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Vijay Hadda
- Department of Pulmonary Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Karan Madan
- Department of Pulmonary Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
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12
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Liao SY, Jacobson S, Hamzeh NY, Culver DA, Barkes BQ, Mroz M, Macphail K, Pacheco K, Patel DC, Wasfi YS, Koth LL, Langefeld CD, Leach SM, White E, Montgomery C, Maier LA, Fingerlin TE. Genome-wide association study identifies multiple HLA loci for sarcoidosis susceptibility. Hum Mol Genet 2023; 32:2669-2678. [PMID: 37399103 PMCID: PMC10407706 DOI: 10.1093/hmg/ddad067] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/30/2023] [Accepted: 04/19/2023] [Indexed: 07/05/2023] Open
Abstract
Sarcoidosis is a complex systemic disease. Our study aimed to (1) identify novel alleles associated with sarcoidosis susceptibility; (2) provide an in-depth evaluation of HLA alleles and sarcoidosis susceptibility and (3) integrate genetic and transcription data to identify risk loci that may more directly impact disease pathogenesis. We report a genome-wide association study of 1335 sarcoidosis cases and 1264 controls of European descent (EA) and investigate associated alleles in a study of African Americans (AA: 1487 cases and 1504 controls). The EA and AA cohort was recruited from multiple United States sites. HLA alleles were imputed and tested for association with sarcoidosis susceptibility. Expression quantitative locus and colocalization analysis were performed using a subset of subjects with transcriptome data. Forty-nine SNPs in the HLA region in HLA-DRA, -DRB9, -DRB5, -DQA1 and BRD2 genes were significantly associated with sarcoidosis susceptibility in EA, rs3129888 was also a risk variant for sarcoidosis in AA. Classical HLA alleles DRB1*0101, DQA1*0101 and DQB1*0501, which are highly correlated, were also associated with sarcoidosis. rs3135287 near HLA-DRA was associated with HLA-DRA expression in peripheral blood mononuclear cells and bronchoalveolar lavage from subjects and lung tissue and whole blood from GTEx. We identified six novel SNPs (out of the seven SNPs representing the 49 significant SNPs) and nine HLA alleles associated with sarcoidosis susceptibility in the largest EA population. We also replicated our findings in an AA population. Our study reiterates the potential role of antigen recognition and/or presentation HLA class II genes in sarcoidosis pathogenesis.
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Affiliation(s)
- Shu-Yi Liao
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado School of Public Health, University of Colorado Denver–Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sean Jacobson
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Nabeel Y Hamzeh
- Department of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Daniel A Culver
- Department of Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Briana Q Barkes
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Margarita Mroz
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Kristyn Macphail
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Karin Pacheco
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado School of Public Health, University of Colorado Denver–Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Divya C Patel
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, FL 32610, USA
| | | | - Laura L Koth
- Department of Medicine, University of California-San Fransisco, San Fransisco, CA 94143, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
- Wake Forest University School of Medicine, Center for Precision Medicine, Winston-Salem, NC 27101, USA
| | - Sonia M Leach
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Elizabeth White
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | | | - Lisa A Maier
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado School of Public Health, University of Colorado Denver–Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tasha E Fingerlin
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado School of Public Health, University of Colorado Denver–Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA
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13
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Sharygin D, Koniaris LG, Wells C, Zimmers TA, Hamidi T. Role of CD14 in human disease. Immunology 2023; 169:260-270. [PMID: 36840585 PMCID: PMC10591340 DOI: 10.1111/imm.13634] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
The cell surface antigen CD14 is primarily understood to act as a co-receptor for toll-like receptors (TLRs) to activate innate immunity responses to pathogens and tissue injury in macrophages and monocytes. However, roles for CD14 are increasingly being uncovered in disease responses in epithelial and endothelial cells. Consistent with these broader functions, CD14 expression is altered in a variety of non-immune cell types in response to a several of disease states. Moreover, soluble CD14 activated by factors from both pathogens and tissue damage may initiate signalling in a variety of non-immune cells. This review examined the current understanding CD14 in innate immunity as well as its potential functions in nonimmune cells and associated human diseases.
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Affiliation(s)
- Daniel Sharygin
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Chemistry, Massachusetts institute of technology, Cambridge, MA, USA
| | - Leonidas G. Koniaris
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Clark Wells
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Teresa A. Zimmers
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
- Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN, USA
| | - Tewfik Hamidi
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, USA
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14
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Perryman AN, Kim HYH, Payton A, Rager JE, McNell EE, Rebuli ME, Wells H, Almond M, Antinori J, Alexis NE, Porter NA, Jaspers I. Plasma sterols and vitamin D are correlates and predictors of ozone-induced inflammation in the lung: A pilot study. PLoS One 2023; 18:e0285721. [PMID: 37186612 PMCID: PMC10184915 DOI: 10.1371/journal.pone.0285721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/27/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Ozone (O3) exposure causes respiratory effects including lung function decrements, increased lung permeability, and airway inflammation. Additionally, baseline metabolic state can predispose individuals to adverse health effects from O3. For this reason, we conducted an exploratory study to examine the effect of O3 exposure on derivatives of cholesterol biosynthesis: sterols, oxysterols, and secosteroid (25-hydroxyvitamin D) not only in the lung, but also in circulation. METHODS We obtained plasma and induced sputum samples from non-asthmatic (n = 12) and asthmatic (n = 12) adult volunteers 6 hours following exposure to 0.4ppm O3 for 2 hours. We quantified the concentrations of 24 cholesterol precursors and derivatives by UPLC-MS and 30 cytokines by ELISA. We use computational analyses including machine learning to determine whether baseline plasma sterols are predictive of O3 responsiveness. RESULTS We observed an overall decrease in the concentration of cholesterol precursors and derivatives (e.g. 27-hydroxycholesterol) and an increase in concentration of autooxidation products (e.g. secosterol-B) in sputum samples. In plasma, we saw a significant increase in the concentration of secosterol-B after O3 exposure. Machine learning algorithms showed that plasma cholesterol was a top predictor of O3 responder status based on decrease in FEV1 (>5%). Further, 25-hydroxyvitamin D was positively associated with lung function in non-asthmatic subjects and with sputum uteroglobin, whereas it was inversely associated with sputum myeloperoxidase and neutrophil counts. CONCLUSION This study highlights alterations in sterol metabolites in the airway and circulation as potential contributors to systemic health outcomes and predictors of pulmonary and inflammatory responsiveness following O3 exposure.
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Affiliation(s)
- Alexia N. Perryman
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Hye-Young H. Kim
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
| | - Alexis Payton
- Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Julia E. Rager
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Erin E. McNell
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Meghan E. Rebuli
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Heather Wells
- Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Martha Almond
- Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Jamie Antinori
- Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Neil E. Alexis
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Ned A. Porter
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
| | - Ilona Jaspers
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
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15
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Kudryavtsev I, Zinchenko Y, Starshinova A, Serebriakova M, Malkova A, Akisheva T, Kudlay D, Glushkova A, Yablonskiy P, Shoenfeld Y. Circulating Regulatory T Cell Subsets in Patients with Sarcoidosis. Diagnostics (Basel) 2023; 13:1378. [PMID: 37189479 PMCID: PMC10137313 DOI: 10.3390/diagnostics13081378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Over recent years, many researchers have supported the autoimmune theory of sarcoidosis. The presence of uncontrolled inflammatory response on local and system levels in patients with sarcoidosis did not define that the immunoregulatory mechanisms could be affected. The aim of this study was to evaluate the distribution and the disturbance circulating Treg cell subsets in the peripheral blood in patients with sarcoidosis. MATERIALS AND METHODS A prospective comparative study was performed in 2016-2018 (34 patients with sarcoidosis (men (67.6%), women (32.3%)) were examined). Healthy subjects-the control group (n = 40). The diagnosis of pulmonary sarcoidosis was performed according to the standard criteria. We used two ten-color combinations of antibodies for Treg immunophenotyping. The first one contained CD39-FITC, CD127-PE, CCR4-PE/Dazzle™ 594, CD25-PC5.5, CD161-PC7, CD4-APC, CD8-APC-AF700, CD3-APC/Cy7, HLA-DR-PacBlue, and CD45 RA-BV 510™, while the second consisted of CXCR3-Alexa Fluor 488, CD25-РЕ, CXCR5-РЕ/Dazzle™ 594, CCR4-PerСP/Сy5.5, CCR6-РЕ/Cy7, CD4-АPC, CD8 АPC-AF700, CD3-АPC/Cy7, CCR7-BV 421, and CD45 RA-BV 510. The flow cytometry data were analyzed by using Kaluza software v2.3. A statistical analysis was performed with Statistica 7.0 and GraphPad Prism 8 software packages. RESULTS OF THE STUDY Primarily, we found that patients with sarcoidosis had decreased absolute numbers of Treg cells in circulation. We noted that the level of CCR7-expressing Tregs decreased in patients with sarcoidosis vs. the control group (65.55% (60.08; 70.60) vs. 76.93% (69.59; 79.86) with p < 0.001). We noticed that the relative numbers of CD45RA-CCR7+ Tregs decreased in patients with sarcoidosis (27.11% vs. 35.43%, p < 0.001), while the frequency of CD45 RA-CCR7- and CD45RA+ CCR7- Tregs increased compared to the control group (33.3% vs. 22.73% and 0.76% vs. 0.51% with p < 0.001 and p = 0.028, respectively). CXCR3-expressing Treg cell subsets-Th1-like CCR60078CXCR3+ Tregs and Th17.1-like CCR6+ CXCR3+ Tregs-significantly increased in patients with sarcoidosis vs. the control group (14.4% vs. 10.5% with p < 0.01 and 27.9% vs. 22.8% with p < 0.01, respectively). Furthermore, the levels of peripheral blood EM Th17-like Tregs significantly decreased in the sarcoidosis group vs. the control group (36.38% vs. 46.70% with p < 0.001). Finally, we found that CXCR5 expression was increased in CM Tregs cell subsets in patients with sarcoidosis. CONCLUSIONS Our data indicated a decrease in circulating Tregs absolute numbers and several alterations in Treg cell subsets. Moreover, our results highlight the presence of increased levels of CM CXCR5+ follicular Tregs in the periphery that could be linked with the imbalance of follicular Th cell subsets and alterations in B cell, based on the immune response. The balance between the two functionally distinct Treg cell populations-Th1-like and Th17-like Tregs-could be used in sarcoidosis diagnosis and the determination of prognosis and disease outcomes. Furthermore, we want to declare that analysis of Treg numbers of phenotypes could fully characterize their functional activity in peripherally inflamed tissues.
