Milica Vukmirovic1,2,3, Xiting Yan1,4,3, Kevin F Gibson5, Mridu Gulati1, Jonas C Schupp1, Giuseppe DeIuliis1, Taylor S Adams1, Buqu Hu1, Antun Mihaljinec1, Tony N Woolard1, Heather Lynn1,6, Nkiruka Emeagwali1, Erica L Herzog1, Edward S Chen7, Alison Morris5, Joseph K Leader8, Yingze Zhang5, Joe G N Garcia6, Lisa A Maier9, Ronald G Collman10, Wonder P Drake11, Michael J Becich12, Harry Hochheiser12, Steven R Wisniewski5, Panayiotis V Benos13, David R Moller7, Antje Prasse14,15, Laura L Koth16, Naftali Kaminski17. 1. Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA. 2. Dept of Medicine, Division of Respirology, McMaster University, Hamilton, ON, Canada. 3. Equally contributing authors. 4. Dept of Biostatistics, Yale School of Public Health, New Haven, CT, USA. 5. Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US. 6. University of Arizona Health Sciences, Tucson, AZ, USA. 7. Johns Hopkins University, Baltimore, MD, USA. 8. Dept of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. 9. National Jewish Health, Denver, CO, USA. 10. University of Pennsylvania School of Medicine, PA, USA. 11. Vanderbilt University, Nashville, TN, USA. 12. Dept of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. 13. Dept of Computational and Systems Biology and Department of Computer Science, University of Pittsburgh, Pittsburgh, PA, USA. 14. Hannover Medical School (MHH), Hannover, Germany. 15. Fraunhofer ITEM, Hannover, Germany. 16. University of California San Francisco, San Francisco, CA, USA. 17. Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA naftali.kaminski@yale.edu.
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.
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.