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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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Lower EE, Baughman RP. Hematologic and Oncologic Aspects of Sarcoidosis: Some of the Least Studied but Most Common Dilemmas. Clin Chest Med 2024; 45:119-129. [PMID: 38245361 DOI: 10.1016/j.ccm.2023.08.008] [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] [Indexed: 01/22/2024]
Abstract
The hematologic system is frequently involved in sarcoidosis. Lymphopenia is the most common hematologic manifestation noted, although anemia and thrombocytopenia also occur. The etiology of these common manifestations can be direct granulomatous infiltration of bone marrow, lymph nodes, or spleen or related to immunologic dysfunction. Although not life threatening, these problems can lead to cytopenias requiring close monitoring in patients receiving a variety of disease treatments. The relationship between sarcoidosis and malignancy remains complex. However, some sarcoidosis patients are at increased risk for the development of malignancies, particularly lymphomas and gastrointestinal cancers. Conversely, cancer patients can experience an increase in the likelihood for the development of breast cancer and lymphomas.
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Affiliation(s)
- Elyse E Lower
- Department of Medicine, University of Cincinnati Medical Center, 200 Eden Avenue, Cincinnati, OH 45219, USA.
| | - Robert P Baughman
- Department of Medicine, University of Cincinnati Medical Center, 200 Eden Avenue, Cincinnati, OH 45219, USA
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Abdelghaffar M, Hwang E, Damsky W. Cutaneous Sarcoidosis. Clin Chest Med 2024; 45:71-89. [PMID: 38245372 DOI: 10.1016/j.ccm.2023.08.004] [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] [Indexed: 01/22/2024]
Abstract
Sarcoidosis is a multisystem disease that most commonly affects the lungs, lymphatic system, eyes, and skin but any organ may be involved. Cutaneous sarcoidosis most commonly presents as pink-red to red-brown papules and plaques that commonly affect the head and neck. With the skin being readily accessible for evaluation and biopsy, when sarcoidosis is suspected, dermatologic evaluation may be helpful for establishing a definitive diagnosis. Treatment strategy depends on the severity and distribution of skin lesions and should incorporate patient preference and treatment considerations for other organs that may be involved.
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Affiliation(s)
- Mariam Abdelghaffar
- School of Medicine, Royal College of Surgeons in Ireland, Smurfit Building, Beaumont Hospital, Dublin 9, Ireland
| | - Erica Hwang
- Department of Dermatology, Yale School of Medicine, 333 Cedar Street, LCI 501 PO Box 208059, New Haven, CT 06520, USA
| | - William Damsky
- Department of Dermatology, Yale School of Medicine, 333 Cedar Street, LCI 501 PO Box 208059, New Haven, CT 06520, USA; Department of Pathology, Yale School of Medicine, 310 Cedar Street, LH 108, PO Box 208023, New Haven, CT 06520, USA.
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4
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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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Celada SI, Lim CX, Carisey AF, Ochsner SA, Arce Deza CF, Rexie P, Poli De Frias F, Cardenas-Castillo R, Polverino F, Hengstschläger M, Tsoyi K, McKenna NJ, Kheradmand F, Weichhart T, Rosas IO, Van Kaer L, Celada LJ. SHP2 promotes sarcoidosis severity by inhibiting SKP2-targeted ubiquitination of TBET in CD8 + T cells. Sci Transl Med 2023; 15:eade2581. [PMID: 37703351 PMCID: PMC11126869 DOI: 10.1126/scitranslmed.ade2581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/24/2023] [Indexed: 09/15/2023]
Abstract
Sarcoidosis is an interstitial lung disease (ILD) characterized by interferon-γ (IFN-γ) and T-box expressed in T cells (TBET) dysregulation. Although one-third of patients progress from granulomatous inflammation to severe lung damage, the molecular mechanisms underlying this process remain unclear. Here, we found that pharmacological inhibition of phosphorylated SH2-containing protein tyrosine phosphatase-2 (pSHP2), a facilitator of aberrant IFN-γ abundance, decreased large granuloma formation and macrophage infiltration in the lungs of mice with sarcoidosis-like disease. Positive treatment outcomes were dependent on the effective enhancement of TBET ubiquitination within CD8+ T cells. Mechanistically, we identified a posttranslational modification pathway in which the E3 F-box protein S-phase kinase-associated protein 2 (SKP2) targets TBET for ubiquitination in T cells under normal conditions. However, this pathway was disrupted by aberrant pSHP2 signaling in CD8+ T cells from patients with progressive pulmonary sarcoidosis and end-stage disease. Ex vivo inhibition of pSHP2 in CD8+ T cells from patients with end-stage sarcoidosis enhanced TBET ubiquitination and suppressed IFN-γ and collagen synthesis. Therefore, these studies provided new mechanistic insights into the SHP2-dependent posttranslational regulation of TBET and identified SHP2 inhibition as a potential therapeutic intervention against severe sarcoidosis. Furthermore, these studies also suggest that the small-molecule SHP2 inhibitor SHP099 might be used as a therapeutic measure against human diseases linked to TBET or ubiquitination.
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Affiliation(s)
- Sherly I. Celada
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Clarice X. Lim
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Alexandre F. Carisey
- William T. Shearer Center for Human Immunobiology, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Cell and Molecular Biology, St. Jude Children’s Hospital, Memphis, TN 38105, USA
| | - Scott A. Ochsner
- Department of Molecular and Cellular Biology, Houston, TX 77030, USA
| | - Carlos F. Arce Deza
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Praveen Rexie
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Fernando Poli De Frias
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Mout Sinai Medical Center, Miami Beach, FL 33140, USA
| | - Rafael Cardenas-Castillo
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francesca Polverino
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Markus Hengstschläger
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Konstantin Tsoyi
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil J. McKenna
- Department of Molecular and Cellular Biology, Houston, TX 77030, USA
| | - Farrah Kheradmand
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey, Houston, TX 77030, USA
| | - Thomas Weichhart
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Ivan O. Rosas
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Luc Van Kaer
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
| | - Lindsay J. Celada
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
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Abo Al Hayja M, Kullberg S, Eklund A, Padyukov L, Grunewald J, Rivera NV. Functional link between sarcoidosis-associated gene variants and quantitative levels of bronchoalveolar lavage fluid cell types. Front Med (Lausanne) 2023; 10:1061654. [PMID: 36824606 PMCID: PMC9941743 DOI: 10.3389/fmed.2023.1061654] [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: 10/04/2022] [Accepted: 01/11/2023] [Indexed: 02/09/2023] Open
Abstract
Background Sarcoidosis is an inflammatory disease that affects multiple organs. Cell analysis from bronchoalveolar lavage fluid (BALF) is a valuable tool in the diagnostic workup and differential diagnosis of sarcoidosis. Besides the expansion of lymphocyte expression-specific receptor segments (Vα2.3 and Vβ22) in some patients with certain HLA types, the relation between sarcoidosis susceptibility and BAL cell populations' quantitative levels is not well-understood. Methods Quantitative levels defined by cell concentrations of BAL cells and CD4+/CD8+ ratio were evaluated together with genetic variants associated with sarcoidosis in 692 patients with extensive clinical data. Genetic variants associated with clinical phenotypes, Löfgren's syndrome (LS) and non-Löfgren's syndrome (non-LS), were examined separately. An association test via linear regression using an additive model adjusted for sex, age, and correlated cell type was applied. To infer the biological function of genetic associations, enrichment analysis of expression quantitative trait (eQTLs) across publicly available eQTL databases was conducted. Results Multiple genetic variants associated with sarcoidosis were significantly associated with quantitative levels of BAL cells. Specifically, LS genetic variants, mainly from the HLA locus, were associated with quantitative levels of BAL macrophages, lymphocytes, CD3+ cells, CD4+ cells, CD8+ cells, CD4+/CD8+ ratio, neutrophils, basophils, and eosinophils. Non-LS genetic variants were associated with quantitative levels of BAL macrophages, CD8+ cells, basophils, and eosinophils. eQTL enrichment revealed an influence of sarcoidosis-associated SNPs and regulation of gene expression in the lung, blood, and immune cells. Conclusion Genetic variants associated with sarcoidosis are likely to modulate quantitative levels of BAL cell types and may regulate gene expression in immune cell populations. Thus, the role of sarcoidosis-associated gene-variants may be to influence cellular phenotypes underlying the disease immunopathology.
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Affiliation(s)
- Muntasir Abo Al Hayja
- Division of Respiratory Medicine, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Susanna Kullberg
- Division of Respiratory Medicine, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anders Eklund
- Division of Respiratory Medicine, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden,Center of Molecular Medicine (CMM), Karolinska Institutet, Stockholm, Sweden
| | - Johan Grunewald
- Division of Respiratory Medicine, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden,Center of Molecular Medicine (CMM), Karolinska Institutet, Stockholm, Sweden
| | - Natalia V. Rivera
- Division of Respiratory Medicine, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden,Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden,Center of Molecular Medicine (CMM), Karolinska Institutet, Stockholm, Sweden,*Correspondence: Natalia V. Rivera, ✉
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Adalimumab in the treatment of cardiac sarcoidosis: Single center case series and narrative literature review. Respir Med Case Rep 2022; 40:101766. [PMID: 36340865 PMCID: PMC9627097 DOI: 10.1016/j.rmcr.2022.101766] [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: 08/27/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
Background Tumor necrosis factor (TNF) inhibitors have been used in the treatment of cardiac sarcoidosis, infliximab being the most commonly used. We have previously reported a case of effective treatment of cardiac sarcoidosis using adalimumab. Objective To describe our experience of using adalimumab in the treatment of cardiac sarcoidosis. Methods We conducted a retrospective study to evaluate patients with cardiac sarcoidosis who received adalimumab treatment at the University of Illinois Health between 2011 and 2022. The outcome was evaluated by assessing safety, tolerability, and ability to taper systemic corticosteroids therapy following initiation of adalimumab. Results Seven patients met the inclusion criteria. Clinical responses to adalimumab were universally positive. Corticosteroid therapy was discontinued in five patients and the dose was reduced in two patients. Furthermore, adalimumab was well tolerated, and no adverse events were reported. Conclusion Adalimumab was safe and well-tolerated in seven patients with cardiac sarcoidosis seen at our medical center and exhibited corticosteroid-sparing effects. Our observation further warrants large prospective studies to evaluate the safety and efficacy of adalimumab in the treatment of cardiac sarcoidosis.