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Affiliation(s)
- Igor Kudryavtsev
- Department of Immunology, Institution of Experimental Medicine, 197376 St. Petersburg, Russia
| | - Yulia Zinchenko
- Phthisiopulmonology Department, St. Petersburg Research Institute of Phthisiopulmonology, 194064 St. Petersburg, Russia
| | - Anna Starshinova
- Almazov National Medical Research Centre, 197341 St. Petersburg, Russia
| | - Maria Serebriakova
- Department of Immunology, Institution of Experimental Medicine, 197376 St. Petersburg, Russia
| | - Anna Malkova
- Laboratory of the Mosaic of Autoimmunity, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Tatiana Akisheva
- Department of Immunology, Institution of Experimental Medicine, 197376 St. Petersburg, Russia
| | - Dmitriy Kudlay
- Department of Pharmacology, Sechenov First Moscow State Medical University, 119992 Moscow, Russia
- Institute of Immunology, 115552 Moscow, Russia
| | - Anzhela Glushkova
- Bekhterev National Research Medical Center for Psychiatry and Neurology, 19201 St. Petersburg, Russia
| | - Piotr Yablonskiy
- Phthisiopulmonology Department, St. Petersburg Research Institute of Phthisiopulmonology, 194064 St. Petersburg, Russia
- Laboratory of the Mosaic of Autoimmunity, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Yehuda Shoenfeld
- Laboratory of the Mosaic of Autoimmunity, St. Petersburg State University, 199034 St. Petersburg, Russia
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel Hashomer 5265601, Israel
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16
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Macrophage Biology in Human Granulomatous Skin Inflammation. Int J Mol Sci 2023; 24:ijms24054624. [PMID: 36902053 PMCID: PMC10003716 DOI: 10.3390/ijms24054624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/04/2023] Open
Abstract
Cutaneous granulomatoses represent a heterogeneous group of diseases, which are defined by macrophage infiltration in the skin. Skin granuloma can be formed in the context of infectious and non-infectious conditions. Recent technological advances have deepened our understanding of the pathophysiology of granulomatous skin inflammation, and they provide novel insights into human tissue macrophage biology at the site of ongoing disease. Here, we discuss findings on macrophage immune function and metabolism derived from three prototypic cutaneous granulomatoses: granuloma annulare, sarcoidosis, and leprosy.
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17
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Weeratunga P, Moller DR, Ho LP. Immune mechanisms in fibrotic pulmonary sarcoidosis. Eur Respir Rev 2022; 31:220178. [PMID: 36543347 PMCID: PMC9879330 DOI: 10.1183/16000617.0178-2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/21/2022] [Indexed: 12/24/2022] Open
Abstract
Sarcoidosis is an immune-mediated disorder. Its immunopathology has been steadily mapped out over the past few decades. Despite this, the underpinning mechanisms for progressive fibrotic sarcoidosis is an almost uncharted area. Consequently, there has been little change in the clinical management of fibrotic sarcoidosis over the decades and an unfocused search for new therapeutics. In this review, we provide a comprehensive examination of the relevant immune findings in fibrotic and/or progressive pulmonary sarcoidosis and propose a unifying mechanism for the pathobiology of fibrosis in sarcoidosis.
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Affiliation(s)
- Praveen Weeratunga
- Oxford Sarcoidosis Clinic, Oxford Interstitial Lung Disease Service, Oxford, UK
- MRC Human Immunology Unit, University of Oxford, Oxford, UK
| | - David R Moller
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ling-Pei Ho
- Oxford Sarcoidosis Clinic, Oxford Interstitial Lung Disease Service, Oxford, UK
- MRC Human Immunology Unit, University of Oxford, Oxford, UK
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18
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Ascoli C, Schott CA, Huang Y, Turturice BA, Wang W, Ecanow N, Sweiss NJ, Perkins DL, Finn PW. Altered transcription factor targeting is associated with differential peripheral blood mononuclear cell proportions in sarcoidosis. Front Immunol 2022; 13:848759. [PMID: 36311769 PMCID: PMC9608777 DOI: 10.3389/fimmu.2022.848759] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
IntroductionIn sarcoidosis, peripheral lymphopenia and anergy have been associated with increased inflammation and maladaptive immune activity, likely promoting development of chronic and progressive disease. However, the molecular mechanisms that lead to reduced lymphocyte proportions, particularly CD4+ T-cells, have not been fully elucidated. We posit that paradoxical peripheral lymphopenia is characterized by a dysregulated transcriptomic network associated with cell function and fate that results from altered transcription factor targeting activity.MethodsMessenger RNA-sequencing (mRNA-seq) was performed on peripheral blood mononuclear cells (PBMCs) from ACCESS study subjects with sarcoidosis and matched controls and findings validated on a sarcoidosis case-control cohort and a sarcoidosis case series. Preserved PBMC transcriptomic networks between case-control cohorts were assessed to establish cellular associations with gene modules and define regulatory targeting involved in sarcoidosis immune dysregulation utilizing weighted gene co-expression network analysis and differential transcription factor involvement analysis. Network centrality measures identified master transcriptional regulators of subnetworks related to cell proliferation and death. Predictive models of differential PBMC proportions constructed from ACCESS target gene expression corroborated the relationship between aberrant transcription factor regulatory activity and imputed and clinical PBMC populations in the validation cohorts.ResultsWe identified two unique and preserved gene modules significantly associated with sarcoidosis immune dysregulation. Strikingly, increased expression of a monocyte-driven, and not a lymphocyte-driven, gene module related to innate immunity and cell death was the best predictor of peripheral CD4+ T-cell proportions. Within the gene network of this monocyte-driven module, TLE3 and CBX8 were determined to be master regulators of the cell death subnetwork. A core gene signature of differentially over-expressed target genes of TLE3 and CBX8 involved in cellular communication and immune response regulation accurately predicted imputed and clinical monocyte expansion and CD4+ T-cell depletion.ConclusionsAltered transcriptional regulation associated with aberrant gene expression of a monocyte-driven transcriptional network likely influences lymphocyte function and survival. Although further investigation is warranted, this indicates that crosstalk between hyperactive monocytes and lymphocytes may instigate peripheral lymphopenia and underlie sarcoidosis immune dysregulation and pathogenesis. Future therapies selectively targeting master regulators, or their targets, may mitigate dysregulated immune processes in sarcoidosis and disease progression.
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Affiliation(s)
- Christian Ascoli
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Cody A. Schott
- University of Illinois at Chicago College of Medicine, Chicago, IL, United States
| | - Yue Huang
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | | | - Wangfei Wang
- Department of Bioengineering, University of Illinois at Chicago College of Engineering and Medicine, Chicago, IL, United States
| | - Naomi Ecanow
- University of Illinois at Chicago College of Medicine, Chicago, IL, United States
| | - Nadera J. Sweiss
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
- Division of Rheumatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - David L. Perkins
- Division of Nephrology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Patricia W. Finn
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
- *Correspondence: Patricia W. Finn,
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19
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Jiang Y, Jiang D, Costabel U, Dai H, Wang C. A transcriptomics-based meta-analysis identifies a cross-tissue signature for sarcoidosis. Front Med (Lausanne) 2022; 9:960266. [PMID: 36203777 PMCID: PMC9530451 DOI: 10.3389/fmed.2022.960266] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/30/2022] [Indexed: 11/22/2022] Open
Abstract
Sarcoidosis is a granulomatous disease of unknown etiology, immunologically characterized by a Th1 immune response. Transcriptome-wide expression studies in various types of sarcoid tissues contributed to better understanding of disease mechanisms. We performed a systematic database search on Gene Expression Omnibus (GEO) and utilized transcriptomic data from blood and sarcoidosis-affected tissues in a meta-analysis to identify a cross-tissue, cross-platform signature. Datasets were further separated into training and testing sets for development of a diagnostic classifier for sarcoidosis. A total of 690 differentially expressed genes were identified in the analysis among various tissues. 29 of the genes were robustly associated with sarcoidosis in the meta-analysis both in blood and in lung-associated tissues. Top genes included LINC01278 (P = 3.11 × 10–13), GBP5 (P = 5.56 × 10–07), and PSMB9 (P = 1.11 × 10–06). Pathway enrichment analysis revealed activated IFN-γ, IL-1, and IL-18, autophagy, and viral infection response. IL-17 was observed to be enriched in peripheral blood specific signature genes. A 16-gene classifier achieved excellent performance in the independent validation data (AUC 0.711–0.964). This study provides a cross-tissue meta-analysis for expression profiles of sarcoidosis and identifies a diagnostic classifier that potentially can complement more invasive procedures.
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Affiliation(s)
- Yale Jiang
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
- Clinical Trial Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- School of Medicine, Tsinghua University, Beijing, China
| | - Dingyuan Jiang
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
- National Center for Respiratory Medicine, Institute of Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Chinese Academy of Medical Sciences, Beijing, China
| | - Ulrich Costabel
- Department of Pneumology, Center for Interstitial and Rare Lung Diseases, Ruhrlandklinik, University Hospital, Essen, Germany
| | - Huaping Dai
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
- National Center for Respiratory Medicine, Institute of Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Huaping Dai,
| | - Chen Wang
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
- National Center for Respiratory Medicine, Institute of Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Chinese Academy of Medical Sciences, Beijing, China
- Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
- Peking Union Medical College, Beijing, China
- Chen Wang,
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20
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Garneret E, Jamilloux Y, Gerfaud-Valentin M, Kodjikian L, Trad S, Sève P. Prevalence of Positive QuantiFERON-TB Test among Sarcoid Uveitis Patients and its Clinical Implications in a Country Non-endemic for Tuberculosis. Ocul Immunol Inflamm 2022:1-9. [PMID: 35797278 DOI: 10.1080/09273948.2022.2073238] [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: 10/17/2022]
Abstract
AIM To report on the prevalence and clinical implications of positive QuantiFERON-TB (QFT) test results in the diagnostic evaluation of a cohort of consecutive sarcoid uveitis patients in France. DESIGN Retrospective cross-sectional study. METHODS This study included consecutive sarcoid uveitis patients who all underwent QFT testing. RESULTS A total of 234 patients were included in the study, among them 28 (12%) were QFT-positive. Previously treated tuberculosis (TB) was documented in 2 patients. QFT-positive patients were older (59 ± 16 years vs. 51 ± 18 years, p = .025) and more in proportion to suffer from chronic uveitis and panuveitis compared to QFT-negative patients. Moderate and severe visual impairment were significantly more frequent in the QFT-positive group (35.7% vs. 18.9%, p = .049 and 25.0% vs. 9.2%, p = .022, respectively). CONCLUSION The significant proportion of QFT-positive patients (12%) in this large series of sarcoid uveitis patients makes us suggest not to exclude the diagnosis of sarcoidosis in case of positive QFT in a low-endemic country for tuberculosis, and to manage these patients early by initiating without delay systemic steroids associated with latent tuberculosis therapy.
