Spatial transcriptomics reveals altered communities and drivers of aberrant epithelia and pro-fibrotic fibroblasts in interstitial lung diseases
Ramnik J. Xavier1, Alok Jaiswal1, Benjamin D. Medoff2, Jacques Deguine1
1The Broad Institute, 2Harvard Medical School, *Corresponding author
Aberrant basaloid cell marker genesAdventitial fibroblast HP vs healthy DEGsAdventitial fibroblast marker genesAirway basal COPD vs healthy DEGsAirway basal HP vs healthy DEGsAirway basal IPF vs healthy DEGsAirway basal NSIP vs healthy DEGsAirway basal PH vs healthy DEGsAirway basal RA-ILD vs healthy DEGsAirway basal marker genesAirway smooth muscle COPD vs healthy DEGsAirway smooth muscle HP vs healthy DEGsAirway smooth muscle IPF vs healthy DEGsAirway smooth muscle PH vs healthy DEGsAirway smooth muscle RA-ILD vs healthy DEGsAirway smooth muscle marker genesAlveolar duct myofibroblast (contractile) marker genesAlveolar epithelial transitional (AT2-AT1) marker genesAlveolar fibroblast marker genesAlveolar macrophage (lipid homeostatic) IPF vs healthy DEGsAlveolar macrophage (lipid homeostatic) marker genesAlveolar macrophage IPF vs healthy DEGsAlveolar macrophage marker genesAlveolar type 1 COPD vs healthy DEGsAlveolar type 1 HP vs healthy DEGsAlveolar type 1 IPAF vs healthy DEGsAlveolar type 1 IPF vs healthy DEGsAlveolar type 1 NSIP vs healthy DEGsAlveolar type 1 PAH vs healthy DEGsAlveolar type 1 PH vs healthy DEGsAlveolar type 1 RA-ILD vs healthy DEGsAlveolar type 1 marker genesAlveolar type 2 COPD vs healthy DEGsAlveolar type 2 HP vs healthy DEGsAlveolar type 2 IPAF vs healthy DEGsAlveolar type 2 IPF vs healthy DEGsAlveolar type 2 NSIP vs healthy DEGsAlveolar type 2 PAH vs healthy DEGsAlveolar type 2 PH vs healthy DEGsAlveolar type 2 RA-ILD vs healthy DEGsAlveolar type 2 cell proliferating marker genesAlveolar type 2 marker genesB COPD vs healthy DEGsB IPAF vs healthy DEGsB IPF vs healthy DEGsB marker genesCD141+ conventional dendritic cell (cDC1) COPD vs healthy DEGsCD141+ conventional dendritic cell (cDC1) HP vs healthy DEGsCD141+ conventional dendritic cell (cDC1) IPAF vs healthy DEGsCD141+ conventional dendritic cell (cDC1) IPF vs healthy DEGsCD141+ conventional dendritic cell (cDC1) NSIP vs healthy DEGsCD141+ conventional dendritic cell (cDC1) marker genesCD4+, alpha-beta T marker genesCD4+, regulatory T IPAF vs healthy DEGsCD4+, regulatory T marker genesCD8+, alpha-beta T marker genesCapillary 1 IPF vs healthy DEGsCapillary 1 marker genesCapillary 2 marker genesCapillary intermediate 1 COPD vs healthy DEGsCapillary intermediate 1 HP vs healthy DEGsCapillary intermediate 1 IPAF vs healthy DEGsCapillary intermediate 1 IPF vs healthy DEGsCapillary intermediate 1 NSIP vs healthy DEGsCapillary intermediate 1 PAH vs healthy DEGsCapillary intermediate 1 PH vs healthy DEGsCapillary intermediate 1 RA-ILD vs healthy DEGsCapillary intermediate 1 marker genesCapillary intermediate 2 marker genesClassical monocyte COPD vs healthy DEGsClassical monocyte IPAF vs healthy DEGsClassical monocyte IPF vs healthy DEGsClassical monocyte marker genesClub (Bronchioles) marker genesClub (Trachea & Bronchus) marker genesCycling lymphatic endothelial cell of lung COPD vs healthy DEGsCycling lymphatic endothelial cell of lung HP vs healthy DEGsCycling lymphatic endothelial cell of lung IPAF vs healthy DEGsCycling lymphatic endothelial cell of lung IPF vs healthy DEGsCycling lymphatic endothelial cell of lung NSIP vs healthy DEGsCycling lymphatic endothelial cell of lung PAH vs healthy DEGsCycling lymphatic endothelial cell of lung PH vs healthy DEGsCycling lymphatic endothelial cell of lung RA-ILD vs healthy