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Casanova NG, Reyes-Hernon V, Gregory T, Sun B, Bermudez T, Hufford MK, Oita RC, Camp SM, Hernandez-Molina G, Serrano JR, Sun X, Fimbres J, Mirsaeidi M, Sammani S, Bime C, Garcia JGN. Biochemical and genomic identification of novel biomarkers in progressive sarcoidosis: HBEGF, eNAMPT, and ANG-2. Front Med (Lausanne) 2022; 9:1012827. [PMID: 36388923 PMCID: PMC9640603 DOI: 10.3389/fmed.2022.1012827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/07/2022] [Indexed: 11/29/2022] Open
Abstract
Background Progressive pulmonary fibrosis is a serious complication in subjects with sarcoidosis. The absence of reliable, non-invasive biomarkers that detect early progression exacerbates the difficulty in predicting sarcoidosis severity. To potentially address this unmet need, we evaluated a panel of markers for an association with sarcoidosis progression (HBEGF, NAMPT, IL1-RA, IL-6, IL-8, ANG-2). This panel encompasses proteins related to inflammation, vascular injury, cell proliferation, and fibroblast mitogenesis processes. Methods Plasma biomarker levels and biomarker protein expression in lung and lymph nodes tissues (immunohistochemical studies) from sarcoidosis subjects with limited disease and progressive (complicated) sarcoidosis were performed. Gene expression of the protein-coding genes included in this panel was analyzed using RNAseq in sarcoidosis granulomatous tissues from lung and lymph nodes. Results Except for IL-8, plasma levels of each biomarker—eNAMPT, IL-1RA, IL-6, ANG-2, and HBEGF—were significantly elevated in sarcoidosis subjects compared to controls. In addition, plasma levels of HBEGF were elevated in complicated sarcoidosis, while eNAMPT and ANG-2 were observed to serve as markers of lung fibrosis in a subgroup of complicated sarcoidosis. Genomic studies corroborated HBEGF and NAMPT among the top dysregulated genes and identified cytokine-related and fibrotic pathways in lung granulomatous tissues from sarcoidosis. Conclusion These findings suggest HBEGF, eNAMPT, and ANG-2 may serve as potential novel indicators of the clinical severity of sarcoidosis disease.
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Affiliation(s)
- Nancy G. Casanova
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Vivian Reyes-Hernon
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Taylor Gregory
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Belinda Sun
- Department of Pathology, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Tadeo Bermudez
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Matthew K. Hufford
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Radu C. Oita
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Sara M. Camp
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | | | | | - Xiaoguang Sun
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Jocelyn Fimbres
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, Mexico
| | - Mehdi Mirsaeidi
- Department of Medicine, College of Medicine, University of Florida, Jacksonville, FL, United States
| | - Saad Sammani
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Christian Bime
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Joe G. N. Garcia
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
- *Correspondence: Joe G. N. Garcia,
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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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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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11
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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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12
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Yoshioka K, Sato H, Kawasaki T, Ishii D, Imamoto T, Abe M, Hasegawa Y, Ohara O, Tatsumi K, Suzuki T. Transcriptome Analysis of Peripheral Blood Mononuclear Cells in Pulmonary Sarcoidosis. Front Med (Lausanne) 2022; 9:822094. [PMID: 35141260 PMCID: PMC8818883 DOI: 10.3389/fmed.2022.822094] [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: 11/25/2021] [Accepted: 01/03/2022] [Indexed: 12/14/2022] Open
Abstract
Background Sarcoidosis is a granulomatous systemic disease of unknown etiology. Mononuclear cells such as macrophages or lymphocytes in lung tissue and hilar or mediastinal lymph nodes have been recognized to play an essential role in granuloma formation in pulmonary sarcoidosis. Peripheral blood mononuclear cells (PBMCs) consist of several immunocompetent cells and have been shown to play a mechanistic role in the pathogenesis of sarcoidosis. However, the genetic modifications that occur in bulk PBMCs of sarcoidosis remain to be elucidated. Purpose This study aimed to explore the pathobiological markers of sarcoidosis in PBMCs by comparing the transcriptional signature of PBMCs from patients with pulmonary sarcoidosis with those of healthy controls by RNA sequencing. Methods PBMC samples were collected from subjects with pulmonary sarcoidosis with no steroid/immunosuppressant drugs (n = 8) and healthy controls (n = 11) from August 2020 to April 2021, and RNA sequencing was performed with the PBMC samples. Results Principal component analysis using RNA sequencing datasets comparing pulmonary sarcoidosis with healthy controls revealed that the two groups appeared to be differentiated, in which 270 differentially expressed genes were found in PBMCs between sarcoidosis and healthy controls. Enrichment analysis for gene ontology suggested that some biological processes related to the pathobiology of sarcoidosis, such as cellular response to interleukin (IL)-1 and IFN-γ, regulation of IL-6 production, IL-8 secretion, regulation of mononuclear cell migration, and response to lipopolysaccharide, were involved. Enrichment analysis of the KEGG pathway indicated the involvement of tumor necrosis factor (TNF), toll-like receptor signaling, IL-17 signaling pathways, phagosomes, and ribosomes. Most of the genes involved in TNF and IL-17 signaling pathways and phagosomes were upregulated, while most of the ribosome-related genes were downregulated. Conclusion The present study demonstrated that bulk gene expression patterns in PBMCs were different between patients with pulmonary sarcoidosis and healthy controls. The changes in the gene expression pattern of PBMCs could reflect the existence of sarcoidosis lesions and influence granuloma formation in sarcoidosis. These new findings are important to strengthen our understanding of the etiology and pathobiology of sarcoidosis and indicate a potential therapeutic target for sarcoidosis.
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Affiliation(s)
- Keiichiro Yoshioka
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hironori Sato
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan.,Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takeshi Kawasaki
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Daisuke Ishii
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takuro Imamoto
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Mitsuhiro Abe
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoshinori Hasegawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Koichiro Tatsumi
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takuji Suzuki
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
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13
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Seedahmed MI, Mogilnicka I, Zeng S, Luo G, Whooley MA, McCulloch CE, Koth L, Arjomandi M. Performance of a Computational Phenotyping Algorithm for Sarcoidosis Using Diagnostic Codes in Electronic Medical Records: A Pilot Study from Two Veterans Affairs Medical Centers. JMIR Form Res 2022; 6:e31615. [PMID: 35081036 PMCID: PMC8928044 DOI: 10.2196/31615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 11/29/2022] Open
Abstract
Background Electronic medical records (EMRs) offer the promise of computationally identifying sarcoidosis cases. However, the accuracy of identifying these cases in the EMR is unknown. Objective The aim of this study is to determine the statistical performance of using the International Classification of Diseases (ICD) diagnostic codes to identify patients with sarcoidosis in the EMR. Methods We used the ICD diagnostic codes to identify sarcoidosis cases by searching the EMRs of the San Francisco and Palo Alto Veterans Affairs medical centers and randomly selecting 200 patients. To improve the diagnostic accuracy of the computational algorithm in cases where histopathological data are unavailable, we developed an index of suspicion to identify cases with a high index of suspicion for sarcoidosis (confirmed and probable) based on clinical and radiographic features alone using the American Thoracic Society practice guideline. Through medical record review, we determined the positive predictive value (PPV) of diagnosing sarcoidosis by two computational methods: using ICD codes alone and using ICD codes plus the high index of suspicion. Results Among the 200 patients, 158 (79%) had a high index of suspicion for sarcoidosis. Of these 158 patients, 142 (89.9%) had documentation of nonnecrotizing granuloma, confirming biopsy-proven sarcoidosis. The PPV of using ICD codes alone was 79% (95% CI 78.6%-80.5%) for identifying sarcoidosis cases and 71% (95% CI 64.7%-77.3%) for identifying histopathologically confirmed sarcoidosis in the EMRs. The inclusion of the generated high index of suspicion to identify confirmed sarcoidosis cases increased the PPV significantly to 100% (95% CI 96.5%-100%). Histopathology documentation alone was 90% sensitive compared with high index of suspicion. Conclusions ICD codes are reasonable classifiers for identifying sarcoidosis cases within EMRs with a PPV of 79%. Using a computational algorithm to capture index of suspicion data elements could significantly improve the case-identification accuracy.