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Affiliation(s)
- Etienne Garneret
- Department of Internal Medicine, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Yvan Jamilloux
- Department of Internal Medicine, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.,Université Claude Bernard Lyon 1, Lyon, France
| | - Mathieu Gerfaud-Valentin
- Department of Internal Medicine, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.,Université Claude Bernard Lyon 1, Lyon, France
| | - Laurent Kodjikian
- Université Claude Bernard Lyon 1, Lyon, France.,Department of Ophthalmology, Hôpital de la Croix Rousse, Université Claude Bernard Lyon 1, Lyon, France
| | - Salim Trad
- Department of Internal Medicine, Hôpital Ambroise Paré, AP-HP, Boulogne-Billancourt, France
| | - Pascal Sève
- Department of Internal Medicine, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.,Université Claude Bernard Lyon 1, Lyon, France.,Research on Healthcare Performance (RESHAPE), INSERM U1290, Université Claude Bernard Lyon 1, Lyon, France
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21
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Gonzales JA, Takhar JS, Joye A, Acharya NR, Chen C, Hinterwirth A, Doan T. Peripheral Blood Transcriptome in Patients with Sarcoidosis-Associated Uveitis. Ocul Immunol Inflamm 2022; 30:1074-1077. [PMID: 33661066 PMCID: PMC9993430 DOI: 10.1080/09273948.2020.1861306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
PURPOSE To identify peripheral blood transcriptome differences in uveitis patients with sarcoidosis compared to those with Vogt-Koyanagi-Harada (VKH) syndrome and controls. METHODS Ten patients with uveitis compatible with sarcoidosis (eight with pulmonary sarcoidosis, one with central nervous system sarcoidosis, and one with conjunctival sarcoidosis), nine patients with VKH, and nine healthy controls were prospectively enrolled. RESULTS Ten genes exhibited a four-fold difference in expression in sarcoidosis patients compared to controls, many being involved in regulating inflammatory processes or cellular responses to microbes. CONCLUSIONS This research suggests that the transcriptome in sarcoidosis is robust enough to be detected in the peripheral blood and that sarcoidosis can be distinguished from healthy controls. Differentially expressed genes may serve as candidates warranting further investigation with respect to disease pathophysiology and may provide additional information, such as ability to stratify patients based on associated disease severity and anatomical location of inflammation within the eye.
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Affiliation(s)
- John A Gonzales
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA.,Department of Ophthalmology, University of California, San Francisco, California, USA
| | - Jaskirat S Takhar
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA.,John Burns Medical School, University of Hawaii, Honolulu, Hawaii, USA
| | - Ashlin Joye
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Nisha R Acharya
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA.,Department of Ophthalmology, University of California, San Francisco, California, USA
| | - Cindi Chen
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Armin Hinterwirth
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Thuy Doan
- Francis I. Proctor Foundation, University of California, San Francisco, California, USA.,Department of Ophthalmology, University of California, San Francisco, California, USA
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22
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Melin A, Routier É, Roy S, Pradere P, Le Pavec J, Pierre T, Chanson N, Scoazec JY, Lambotte O, Robert C. Sarcoid-like Granulomatosis Associated with Immune Checkpoint Inhibitors in Melanoma. Cancers (Basel) 2022; 14:cancers14122937. [PMID: 35740604 PMCID: PMC9221061 DOI: 10.3390/cancers14122937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 02/05/2023] Open
Abstract
We aimed to review the clinical and biological presentation of granulomatosis associated with immune-checkpoint inhibitors (ICI) in patients with melanoma and to explore its association with classical sarcoidosis as well as with cancer response to ICI. To this end, a retrospective study on 18 melanoma patients with histologically proven ICI-induced granulomatosis over a 12-year period in a single center, as well as on 67 similar cases reported in the literature, was conducted. Results indicate ICI-induced granulomatosis is an early side effect (median time to onset: 2 months). Its clinical presentation, with predominant (90%) thoracic involvement, histopathological appearance and supposed underlying biology (involving the mTOR pathway in immune cells, Th17 polarization and TReg dysfunction) are indistinguishable from those of sarcoidosis. Moreover, it appears to be associated with ICI benefit (>65% objective response rate). Evolution is generally favorable, and symptomatic steroid treatment and/or ICI discontinuation are rarely necessary. ICI-associated granulomatosis is critical to explore for several reasons. Practically, it is essential to differentiate it from cancer progression. Secondly, this “experimental” sarcoidosis brings new elements that may help to address sarcoidosis origin and pathophysiology. Its association with ICI efficacy must be confirmed on a larger scale but could have significant impacts on patient management and biomarker definition.
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Affiliation(s)
- Audrey Melin
- Department of Dermatology, Gustave Roussy, 114 rue Edouard-Vaillant, 94800 Villejuif, France; (É.R.); (S.R.)
- Correspondence: (A.M.); (C.R.)
| | - Émilie Routier
- Department of Dermatology, Gustave Roussy, 114 rue Edouard-Vaillant, 94800 Villejuif, France; (É.R.); (S.R.)
| | - Séverine Roy
- Department of Dermatology, Gustave Roussy, 114 rue Edouard-Vaillant, 94800 Villejuif, France; (É.R.); (S.R.)
| | - Pauline Pradere
- Service de Pneumologie et Transplantation Pulmonaire, Hôpital Marie-Lannelongue, Groupe Hospitalier Paris-Saint Joseph, 133 Av. de la Résistance, 92350 Le Plessis-Robinson, France; (P.P.); (J.L.P.)
| | - Jerome Le Pavec
- Service de Pneumologie et Transplantation Pulmonaire, Hôpital Marie-Lannelongue, Groupe Hospitalier Paris-Saint Joseph, 133 Av. de la Résistance, 92350 Le Plessis-Robinson, France; (P.P.); (J.L.P.)
| | - Thibaut Pierre
- Department of Medical Imaging, Gustave Roussy, 114 rue Edouard-Vaillant, 94800 Villejuif, France;
| | - Noémie Chanson
- Department of Internal Medicine, Kremlin Bicêtre Hospital, 78 rue du Général Leclerc, 94270 Le Kremlin Bicêtre, France; (N.C.); (O.L.)
| | - Jean-Yves Scoazec
- Université Paris Saclay, AP-HP, 63 rue Gabriel Péri, 94270 Le Kremlin Bicêtre, France;
- Department of Pathology, Gustave Roussy, 114 rue Edouard-Vaillant, 94800 Villejuif, France
| | - Olivier Lambotte
- Department of Internal Medicine, Kremlin Bicêtre Hospital, 78 rue du Général Leclerc, 94270 Le Kremlin Bicêtre, France; (N.C.); (O.L.)
- Université Paris Saclay, AP-HP, 63 rue Gabriel Péri, 94270 Le Kremlin Bicêtre, France;
| | - Caroline Robert
- Department of Dermatology, Gustave Roussy, 114 rue Edouard-Vaillant, 94800 Villejuif, France; (É.R.); (S.R.)
- Université Paris Saclay, AP-HP, 63 rue Gabriel Péri, 94270 Le Kremlin Bicêtre, France;
- Correspondence: (A.M.); (C.R.)
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23
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Futami Y, Takeda Y, Koba T, Narumi R, Nojima Y, Ito M, Nakayama M, Ishida M, Yoshimura H, Naito Y, Fukushima K, Takimoto T, Edahiro R, Matsuki T, Nojima S, Hirata H, Koyama S, Iwahori K, Nagatomo I, Shirai Y, Suga Y, Satoh S, Futami S, Miyake K, Shiroyama T, Inoue Y, Adachi J, Tomonaga T, Ueda K, Kumanogoh A. Identification of CD14 and lipopolysaccharide-binding protein as novel biomarkers for sarcoidosis using proteomics of serum extracellular vesicles. Int Immunol 2022; 34:327-340. [PMID: 35294531 PMCID: PMC9166566 DOI: 10.1093/intimm/dxac009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/15/2022] [Indexed: 11/14/2022] Open
Abstract
Sarcoidosis is a complex, polygenic, inflammatory granulomatous multi-organ disease of unknown cause. The granulomatous inflammation in sarcoidosis is driven by the interplay between T cells and macrophages. Extracellular vesicles (EVs) play important roles in intercellular communication. We subjected serum EVs, isolated by size exclusion chromatography, from seven patients with sarcoidosis and five control subjects to non-targeted proteomics analysis. Non-targeted, label-free proteomics analysis detected 2292 proteins in serum EVs; 42 proteins were up-regulated in patients with sarcoidosis relative to control subjects; and 324 proteins were down-regulated. The protein signature of EVs from patients with sarcoidosis reflected disease characteristics such as antigen presentation and immunological disease. Candidate biomarkers were further verified by targeted proteomics analysis (selected reaction monitoring) in 46 patients and 10 control subjects. Notably, CD14 and lipopolysaccharide-binding protein (LBP) were validated by targeted proteomics analysis. Up-regulation of these proteins was further confirmed by immunoblotting, and their expression was strongly increased in macrophages of lung granulomatous lesions. Consistent with these findings, CD14 levels were increased in lipopolysaccharide-stimulated macrophages during multinucleation, concomitant with increased levels of CD14 and LBP in EVs. The area under the curve values of CD14 and LBP were 0.81 and 0.84, respectively, and further increased to 0.98 in combination with angiotensin-converting enzyme and soluble interleukin-2 receptor. These findings suggest that CD14 and LBP in serum EVs, which are associated with granulomatous pathogenesis, can improve the diagnostic accuracy in patients with sarcoidosis.
