{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T16:22:18Z","timestamp":1790266938563,"version":"4.1.0"},"reference-count":55,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2020,12,8]],"date-time":"2020-12-08T00:00:00Z","timestamp":1607385600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100015131","name":"Foundation for Sarcoidosis Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100015131","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HL113326-05, P30 GM110766-01, U54GM104938-06, R01HL117074, K24HL127301"],"award-info":[{"award-number":["R01HL113326-05, P30 GM110766-01, U54GM104938-06, R01HL117074, K24HL127301"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:p>Sarcoidosis is a systemic inflammatory disease characterized by infiltration of immune cells into granulomas. Previous gene expression studies using heterogeneous cell mixtures lack insight into cell-type-specific immune dysregulation. We performed the first single-cell RNA-sequencing study of sarcoidosis in peripheral immune cells in 48 patients and controls. Following unbiased clustering, differentially expressed genes were identified for 18 cell types and bioinformatically assessed for function and pathway enrichment. Our results reveal persistent activation of circulating classical monocytes with subsequent upregulation of trafficking molecules. Specifically, classical monocytes upregulated distinct markers of activation including adhesion molecules, pattern recognition receptors, and chemokine receptors, as well as enrichment of immunoregulatory pathways HMGB1, mTOR, and ephrin receptor signaling. Predictive modeling implicated TGF\u03b2 and mTOR signaling as drivers of persistent monocyte activation. Additionally, sarcoidosis T cell subsets displayed patterns of dysregulation. CD4 na\u00efve T cells were enriched for markers of apoptosis and Th17\/T<jats:sub>reg<\/jats:sub> differentiation, while effector T cells showed enrichment of anergy-related pathways. Differentially expressed genes in regulatory T cells suggested dysfunctional p53, cell death, and TNFR2 signaling. Using more sensitive technology and more precise units of measure, we identify cell-type specific, novel inflammatory and regulatory pathways. Based on our findings, we suggest a novel model involving four convergent arms of dysregulation: persistent hyperactivation of innate and adaptive immunity <jats:italic>via<\/jats:italic> classical monocytes and CD4 na\u00efve T cells, regulatory T cell dysfunction, and effector T cell anergy. We further our understanding of the immunopathology of sarcoidosis and point to novel therapeutic targets.<\/jats:p>","DOI":"10.3389\/fimmu.2020.567342","type":"journal-article","created":{"date-parts":[[2020,12,8]],"date-time":"2020-12-08T06:03:39Z","timestamp":1607407419000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":49,"title":["Single Cell Transcriptomics Implicate Novel Monocyte and T Cell Immune Dysregulation in Sarcoidosis"],"prefix":"10.3389","volume":"11","author":[{"given":"Lori","family":"Garman","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard C.","family":"Pelikan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Astrid","family":"Rasmussen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caleb A.","family":"Lareau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn A.","family":"Savoy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Umesh S.","family":"Deshmukh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harini","family":"Bagavant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Albert M.","family":"Levin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salim","family":"Daouk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wonder P.","family":"Drake","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Courtney G.","family":"Montgomery","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2020,12,8]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1513\/AnnalsATS.201707-565OT","article-title":"Genetic, immunologic, and environmental basis of sarcoidosis","volume":"14","author":"Moller","year":"2017","journal-title":"Ann Am Thorac Soc"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201507-1344LE","article-title":"Role of NOD2 pathway genes in sarcoidosis cases with clinical characteristics of blau syndrome","volume":"192","author":"Bello","year":"2015","journal-title":"Am J Respir Crit Care Med"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1002\/gepi.22196","article-title":"Extended methods for gene-environment-wide interaction scans in studies of admixed individuals with varying degrees