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Affiliation(s)
- Mohamed Ismail Seedahmed
- Division of Pulmonary, Critical care, allergy and Immunology, and Sleep., Department of Medicine, University of California San Francisco, 513 Parnassus Ave.HSE 1314, Box 0111, San Francisco, US.,San Francisco Veterans Affairs Medical Center, 4150 Clement Street, San Francisco, US
| | - Izabella Mogilnicka
- Department of Experimental Physiology and Pathophysiology, Laboratory of the Centre for Preclinical Research, Medical University of Warsaw, Warsaw, PL
| | - Siyang Zeng
- San Francisco Veterans Affairs Medical Center, 4150 Clement Street, San Francisco, US.,Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, US
| | - Gang Luo
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, US
| | - Mary A Whooley
- San Francisco Veterans Affairs Medical Center, 4150 Clement Street, San Francisco, US.,Department of Medicine, University of California San Francisco, San Francisco, US.,Measurement Science Quality Enhancement Research Initiative, San Francisco Veterans Affairs Healthcare System, San Francisco, US
| | - Charles E McCulloch
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, US
| | - Laura Koth
- Division of Pulmonary, Critical care, allergy and Immunology, and Sleep., Department of Medicine, University of California San Francisco, 513 Parnassus Ave.HSE 1314, Box 0111, San Francisco, US
| | - Mehrdad Arjomandi
- San Francisco Veterans Affairs Medical Center, 4150 Clement Street, San Francisco, US.,Division of Pulmonary, Critical care, allergy and Immunology, and Sleep., Department of Medicine, University of California San Francisco, 513 Parnassus Ave.HSE 1314, Box 0111, San Francisco, US
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14
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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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15
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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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16
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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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17
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Zhang S, Cai Z, Mo X, Zeng H. Tofacitinib effectiveness in Blau syndrome: a case series of Chinese paediatric patients. Pediatr Rheumatol Online J 2021; 19:160. [PMID: 34781959 PMCID: PMC8594202 DOI: 10.1186/s12969-021-00634-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/25/2021] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVE Blau syndrome (BS), a rare, autosomal-dominant autoinflammatory syndrome, is characterized by a clinical triad of granulomatous recurrent uveitis, dermatitis, and symmetric arthritis and associated with mutations of the nucleotide-binding oligomerization domain containing 2 (NOD2) gene. Aim of this study was to assess the efficacy of tofacitinib in Chinese paediatric patients with BS. METHODS Tofacitinib was regularly administered to three BS patients (Patient 1, Patient 2, and Patient 3) at different dosages: 1.7 mg/day (0.11 mg/kg), 2.5 mg/day (0.12 mg/kg), and 2.5 mg/day (0.33 mg/kg). The clinical manifestations of the patients, magnetic resonance imaging results, serological diagnoses, therapeutic measures and outcomes of treatments are described in this report. RESULTS The clinical characteristics and serological diagnoses of all BS patients were greatly improved after the administration of tofacitinib treatment. All patients reached clinical remission of polyarthritis and improvements in the erythrocyte sedimentation rate (ESR) and levels of C-reactive protein (CRP) and inflammatory cytokines. CONCLUSION Tofacitinib, a Janus kinase (JAK) inhibitor, is a promising agent for BS patients who have unsatisfactory responses to corticosteroids, traditional disease-modifying antirheumatic drugs, and biological agents.
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Affiliation(s)
- Song Zhang
- grid.413428.80000 0004 1757 8466Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children’s Medical Center, Guangzhou, 510120 Guangdong China
| | - Zhe Cai
- grid.413428.80000 0004 1757 8466Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children’s Medical Center, Guangzhou, 510120 Guangdong China
| | - Xiaolan Mo
- grid.410737.60000 0000 8653 1072Department of Pharmacy, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huasong Zeng
- Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children's Medical Center, Guangzhou, 510120, Guangdong, China.
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18
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Laubach ZM, Greenberg JR, Turner JW, Montgomery TM, Pioon MO, Sawdy MA, Smale L, Cavalcante RG, Padmanabhan KR, Lalancette C, vonHoldt B, Faulk CD, Dolinoy DC, Holekamp KE, Perng W. Early-life social experience affects offspring DNA methylation and later life stress phenotype. Nat Commun 2021; 12:4398. [PMID: 34285226 PMCID: PMC8292380 DOI: 10.1038/s41467-021-24583-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 06/24/2021] [Indexed: 02/06/2023] Open
Abstract
Studies in rodents and captive primates suggest that the early-life social environment affects future phenotype, potentially through alterations to DNA methylation. Little is known of these associations in wild animals. In a wild population of spotted hyenas, we test the hypothesis that maternal care during the first year of life and social connectedness during two periods of early development leads to differences in DNA methylation and fecal glucocorticoid metabolites (fGCMs) later in life. Here we report that although maternal care and social connectedness during the den-dependent life stage are not associated with fGCMs, greater social connectedness during the subadult den-independent life stage is associated with lower adult fGCMs. Additionally, more maternal care and social connectedness after den independence correspond with higher global (%CCGG) DNA methylation. We also note differential DNA methylation near 5 genes involved in inflammation, immune response, and aging that may link maternal care with stress phenotype.
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Affiliation(s)
- Zachary M Laubach
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA.
- BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| | - Julia R Greenberg
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
| | - Julie W Turner
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
- BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
| | - Tracy M Montgomery
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
- Max Planck Institute of Animal Behavior, Department for the Ecology of Animal Societies, Konstanz, Germany
| | - Malit O Pioon
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
| | - Maggie A Sawdy
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
| | - Laura Smale
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Department of Psychology, Michigan State University, East Lansing, MI, USA
| | | | | | | | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | - Dana C Dolinoy
- Epigenomics Core, University of Michigan, Ann Arbor, MI, USA
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kay E Holekamp
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
- BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
| | - Wei Perng
- Department of Epidemiology and Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Denver, Aurora, CO, USA
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19
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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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20
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Boleto G, Vieira M, Desbois AC, Saadoun D, Cacoub P. Emerging Molecular Targets for the Treatment of Refractory Sarcoidosis. Front Med (Lausanne) 2020; 7:594133. [PMID: 33330556 PMCID: PMC7732552 DOI: 10.3389/fmed.2020.594133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/02/2020] [Indexed: 12/19/2022] Open
Abstract
Sarcoidosis is a multisystem granulomatous disease of unknown origin that has variable clinical course and can affect nearly any organ. It has a chronic course in about 25% of patients. Corticosteroids (CS) are the cornerstone of therapy but their long-term use is associated with cumulative toxicity. Commonly used CS-sparing agents include methotrexate, cyclophosphamide, azathioprine, and mycophenolate mofetil. Twenty to forty percentage of sarcoidosis patients are refractory to these therapies or develop severe adverse events. Therefore, additional and targeted CS-sparing agents are needed for chronic sarcoidosis. Macrophage activation, interferon response, and formation of the granuloma are mainly mediated by T helper-1 responses. Different pro-inflammatory cytokines such as interleukin (IL)-8, IL-12, IL-6, and tumor necrosis factor-alpha (TNF-α) have been shown to be highly expressed in sarcoidosis-affected tissues. As a result of increased production of these cytokines, Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling is constitutively active in sarcoidosis. Several studies of biological agents that target TNF-α have reported their efficacy and appear today as a second line option in refractory sarcoidosis. Some case series report a positive effect of tocilizumab an anti-IL-6 monoclonal antibody in this setting. More recently, JAK inhibition appears as a new promising strategy. This review highlights key advances on the management of chronic refractory sarcoidosis. Novel therapeutic strategies and treatment agents to manage the disease are described.
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Affiliation(s)
- Gonçalo Boleto
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Department of Internal Medicine and Clinical Immunology, Paris, France.,Centre de Référence des Maladies Auto-Immunes et Systémiques Rares, Centre de Référence des Maladies Auto-Inflammatoires et de l'Amylose, Bordeaux, France
| | - Matheus Vieira
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Department of Internal Medicine and Clinical Immunology, Paris, France.,Centre de Référence des Maladies Auto-Immunes et Systémiques Rares, Centre de Référence des Maladies Auto-Inflammatoires et de l'Amylose, Bordeaux, France
| | - Anne Claire Desbois
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Department of Internal Medicine and Clinical Immunology, Paris, France.,Centre de Référence des Maladies Auto-Immunes et Systémiques Rares, Centre de Référence des Maladies Auto-Inflammatoires et de l'Amylose, Bordeaux, France.,Sorbonne Université, UPMC Univ Paris 06, UMR 7211, Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.,INSERM, UMR_S 959, Paris, France.,CNRS, FRE3632, Paris, France
| | - David Saadoun
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Department of Internal Medicine and Clinical Immunology, Paris, France.,Centre de Référence des Maladies Auto-Immunes et Systémiques Rares, Centre de Référence des Maladies Auto-Inflammatoires et de l'Amylose, Bordeaux, France.,Sorbonne Université, UPMC Univ Paris 06, UMR 7211, Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.,INSERM, UMR_S 959, Paris, France.,CNRS, FRE3632, Paris, France
| | - Patrice Cacoub
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Department of Internal Medicine and Clinical Immunology, Paris, France.,Centre de Référence des Maladies Auto-Immunes et Systémiques Rares, Centre de Référence des Maladies Auto-Inflammatoires et de l'Amylose, Bordeaux, France.,Sorbonne Université, UPMC Univ Paris 06, UMR 7211, Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.,INSERM, UMR_S 959, Paris, France.,CNRS, FRE3632, Paris, France
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21
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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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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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23
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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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24
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Schott CA, Ascoli C, Huang Y, Perkins DL, Finn PW. Declining Pulmonary Function in Interstitial Lung Disease Linked to Lymphocyte Dysfunction. Am J Respir Crit Care Med 2020; 201:610-613. [PMID: 31661301 PMCID: PMC7047459 DOI: 10.1164/rccm.201910-1909le] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Cody A. Schott
- University of Illinois at Chicago College of MedicineChicago, Illinois
| | - Christian Ascoli
- University of Illinois at Chicago College of MedicineChicago, Illinois
| | - Yue Huang
- University of Illinois at Chicago College of MedicineChicago, Illinois
| | - David L. Perkins
- University of Illinois at Chicago College of MedicineChicago, Illinois
| | - Patricia W. Finn
- University of Illinois at Chicago College of MedicineChicago, Illinois
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25
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Damsky W, Young BD, Sloan B, Miller EJ, Obando JA, King B. Treatment of Multiorgan Sarcoidosis With Tofacitinib. ACR Open Rheumatol 2020; 2:106-109. [PMID: 31916703 PMCID: PMC7011417 DOI: 10.1002/acr2.11112] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/27/2019] [Indexed: 12/15/2022] Open
Abstract
Objective Sarcoidosis is an idiopathic inflammatory disorder that is difficult to treat. There is accumulating evidence that constitutive activation of Janus kinase–signal transducer and activator of transcription (JAK‐STAT) signaling occurs in sarcoidosis and represents a target for treatment. Here we report the efficacy of tofacitinib, a Janus kinase (JAK) inhibitor, in a single patient with multiorgan sarcoidosis. Methods A patient with long‐standing multiorgan sarcoidosis who was unresponsive to other commonly used therapies, including methotrexate, prednisone, and tumor necrosis factor α blockade, was treated with tofacitinib. Results Tofacitinib treatment resulted in clinical remission of cutaneous sarcoidosis lesions and resolution of positron emission tomography avid lesions in internal organs after 6 months. An evaluation of lesional tissue and blood before and during treatment showed resolution of granulomatous inflammation and normalization of disease biomarkers. Conclusion This case illustrates the promise of JAK inhibition as a strategy to treat recalcitrant sarcoidosis and suggests that further study of JAK inhibitors in sarcoidosis is needed.