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Affiliation(s)
- Yu Futami
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Taro Koba
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Ryohei Narumi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Yosui Nojima
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Mari Ito
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Mana Nakayama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Mimiko Ishida
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Hanako Yoshimura
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Yujiro Naito
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Kiyoharu Fukushima
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Takayuki Takimoto
- Department of Respiratory Internal Medicine, National Hospital Organization Kinki-Chuo Chest Medical Centre, Nagasone-Cho 1180, Kita-Ku, Sakai, Osaka 591-8555, Japan
| | - Ryuya Edahiro
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Takanori Matsuki
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Satoshi Nojima
- Department of Pathology, Osaka University Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Haruhiko Hirata
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Shohei Koyama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Kota Iwahori
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Izumi Nagatomo
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Yuya Shirai
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Yasuhiko Suga
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Shingo Satoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Shinji Futami
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Kotaro Miyake
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Takayuki Shiroyama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Yoshikazu Inoue
- Clinical Research Centre, National Hospital Organization Kinki-Chuo Chest Medical Centre, 1180 Nagasone-Cho, Kita-Ku, Sakai City, Osaka 591-8555, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Centre, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto, Tokyo 135-8550, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Laboratory of Immunopathology, World Premier International Immunology Frontier Research Centre, Osaka University, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 2-2 Yamada-Oka, Suita, Osaka 565-0871, Japan
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24
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Abstract
Tuberculosis (TB) in humans is characterized by formation of immune-rich granulomas in infected tissues, the architecture and composition of which are thought to affect disease outcome. However, our understanding of the spatial relationships that control human granulomas is limited. Here, we used multiplexed ion beam imaging by time of flight (MIBI-TOF) to image 37 proteins in tissues from patients with active TB. We constructed a comprehensive atlas that maps 19 cell subsets across 8 spatial microenvironments. This atlas shows an IFN-γ-depleted microenvironment enriched for TGF-β, regulatory T cells and IDO1+ PD-L1+ myeloid cells. In a further transcriptomic meta-analysis of peripheral blood from patients with TB, immunoregulatory trends mirror those identified by granuloma imaging. Notably, PD-L1 expression is associated with progression to active TB and treatment response. These data indicate that in TB granulomas, there are local spatially coordinated immunoregulatory programs with systemic manifestations that define active TB.
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25
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Identification of key regulators in Sarcoidosis through multidimensional systems biological approach. Sci Rep 2022; 12:1236. [PMID: 35075176 PMCID: PMC8786862 DOI: 10.1038/s41598-022-05129-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 12/30/2021] [Indexed: 01/13/2023] Open
Abstract
Sarcoidosis is a multi-organ disorder where immunology, genetic and environmental factors play a key role in causing Sarcoidosis, but its molecular mechanism remains unclear. Identification of its genetics profiling that regulates the Sarcoidosis network will be one of the main challenges to understand its aetiology. We have identified differentially expressed genes (DEGs) by analyzing the gene expression profiling of Sarcoidosis and compared it with healthy control. Gene set enrichment analysis showed that these DEGs were mainly enriched in the inflammatory response, immune system, and pathways in cancer. Sarcoidosis protein interaction network was constructed by a total of 877 DEGs (up-down) and calculated its network topological properties, which follow hierarchical scale-free fractal nature up to six levels of the organization. We identified a large number of leading hubs that contain six key regulators (KRs) including ICOS, CTLA4, FLT3LG, CD33, GPR29 and ITGA4 are deeply rooted in the network from top to bottom, considering a backbone of the network. We identified the transcriptional factors (TFs) which are closely interacted with KRs. These genes and their TFs regulating the Sarcoidosis network are expected to be the main target for the therapeutic approaches and potential biomarkers. However, experimental validations of KRs needed to confirm their efficacy.
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26
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Kök GF, Türsen Ü. The Immunogenetics of Granulomatous Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:349-368. [DOI: 10.1007/978-3-030-92616-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Dasgupta S, Ghosh N, Choudhury P, Joshi M, Chowdhury SR, Bhattacharyya P, Chaudhury K. NMR metabolomic and microarray-based transcriptomic data integration identifies unique molecular signatures of hypersensitivity pneumonitis. Mol Omics 2021; 18:101-111. [PMID: 34881764 DOI: 10.1039/d1mo00209k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hypersensitivity pneumonitis (HP) is an immune-mediated granulomatous interstitial lung disease (ILD) that results from repeated inhalation of certain antigens. Despite major advances in research, pathophysiology of the disease remains poorly understood. The present study combines metabolomic and transcriptomic data to determine alterations in HP subjects as compared with healthy controls. Metabolic signatures were identified in serum, exhaled breath condensate (EBC) and bronchoalveolar lavage fluid (BALF) of HP patients using proton nuclear magnetic resonance (NMR) metabolomics. The expression of three metabolites, i.e., lactate, pyruvate, and proline, was found to be significantly altered in all three biofluids. The potential of differential diagnosis based on these three metabolites was investigated by including a group of patients with sarcoidosis, which is another type of granulomatous ILD. In addition, differentially expressed transcriptomic fingerprints in blood samples were identified by analyzing a Gene Expression Omnibus (GEO) database. The transcriptomics analysis of these microarray-based data revealed 59 genes to be significantly dysregulated in patients with HP. Over representation analysis of the metabolites and genes of interest was performed using IMPaLA (Integrated Molecular Pathway Level Analysis) version 12. Integrated analysis of serum metabolite signatures and blood gene expression suggests dysregulation of PI3K-AKT signaling and TCA cycle pathways in these patients. This preliminary study is a step towards better understanding of the pathogenesis of HP by identification of differentially expressed metabolites and transcriptomic fingerprints. These molecular signatures may be explored as diagnostic markers for differentiating HP from other lung diseases.
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Affiliation(s)
- Sanjukta Dasgupta
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Nilanjana Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Priyanka Choudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Mamata Joshi
- National Facility for High-field NMR, Tata Institute of Fundamental Research, Mumbai, India
| | | | | | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
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28
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Bhargava M, Liao SY, Crouser ED, Maier LA, Leach SM. The landscape of transcriptomic and proteomic studies in sarcoidosis. ERJ Open Res 2021; 8:00621-2021. [PMID: 35237683 PMCID: PMC8883173 DOI: 10.1183/23120541.00621-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 11/16/2021] [Indexed: 11/05/2022] Open
Abstract
Sarcoidosis is a systemic disease with gene/protein expression patterns that may be different among different tissues, based on the presence or absence of granulomas, and on subphenotypes with progressive or nonprogressive disease manifestations. There is a growing body of data evaluating global transcriptomic changes across multiple tissue compartments in sarcoidosis. However, whether similar biological pathways are involved is unknown. Furthermore, an understanding of the transcriptional impact on the proteome is required to validate molecular pathways driving heterogeneity in sarcoidosis. The purpose of this study was to compare biological inferences from published datasets and explore the compartment specificity of these responses in sarcoidosis. Common pathways identified across datasets or tissue types may serve as convenient biomarkers and could lead to the discovery of novel therapeutic targets. Multiple overlapping pathways are identified in tissue, BAL cells, PBMCs and a sarcoidosis in vitro granuloma model. Inferences from omic studies are constrained by small sample sizes. Studies comparing differences between sarcoidosis phenotypes are needed.https://bit.ly/30NaHz4
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29
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Vukmirovic M, Yan X, Gibson KF, Gulati M, Schupp JC, DeIuliis G, Adams TS, Hu B, Mihaljinec A, Woolard TN, Lynn H, Emeagwali N, Herzog EL, Chen ES, Morris A, Leader JK, Zhang Y, Garcia JGN, Maier LA, Collman RG, Drake WP, Becich MJ, Hochheiser H, Wisniewski SR, Benos PV, Moller DR, Prasse A, Koth LL, Kaminski N. Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis. Eur Respir J 2021; 58:2002950. [PMID: 34083402 PMCID: PMC9759791 DOI: 10.1183/13993003.02950-2020] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/20/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Sarcoidosis is a multisystem granulomatous disease of unknown origin with a variable and often unpredictable course and pattern of organ involvement. In this study we sought to identify specific bronchoalveolar lavage (BAL) cell gene expression patterns indicative of distinct disease phenotypic traits. METHODS RNA sequencing by Ion Torrent Proton was performed on BAL cells obtained from 215 well-characterised patients with pulmonary sarcoidosis enrolled in the multicentre Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Weighted gene co-expression network analysis and nonparametric statistics were used to analyse genome-wide BAL transcriptome. Validation of results was performed using a microarray expression dataset of an independent sarcoidosis cohort (Freiburg, Germany; n=50). RESULTS Our supervised analysis found associations between distinct transcriptional programmes and major pulmonary phenotypic manifestations of sarcoidosis including T-helper type 1 (Th1) and Th17 pathways associated with hilar lymphadenopathy, transforming growth factor-β1 (TGFB1) and mechanistic target of rapamycin (MTOR) signalling with parenchymal involvement, and interleukin (IL)-7 and IL-2 with airway involvement. Our unsupervised analysis revealed gene modules that uncovered four potential sarcoidosis endotypes including hilar lymphadenopathy with increased acute T-cell immune response; extraocular organ involvement with PI3K activation pathways; chronic and multiorgan disease with increased immune response pathways; and multiorgan involvement, with increased IL-1 and IL-18 immune and inflammatory responses. We validated the occurrence of these endotypes using gene expression, pulmonary function tests and cell differentials from Freiburg. CONCLUSION Taken together, our results identify BAL gene expression programmes that characterise major pulmonary sarcoidosis phenotypes and suggest the presence of distinct disease molecular endotypes.
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Affiliation(s)
- Milica Vukmirovic
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Dept of Medicine, Division of Respirology, McMaster University, Hamilton, ON, Canada
- Equally contributing authors
| | - Xiting Yan
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Dept of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Equally contributing authors
| | - Kevin F Gibson
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | - Mridu Gulati
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Giuseppe DeIuliis
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Buqu Hu
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Antun Mihaljinec
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Tony N Woolard
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Heather Lynn
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- University of Arizona Health Sciences, Tucson, AZ, USA
| | - Nkiruka Emeagwali
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Erica L Herzog
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | | | - Alison Morris
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | - Joseph K Leader
- Dept of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yingze Zhang
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | | | | | | | | | - Michael J Becich
- Dept of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Harry Hochheiser
- Dept of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven R Wisniewski
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | - Panayiotis V Benos
- Dept of Computational and Systems Biology and Department of Computer Science, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Antje Prasse
- Hannover Medical School (MHH), Hannover, Germany
- Fraunhofer ITEM, Hannover, Germany
| | - Laura L Koth
- University of California San Francisco, San Francisco, CA, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
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Bradshaw MJ, Pawate S, Koth LL, Cho TA, Gelfand JM. Neurosarcoidosis: Pathophysiology, Diagnosis, and Treatment. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2021; 8:8/6/e1084. [PMID: 34607912 PMCID: PMC8495503 DOI: 10.1212/nxi.0000000000001084] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/12/2021] [Indexed: 12/23/2022]
Abstract
Although often regarded as a protean illness with myriad clinical and imaging manifestations, neurosarcoidosis typically presents as recognizable syndromes that can be approached in a rational, systematic fashion. Understanding of neurosarcoidosis has progressed significantly in recent years, including updated diagnostic criteria and advances in treatment. The diagnosis of neurosarcoidosis is established by the clinical syndrome, imaging and histopathological findings, and exclusion of other causes. Mounting evidence supports the use of tumor necrosis factor inhibitors as an important addition to the therapeutic armamentarium, along with glucocorticoids and steroid-sparing cytotoxic immunosuppressants. In this narrative review, we summarize recent advances in the diagnosis and treatment of neurosarcoidosis.