DEGsCycling lymphatic endothelial cell of lung marker genesDeuterosomal cell marker genesDuct, basal marker genesGoblet COPD vs healthy DEGsGoblet HP vs healthy DEGsGoblet IPAF vs healthy DEGsGoblet IPF vs healthy DEGsGoblet NSIP vs healthy DEGsGoblet PH vs healthy DEGsGoblet RA-ILD vs healthy DEGsGoblet marker genesGroup 1 ILC marker genesHematopoietic stem cell marker genesHillock basal marker genesHillock squamous marker genesInflammatory alveolar fibroblast COPD vs healthy DEGsInflammatory alveolar fibroblast HP vs healthy DEGsInflammatory alveolar fibroblast IPAF vs healthy DEGsInflammatory alveolar fibroblast IPF vs healthy DEGsInflammatory alveolar fibroblast NSIP vs healthy DEGsInflammatory alveolar fibroblast PAH vs healthy DEGsInflammatory alveolar fibroblast RA-ILD vs healthy DEGsInflammatory alveolar fibroblast marker genesInterstitial fibroblast COPD vs healthy DEGsInterstitial fibroblast HP vs healthy DEGsInterstitial fibroblast IPAF vs healthy DEGsInterstitial fibroblast IPF vs healthy DEGsInterstitial fibroblast NSIP vs healthy DEGsInterstitial fibroblast PAH vs healthy DEGsInterstitial fibroblast PH vs healthy DEGsInterstitial fibroblast RA-ILD vs healthy DEGsInterstitial fibroblast marker genesInterstitial macrophage COPD vs healthy DEGsInterstitial macrophage HP vs healthy DEGsInterstitial macrophage IPAF vs healthy DEGsInterstitial macrophage IPF vs healthy DEGsInterstitial macrophage NSIP vs healthy DEGsInterstitial macrophage RA-ILD vs healthy DEGsInterstitial macrophage marker genesLangerhans cell IPAF vs healthy DEGsLangerhans cell IPF vs healthy DEGsLangerhans cell marker genesLipofibroblast 1 marker genesLymphatic endothelial marker genesLymphocyte of B lineage marker genesMGH ILD cell-state marker genesMast cell COPD vs healthy DEGsMast cell NSIP vs healthy DEGsMast cell RA-ILD vs healthy DEGsMast cell marker genesMegakaryocyte marker genesMesothelial PAH vs healthy DEGsMesothelial marker genesMetallothionein+ AM marker genesMigratory lung dendritic cell marker genesMulticiliated (Bronchioles) marker genesMulticiliated (Trachea & Bronchus) marker genesMulticiliated (axonemal) COPD vs healthy DEGsMulticiliated (axonemal) HP vs healthy DEGsMulticiliated (axonemal) IPAF vs healthy DEGsMulticiliated (axonemal) IPF vs healthy DEGsMulticiliated (axonemal) NSIP vs healthy DEGsMulticiliated (axonemal) PH vs healthy DEGsMulticiliated (axonemal) RA-ILD vs healthy DEGsMulticiliated (axonemal) marker genesNK COPD vs healthy DEGsNK HP vs healthy DEGsNK IPAF vs healthy DEGsNK IPF vs healthy DEGsNK marker genesNasal club cell marker genesNasal goblet cell marker genesNasal serous cell marker genesNeutrophil COPD vs healthy DEGsNeutrophil IPAF vs healthy DEGsNeutrophil IPF vs healthy DEGsNeutrophil marker genesNon-classical monocyte COPD vs healthy DEGsNon-classical monocyte HP vs healthy DEGsNon-classical monocyte IPAF vs healthy DEGsNon-classical monocyte IPF vs healthy DEGsNon-classical monocyte NSIP vs healthy DEGsNon-classical monocyte marker genesPeribronchial fibroblast HP vs healthy DEGsPeribronchial fibroblast IPF vs healthy DEGsPeribronchial fibroblast NSIP vs healthy DEGsPeribronchial fibroblast marker genesPerichondrial chondroprogenitor marker genesPericytes COPD vs healthy DEGsPericytes HP vs healthy DEGsPericytes IPAF vs healthy DEGsPericytes IPF vs healthy DEGsPericytes NSIP vs healthy DEGsPericytes PAH vs healthy DEGsPericytes RA-ILD vs healthy DEGsPericytes marker genesPlasma IPAF vs healthy DEGsPlasma marker genesPlasmacytoid dendritic cell marker genesProliferating AM marker genesPulmonary alveolar duct myofibroblast IPF vs healthy DEGsPulmonary