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Affiliation(s)
| | | | - Brett Sloan
- University of Connecticut School of Medicine, Farmington
| | | | | | - Brett King
- Yale School of Medicine, New Haven, Connecticut
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26
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Abstract
Sarcoidosis is a highly variable granulomatous multisystem syndrome. It affects individuals in the prime years of life; both the frequency and severity of sarcoidosis are greater in economically disadvantaged populations. The diagnosis, assessment, and management of pulmonary sarcoidosis have evolved as new technologies and therapies have been adopted. Transbronchial needle aspiration guided by endobronchial ultrasound has replaced mediastinoscopy in many centers. Advanced imaging modalities, such as fluorodeoxyglucose positron emission tomography scanning, and the widespread availability of magnetic resonance imaging have led to more sensitive assessment of organ involvement and disease activity. Although several new insights about the pathogenesis of sarcoidosis exist, no new therapies have been specifically developed for use in the disease. The current or proposed use of immunosuppressive medications for sarcoidosis has been extrapolated from other disease states; various novel pathways are currently under investigation as therapeutic targets. Coupled with the growing recognition of corticosteroid toxicities for managing sarcoidosis, the use of corticosteroid sparing anti-sarcoidosis medications is likely to increase. Besides treatment of granulomatous inflammation, recognition and management of the non-granulomatous complications of pulmonary sarcoidosis are needed for optimal outcomes in patients with advanced disease.
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Affiliation(s)
- Daniel A Culver
- Department of Pulmonary Medicine, Respiratory Institute, Department of Inflammation and Immunity, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA
| | - Marc A Judson
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, NY, USA
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27
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Casanova N, Zhou T, Gonzalez-Garay ML, Rosas IO, Goldberg HJ, Ryter SW, Collard HR, El-Chemaly S, Flaherty KR, Hunninghake GM, Lasky JA, Lederer DJ, Machado RF, Martinez FJ, Noth I, Raghu G, Choi AMK, Garcia JGN. Low Dose Carbon Monoxide Exposure in Idiopathic Pulmonary Fibrosis Produces a CO Signature Comprised of Oxidative Phosphorylation Genes. Sci Rep 2019; 9:14802. [PMID: 31615996 PMCID: PMC6794274 DOI: 10.1038/s41598-019-50585-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 09/10/2019] [Indexed: 01/22/2023] Open
Abstract
Compelling preclinical studies indicate that low-dose carbon monoxide (CO) abrogates experimental lung fibrosis. We recently reported the results of a multicenter, double-blinded, clinical trial of inhaled CO in patients with idiopathic pulmonary fibrosis (IPF). Identifying no significantly changes in metalloproteinase-7 (MMP7) serum concentration, or secondary endpoints of physiologic measurements, hospitalization, death, or patient-reported outcomes. In the present study, we evaluated the effect of low dose CO exposure (100–200 ppm) for 12 weeks on genome-wide gene expression in peripheral blood mononuclear cells (PBMC) derived from these IPF study subjects. We conducted transcriptome profiling on 38 IPF subjects with time points available at 0, 12, and 24 weeks. Total RNA isolated from PBMCs was hybridized onto the Affymetrix Human Gene 2.0 ST Array. We identified 621 genes significantly upregulated in the 24-week CO exposed group compared with the 12-week. Pathway analysis demonstrated association with Oxidative Phosphorylation (adjusted P < 0.05). We identified a clear CO signature dominated with 23 oxidative phosphorylation-related genes (FDR <10%). We confirmed the expression of nine selected gene products using Nanostring’s nCounter analysis system. These findings suggest this signature may serve as a potential genomic biomarker for CO exposure and for potential titration of dosage to allow precision testing of therapies in future low dose CO therapeutic studies in IPF.
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Affiliation(s)
- Nancy Casanova
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV, USA
| | | | - Ivan O Rosas
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hilary J Goldberg
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stefan W Ryter
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Harold R Collard
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Souheil El-Chemaly
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kevin R Flaherty
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Gary M Hunninghake
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joseph A Lasky
- Pulmonary and Critical Care Medicine Section, Tulane University Medical School, New Orleans, LA, USA
| | - David J Lederer
- Division of Pulmonary and Critical Care Medicine, Columbia University Medical Center, New York, NY, USA
| | - Roberto F Machado
- Division of Pulmonary, Critical Care, Indiana University, Indianapolis, IN, USA
| | | | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, IL, USA
| | - Ganesh Raghu
- Division of Pulmonary and Critical Care Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Augustine M K Choi
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Joe G N Garcia
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA.
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28
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Stern BJ, Royal W, Gelfand JM, Clifford DB, Tavee J, Pawate S, Berger JR, Aksamit AJ, Krumholz A, Pardo CA, Moller DR, Judson MA, Drent M, Baughman RP. Definition and Consensus Diagnostic Criteria for Neurosarcoidosis: From the Neurosarcoidosis Consortium Consensus Group. JAMA Neurol 2019; 75:1546-1553. [PMID: 30167654 DOI: 10.1001/jamaneurol.2018.2295] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Importance The Neurosarcoidosis Consortium Consensus Group, an expert panel of physicians experienced in the management of patients with sarcoidosis and neurosarcoidosis, engaged in an iterative process to define neurosarcoidosis and develop a practical diagnostic approach to patients with suspected neurosarcoidosis. This panel aimed to develop a consensus clinical definition of neurosarcoidosis to enhance the clinical care of patients with suspected neurosarcoidosis and to encourage standardization of research initiatives that address this disease. Observations The work of this collaboration included a review of the manifestations of neurosarcoidosis and the establishment of an approach to the diagnosis of this disorder. The proposed consensus diagnostic criteria, which reflect current knowledge, provide definitions for possible, probable, and definite central and peripheral nervous system sarcoidosis. The definitions emphasize the need to evaluate patients with findings suggestive of neurosarcoidosis for alternate causal factors, including infection and malignant neoplasm. Also emphasized is the need for biopsy, whenever feasible and advisable according to clinical context and affected anatomy, of nonneural tissue to document the presence of systemic sarcoidosis and support a diagnosis of probable neurosarcoidosis or of neural tissue to support a diagnosis of definite neurosarcoidosis. Conclusions and Relevance Diverse disease presentations and lack of specificity of relevant diagnostic tests contribute to diagnostic uncertainty. This uncertainty is compounded by the absence of a pathognomonic histologic tissue examination. The diagnostic criteria we propose are designed to focus investigations on NS as accurately as possible, recognizing that multiple pathophysiologic pathways may lead to the clinical manifestations we currently term NS. Research recognizing the clinical heterogeneity of this diagnosis may open the door to identifying meaningful biologic factors that may ultimately contribute to better treatments.
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Affiliation(s)
- Barney J Stern
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland
| | - Walter Royal
- Department of Neurobiology and the Neuroscience Institute, Morehouse School of Medicine, Atlanta, Georgia
| | - Jeffrey M Gelfand
- Department of Neurology, University of California, San Francisco, San Francisco
| | - David B Clifford
- Department of Neurology, Washington University in St Louis, St Louis, Missouri
| | - Jinny Tavee
- Department of Neurology, Northwestern University, Chicago, Illinois
| | - Siddharama Pawate
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joseph R Berger
- Department of Neurology, University of Pennsylvania, Philadelphia
| | | | - Allan Krumholz
- Department of Neurology, University of Maryland, Baltimore
| | - Carlos A Pardo
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland
| | - David R Moller
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Marc A Judson
- Department of Medicine, Albany Medical College, Albany, New York
| | - Marjolein Drent
- Department of Pharmacology and Toxicology, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, Interstitial Lung Disease Center of Excellence, St. Antonius Hospital, Nieuwegein, the Netherlands
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29
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Cowman SA, Jacob J, Hansell DM, Kelleher P, Wilson R, Cookson WOC, Moffatt MF, Loebinger MR. Whole-Blood Gene Expression in Pulmonary Nontuberculous Mycobacterial Infection. Am J Respir Cell Mol Biol 2019; 58:510-518. [PMID: 29206475 DOI: 10.1165/rcmb.2017-0230oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The factors predisposing toward the development of pulmonary nontuberculous mycobacterial (pNTM) disease and influencing disease progression remain unclear. Impaired immune responses have been reported in individuals with pNTM disease, but data are limited and inconsistent. In this study, we sought to use gene expression profiling to examine the host response to pNTM disease. Microarray analysis of whole-blood gene expression was performed on 25 subjects with pNTM disease and 27 uninfected control subjects with respiratory disease. Gene expression results were compared with phenotypic variables and survival data. Compared with uninfected control subjects, pNTM disease was associated with downregulation of 213 transcripts enriched for terms related to T cell signaling, including IFNG. Reduced IFNG expression was associated with more severe computed tomography changes and impaired lung function. Mortality was associated with the expression of transcripts related to the innate immune response and inflammation, whereas transcripts related to T and B cell function were associated with improved survival. These findings suggest that pNTM disease is associated with an aberrant immune response, which may reflect an underlying propensity to infection or result from NTM infection itself. There were important differences in the immune response associated with survival and mortality in pNTM disease.