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Affiliation(s)
- Michael J Bradshaw
- From the University of Washington and Billings Clinic, (M.J.B.); Vanderbilt University Medical Center (S.P.), Nashville, TN; Division of Pulmonary and Critical Care (L.L.K.), Department of Medicine, University of California, San Francisco; Division of Pulmonary and Critical Care, Department of Medicine; Univeristy of Iowa (T.A.C.), Iowa City; Department of Neurology (J.M.G.), Division of Neuroimmunology and Glial Biology, University of California, San Francisco.
| | - Siddharama Pawate
- From the University of Washington and Billings Clinic, (M.J.B.); Vanderbilt University Medical Center (S.P.), Nashville, TN; Division of Pulmonary and Critical Care (L.L.K.), Department of Medicine, University of California, San Francisco; Division of Pulmonary and Critical Care, Department of Medicine; Univeristy of Iowa (T.A.C.), Iowa City; Department of Neurology (J.M.G.), Division of Neuroimmunology and Glial Biology, University of California, San Francisco
| | - Laura L Koth
- From the University of Washington and Billings Clinic, (M.J.B.); Vanderbilt University Medical Center (S.P.), Nashville, TN; Division of Pulmonary and Critical Care (L.L.K.), Department of Medicine, University of California, San Francisco; Division of Pulmonary and Critical Care, Department of Medicine; Univeristy of Iowa (T.A.C.), Iowa City; Department of Neurology (J.M.G.), Division of Neuroimmunology and Glial Biology, University of California, San Francisco
| | - Tracey A Cho
- From the University of Washington and Billings Clinic, (M.J.B.); Vanderbilt University Medical Center (S.P.), Nashville, TN; Division of Pulmonary and Critical Care (L.L.K.), Department of Medicine, University of California, San Francisco; Division of Pulmonary and Critical Care, Department of Medicine; Univeristy of Iowa (T.A.C.), Iowa City; Department of Neurology (J.M.G.), Division of Neuroimmunology and Glial Biology, University of California, San Francisco
| | - Jeffrey M Gelfand
- From the University of Washington and Billings Clinic, (M.J.B.); Vanderbilt University Medical Center (S.P.), Nashville, TN; Division of Pulmonary and Critical Care (L.L.K.), Department of Medicine, University of California, San Francisco; Division of Pulmonary and Critical Care, Department of Medicine; Univeristy of Iowa (T.A.C.), Iowa City; Department of Neurology (J.M.G.), Division of Neuroimmunology and Glial Biology, University of California, San Francisco
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31
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Francesqui J, Hernández-González F, Sellarés J. Sarcoidosis Phenotypes. OPEN RESPIRATORY ARCHIVES 2021. [PMID: 37496847 PMCID: PMC10369535 DOI: 10.1016/j.opresp.2021.100137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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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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Abstract
PURPOSE OF REVIEW Epidemiological and clinical observations as well as familial clustering support the existence of a genetic predisposition to sarcoidosis. In this article, we review the most recent findings in genetics of sarcoidosis and discuss how the identification of risk alleles may help advancing our understanding of disease etiology and development. RECENT FINDINGS Genetic studies of sarcoidosis phenotypes have identified novel and ancestry-specific associations. Gene-environment interaction studies highlighted the importance of integrating genetic information when assessing the relationship between sarcoidosis and environmental exposures. A case-control-family study revealed that the heritability of sarcoidosis is only 49%, suggesting the existence of additional important contributors to disease risk. The application of whole-exome sequencing has identified associations with disease activity and prognosis. Finally, gene expression studies of circulating immune cells have identified shared and unique pathways between sarcoidosis and other granulomatous diseases. SUMMARY Sarcoidosis genetic research has led to the identification of a number of associations with both sarcoidoses per se and disease phenotypes. Newer sequencing technologies are likely to increase the number of genetic variants associated with sarcoidosis. However, studying phenotypically and ethnically homogeneous patient subsets remains critically important regardless of the genetic approach used.
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34
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Tofacitinib as a Steroid-Sparing Therapy in Pulmonary Sarcoidosis, an Open-Label Prospective Proof-of-Concept Study. Lung 2021; 199:147-153. [PMID: 33825964 DOI: 10.1007/s00408-021-00436-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/04/2021] [Indexed: 12/12/2022]
Abstract
This is a prospective, open-label, proof-of-concept study of tofacitinib, a Janus kinase inhibitor, as a steroid-sparing therapy in corticosteroid-dependent pulmonary sarcoidosis. Five patients with corticosteroid-dependent pulmonary sarcoidosis were treated with tofacitinib 5 mg twice daily. The primary endpoint was a ≥ 50% reduction in corticosteroids at week 16 with no worsening in pulmonary function or respiratory symptoms. 60% of patients (3/5) met the primary endpoint. One patient was lost to follow up prior to steroid taper, and another was withdrawn due to worsening of known neurosarcoidosis. The three patients who met the primary endpoint each tapered to ≤ 5 mg/day prednisone, respiratory symptoms improved, and spirometry remained stable. In this proof-of-concept study, the addition of a JAK-inhibitor allowed 60% of patients with pulmonary sarcoidosis to successfully taper corticosteroids. JAK-inhibitors are a promising therapy for pulmonary sarcoidosis, which require further investigation in randomized trials.Trial Registration clinicaltrials.gov NCT03793439; registered Jan 4, 2019.
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35
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Crouser ED, Locke LW, Julian MW, Bicer S, Sadee W, White P, Schlesinger LS. Phagosome-regulated mTOR signalling during sarcoidosis granuloma biogenesis. Eur Respir J 2021; 57:13993003.02695-2020. [PMID: 32943400 DOI: 10.1183/13993003.02695-2020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/03/2020] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Sarcoidosis and tuberculosis are granulomatous pulmonary diseases characterised by heightened immune reactivity to Mycobacterium tuberculosis antigens. We hypothesised that an unsupervised analysis comparing the molecular characteristics of granulomas formed in response to M. tuberculosis antigens in patients with sarcoidosis or latent tuberculosis infection (LTBI) would provide novel insights into the pathogenesis of sarcoidosis. METHODS A genomic analysis identified differentially expressed genes in granuloma-like cell aggregates formed by sarcoidosis (n=12) or LTBI patients (n=5) in an established in vitro human granuloma model wherein peripheral blood mononuclear cells were exposed to M. tuberculosis antigens (beads coated with purified protein derivative) and cultured for 7 days. Pathway analysis of differentially expressed genes identified canonical pathways, most notably antigen processing and presentation via phagolysosomes, as a prominent pathway in sarcoidosis granuloma formation. The phagolysosomal pathway promoted mechanistic target of rapamycin complex 1 (mTORc1)/STAT3 signal transduction. Thus, granuloma formation and related immune mediators were evaluated in the absence or presence of various pre-treatments known to prevent phagolysosome formation (chloroquine) or phagosome acidification (bafilomycin A1) or directly inhibit mTORc1 activation (rapamycin). RESULTS In keeping with genomic analyses indicating enhanced phagolysosomal activation and predicted mTORc1 signalling, it was determined that sarcoidosis granuloma formation and related inflammatory mediator release was dependent upon phagolysosome assembly and acidification and mTORc1/S6/STAT3 signal transduction. CONCLUSIONS Sarcoidosis granulomas exhibit enhanced and sustained intracellular antigen processing and presentation capacities, and related phagolysosome assembly and acidification are required to support mTORc1 signalling to promote sarcoidosis granuloma formation.
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Affiliation(s)
- Elliott D Crouser
- Division of Pulmonary, Critical Care, and Sleep Medicine, The Dorothy M. Davis Heart and Lung Research Institute, Columbus, OH, USA
| | - Landon W Locke
- Dept of Microbial Infection and Immunity, Center for Microbial Interface Biology, Columbus, OH, USA
| | - Mark W Julian
- Division of Pulmonary, Critical Care, and Sleep Medicine, The Dorothy M. Davis Heart and Lung Research Institute, Columbus, OH, USA
| | - Sabahattin Bicer
- Division of Pulmonary, Critical Care, and Sleep Medicine, The Dorothy M. Davis Heart and Lung Research Institute, Columbus, OH, USA
| | - Wolfgang Sadee
- Dept of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Peter White
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Dept of Pediatrics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
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Baguma R, Mbandi SK, Rodo MJ, Erasmus M, Day J, Makhethe L, de Kock M, van Rooyen M, Stone L, Bilek N, Steyn M, Africa H, Darboe F, Chegou NN, Tromp G, Walzl G, Hatherill M, Penn-Nicholson A, Scriba TJ. Inflammatory Determinants of Differential Tuberculosis Risk in Pre-Adolescent Children and Young Adults. Front Immunol 2021; 12:639965. [PMID: 33717192 PMCID: PMC7947716 DOI: 10.3389/fimmu.2021.639965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/14/2021] [Indexed: 01/16/2023] Open
Abstract
The risk of progression from Mycobacterium tuberculosis (M.tb) infection to active tuberculosis (TB) disease varies markedly with age. TB disease is significantly less likely in pre-adolescent children above 4 years of age than in very young children or post-pubescent adolescents and young adults. We hypothesized that pro-inflammatory responses to M.tb in pre-adolescent children are either less pronounced or more regulated, than in young adults. Inflammatory and antimicrobial mediators, measured by microfluidic RT-qPCR and protein bead arrays, or by analyzing published microarray data from TB patients and controls, were compared in pre-adolescent children and adults. Multivariate analysis revealed that M.tb-uninfected 8-year-old children had lower levels of myeloid-associated pro-inflammatory mediators than uninfected 18-year-old young adults. Relative to uninfected children, those with M.tb-infection had higher levels of similar myeloid inflammatory responses. These inflammatory mediators were also expressed after in vitro stimulation of whole blood from uninfected children with live M.tb. Our findings suggest that myeloid inflammation is intrinsically lower in pre-pubescent children than in young adults. The lower or more regulated pro-inflammatory responses may play a role in the lower risk of TB disease in this age group.