alveolar duct myofibroblast marker genesPulmonary arteriole endothelial marker genesPulmonary artery endothelial COPD vs healthy DEGsPulmonary artery endothelial HP vs healthy DEGsPulmonary artery endothelial IPAF vs healthy DEGsPulmonary artery endothelial IPF vs healthy DEGsPulmonary artery endothelial NSIP vs healthy DEGsPulmonary artery endothelial RA-ILD vs healthy DEGsPulmonary artery endothelial marker genesPulmonary capillary endothelial marker genesPulmonary ionocyte marker genesPulmonary neuroendocrine cell marker genesPulmonary vein endothelial IPF vs healthy DEGsPulmonary vein endothelial NSIP vs healthy DEGsPulmonary vein endothelial marker genesRASC COPD vs healthy DEGsRASC HP vs healthy DEGsRASC IPAF vs healthy DEGsRASC IPF vs healthy DEGsRASC NSIP vs healthy DEGsRASC PAH vs healthy DEGsRASC PH vs healthy DEGsRASC RA-ILD vs healthy DEGsRASC marker genesSchwann cell marker genesSecondary crest myofibroblast COPD vs healthy DEGsSecondary crest myofibroblast HP vs healthy DEGsSecondary crest myofibroblast IPAF vs healthy DEGsSecondary crest myofibroblast IPF vs healthy DEGsSecondary crest myofibroblast NSIP vs healthy DEGsSecondary crest myofibroblast PAH vs healthy DEGsSecondary crest myofibroblast PH vs healthy DEGsSecondary crest myofibroblast RA-ILD vs healthy DEGsSecondary crest myofibroblast marker genesSmooth muscle lymphatic marker genesSubpleural fibroblast marker genesSystemic artery endothelial COPD vs healthy DEGsSystemic artery endothelial HP vs healthy DEGsSystemic artery endothelial IPAF vs healthy DEGsSystemic artery endothelial IPF vs healthy DEGsSystemic artery endothelial NSIP vs healthy DEGsSystemic artery endothelial PAH vs healthy DEGsSystemic artery endothelial PH vs healthy DEGsSystemic artery endothelial RA-ILD vs healthy DEGsSystemic artery endothelial marker genesSystemic venous endothelial (activated) marker genesSystemic venous endothelial marker genesT cell proliferating marker genesTransitioning monocyte-derived macrophage COPD vs healthy DEGsTransitioning monocyte-derived macrophage HP vs healthy DEGsTransitioning monocyte-derived macrophage IPAF vs healthy DEGsTransitioning monocyte-derived macrophage IPF vs healthy DEGsTransitioning monocyte-derived macrophage NSIP vs healthy DEGsTransitioning monocyte-derived macrophage PAH vs healthy DEGsTransitioning monocyte-derived macrophage PH vs healthy DEGsTransitioning monocyte-derived macrophage RA-ILD vs healthy DEGsTransitioning monocyte-derived macrophage marker genesTuft COPD vs healthy DEGsTuft HP vs healthy DEGsTuft IPAF vs healthy DEGsTuft IPF vs healthy DEGsTuft NSIP vs healthy DEGsTuft PH vs healthy DEGsTuft RA-ILD vs healthy DEGsTuft marker genesVascular smooth muscle (contractile) COPD vs healthy DEGsVascular smooth muscle (contractile) HP vs healthy DEGsVascular smooth muscle (contractile) IPAF vs healthy DEGsVascular smooth muscle (contractile) IPF vs healthy DEGsVascular smooth muscle (contractile) NSIP vs healthy DEGsVascular smooth muscle (contractile) PAH vs healthy DEGsVascular smooth muscle (contractile) PH vs healthy DEGsVascular smooth muscle (contractile) RA-ILD vs healthy DEGsVascular smooth muscle (contractile) marker genesVascular smooth muscle marker genesiNKT COPD vs healthy DEGsiNKT HP vs healthy DEGsiNKT IPAF vs healthy DEGsiNKT IPF vs healthy DEGsiNKT NSIP vs healthy DEGsiNKT RA-ILD vs healthy DEGsiNKT marker genes
Gene symbols or identifiers, one per line.
MGH ILD cell-state marker genes
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Derived locally from the configured pseudobulk table, scale recorded above. Not fetched from www.lungmap.net.