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Affiliation(s)
- Steven A Cowman
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom.,2 Host Defence Unit and
| | - Joseph Jacob
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom.,3 Department of Radiology, Royal Brompton Hospital, London, United Kingdom
| | - David M Hansell
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom.,3 Department of Radiology, Royal Brompton Hospital, London, United Kingdom
| | - Peter Kelleher
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom.,2 Host Defence Unit and
| | - Robert Wilson
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom.,2 Host Defence Unit and
| | - William O C Cookson
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Miriam F Moffatt
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Michael R Loebinger
- 1 National Heart and Lung Institute, Imperial College London, London, United Kingdom.,2 Host Defence Unit and
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30
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Damsky W, Thakral D, McGeary MK, Leventhal J, Galan A, King B. Janus kinase inhibition induces disease remission in cutaneous sarcoidosis and granuloma annulare. J Am Acad Dermatol 2019; 82:612-621. [PMID: 31185230 DOI: 10.1016/j.jaad.2019.05.098] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/20/2019] [Accepted: 05/24/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Sarcoidosis and granuloma annulare (GA) are cutaneous granulomatous disorders that can be difficult to treat. There is evidence of underlying Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway activation in sarcoidosis, suggesting that JAK inhibition might be effective. OBJECTIVE To evaluate treatment with tofacitinib, a JAK inhibitor, in patients with recalcitrant sarcoidosis and GA. METHODS A prospective evaluation of tofacitinib in 4 consecutive patients with recalcitrant cutaneous sarcoidosis (n = 3) and generalized GA (n = 1) was conducted. Immunohistochemical analysis of skin biopsy specimens from other patients with sarcoidosis (n = 21) and GA (n = 17) was performed to characterize patterns of JAK-STAT pathway activation. RESULTS Tofacitinib resulted in a mean improvement in the baseline Cutaneous Sarcoidosis Activity and Morphology Instrument and Granuloma Annulare Scoring Index scores of 96% (standard deviation, 2%). Histologic resolution of disease was documented in all patients (3 out of 3) who had skin biopsies while receiving therapy. Constitutive STAT1 and STAT3 activation was observed in both sarcoidosis and GA, albeit in different patterns. Signal regulatory protein α may explain the differences in JAK-STAT signaling between sarcoidosis and GA. LIMITATIONS The study is limited by the small number of participants. CONCLUSIONS Tofacitinib resulted in dramatic improvement in 4 patients with cutaneous sarcoidosis and GA. Larger studies are underway to better understand this effect.
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Affiliation(s)
- William Damsky
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut.
| | - Durga Thakral
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
| | - Meaghan K McGeary
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
| | - Jonathan Leventhal
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
| | - Anjela Galan
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
| | - Brett King
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut.
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31
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Damsky W, Thakral D, Emeagwali N, Galan A, King B. Tofacitinib Treatment and Molecular Analysis of Cutaneous Sarcoidosis. N Engl J Med 2018; 379:2540-2546. [PMID: 30586518 PMCID: PMC6351852 DOI: 10.1056/nejmoa1805958] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There is evidence that Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling plays a role in the pathogenesis of sarcoidosis. We treated a patient with cutaneous sarcoidosis with the JAK inhibitor tofacitinib; the patient had not previously had a response to medications and had not received systemic glucocorticoids. This treatment resulted in clinical and histologic remission of her skin disease. Sequencing of RNA and immunohistochemical examination of skin-lesion samples obtained from the patient before and during therapy and immunohistochemical testing of lesion samples obtained from other patients with cutaneous sarcoidosis support a role for JAK-STAT signaling in cutaneous sarcoidosis. (Funded by the Ranjini and Ajay Poddar Resource Fund for Dermatologic Diseases Research and others.).
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Affiliation(s)
- William Damsky
- From the Departments of Dermatology (W.D., D.T., A.G., B.K.), Immunobiology (W.D.), and Pathology (A.G.) and the Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine (N.E.), Yale School of Medicine, New Haven, CT
| | - Durga Thakral
- From the Departments of Dermatology (W.D., D.T., A.G., B.K.), Immunobiology (W.D.), and Pathology (A.G.) and the Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine (N.E.), Yale School of Medicine, New Haven, CT
| | - Nkiruka Emeagwali
- From the Departments of Dermatology (W.D., D.T., A.G., B.K.), Immunobiology (W.D.), and Pathology (A.G.) and the Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine (N.E.), Yale School of Medicine, New Haven, CT
| | - Anjela Galan
- From the Departments of Dermatology (W.D., D.T., A.G., B.K.), Immunobiology (W.D.), and Pathology (A.G.) and the Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine (N.E.), Yale School of Medicine, New Haven, CT
| | - Brett King
- From the Departments of Dermatology (W.D., D.T., A.G., B.K.), Immunobiology (W.D.), and Pathology (A.G.) and the Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine (N.E.), Yale School of Medicine, New Haven, CT
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Rotenberg C, Besnard V, Brillet PY, Giraudier S, Nunes H, Valeyre D. Dramatic response of refractory sarcoidosis under ruxolitinib in a patient with associated JAK2-mutated polycythemia. Eur Respir J 2018; 52:13993003.01482-2018. [DOI: 10.1183/13993003.01482-2018] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/27/2018] [Indexed: 11/05/2022]
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Abstract
Sarcoidosis is a disease with heterogeneous manifestations and outcomes, varying in part on the basis of organ involvement. Specifically, patients with sarcoidosis at risk for poor outcomes include individuals with treatment-resistant pulmonary sarcoidosis, including fibrotic pulmonary disease and pulmonary hypertension, as well as those with cardiac, neurologic, and multiorgan disease. The limited but available data relating to these patients with high-risk sarcoidosis, defined as those patients with presentations requiring medical intervention to avoid progressive disability or premature death, was evaluated as part of the National Heart, Lung, and Blood Institute's workshop to improve understanding of these disease manifestations. In particular, knowledge gaps that preclude a greater understanding of the pathogenesis and management of these severe sarcoidosis clinical phenotypes were identified in the workshop. Research strategies are proposed to address critical knowledge gaps that would further our understanding of these disease manifestations and enhance the care of these patients.
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Hočevar K, Maver A, Kunej T, Peterlin B. Sarcoidosis Related Novel Candidate Genes Identified by Multi-Omics Integrative Analyses. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 22:322-331. [PMID: 29688803 DOI: 10.1089/omi.2018.0027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Sarcoidosis is a multifactorial systemic disease characterized by granulomatous inflammation and greatly impacting on global public health. The etiology and mechanisms of sarcoidosis are not fully understood. Recent high-throughput biological research has generated vast amounts of multi-omics big data on sarcoidosis, but their significance remains to be determined. We sought to identify novel candidate regions, and genes consistently altered in heterogeneous omics studies so as to reveal the underlying molecular mechanisms. We conducted a comprehensive integrative literature analysis on global data on sarcoidosis, including genomic, transcriptomic, proteomic, and phenomic studies. We performed positional integration analysis of 38 eligible datasets originating from 17 different biological layers. Using the integration interval length of 50 kb, we identified 54 regions reaching significance value p ≤ 0.0001 and 15 regions with significance value p ≤ 0.00001, when applying more stringent criteria. Secondary literature analysis of the top 20 regions, with the most significant accumulation of signals, revealed several novel candidate genes for which associations with sarcoidosis have not yet been established, but have considerable support for their involvement based on omic data. These new plausible candidate genes include NELFE, CFB, EGFL7, AGPAT2, FKBPL, NRC3, and NEU1. Furthermore, annotated data were prepared to enable custom visualization and browsing of these sarcoidosis related omics evidence in the University of California Santa Cruz (UCSC) Genome Browser. Further multi-omics approaches are called for sarcoidosis biomarkers and diagnostic and therapeutic innovation. Our approach for harnessing multi-omics data and the findings presented herein reflect important steps toward understanding the etiology and underlying pathological mechanisms of sarcoidosis.
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Affiliation(s)
- Keli Hočevar
- 1 Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
| | - Aleš Maver
- 1 Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
| | - Tanja Kunej
- 2 Biotechnical Faculty, Department of Animal Science, University of Ljubljana , Jamnikarjeva 101, Ljubljana, Slovenia
| | - Borut Peterlin
- 1 Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
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35
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Transcriptome profiles in sarcoidosis and their potential role in disease prediction. Curr Opin Pulm Med 2018; 23:487-492. [PMID: 28590292 DOI: 10.1097/mcp.0000000000000403] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE OF REVIEW Sarcoidosis is a systemic disease defined by the presence of nonnecrotizing granuloma in the absence of any known cause. Although the heterogeneity of sarcoidosis is well characterized clinically, the transcriptome of sarcoidosis and underlying molecular mechanisms are not. The signal of all transcripts, small and long noncoding RNAs, can be detected using microarrays or RNA-Sequencing. Analyzing the transcriptome of tissues that are directly affected by granulomas is of great importance to understand biology of the disease and may be predictive of disease and treatment outcome. RECENT FINDINGS Multiple genome wide expression studies performed on sarcoidosis affected tissues were published in the last 11 years. Published studies focused on differences in gene expression between sarcoidosis vs. control tissues, stable vs. progressive sarcoidosis, as well as sarcoidosis vs. other diseases. Strikingly, all these transcriptomics data confirm the key role of TH1 immune response in sarcoidosis and particularly of interferon-γ (IFN-γ) and type I IFN-driven signaling pathways. SUMMARY The steps toward transcriptomics of sarcoidosis in precision medicine highlight the potentials of this approach. Large prospective follow-up studies are required to identify signatures predictive of disease progression and outcome.