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Affiliation(s)
- Richard Baguma
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Miguel J. Rodo
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Mzwandile Erasmus
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Jonathan Day
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Lebohang Makhethe
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Marwou de Kock
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Michele van Rooyen
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Lynnett Stone
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Nicole Bilek
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Marcia Steyn
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Hadn Africa
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Fatoumatta Darboe
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Novel N. Chegou
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerard Tromp
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerhard Walzl
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Adam Penn-Nicholson
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative (SATVI), Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
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Odia T, Malherbe ST, Meier S, Maasdorp E, Kleynhans L, du Plessis N, Loxton AG, Zak DE, Thompson E, Duffy FJ, Kuivaniemi H, Ronacher K, Winter J, Walzl G, Tromp G. The Peripheral Blood Transcriptome Is Correlated With PET Measures of Lung Inflammation During Successful Tuberculosis Treatment. Front Immunol 2021; 11:596173. [PMID: 33643286 PMCID: PMC7902901 DOI: 10.3389/fimmu.2020.596173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022] Open
Abstract
Pulmonary tuberculosis (PTB) is characterized by lung granulomas, inflammation and tissue destruction. Here we used within-subject peripheral blood gene expression over time to correlate with the within-subject lung metabolic activity, as measured by positron emission tomography (PET) to identify biological processes and pathways underlying overall resolution of lung inflammation. We used next-generation RNA sequencing and [18F]FDG PET-CT data, collected at diagnosis, week 4, and week 24, from 75 successfully cured PTB patients, with the [18F]FDG activity as a surrogate for lung inflammation. Our linear mixed-effects models required that for each individual the slope of the line of [18F]FDG data in the outcome and the slope of the peripheral blood transcript expression data correlate, i.e., the slopes of the outcome and explanatory variables had to be similar. Of 10,295 genes that changed as a function of time, we identified 639 genes whose expression profiles correlated with decreasing [18F]FDG uptake levels in the lungs. Gene enrichment over-representation analysis revealed that numerous biological processes were significantly enriched in the 639 genes, including several well known in TB transcriptomics such as platelet degranulation and response to interferon gamma, thus validating our novel approach. Others not previously associated with TB pathobiology included smooth muscle contraction, a set of pathways related to mitochondrial function and cell death, as well as a set of pathways connecting transcription, translation and vesicle formation. We observed up-regulation in genes associated with B cells, and down-regulation in genes associated with platelet activation. We found 254 transcription factor binding sites to be enriched among the 639 gene promoters. In conclusion, we demonstrated that of the 10,295 gene expression changes in peripheral blood, only a subset of 639 genes correlated with inflammation in the lungs, and the enriched pathways provide a description of the biology of resolution of lung inflammation as detectable in peripheral blood. Surprisingly, resolution of PTB inflammation is positively correlated with smooth muscle contraction and, extending our previous observation on mitochondrial genes, shows the presence of mitochondrial stress. We focused on pathway analysis which can enable therapeutic target discovery and potential modulation of the host response to TB.
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Affiliation(s)
- Trust Odia
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Stephanus T Malherbe
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Stuart Meier
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Elizna Maasdorp
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Léanie Kleynhans
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Nelita du Plessis
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Andre G Loxton
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Daniel E Zak
- Center for Infectious Disease Research, Seattle, WA, United States
| | - Ethan Thompson
- Center for Infectious Disease Research, Seattle, WA, United States
| | - Fergal J Duffy
- Center for Infectious Disease Research, Seattle, WA, United States.,Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Helena Kuivaniemi
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Katharina Ronacher
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Translational Research Institute, Mater Research Institute - The University of Queensland, Brisbane, QLD, Australia
| | - Jill Winter
- Catalysis Foundation for Health, San Ramon, CA, United States
| | - Gerhard Walzl
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa
| | - Gerard Tromp
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
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Casanova NG, Zhou T, Gonzalez-Garay ML, Lussier YA, Sweiss N, Ma SF, Noth I, Knox KS, Garcia JGN. MicroRNA and protein-coding gene expression analysis in idiopathic pulmonary fibrosis yields novel biomarker signatures associated to survival. Transl Res 2021; 228:1-12. [PMID: 32711186 PMCID: PMC7779721 DOI: 10.1016/j.trsl.2020.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 07/09/2020] [Accepted: 07/16/2020] [Indexed: 02/04/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive interstitial lung disease of unknown etiology that poses significant challenges in early diagnosis and prediction of progression. Analyses of microRNA and gene expression in IPF have yielded potentially predictive information. However, the relationship between microRNA/gene expression and quantitative phenotypic value in IPF remains controversial, as is the added value of this approach to current molecular signatures in IPF. To identify biomarkers predictive of survival in IPF via a microRNA-driven strategy. We profiled microRNA and protein-coding gene expression in peripheral blood mononuclear cells from 70 IPF subjects in a discovery cohort. We linked the microRNA/gene expression level with the quantitative phenotypic variation in IPF, including diffusing capacity of the lung for carbon monoxide and the forced vital capacity percent predicted. In silico analyses of expression profiles and quantitative phenotypic data allowed the generation of 2 sets of IPF molecular signatures (unique for microRNAs and protein-coding genes) that predict IPF survival. Each signature performed well in a validation cohort comprised of IPF patients aggregated from distinct patient populations recruited from different sites. Resampling test suggests that the protein-coding gene based signature is comparable and potentially superior to published IPF prognostic gene signatures. In conclusion, these results highlight the utility of microRNA-driven peripheral blood molecular signatures as valuable and novel biomarkers associated to individuals at high survival risk and for potentially facilitating individualized therapies in this enigmatic disorder.
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Affiliation(s)
- Nancy G Casanova
- Department of Medicine, University of Arizona Health Sciences, Tucson, Arizona
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada
| | | | - Yves A Lussier
- Center for Biomedical Informatics and Biostatistics, University of Arizona, Tucson, Arizona
| | - Nadera Sweiss
- Section of Rheumatology Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Shwu-Fan Ma
- Section of Pulmonary/Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Imre Noth
- Division of Pulmonary and Critical Care Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Kenneth S Knox
- Department of Medicine, College of Medicine-Phoenix, University of Arizona Health Sciences, Phoenix, Arizona
| | - Joe G N Garcia
- Department of Medicine, University of Arizona Health Sciences, Tucson, Arizona.
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Garman L, Pelikan RC, Rasmussen A, Lareau CA, Savoy KA, Deshmukh US, Bagavant H, Levin AM, Daouk S, Drake WP, Montgomery CG. Single Cell Transcriptomics Implicate Novel Monocyte and T Cell Immune Dysregulation in Sarcoidosis. Front Immunol 2020; 11:567342. [PMID: 33363531 PMCID: PMC7753017 DOI: 10.3389/fimmu.2020.567342] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/03/2020] [Indexed: 12/19/2022] Open
Abstract
Sarcoidosis is a systemic inflammatory disease characterized by infiltration of immune cells into granulomas. Previous gene expression studies using heterogeneous cell mixtures lack insight into cell-type-specific immune dysregulation. We performed the first single-cell RNA-sequencing study of sarcoidosis in peripheral immune cells in 48 patients and controls. Following unbiased clustering, differentially expressed genes were identified for 18 cell types and bioinformatically assessed for function and pathway enrichment. Our results reveal persistent activation of circulating classical monocytes with subsequent upregulation of trafficking molecules. Specifically, classical monocytes upregulated distinct markers of activation including adhesion molecules, pattern recognition receptors, and chemokine receptors, as well as enrichment of immunoregulatory pathways HMGB1, mTOR, and ephrin receptor signaling. Predictive modeling implicated TGFβ and mTOR signaling as drivers of persistent monocyte activation. Additionally, sarcoidosis T cell subsets displayed patterns of dysregulation. CD4 naïve T cells were enriched for markers of apoptosis and Th17/Treg differentiation, while effector T cells showed enrichment of anergy-related pathways. Differentially expressed genes in regulatory T cells suggested dysfunctional p53, cell death, and TNFR2 signaling. Using more sensitive technology and more precise units of measure, we identify cell-type specific, novel inflammatory and regulatory pathways. Based on our findings, we suggest a novel model involving four convergent arms of dysregulation: persistent hyperactivation of innate and adaptive immunity via classical monocytes and CD4 naïve T cells, regulatory T cell dysfunction, and effector T cell anergy. We further our understanding of the immunopathology of sarcoidosis and point to novel therapeutic targets.
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Affiliation(s)
- Lori Garman
- Oklahoma Medical Research Foundation, Genes and Human Disease, Oklahoma City, OK, United States
| | - Richard C Pelikan
- Oklahoma Medical Research Foundation, Genes and Human Disease, Oklahoma City, OK, United States
| | - Astrid Rasmussen
- Oklahoma Medical Research Foundation, Genes and Human Disease, Oklahoma City, OK, United States
| | - Caleb A Lareau
- Cell Circuits and Epigenomics Program, Broad Institute, Cambridge, MA, United States
| | - Kathryn A Savoy
- Oklahoma Medical Research Foundation, Genes and Human Disease, Oklahoma City, OK, United States
| | - Umesh S Deshmukh
- Oklahoma Medical Research Foundation, Arthritis and Clinical Immunology, Oklahoma City, OK, United States
| | - Harini Bagavant
- Oklahoma Medical Research Foundation, Arthritis and Clinical Immunology, Oklahoma City, OK, United States
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, United States
| | - Salim Daouk
- Cardiovascular Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Wonder P Drake
- Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Courtney G Montgomery
- Oklahoma Medical Research Foundation, Genes and Human Disease, Oklahoma City, OK, United States
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40
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Casanova NG, Gonzalez-Garay ML, Sun B, Bime C, Sun X, Knox KS, Crouser ED, Sammani N, Gonzales T, Natt B, Chaudhary S, Lussier Y, Garcia JGN. Differential transcriptomics in sarcoidosis lung and lymph node granulomas with comparisons to pathogen-specific granulomas. Respir Res 2020; 21:321. [PMID: 33276795 PMCID: PMC7716494 DOI: 10.1186/s12931-020-01537-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/06/2020] [Indexed: 12/15/2022] Open
Abstract
RATIONALE Despite the availability of multi-"omics" strategies, insights into the etiology and pathogenesis of sarcoidosis have been elusive. This is partly due to the lack of reliable preclinical models and a paucity of validated biomarkers. As granulomas are a key feature of sarcoidosis, we speculate that direct genomic interrogation of sarcoid tissues, may lead to identification of dysregulated gene pathways or biomarker signatures. OBJECTIVE To facilitate the development sarcoidosis genomic biomarkers by gene expression profiling of sarcoidosis granulomas in lung and lymph node tissues (most commonly affected organs) and comparison to infectious granulomas (coccidiodomycosis and tuberculosis). METHODS Transcriptomic profiles of immune-related gene from micro-dissected sarcoidosis granulomas within lung and mediastinal lymph node tissues and compared to infectious granulomas from paraffin-embedded blocks. Differentially-expressed genes (DEGs) were profiled, compared among the three granulomatous diseases and analyzed for functional enrichment pathways. RESULTS Despite histologic similarities, DEGs and pathway enrichment markedly differed in sarcoidosis granulomas from lymph nodes and lung. Lymph nodes showed a clear immunological response, whereas a structural regenerative response was observed in lung. Sarcoidosis granuloma gene expression data corroborated previously reported genomic biomarkers (STAB1, HBEGF, and NOTCH4), excluded others and identified new genomic markers present in lung and lymph nodes, ADAMTS1, NPR1 and CXCL2. Comparisons between sarcoidosis and pathogen granulomas identified pathway divergences and commonalities at gene expression level. CONCLUSION These findings suggest the importance of tissue and disease-specificity evaluation when exploring sarcoidosis genomic markers. This relevant translational information in sarcoidosis and other two histopathological similar infections provides meaningful specific genomic-derived biomarkers for sarcoidosis diagnosis and prognosis.