of relationships","volume":"43","author":"Chen","year":"2019","journal-title":"Genet Epidemiol"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1002\/gepi.21811","article-title":"Efficient generalized least squares method for mixed population and family-based samples in genome-wide association studies","volume":"38","author":"Li","year":"2014","journal-title":"Genet Epidemiol"},{"key":"B5","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1513\/AnnalsATS.201508-568BC","article-title":"Epidemiology of sarcoidosis in a prospective cohort study of U.S. women","volume":"13","author":"Dumas","year":"2016","journal-title":"Ann Am Thorac Soc"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1513\/AnnalsATS.201707-564OT","article-title":"Disease burden and variability in sarcoidosis","volume":"14","author":"Gerke","year":"2017","journal-title":"Ann Am Thorac Soc"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20050648","article-title":"The immune paradox of sarcoidosis and regulatory T cells","volume":"203","author":"Miyara","year":"2006","journal-title":"J Exp Med"},{"key":"B8","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1038\/gene.2017.3","article-title":"Polygenic risk assessment reveals pleiotropy between sarcoidosis and inflammatory disorders in the context of genetic ancestry","volume":"18","author":"Lareau","year":"2017","journal-title":"Genes Immun"},{"key":"B9","doi-asserted-by":"publisher","first-page":"1802153","DOI":"10.1183\/13993003.021532018","article-title":"Moving target: shifting the focus to pulmonary sarcoidosis as an autoimmune spectrum disorder","volume":"54","author":"Kaiser","year":"2019","journal-title":"Eur Respir J"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.181.12.8784","article-title":"T cell responses to mycobacterial catalase-peroxidase profile a pathogenic antigen in systemic sarcoidosis","volume":"181","author":"Chen","year":"2008","journal-title":"J Immunol"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1007\/s10875-009-9311-y","article-title":"Mycobacterial ESAT-6 and katG are recognized by sarcoidosis CD4+ T cells when presented by the American sarcoidosis susceptibility allele, DRB1*1101","volume":"30","author":"Oswald-Richter","year":"2010","journal-title":"J Clin Immunol"},{"key":"B12","article-title":"Effects of broad-spectrum antimycobacterial therapy on chronic pulmonary sarcoidosis","volume":"30","author":"Drake","year":"2013","journal-title":"Sarcoidosis Vasc Diffuse Lung Dis"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201106-1143OC","article-title":"Sarcoidosis blood transcriptome reflects lung inflammation and overlaps with tuberculosis","volume":"184","author":"Koth","year":"2011","journal-title":"Am J Respir Crit Care Med"},{"key":"B14","doi-asserted-by":"publisher","first-page":"2720","DOI":"10.1038\/s41598-017-02941-4","article-title":"RNA-sequencing identifies novel pathways in sarcoidosis monocytes","volume":"7","author":"Talreja","year":"2017","journal-title":"Sci Rep"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201401-0188OC","article-title":"Blockade of the programmed death-1 pathway restores sarcoidosis CD4(+) T-cell proliferative capacity","volume":"190","author":"Braun","year":"2014","journal-title":"Am J Respir Crit Care Med"},{"key":"B16","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1016\/j.jaut.2018.07.012","article-title":"Molecular profiling of regulatory T cells in pulmonary sarcoidosis","volume":"94","author":"Kachamakova-Trojanowska","year":"2018","journal-title":"J Autoimmun"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1164\/ajrccm.164.10.2104046","article-title":"Clinical characteristics of patients in a case control study of sarcoidosis","volume":"164","author":"Baughman","year":"2001","journal-title":"Am J Respir Crit Care Med"},{"key":"B18","first-page":"75","article-title":"Defining organ involvement in sarcoidosis: the ACCESS proposed instrument. ACCESS Research Group. A Case Control Etiologic Study of Sarcoidosis","volume":"16","author":"Judson","year":"1999","journal-title":"Sarcoidosis Vasc Diffuse Lung Dis"},{"key":"B19","first-page":"19","article-title":"The WASOG Sarcoidosis Organ Assessment Instrument: An update of a previous clinical tool","volume":"31","author":"Judson","year":"2014","journal-title":"Sarcoidosis Vasc Diffuse Lung Dis"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1053\/j.semdp.2007.06.002","article-title":"The pathology of pulmonary sarcoidosis: update","volume":"24","author":"Ma","year":"2007","journal-title":"Semin Diagn Pathol"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.202002-0251ST","article-title":"Diagnosis