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Ascoli C, Huang Y, Schott C, Turturice BA, Metwally A, Perkins DL, Finn PW. A Circulating MicroRNA Signature Serves as a Diagnostic and Prognostic Indicator in Sarcoidosis. Am J Respir Cell Mol Biol 2018; 58:40-54. [PMID: 28812922 DOI: 10.1165/rcmb.2017-0207oc] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) act as post-transcriptional regulators of gene expression. In sarcoidosis, aberrant miRNA expression may enhance immune responses mounted against an unknown antigenic agent. We tested whether a distinct miRNA signature functions as a diagnostic biomarker and explored its role as an immune modulator in sarcoidosis. The expression of miRNAs in peripheral blood mononuclear cells from subjects who met clinical and histopathologic criteria for sarcoidosis was compared with that observed in matched controls in the ACCESS (A Case Controlled Etiologic Study of Sarcoidosis) study. Signature miRNAs were determined by miRNA microarray analysis and validated by quantitative RT-PCR. Microarray analysis identified 54 mature, human feature miRNAs that were differentially expressed between the groups. Significant feature miRNAs that distinguished subjects with sarcoidosis from controls were selected by means of probabilistic models adjusted for clinical variables. Eight signature miRNAs were chosen to verify the diagnosis of sarcoidosis in a validation cohort, and distinguished subjects with sarcoidosis from controls with a positive predictive value of 88%. We identified both novel and previously described genes and molecular pathways associated with sarcoidosis as targets of these signature miRNAs. Additionally, we demonstrate that signature miRNAs (hsa-miR-150-3p and hsa-miR-342-5p) are significantly associated with reduced lymphocytes and airflow limitations, both of which are known markers of a poor prognosis. Together, these findings suggest that a circulating miRNA signature serves as a noninvasive biomarker that supports the diagnosis of sarcoidosis. Future studies will test the miRNA signature as a prognostication tool to identify unfavorable changes associated with poor clinical outcomes in sarcoidosis.
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Affiliation(s)
- Christian Ascoli
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine
| | - Yue Huang
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine
| | - Cody Schott
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine.,Department of Microbiology and Immunology
| | - Benjamin A Turturice
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine.,Department of Microbiology and Immunology
| | | | - David L Perkins
- Department of Bioengineering.,Division of Nephrology, Department of Medicine, and.,Department of Surgery, University of Illinois at Chicago, Chicago, Illinois
| | - Patricia W Finn
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine.,Department of Microbiology and Immunology
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The Pathogenesis of Pulmonary Sarcoidosis and Implications for Treatment. Chest 2017; 153:1432-1442. [PMID: 29224832 DOI: 10.1016/j.chest.2017.11.030] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/20/2017] [Accepted: 11/26/2017] [Indexed: 12/31/2022] Open
Abstract
Thoracic sarcoidosis is the most common form of sarcoidosis, encompassing a heterogeneous group of patients with a wide range of clinical features and associated outcomes. The distinction between isolated thoracic lymphadenopathy and pulmonary involvement matters. Morbidity is often higher, and long-term outcomes are worse for the latter. Although inflammatory infiltrates in pulmonary sarcoidosis may resolve, persistent disease activity is common and can result in lung fibrosis. Given the distinct clinical features and natural history of pulmonary sarcoidosis, its pathogenesis may differ in important ways from other sarcoidosis manifestations. This review highlights recent advances in the pathogenesis of pulmonary sarcoidosis, including the nature of the sarcoidosis antigen, the role of serum amyloid A and other host factors that contribute to alterations in innate immunity, factors that shape adaptive T-cell profiles in the lung, and how these mechanisms influence the maintenance of granulomatous inflammation in sarcoidosis. We discuss questions raised by recent findings, including the role of innate immunity in the pathogenesis, the meaning of immune cell exhaustion, and mechanisms that may contribute to lung fibrosis in sarcoidosis. We conclude with a reflection on when and how immunosuppressive therapies may be helpful for pulmonary sarcoidosis, a consideration of nonpharmacologic management strategies, and a survey of potential novel therapeutic targets for this vexing disease.
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38
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Moller DR, Rybicki BA, Hamzeh NY, Montgomery CG, Chen ES, Drake W, Fontenot AP. Genetic, Immunologic, and Environmental Basis of Sarcoidosis. Ann Am Thorac Soc 2017; 14:S429-S436. [PMID: 29073364 PMCID: PMC5822412 DOI: 10.1513/annalsats.201707-565ot] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/24/2017] [Indexed: 12/24/2022] Open
Abstract
Sarcoidosis is a multisystem disease with tremendous heterogeneity in disease manifestations, severity, and clinical course that varies among different ethnic and racial groups. To better understand this disease and to improve the outcomes of patients, a National Heart, Lung, and Blood Institute workshop was convened to assess the current state of knowledge, gaps, and research needs across the clinical, genetic, environmental, and immunologic arenas. We also explored to what extent the interplay of the genetic, environmental, and immunologic factors could explain the different phenotypes and outcomes of patients with sarcoidosis, including the chronic phenotypes that have the greatest healthcare burden. The potential use of current genetic, epigenetic, and immunologic tools along with study approaches that integrate environmental exposures and precise clinical phenotyping were also explored. Finally, we made expert panel-based consensus recommendations for research approaches and priorities to improve our understanding of the effect of these factors on the health outcomes in sarcoidosis.
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Affiliation(s)
- David R. Moller
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore Maryland
| | - Ben A. Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, Michigan
| | | | - Courtney G. Montgomery
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Edward S. Chen
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore Maryland
| | - Wonder Drake
- Vanderbilt University School of Medicine, Nashville, Tennessee; and
| | - Andrew P. Fontenot
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
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Celada LJ, Rotsinger JE, Young A, Shaginurova G, Shelton D, Hawkins C, Drake WP. Programmed Death-1 Inhibition of Phosphatidylinositol 3-Kinase/AKT/Mechanistic Target of Rapamycin Signaling Impairs Sarcoidosis CD4 + T Cell Proliferation. Am J Respir Cell Mol Biol 2017; 56:74-82. [PMID: 27564547 DOI: 10.1165/rcmb.2016-0037oc] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Patients with progressive sarcoidosis exhibit increased expression of programmed death-1 (PD-1) receptor on their CD4+ T cells. Up-regulation of this marker of T cell exhaustion is associated with a reduction in the proliferative response to T cell receptor (TCR) stimulation, a defect that is reversed by PD-1 pathway blockade. Genome-wide association studies and microarray analyses have correlated signaling downstream from the TCR with sarcoidosis disease severity, but the mechanism is not yet known. Reduced phosphatidylinositol 3-kinase (PI3K)/AKT expression inhibits proliferation by inhibiting cell cycle progression. To test the hypothesis that PD-1 expression attenuates TCR-dependent activation of PI3K/AKT activity in progressive systemic sarcoidosis, we analyzed PI3K/AKT/mechanistic target of rapamycin (mTOR) expression at baseline and after PD-1 pathway blockade in CD4+ T cells isolated from patients with sarcoidosis and healthy control subjects. We confirmed an increased percentage of PD-1+ CD4+ T cells and reduced proliferative capacity in patients with sarcoidosis compared with healthy control subjects (P < 0.001). There was a negative correlation with PD-1 expression and proliferative capacity (r = -0.70, P < 0.001). Expression of key mediators of cell cycle progression, including PI3K and AKT, were significantly decreased. Gene and protein expression levels reverted to healthy control levels after PD-1 pathway blockade. Reduction in sarcoidosis CD4+ T cell proliferative capacity is secondary to altered expression of key mediators of cell cycle progression, including the PI3K/AKT/mTOR pathway, via PD-1 up-regulation. This supports the concept that PD-1 up-regulation drives the immunologic deficits associated with sarcoidosis severity by inducing signaling aberrancies in key mediators of cell cycle progression.
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Affiliation(s)
- Lindsay J Celada
- 1 Division of Infectious Diseases, Department of Medicine, and.,2 Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | - Anjuli Young
- 1 Division of Infectious Diseases, Department of Medicine, and
| | - Guzel Shaginurova
- 2 Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | | | - Wonder P Drake
- 1 Division of Infectious Diseases, Department of Medicine, and.,2 Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee
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40
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Zhou T, Casanova N, Pouladi N, Wang T, Lussier Y, Knox KS, Garcia JGN. Identification of Jak-STAT signaling involvement in sarcoidosis severity via a novel microRNA-regulated peripheral blood mononuclear cell gene signature. Sci Rep 2017; 7:4237. [PMID: 28652588 PMCID: PMC5484682 DOI: 10.1038/s41598-017-04109-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 05/10/2017] [Indexed: 11/28/2022] Open
Abstract
Sarcoidosis is a granulomatous lung disorder of unknown cause. The majority of individuals with sarcoidosis spontaneously achieve full remission (uncomplicated sarcoidosis), however, ~20% of sarcoidosis-affected individuals experience progressive lung disease or cardiac and nervous system involvement (complicated sarcoidosis). We investigated peripheral blood mononuclear cell (PBMC) microRNA and protein-coding gene expression data from healthy controls and patients with uncomplicated or complicated sarcoidosis. We identified 46 microRNAs and 1,559 genes that were differentially expressed across a continuum of sarcoidosis severity (healthy control → uncomplicated sarcoidosis → complicated sarcoidosis). A total of 19 microRNA-mRNA regulatory pairs were identified within these deregulated microRNAs and mRNAs, which consisted of 17 unique protein-coding genes yielding a 17-gene signature. Pathway analysis of the 17-gene signature revealed Jak-STAT signaling pathway as the most significantly represented pathway. A severity score was assigned to each patient based on the expression of the 17-gene signature and a significant increasing trend in the severity score was observed from healthy control, to uncomplicated sarcoidosis, and finally to complicated sarcoidosis. In addition, this microRNA-regulated gene signature differentiates sarcoidosis patients from healthy controls in independent validation cohorts. Our study suggests that PBMC gene expression is useful in diagnosis of sarcoidosis.
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Affiliation(s)
- Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Nancy Casanova
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Nima Pouladi
- Center for Bioinformatics and Biostatistics, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Ting Wang
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Yves Lussier
- Center for Bioinformatics and Biostatistics, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Kenneth S Knox
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Joe G N Garcia
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA.