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Affiliation(s)
- Nancy G Casanova
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Manuel L Gonzalez-Garay
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Belinda Sun
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Christian Bime
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Xiaoguang Sun
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Kenneth S Knox
- Department of Medicine, College of Medicine, University of Arizona, Phoenix, AZ, USA
| | - Elliott D Crouser
- Division of Pulmonary and Critical Care Medicine, The Ohio State University, Columbus, OH, USA
| | - Nora Sammani
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Taylor Gonzales
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Bhupinder Natt
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Sachin Chaudhary
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Yves Lussier
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Joe G N Garcia
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA.
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41
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Guerrero CR, Maier LA, Griffin TJ, Higgins L, Najt CP, Perlman DM, Bhargava M. Application of Proteomics in Sarcoidosis. Am J Respir Cell Mol Biol 2020; 63:727-738. [PMID: 32804537 DOI: 10.1165/rcmb.2020-0070ps] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/17/2020] [Indexed: 02/03/2023] Open
Abstract
Sarcoidosis is a multisystem disease with heterogeneity in manifestations and outcomes. System-level studies leveraging "omics" technologies are expected to define mechanisms contributing to sarcoidosis heterogeneous manifestations and course. With improvements in mass spectrometry (MS) and bioinformatics, it is possible to study protein abundance for a large number of proteins simultaneously. Contemporary fast-scanning MS enables the acquisition of spectral data for deep coverage of the proteins with data-dependent or data-independent acquisition MS modes. Studies leveraging MS-based proteomics in sarcoidosis have characterized BAL fluid (BALF), alveolar macrophages, plasma, and exosomes. These studies identified several differentially expressed proteins, including protocadherin-2 precursor, annexin A2, pulmonary surfactant A2, complement factors C3, vitamin-D-binding protein, cystatin B, and amyloid P, comparing subjects with sarcoidosis with control subjects. Other studies identified ceruloplasmin, complement factors B, C3, and 1, and others with differential abundance in sarcoidosis compared with other interstitial lung diseases. Using quantitative proteomics, most recent studies found differences in PI3K/Akt/mTOR, MAP kinase, pluripotency-associated transcriptional factor, and hypoxia response pathways. Other studies identified increased clathrin-mediated endocytosis and Fcγ receptor-mediated phagocytosis pathways in sarcoidosis alveolar macrophages. Although studies in mixed BAL and blood cells or plasma are limited, some of the changes in lung compartment are detected in the blood cells and plasma. We review proteomics for sarcoidosis with a focus on the existing MS data acquisition strategies, bioinformatics for spectral data analysis to infer protein identity and quantity, unique aspects about biospecimen collection and processing for lung-related proteomics, and proteomics studies conducted to date in sarcoidosis.
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Affiliation(s)
- Candance R Guerrero
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences and
| | - Lisa A Maier
- Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, Colorado
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences and
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences and
| | - Charles P Najt
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences and
| | - David M Perlman
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Minnesota, Minneapolis, Minnesota; and
| | - Maneesh Bhargava
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Minnesota, Minneapolis, Minnesota; and
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42
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Lung gene expression signatures suggest pathogenic links and molecular markers for pulmonary tuberculosis, adenocarcinoma and sarcoidosis. Commun Biol 2020; 3:604. [PMID: 33097805 PMCID: PMC7584606 DOI: 10.1038/s42003-020-01318-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/25/2020] [Indexed: 12/22/2022] Open
Abstract
Previous reports have suggested a link between pulmonary tuberculosis (TB), which is caused by Mycobacterium tuberculosis (Mtb), and the development of lung adenocarcinoma (LUAD) and sarcoidosis. Furthermore, these lung diseases share certain clinical similarities that can challenge differential diagnosis in some cases. Here, through comparison of lung transcriptome-derived molecular signatures of TB, LUAD and sarcoidosis patients, we identify certain shared disease-related expression patterns. We also demonstrate that MKI67, an over-expressed gene shared by TB and LUAD, is a key mediator in Mtb-promoted tumor cell proliferation, migration, and invasion. Moreover, we reveal a distinct ossification-related TB lung signature, which may be associated with the activation of the BMP/SMAD/RUNX2 pathway in Mtb-infected macrophages that can restrain mycobacterial survival and promote osteogenic differentiation of mesenchymal stem cells. Taken together, these findings provide novel pathogenic links and potential molecular markers for better understanding and differential diagnosis of pulmonary TB, LUAD and sarcoidosis. Previous work has suggested potential links between Mycobacterium tuberculosis infection and the development of both lung cancer and sarcoidosis, in addition to tuberculosis. Here, Qiyao Chai, Zhe Lu, Zhidong Liu and colleagues report a transcriptomic analysis of lung tissue from tuberculosis, lung adenocarcinoma, and sarcoidosis patients and find that while many disease-linked expression changes are shared between the three diseases, each also has distinct transcriptional signatures that could be useful as molecular markers.
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43
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Schrijver B, Dijkstra DJ, Borggreven NV, La Distia Nora R, Huijser E, Versnel MA, van Hagen PM, Joosten SA, Trouw LA, Dik WA. Inverse correlation between serum complement component C1q levels and whole blood type-1 interferon signature in active tuberculosis and QuantiFERON-positive uveitis: implications for diagnosis. Clin Transl Immunology 2020; 9:e1196. [PMID: 33088504 PMCID: PMC7563643 DOI: 10.1002/cti2.1196] [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: 04/24/2020] [Revised: 08/20/2020] [Accepted: 09/25/2020] [Indexed: 01/16/2023] Open
Abstract
Objectives To examine the relation between serum C1q levels and blood type‐1 interferon signature (type‐1 IFN signature) in active pulmonary tuberculosis (APTB) and to determine whether combined measurement of serum C1q and type‐1 IFN signature may add to the diagnosis of QuantiFERON‐positive (QFT+) patients with uveitis of unknown cause. Methods C1q was determined (ELISA) in serum from two distinct Indonesian cohorts, and in total, APTB (n = 72), QFT+ uveitis of unknown aetiology (n = 58), QFT− uveitis (n = 51) patients and healthy controls (HC; n = 73) were included. The type‐1 IFN signature scores were previously determined. Results Serum C1q was higher in APTB than HC (P < 0.001). APTB patients with uveitis had higher serum C1q than APTB patients without uveitis (P = 0.0207). Serum C1q correlated inversely with type‐1 IFN signature scores in APTB (P = 0.0036, r2 = 0.3526), revealing that these biomarkers for active TB disease can be mutually exclusive. Stratification of QFT+ patients with uveitis of unknown cause, by serum C1q and type‐1 IFN signature, yielded four groups with different likelihood of suffering from active TB uveitis. Conclusion Serum C1q is elevated in APTB, especially in those cases with uveitis. We propose that combined measurement of blood type‐1 IFN signature and serum C1q may provide added value in the diagnosis of active TB disease. Combined measurement of type‐1 IFN signature and serum C1q in QFT+ patients without signs of active TB disease, but suffering from uveitis of unknown cause, may be of help to identify cases with low or high likelihood of having active TB uveitis, which may facilitate clinical management decisions.
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Affiliation(s)
- Benjamin Schrijver
- Department of Immunology Laboratory Medical Immunology Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | - Douwe J Dijkstra
- Department of Immunohematology and Blood Transfusion Leiden University Medical Center Leiden The Netherlands
| | - Nicole V Borggreven
- Department of Immunohematology and Blood Transfusion Leiden University Medical Center Leiden The Netherlands
| | - Rina La Distia Nora
- Department of Ophthalmology Faculty of Medicine University of Indonesia and Cipto Mangunkusumo Hospital Jakarta Indonesia
| | - Erika Huijser
- Department of Immunology Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | - Marjan A Versnel
- Department of Immunology Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | - P Martin van Hagen
- Department of Immunology Laboratory Medical Immunology Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands.,Department of Internal Medicine Division Clinical Immunology Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | - Simone A Joosten
- Department of Infectious Diseases Leiden University Medical Center Leiden The Netherlands
| | - Leendert A Trouw
- Department of Immunohematology and Blood Transfusion Leiden University Medical Center Leiden The Netherlands
| | - Willem A Dik
- Department of Immunology Laboratory Medical Immunology Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands.,Department of Internal Medicine Division Clinical Immunology Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
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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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Garman L, Montgomery CG, Rivera NV. Recent advances in sarcoidosis genomics: epigenetics, gene expression, and gene by environment (G × E) interaction studies. Curr Opin Pulm Med 2020; 26:544-553. [PMID: 32701681 PMCID: PMC7735660 DOI: 10.1097/mcp.0000000000000719] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW We aim to review the most recent findings in genomics of sarcoidosis and highlight the gaps in the field. RECENT FINDINGS Original explorations of sarcoidosis subphenotypes, including cases associated with the World Trade Center and ocular sarcoidosis, have identified novel risk loci. Innovative gene--environment interaction studies utilizing modern analytical techniques have discovered risk loci associated with smoking and insecticide exposure. The application of whole-exome sequencing has identified genetic variants associated with persistent sarcoidosis and rare functional variations. A single epigenomics study has provided background knowledge of DNA methylation mechanisms in comparison with gene expression data. The application of machine-learning techniques has suggested new drug repositioning for the treatment of sarcoidosis. Several gene expression studies have identified prominent inflammatory pathways enriched in the affected tissue. SUMMARY Certainly, sarcoidosis research has recently advanced in the exploration of disease subphenotypes, utilizing novel analytical techniques, and including measures of clinical variation. Nevertheless, large-scale and diverse cohorts investigated with advanced sequencing methods, such as whole-genome and single-cell RNA sequencing, epigenomics, and meta-analysis coupled with cutting-edge analytic approaches, when employed, will broaden and translate genomics findings into clinical applications, and ultimately open venues for personalized medicine.