and detection of sarcoidosis. An official American Thoracic Society clinical practice guideline","volume":"201","author":"Crouser","year":"2020","journal-title":"Am J Respir Crit Care Med"},{"key":"B22","article-title":"ATS\/ERS\/WASOG statement on sarcoidosis. American Thoracic Society\/European Respiratory Society\/World Association of Sarcoidosis and other Granulomatous Disorders","volume":"16","author":"Hunninghake","year":"1999","journal-title":"Sarcoidosis Vasc Diffuse Lung Dis"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1097\/MCP.0000000000000596","article-title":"The diagnosis of sarcoidosis","volume":"25","author":"Judson","year":"2019","journal-title":"Curr Opin Pulm Med"},{"key":"B24","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra071714","article-title":"Sarcoidosis","volume":"357","author":"Iannuzzi","year":"2007","journal-title":"N Engl J Med"},{"key":"B26","article-title":"The clinical course of sarcoidosis: presentation, diagnosis, and treatment in a large white and black cohort in the United States","volume":"29","author":"Judson","year":"2012","journal-title":"Sarcoidosis Vasc Diffuse Lung Dis"},{"key":"B27","doi-asserted-by":"publisher","first-page":"1901626","DOI":"10.1183\/13993003.01626-2019","article-title":"Monocytes and macrophages in chronic sarcoidosis pathology","volume":"54","author":"Fraser","year":"2019","journal-title":"Eur Respir J"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2018.01726","article-title":"Monocyte subsets: phenotypes and function in tuberculosis infection","volume":"9","author":"Sampath","year":"2018","journal-title":"Front Immunol"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbrc.2016.07.078","article-title":"Platelet-derived high-mobility group box 1 promotes recruitment and suppresses apoptosis of monocytes","volume":"478","author":"Vogel","year":"2016","journal-title":"Biochem Biophys Res Commun"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.01473","article-title":"Emerging roles for eph receptors and ephrin ligands in immunity","volume":"10","author":"Darling","year":"2019","journal-title":"Front Immunol"},{"key":"B31","doi-asserted-by":"publisher","first-page":"e87157","DOI":"10.1172\/jci.insight.87157","article-title":"IL-3 promotes the development of experimental autoimmune encephalitis","volume":"1","author":"Renner","year":"2016","journal-title":"JCI Insight"},{"key":"B32","doi-asserted-by":"publisher","first-page":"e0224543","DOI":"10.1371\/journal.pone.0224543","article-title":"ITGAM is a risk factor to systemic lupus erythematosus and possibly a protection factor to rheumatoid arthritis in patients from Mexico","volume":"14","author":"Ramirez-Bello","year":"2019","journal-title":"PLoS One"},{"key":"B33","doi-asserted-by":"publisher","first-page":"e44519","DOI":"10.7554\/eLife.44519","article-title":"HIF-1alpha regulates IL-1beta and IL-17 in sarcoidosis","volume":"8","author":"Talreja","year":"2019","journal-title":"Elife"},{"key":"B34","doi-asserted-by":"publisher","first-page":"ra86","DOI":"10.1126\/scisignal.aaa3206","article-title":"Extracellular signal-regulated kinase 5 promotes acute cellular and systemic inflammation","volume":"8","author":"Wilhelmsen","year":"2015","journal-title":"Sci Signal"},{"key":"B35","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1038\/ni.3655","article-title":"Chronic signaling via the metabolic checkpoint kinase mTORC1 induces macrophage granuloma formation and marks sarcoidosis progression","volume":"18","author":"Linke","year":"2017","journal-title":"Nat Immunol"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1378\/chest.08-0443","article-title":"Increased expression of CD16, CD69, and very late antigen-1 on blood monocytes in active sarcoidosis","volume":"134","author":"Heron","year":"2008","journal-title":"Chest"},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2249.2007.03578.x","article-title":"Neurotrophins modulate monocyte chemotaxis without affecting macrophage function","volume":"151","author":"Samah","year":"2008","journal-title":"Clin Exp Immunol"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1007\/s10059-012-2297-y","article-title":"The nuclear receptor PPARs as important regulators of T-cell functions and autoimmune diseases","volume":"33","author":"Choi","year":"2012","journal-title":"Mol Cells"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1084\/jem.174.6.1323","article-title":"Platelet-derived growth factor is a potent biologic response modifier of T cells","volume":"174","author":"Daynes","year":"1991","journal-title":"J Exp