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41
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RNA-sequencing Identifies Novel Pathways in Sarcoidosis Monocytes. Sci Rep 2017; 7:2720. [PMID: 28577019 PMCID: PMC5457404 DOI: 10.1038/s41598-017-02941-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/25/2017] [Indexed: 12/21/2022] Open
Abstract
Sarcoidosis is a complex systemic granulomatous disorder of unknown etiology. Genome-wide association studies have not been able to explain a causative role for nucleotide variation in its pathogenesis. The goal of the present study was to identify the gene expression profile and the cellular pathways altered in sarcoidosis monocytes via RNA-sequencing. Peripheral blood monocytes play a role in sarcoidosis inflammation. Therefore, we determined and compared the transcriptional signature of monocytes from peripheral blood from sarcoidosis patients and healthy controls via RNA-sequencing. We found 2,446 differentially expressed (DE) genes between sarcoidosis and healthy control monocytes. Analysis of these DE genes showed enrichment for ribosome, phagocytosis, lysosome, proteasome, oxidative phosphorylation and metabolic pathways. RNA-sequencing identified upregulation of genes involved in phagocytosis and lysosomal pathway in sarcoidosis monocytes, whereas genes involved in proteasome degradation and ribosomal pathways were downregulated. Further studies are needed to investigate the role of specific genes involved in the identified pathways and their possible interaction leading to sarcoidosis pathology.
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42
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Association of circulating transcriptomic profiles with mortality in sickle cell disease. Blood 2017; 129:3009-3016. [PMID: 28373264 DOI: 10.1182/blood-2016-11-752279] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/27/2017] [Indexed: 12/27/2022] Open
Abstract
Sickle cell disease (SCD) complications are associated with increased morbidity and risk of mortality. We sought to identify a circulating transcriptomic profile predictive of these poor outcomes in SCD. Training and testing cohorts consisting of adult patients with SCD were recruited and prospectively followed. A pathway-based signature derived from grouping peripheral blood mononuclear cell transcriptomes distinguished 2 patient clusters with differences in survival in the training cohort. These findings were validated in a testing cohort in which the association between cluster 1 molecular profiling and mortality remained significant in a fully adjusted model. In a third cohort of West African children with SCD, cluster 1 differentiated SCD severity using a published scoring index. Finally, a risk score composed of assigning weights to cluster 1 profiling, along with established clinical risk factors using tricuspid regurgitation velocity, white blood cell count, history of acute chest syndrome, and hemoglobin levels, demonstrated a higher hazard ratio for mortality in both the training and testing cohorts compared with clinical risk factors or cluster 1 data alone. Circulating transcriptomic profiles are a powerful method to risk-stratify severity of disease and poor outcomes in both children and adults, respectively, with SCD and highlight potential associated molecular pathways.
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43
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Monast CS, Li K, Judson MA, Baughman RP, Wadman E, Watt R, Silkoff PE, Barnathan ES, Brodmerkel C. Sarcoidosis extent relates to molecular variability. Clin Exp Immunol 2017; 188:444-454. [PMID: 28205212 DOI: 10.1111/cei.12942] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2017] [Indexed: 12/22/2022] Open
Abstract
The molecular basis of sarcoidosis phenotype heterogeneity and its relationship to effective treatment of sarcoidosis have not been elucidated. Peripheral samples from sarcoidosis subjects who participated in a Phase II study of golimumab [anti-tumour necrosis factor (TNF)-α] and ustekinumab [anti-interleukin (IL)-12p40] were used to measure the whole blood transcriptome and levels of serum proteins. Differential gene and protein expression analyses were used to explore the molecular differences between sarcoidosis phenotypes as defined by extent of organ involvement. The same data were also used in conjunction with an enrichment algorithm to identify gene expression changes associated with treatment with study drugs compared to placebo. Our analyses revealed marked heterogeneity among the three sarcoidosis phenotypes included in the study cohort, including striking differences in enrichment of the interferon pathway. Conversely, enrichments of multiple pathways, including T cell receptor signalling, were similar among phenotypes. We also identify differences between treatment with golimumab and ustekinumab that may explain the differences in trends for clinical efficacy observed in the trial. We find that molecular heterogeneity is associated with sarcoidosis in a manner that may be related to the extent of organ involvement. These findings may help to explain the difficulty in identifying clinically efficacious sarcoidosis treatments and suggest hypotheses for improved therapeutic strategies.
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Affiliation(s)
- C S Monast
- Janssen Research & Development, LLC, Spring House, PA, USA
| | - K Li
- Albany Medical College, Albany, NY, USA
| | | | - R P Baughman
- University of Cincinnati Medical Center, Cincinnati, OH, USA
| | - E Wadman
- Janssen Research & Development, LLC, Spring House, PA, USA
| | - R Watt
- Janssen Research & Development, LLC, Spring House, PA, USA
| | - P E Silkoff
- Janssen Research & Development, LLC, Spring House, PA, USA
| | - E S Barnathan
- Janssen Research & Development, LLC, Spring House, PA, USA
| | - C Brodmerkel
- Janssen Research & Development, LLC, Spring House, PA, USA
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44
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Singla S, Zhou T, Javaid K, Abbasi T, Casanova N, Zhang W, Ma SF, Wade MS, Noth I, Sweiss NJ, Garcia JGN, Machado RF. Expression profiling elucidates a molecular gene signature for pulmonary hypertension in sarcoidosis. Pulm Circ 2016; 6:465-471. [PMID: 28090288 PMCID: PMC5210052 DOI: 10.1086/688316] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/21/2016] [Indexed: 12/11/2022] Open
Abstract
Pulmonary hypertension (PH), when it complicates sarcoidosis, carries a poor prognosis, in part because it is difficult to detect early in patients with worsening respiratory symptoms. Pathogenesis of sarcoidosis occurs via incompletely characterized mechanisms that are distinct from the mechanisms of pulmonary vascular remodeling well known to occur in conjunction with other chronic lung diseases. To address the need for a biomarker to aid in early detection as well as the gap in knowledge regarding the mechanisms of PH in sarcoidosis, we used genome-wide peripheral blood gene expression analysis and identified an 18-gene signature capable of distinguishing sarcoidosis patients with PH (n = 8), sarcoidosis patients without PH (n = 17), and healthy controls (n = 45). The discriminative accuracy of this 18-gene signature was 100% in separating sarcoidosis patients with PH from those without it. If validated in a large replicate cohort, this signature could potentially be used as a diagnostic molecular biomarker for sarcoidosis-associated PH.
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Affiliation(s)
- Sunit Singla
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- These authors contributed equally
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, USA
- These authors contributed equally
| | - Kamran Javaid
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- These authors contributed equally
| | - Taimur Abbasi
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Nancy Casanova
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, Arizona, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shwu-Fan Ma
- Section of Pulmonary/Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Michael S. Wade
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Imre Noth
- Section of Pulmonary/Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Nadera J. Sweiss
- Section of Rheumatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Joe G. N. Garcia
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, Arizona, USA
| | - Roberto F. Machado
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
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45
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Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) Study. Sarcoidosis Protocol. Ann Am Thorac Soc 2016; 12:1561-71. [PMID: 26193069 DOI: 10.1513/annalsats.201503-172ot] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Sarcoidosis is a systemic disease characterized by noncaseating granulomatous inflammation with tremendous clinical heterogeneity and uncertain pathobiology and lacking in clinically useful biomarkers. The Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study is an observational cohort study designed to explore the role of the lung microbiome and genome in these two diseases. This article describes the design and rationale for the GRADS study sarcoidosis protocol. The study addresses the hypothesis that distinct patterns in the lung microbiome are characteristic of sarcoidosis phenotypes and are reflected in changes in systemic inflammatory responses as measured by peripheral blood changes in gene transcription. The goal is to enroll 400 participants, with a minimum of 35 in each of 9 clinical phenotype subgroups prioritized by their clinical relevance to understanding of the pathobiology and clinical heterogeneity of sarcoidosis. Participants with a confirmed diagnosis of sarcoidosis undergo a baseline visit with self-administered questionnaires, chest computed tomography, pulmonary function tests, and blood and urine testing. A research or clinical bronchoscopy with a research bronchoalveolar lavage will be performed to obtain samples for genomic and microbiome analyses. Comparisons will be made by blood genomic analysis and with clinical phenotypic variables. A 6-month follow-up visit is planned to assess each participant's clinical course. By the use of an integrative approach to the analysis of the microbiome and genome in selected clinical phenotypes, the GRADS study is powerfully positioned to inform and direct studies on the pathobiology of sarcoidosis, identify diagnostic or prognostic biomarkers, and provide novel molecular phenotypes that could lead to improved personalized approaches to therapy for sarcoidosis.
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46
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Enhanced LPS-induced activation of IL-27 signalling in sarcoidosis. Respir Med 2016; 117:243-53. [PMID: 27492538 DOI: 10.1016/j.rmed.2016.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 12/13/2022]
Abstract
RATIONALE Granulomas in sarcoidosis have recently been described as containing Interleukin (IL)-27, one of the members of the IL-12 family of cytokines, which also includes IL-35. Levels of these cytokines and the IL-27 receptor subunits were hypothesised to differ between patients with sarcoidosis compared to healthy controls in peripheral blood. METHODS Using a cross-sectional study design, plasma and peripheral blood mononuclear cells (PBMC) were collected from patients and control subjects. Protein and mRNA (in PBMC) levels for IL-27 and IL-35 (IL27, EBI3, IL12A subunits) as well as IL-27 receptor (IL6ST and IL27RA subunits) were assessed spontaneously and following direct (LPS) and indirect (anti-CD3/28 activation beads) macrophage stimulation using RT- PCR, ELISA and flow cytometry. RESULTS Following stimulation with LPS, PBMC of patients with sarcoidosis displayed significantly enhanced expression of IL27 and EBI3 mRNA (p = 0.020 and p = 0.037 respectively) compared to PBMCs from healthy controls. There was also significantly enhanced production of IL-27 by PBMC from patients with sarcoidosis compared to healthy controls in response to LPS stimulation (p = 0.027). IL6ST mRNA and IL6ST protein were significantly lower in patients with sarcoidosis (mRNA p = 0.0002; MFI p = 0.0015) whilst IL27RA protein levels were significantly higher in patients with sarcoidosis compared to healthy controls (MFI p < 0.0001). Plasma IL-35 protein levels did not differ between control and sarcoidosis subjects (p = 0.23). CONCLUSION These results suggest there may be exaggerated activation of IL-27 signalling in response to LPS in sarcoidosis.