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Affiliation(s)
- Lori Garman
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Courtney G. Montgomery
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Natalia V. Rivera
- Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Rheumatology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center of Molecular Medicine (CMM), Karolinska Institutet, Stockholm, Sweden
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46
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Calender A, Weichhart T, Valeyre D, Pacheco Y. Current Insights in Genetics of Sarcoidosis: Functional and Clinical Impacts. J Clin Med 2020; 9:E2633. [PMID: 32823753 PMCID: PMC7465171 DOI: 10.3390/jcm9082633] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Sarcoidosis is a complex disease that belongs to the vast group of autoinflammatory disorders, but the etiological mechanisms of which are not known. At the crosstalk of environmental, infectious, and genetic factors, sarcoidosis is a multifactorial disease that requires a multidisciplinary approach for which genetic research, in particular, next generation sequencing (NGS) tools, has made it possible to identify new pathways and propose mechanistic hypotheses. Codified treatments for the disease cannot always respond to the most progressive forms and the identification of new genetic and metabolic tracks is a challenge for the future management of the most severe patients. Here, we review the current knowledge regarding the genes identified by both genome wide association studies (GWAS) and whole exome sequencing (WES), as well the connection of these pathways with the current research on sarcoidosis immune-related disorders.
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Affiliation(s)
- Alain Calender
- Department of Molecular and Medical genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France;
- CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory, University Claude Bernard Lyon 1, 69007 Lyon, France
| | - Thomas Weichhart
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, 1090 Vienna, Austria;
| | - Dominique Valeyre
- INSERM UMR 1272, Department of Pulmonology, Avicenne Hospital, University Sorbonne Paris Nord, Saint Joseph Hospital, AP-HP, 75014 Paris, France;
| | - Yves Pacheco
- Department of Molecular and Medical genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France;
- CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory, University Claude Bernard Lyon 1, 69007 Lyon, France
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Vijayaraj M, Abhinand PA, Venkatesan P, Ragunath PK. An ANN model for the differential diagnosis of tuberculosis and sarcoidosis. Bioinformation 2020; 16:539-546. [PMID: 32994679 PMCID: PMC7505241 DOI: 10.6026/97320630016539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/08/2020] [Accepted: 06/08/2020] [Indexed: 11/23/2022] Open
Abstract
Sarcoidosis is often misdiagnosed as tuberculosis and consequently mistreated owing to inherent limitations in histopathological and radiological presentations. It is known that the differential diagnosis of Tuberculosis and Sarcoidosis is often non-trivial and requires expertise and experience from clinicians. Therefore, it is of interest to describe a multilayer neural network model to differentiate pulmonary tuberculosis from Sarcoidosis using signal intensity data from blood transcriptional microarray. Genes that are significantly upregulated in Pulmonary Tuberculosis and Sarcoidosis in comparison with healthy controls were used in the model. The model classified Pulmonary Tuberculosis and Sarcoidosis with 95.8% accuracy. The model also helps to identify gene markers that are differentially upregulated in the two clinical conditions.
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Affiliation(s)
- Mahalakshmi Vijayaraj
- Department of Bioinformatics, Faculty of Biomedical Sciences Sri Ramachandra Institute of Higher Education and Research (Deemed To Be University)
| | - PA Abhinand
- Department of Bioinformatics, Faculty of Biomedical Sciences Sri Ramachandra Institute of Higher Education and Research (Deemed To Be University)
| | - P Venkatesan
- Department of Bioinformatics, Faculty of Biomedical Sciences Sri Ramachandra Institute of Higher Education and Research (Deemed To Be University)
| | - PK Ragunath
- Department of Bioinformatics, Faculty of Biomedical Sciences Sri Ramachandra Institute of Higher Education and Research (Deemed To Be University)
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48
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Arger NK, Machiraju S, Allen IE, Woodruff PG, Koth LL. T-bet Expression in Peripheral Th17.0 Cells Is Associated With Pulmonary Function Changes in Sarcoidosis. Front Immunol 2020; 11:1129. [PMID: 32774332 PMCID: PMC7387715 DOI: 10.3389/fimmu.2020.01129] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 05/07/2020] [Indexed: 12/29/2022] Open
Abstract
Background: Interferon-gamma (IFN-γ) is a key mediator of sarcoidosis-related granulomatous inflammation. Previous findings of IFN-γ-producing Th17 cells in bronchoalveolar lavage fluid from sarcoidosis patients invokes the transition of Th17.0 cells to Th17.1 cells in the disease's pathogenesis. Since the T-bet transcription factor is crucial for this transition, the goal of this study was to determine if T-bet expression in Th17.0 cells reflects the extent of granulomatous inflammation in sarcoidosis patients as assessed by clinical outcomes. Methods: Using a case-control study design, we identified two groups of sarcoidosis subjects (total N = 43) with pulmonary function tests (PFTs) that either (1) changed (increased or decreased) longitudinally or (2) were stable. We used flow cytometry to measure the transcription factors T-bet and RORγt in Th1, Th17.0, and Th17.1 cell subsets defined by CCR6, CCR4 and CXCR3 in blood samples. We compared the percentages of T-bet+ cells in RORγt+Th17.0 cells (defined as CCR6+CCR4+CXCR3−) based on subjects' PFT group. We also assessed the relationship between the direction of change in PFTs with the changes in %T-bet+ frequencies using mixed effects modeling. Results: We found that T-bet expression in subjects' RORγt+Th17.0 cells varied based on clinical outcome. The T-bet+ percentage of RORγt+Th17.0 cells was higher in the cases (subject group with PFT changes) as compared to controls (stable group) (27 vs. 16%, p = 0.0040). In comparisons before and after subjects' PFT changes, the T-bet+ frequency of RORγt+Th17.0 cells increased or decreased in the opposite direction of the PFT change. The percentage of these T-bet+ cells was also higher in those with greater numbers of involved organs. Serum levels of interferon-γ-induced chemokines, CXCL9, CXCL10, and CXCL11, and whole blood gene expression of IFN-γ-related genes including GBP1, TAP1, and JAK2 were independently positively associated with the T-bet+ frequencies of RORγt+Th17.0 cells. Conclusions: These data suggest that expression of T-bet in Th17.0 cells could reflect the extent of granulomatous inflammation in sarcoidosis patients because they represent a transition state leading to the Th17.1 cell phenotype. These findings indicate that Th17 plasticity may be part of the disease paradigm.
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Affiliation(s)
- Nicholas K Arger
- Division of Pulmonary and Critical Care, University of California, San Francisco, San Francisco, CA, United States
| | - Siddharth Machiraju
- Division of Pulmonary and Critical Care, University of California, San Francisco, San Francisco, CA, United States
| | - Isabel E Allen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Prescott G Woodruff
- Division of Pulmonary and Critical Care, University of California, San Francisco, San Francisco, CA, United States
| | - Laura L Koth
- Division of Pulmonary and Critical Care, University of California, San Francisco, San Francisco, CA, United States
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Shen H, Liu T, Cui J, Borole P, Benjamin A, Kording K, Issadore D. A web-based automated machine learning platform to analyze liquid biopsy data. LAB ON A CHIP 2020; 20:2166-2174. [PMID: 32420563 DOI: 10.1039/d0lc00096e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Liquid biopsy (LB) technologies continue to improve in sensitivity, specificity, and multiplexing and can measure an ever growing library of disease biomarkers. However, clinical interpretation of the increasingly large sets of data these technologies generate remains a challenge. Machine learning is a popular approach to discover and detect signatures of disease. However, limited machine learning expertise in the LB field has kept the discipline from fully leveraging these tools and risks improper analyses and irreproducible results. In this paper, we develop a web-based automated machine learning tool tailored specifically for LB, where machine learning models can be built without the user's input. We also incorporate a differential privacy algorithm, designed to limit the effects of overfitting that can arise from users iteratively developing a panel with feedback from our platform. We validate our approach by performing a meta-analysis on 11 published LB datasets, and found that we had similar or better performance compared to those reported in the literature. Moreover, we show that our platform's performance improved when incorporating information from prior LB datasets, suggesting that this approach can continue to improve with increased access to LB data. Finally, we show that by using our platform the results achieved in the literature can be matched using 40% of the number of subjects in the training set, potentially reducing study cost and time. This self-improving and overfitting-resistant automatic machine learning platform provides a new standard that can be used to validate machine learning works in the LB field.
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Affiliation(s)
- Hanfei Shen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
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50
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Ho J, Bokil NJ, Nguyen PTB, Nguyen TA, Liu MY, Hare N, Fox GJ, Saunders BM, Marks GB, Britton WJ. A transcriptional blood signature distinguishes early tuberculosis disease from latent tuberculosis infection and uninfected individuals in a Vietnamese cohort. J Infect 2020; 81:72-80. [PMID: 32330522 DOI: 10.1016/j.jinf.2020.03.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Global tuberculosis (TB) control is restricted by the failure to detect an estimated 3.3 million TB cases annually. In the majority of TB endemic settings, sputum smear microscopy is used to diagnose TB, but this test is insensitive for TB in its early stages. The objective of this study is to establish a concise gene signature that discriminates between individuals with early TB disease, latent TB infection (LTBI) and those without infection. METHODS This is a case control study nested within a cluster-randomised trial of population screening for active TB using Xpert MTB/RIF. Whole blood samples from 303 participants with active TB (97), LTBI (92) and uninfected individuals (114) were subject to transcriptomic analysis of selected target genes based on a systematic review of previous studies. RESULTS Analysis of 82 genes identified a pattern of differentially expressed genes in TB disease. A seven gene signature was identified that distinguished between TB disease and no TB disease with an AUC of 0.86 (95% CI: 0.80-0.91), and between TB disease from LTBI with an AUC of 0.88 (95% CI: 0.82-0.93). CONCLUSION This gene signature accurately distinguishes early TB disease from those without TB disease or infection, in the context of community-wide TB screening. It could be used as a non-sputum based screening tool or triage test to detect prevalent cases of TB in the community.
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Affiliation(s)
- Jennifer Ho
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, Australia; Centenary Institute, The University of Sydney, Sydney, Australia.
| | - Nilesh J Bokil
- School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Phuong Thi Bich Nguyen
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia
| | - Thu Anh Nguyen
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia
| | - Michael Y Liu
- The ithree Institute, University of Technology Sydney, Sydney, Australia
| | - Nathan Hare
- Centenary Institute, The University of Sydney, Sydney, Australia
| | - Greg J Fox
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia; Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Bernadette M Saunders
- Centenary Institute, The University of Sydney, Sydney, Australia; School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Guy B Marks
- Woolcock Institute of Medical Research, The University of Sydney, 431 Glebe Point Rd, Glebe NSW 2037, Australia; South Western Sydney Clinical School, University of New South Wales, Sydney, Australia
| | - Warwick J Britton
- Centenary Institute, The University of Sydney, Sydney, Australia; Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
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