Med"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.15252\/emmm.201303376","article-title":"Insulin-like growth factor-1 stimulates regulatory T cells and suppresses autoimmune disease","volume":"6","author":"Bilbao","year":"2014","journal-title":"EMBO Mol Med"},{"key":"B41","doi-asserted-by":"publisher","first-page":"398","DOI":"10.3390\/cells8050398","article-title":"Hippo pathway in mammalian adaptive immune system","volume":"8","author":"Yamauchi","year":"2019","journal-title":"Cells"},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1016\/j.rmed.2012.01.012","article-title":"Peripheral blood responses to specific antigens and CD28 in sarcoidosis","volume":"106","author":"Ahmadzai","year":"2012","journal-title":"Respir Med"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1016\/j.smim.2013.10.010","article-title":"Induction and stability of the anergic phenotype in T cells","volume":"25","author":"Valdor","year":"2013","journal-title":"Semin Immunol"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(02)00767-5","article-title":"Transcriptional mechanisms underlying lymphocyte tolerance","volume":"109","author":"Macian","year":"2002","journal-title":"Cell"},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.1038\/ni1193","article-title":"Egr-2 and Egr-3 are negative regulators of T cell activation","volume":"6","author":"Safford","year":"2005","journal-title":"Nat Immunol"},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1016\/j.molimm.2013.03.006","article-title":"Egr2-dependent gene expression profiling and ChIP-Seq reveal novel biologic targets in T cell anergy","volume":"55","author":"Zheng","year":"2013","journal-title":"Mol Immunol"},{"key":"B47","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1202891","article-title":"Reversal of global CD4+ subset dysfunction is associated with spontaneous clinical resolution of pulmonary sarcoidosis","volume":"190","author":"Oswald-Richter","year":"2013","journal-title":"J Immunol"},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201503-0635LE","article-title":"Decreased cytotoxic T-lymphocyte antigen 4 expression on regulatory T cells and Th17 cells in sarcoidosis: double trouble","volume":"192","author":"Broos","year":"2015","journal-title":"Am J Respir Crit Care Med"},{"key":"B49","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1186\/s12931-015-0265-8","article-title":"Impaired survival of regulatory T cells in pulmonary sarcoidosis","volume":"16","author":"Broos","year":"2015","journal-title":"Respir Res"},{"key":"B50","doi-asserted-by":"publisher","first-page":"12079","DOI":"10.1038\/s41598-018-30621-4","article-title":"TNFR2 ligation in human T regulatory cells enhances IL2-induced cell proliferation through the non-canonical NF-kappaB pathway","volume":"8","author":"Wang","year":"2018","journal-title":"Sci Rep"},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1016\/j.it.2020.01.007","article-title":"Sarcoidosis and the mTOR, Rac1, and autophagy triad","volume":"41","author":"Pacheco","year":"2020","journal-title":"Trends Immunol"},{"key":"B52","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-pharmtox-011112-140226","article-title":"Eph receptors and ephrins: therapeutic opportunities","volume":"55","author":"Barquilla","year":"2015","journal-title":"Annu Rev Pharmacol Toxicol"},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.3389\/fphar.2019.00691","article-title":"Targeting the eph\/ephrin system as anti-inflammatory strategy in IBD","volume":"10","author":"Grandi","year":"2019","journal-title":"Front Pharmacol"},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00149614","article-title":"The role of tyrosine kinases in the pathogenesis of idiopathic pulmonary fibrosis","volume":"45","author":"Grimminger","year":"2015","journal-title":"Eur Respir J"},{"key":"B55","doi-asserted-by":"publisher","DOI":"10.1016\/j.pharmthera.2013.11.001","article-title":"An overview on HMGB1 inhibitors as potential therapeutic agents in HMGB1-related pathologies","volume":"141","author":"Musumeci","year":"2014","journal-title":"Pharmacol Ther"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2020.567342\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,12,8]],"date-time":"2020-12-08T06:03:42Z","timestamp":1607407422000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2020.567342\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,12,8]]},"references-count":55,"alternative-id":["10.3389\/fimmu.2020.567342"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2020.567342","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,12,8]]},"article-number":"567342"}}