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Bime C, Zhou T, Wang T, Slepian MJ, Garcia JGN, Hecker L. Reactive oxygen species-associated molecular signature predicts survival in patients with sepsis. Pulm Circ 2016; 6:196-201. [PMID: 27252846 DOI: 10.1086/685547] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Sepsis-related multiple organ dysfunction syndrome is a leading cause of death in intensive care units. There is overwhelming evidence that oxidative stress plays a significant role in the pathogenesis of sepsis-associated multiple organ failure; however, reactive oxygen species (ROS)-associated biomarkers and/or diagnostics that define mortality or predict survival in sepsis are lacking. Lung or peripheral blood gene expression analysis has gained increasing recognition as a potential prognostic and/or diagnostic tool. The objective of this study was to identify ROS-associated biomarkers predictive of survival in patients with sepsis. In-silico analyses of expression profiles allowed the identification of a 21-gene ROS-associated molecular signature that predicts survival in sepsis patients. Importantly, this signature performed well in a validation cohort consisting of sepsis patients aggregated from distinct patient populations recruited from different sites. Our signature outperforms randomly generated signatures of the same signature gene size. Our findings further validate the critical role of ROSs in the pathogenesis of sepsis and provide a novel gene signature that predicts survival in sepsis patients. These results also highlight the utility of peripheral blood molecular signatures as biomarkers for predicting mortality risk in patients with sepsis, which could facilitate the development of personalized therapies.
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Affiliation(s)
- Christian Bime
- Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Tong Zhou
- Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Ting Wang
- Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Marvin J Slepian
- Department of Medicine, University of Arizona, Tucson, Arizona, USA; Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA
| | - Joe G N Garcia
- Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Louise Hecker
- Department of Medicine, University of Arizona, Tucson, Arizona, USA; Southern Arizona Veterans Administration Health Care System, Tucson, Arizona, USA
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Kiszałkiewicz J, Piotrowski WJ, Pastuszak-Lewandoska D, Górski P, Antczak A, Górski W, Domańska-Senderowska D, Migdalska-Sęk M, Czarnecka KH, Nawrot E, Brzeziańska-Lasota E. Altered Cyclooxygenase-2 Expression in Pulmonary Sarcoidosis is not Related to Clinical Classifications. Inflammation 2016; 39:1302-9. [PMID: 27188849 DOI: 10.1007/s10753-016-0362-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elevated COX-2 activity is associated with the development of chronic lung diseases leading to bronchial obstruction, including sarcoidosis. The aim of the study was to examine expression pattern of COX-2 messenger RNA (mRNA). Expression was performed by q-PCR method in bronchoalveolar lavage (BAL) cells and peripheral blood (PB) lymphocytes in sarcoidosis patients (n = 61) and control group (n = 30). Analysis of COX-2 mRNA expression level in BAL fluid and PB revealed downregulation in sarcoidosis and control groups. In PB lymphocytes, the statistically significant difference between patients and controls was observed (P = 0.003, Mann-Whitney U test), with higher expression in patients. There were no statistically significant differences between patients without and with parenchymal involvement (stages I vs. II-IV), between patients with acute vs. insidious onset of disease and between patients with abnormal vs. normal spirometry (P > 0.05, Mann-Whitney U test). Results suggest that expression of COX-2 mRNA in patients with pulmonary sarcoidosis is not related to clinical classifications.
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Affiliation(s)
- Justyna Kiszałkiewicz
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, St. Pomorska 251, 92-213, Lodz, Poland
| | - Wojciech J Piotrowski
- Department of Pneumonology and Allergy, 1st Chair of Internal Diseases, Medical University of Lodz, St. Kopcińskiego 22, Lodz, 90-153, Poland
| | - Dorota Pastuszak-Lewandoska
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, St. Pomorska 251, 92-213, Lodz, Poland
| | - Paweł Górski
- Department of Pneumonology and Allergy, 1st Chair of Internal Diseases, Medical University of Lodz, St. Kopcińskiego 22, Lodz, 90-153, Poland
| | - Adam Antczak
- Department of General and Oncological Pulmonology, 1st Chair of Internal Diseases, Medical University of Lodz, St. Kopcińskiego 22, Lodz, 90-153, Poland
| | - Witold Górski
- Department of Pneumonology and Allergy, 1st Chair of Internal Diseases, Medical University of Lodz, St. Kopcińskiego 22, Lodz, 90-153, Poland
| | - Daria Domańska-Senderowska
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, St. Pomorska 251, 92-213, Lodz, Poland
| | - Monika Migdalska-Sęk
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, St. Pomorska 251, 92-213, Lodz, Poland
| | - Karolina H Czarnecka
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, St. Pomorska 251, 92-213, Lodz, Poland
| | - Ewa Nawrot
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, St. Pomorska 251, 92-213, Lodz, Poland
| | - Ewa Brzeziańska-Lasota
- Department of Molecular Bases of Medicine, 1st Chair of Internal Diseases, Medical University of Lodz, St. Pomorska 251, 92-213, Lodz, Poland.
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Li L, Silveira LJ, Hamzeh N, Gillespie M, Mroz PM, Mayer AS, Fingerlin TE, Maier LA. Beryllium-induced lung disease exhibits expression profiles similar to sarcoidosis. Eur Respir J 2016; 47:1797-808. [PMID: 27103383 DOI: 10.1183/13993003.01469-2015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/07/2016] [Indexed: 12/21/2022]
Abstract
A subset of beryllium-exposed workers develop beryllium sensitisation (BeS) which precedes chronic beryllium disease (CBD). We conducted an in-depth analysis of differentially expressed candidate genes in CBD.We performed Affymetrix GeneChip 1.0 ST array analysis on peripheral blood mononuclear cells (PBMCs) from 10 CBD, 10 BeS and 10 beryllium-exposed, nondiseased controls stimulated with BeSO4 or medium. The differentially expressed genes were validated by high-throughput real-time PCR in this group and in an additional group of cases and nonexposed controls. The functional roles of the top candidate genes in CBD were assessed using a pharmacological inhibitor. CBD gene expression data were compared with whole blood and lung tissue in sarcoidosis from the Gene Expression Omnibus.We confirmed almost 450 genes that were significantly differentially expressed between CBD and controls. The top enrichment of genes was for JAK (Janus kinase)-STAT (signal transducer and activator of transcription) signalling. A JAK2 inhibitor significantly decreased tumour necrosis factor-α and interferon-γ production. Furthermore, we found 287 differentially expressed genes overlapped in CBD/sarcoidosis. The top shared pathways included cytokine-cytokine receptor interactions, and Toll-like receptor, chemokine and JAK-STAT signalling pathways.We show that PBMCs demonstrate differentially expressed gene profiles relevant to the immunnopathogenesis of CBD. CBD and sarcoidosis share similar differential expression of pathogenic genes and pathways.
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Affiliation(s)
- Li Li
- Dept of Medicine, National Jewish Health, Denver, CO, USA Division of Pulmonary and Critical Care Sciences, Dept of Medicine, School of Medicine, Denver, CO, USA
| | | | - Nabeel Hamzeh
- Dept of Medicine, National Jewish Health, Denver, CO, USA Division of Pulmonary and Critical Care Sciences, Dept of Medicine, School of Medicine, Denver, CO, USA
| | - May Gillespie
- Dept of Medicine, National Jewish Health, Denver, CO, USA
| | - Peggy M Mroz
- Dept of Medicine, National Jewish Health, Denver, CO, USA
| | - Annyce S Mayer
- Dept of Medicine, National Jewish Health, Denver, CO, USA Division of Pulmonary and Critical Care Sciences, Dept of Medicine, School of Medicine, Denver, CO, USA Environmental Occupational Health Dept, School of Public Health, University of Colorado, Denver, CO, USA
| | | | - Lisa A Maier
- Dept of Medicine, National Jewish Health, Denver, CO, USA Division of Pulmonary and Critical Care Sciences, Dept of Medicine, School of Medicine, Denver, CO, USA Environmental Occupational Health Dept, School of Public Health, University of Colorado, Denver, CO, USA
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Abstract
The diagnosis of sarcoidosis, a systemic granulomatous disease, is based on a compatible clinical-radiological picture and the histological evidence of noncaseating granulomas. Other diseases mimicking sarcoidosis, mostly infections and other granulomatoses, have to be excluded. There is no single test for sarcoidosis, and the presence of granulomas alone does not establish the diagnosis. Symptoms of sarcoidosis are not specific and can be markedly different according to organ involvement and disease course. Respiratory symptoms and fatigue are the most common symptoms at any stage of disease. Histological confirmation is not needed for Löfgren's or Heerfordt's syndrome and asymptomatic bihilar lymphadenopathy. The radiological staging system is still based on chest radiography, and computed tomography is not mandatory for routine follow-up. (18)F-fluorodeoxyglucose positron emission tomography may be of value in special cases. For assessment of lung involvement and follow-up, pulmonary function tests are necessary with vital capacity being the most important single parameter and diffusion capacity the most sensitive. Bronchoscopy with biopsy is the most common procedure for detection of granulomas, when there is no easier biopsy site like skin or peripheral lymph nodes. Endobronchial ultrasonography-guided transbronchial needle aspiration has replaced mediastinoscopy for evaluation of mediastinal and hilar lymph nodes with a high diagnostic yield. Despite numerous studies, no single biomarker can be reliably used for correct diagnosis or exclusion of sarcoidosis. Genetic testing, despite promising advances, has still not been included in routine care for sarcoidosis patients. The long-term prognosis of sarcoidosis depends on the different organ manifestations: Cardiac or central nervous involvement, together with respiratory complications, is critical. A multidisciplinary approach is necessary for comprehensive care of the sarcoidosis patient.
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