Expression data from fibroblasts cultured from normal and fibrotic human lung tissue
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE40839 | GEO | 2013/08/05
SECONDARY ACCESSION(S): PRJNA175063
REPOSITORIES: GEO
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Project description:Pulmonary fibrosis develops as a consequence of environmentally induced lung injury and/or an inherent disease susceptibility causing fibroblast activation, proliferation and extracellular matrix deposition. The study was undertaken to characterise global gene expression in pulmonary fibroblasts to better understand the mechanisms underlying the fibrotic fibroblast phenotype. Gene expression was evaluated in lung fibroblasts derived from ten controls (normal periphery of resected tumor), open lung biopsies from eight patients with interstitial lung disease associated with systemic sclerosis (fibrotic non specific interstitial pneumonia pattern on biopsy), and from three patients with usual interstitial pneumonia. Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived for 44 hours in the presence of fibroblast growth medium with the addition of 0.1% bovine serum albumin (Sigma).
2013-08-05 | E-GEOD-40839 | biostudies-arrayexpress
Project description:Fibrosis, the replacement of healthy tissue with collagen-rich matrix, can occur following injury in almost every organ. Mouse lungs follow stereotyped sequences of fibrogenesis-to-resolution after bleomycin injury, and we reasoned that profiling post-injury histological progression could uncover pro- vs. anti-fibrotic features with functional value for human fibrosis. We mapped spatiotemporally-resolved transformations in lung extracellular matrix (ECM) architecture to spatially-resolved, multi-omic data. First, we charted stepwise trajectories of matrix aberration vs. resolution using unsupervised machine learning, denoting a reversible transition in uniform-to-disordered histological architecture. Single-cell sequencing along these trajectories identified temporally-enriched “ECM-secreting” (Csmd1+) and “pro-resolving” (Cd248+) fibroblasts, for which Visium inferred divergent histological signatures and spatial-transcriptional “neighborhoods”. Critically, pro-resolving fibroblast instillation helped ameliorate fibrosis in vivo. Further, fibroblast neighborhood-associated moieties, Serpine2 and Pi16, functionally modulated human lung fibrosis ex vivo. Spatial phenotyping of idiopathic pulmonary fibrosis further uncovered analogous fibroblast subtypes and neighborhoods in human disease. Collectively, these findings establish an atlas of pro-/anti-fibrotic factors underlying lung matrix architecture and implicate fibroblast-centered moieties in modulating fibrotic progression vs. resolution.
2025-01-07 | GSE250395 | GEO
Project description:Fibrosis, the replacement of healthy tissue with collagen-rich matrix, can occur following injury in almost every organ. Mouse lungs follow stereotyped sequences of fibrogenesis-to-resolution after bleomycin injury, and we reasoned that profiling post-injury histological progression could uncover pro- vs. anti-fibrotic features with functional value for human fibrosis. We mapped spatiotemporally-resolved transformations in lung extracellular matrix (ECM) architecture to spatially-resolved, multi-omic data. First, we charted stepwise trajectories of matrix aberration vs. resolution using unsupervised machine learning, denoting a reversible transition in uniform-to-disordered histological architecture. Single-cell sequencing along these trajectories identified temporally-enriched “ECM-secreting” (Csmd1+) and “pro-resolving” (Cd248+) fibroblasts, for which Visium inferred divergent histological signatures and spatial-transcriptional “neighborhoods”. Critically, pro-resolving fibroblast instillation helped ameliorate fibrosis in vivo. Further, fibroblast neighborhood-associated moieties, Serpine2 and Pi16, functionally modulated human lung fibrosis ex vivo. Spatial phenotyping of idiopathic pulmonary fibrosis further uncovered analogous fibroblast subtypes and neighborhoods in human disease. Collectively, these findings establish an atlas of pro-/anti-fibrotic factors underlying lung matrix architecture and implicate fibroblast-centered moieties in modulating fibrotic progression vs. resolution.
2025-01-07 | GSE250397 | GEO
Project description:Fibrosis, the replacement of healthy tissue with collagen-rich matrix, can occur following injury in almost every organ. Mouse lungs follow stereotyped sequences of fibrogenesis-to-resolution after bleomycin injury, and we reasoned that profiling post-injury histological progression could uncover pro- vs. anti-fibrotic features with functional value for human fibrosis. We mapped spatiotemporally-resolved transformations in lung extracellular matrix (ECM) architecture to spatially-resolved, multi-omic data. First, we charted stepwise trajectories of matrix aberration vs. resolution using unsupervised machine learning, denoting a reversible transition in uniform-to-disordered histological architecture. Single-cell sequencing along these trajectories identified temporally-enriched “ECM-secreting” (Csmd1+) and “pro-resolving” (Cd248+) fibroblasts, for which Visium inferred divergent histological signatures and spatial-transcriptional “neighborhoods”. Critically, pro-resolving fibroblast instillation helped ameliorate fibrosis in vivo. Further, fibroblast neighborhood-associated moieties, Serpine2 and Pi16, functionally modulated human lung fibrosis ex vivo. Spatial phenotyping of idiopathic pulmonary fibrosis further uncovered analogous fibroblast subtypes and neighborhoods in human disease. Collectively, these findings establish an atlas of pro-/anti-fibrotic factors underlying lung matrix architecture and implicate fibroblast-centered moieties in modulating fibrotic progression vs. resolution.
2025-01-07 | GSE250396 | GEO
Project description:Idiopathic pulmonary fibrosis (IPF) is a progressive, irreversible fibrotic disease of the distal lung alveoli that culminates in respiratory failure and reduced lifespan. Unlike normal lung repair in response to injury, IPF is associated with the accumulation and persistence of fibroblasts and myofibroblasts and continued production of collagen and other extracellular matrix (ECM) components. Prior in vitro studies have led to the hypothesis that the development of resistance to Fas-induced apoptosis by lung fibroblasts and myofibroblasts contibributes to their accumulation in the distal lung tissues of IPF patients. Here, we test this hypothesis in vivo in the resolving model of bleomycin-induced pulmonary fibrosis in mice. Using genetic loss-of-function approaches to inhibit Fas signaling in fibroblasts, novel flow cytometry strategies to quantify lung fibroblast subsets and transcriptional profiling of lung fibroblasts by bulk and single cell RNA-sequencing, we show that Fas is necessary for lung fibroblast apoptosis during homeostatic resolution of bleomycin-induced pulmonary fibrosis in vivo. Furthermore, we show that loss of Fas signaling leads to the persistence and continued pro-fibrotic functions of lung fibroblasts. Our studies provide novel insights into the mechanisms that contribute to fibroblast survival, persistence and continued ECM deposition in the context of IPF and how failure to undergo Fas-induced apoptosis prevents fibrosis resolution.
2020-11-18 | GSE161648 | GEO
Project description:Skin fibrotic disease representsa major global healthcare burden, characterized by fibroblast hyperproliferation and excessive accumulation of extracellular matrix.Fibroblasts are found to be heterogeneous in multiple fibrotic diseases,but the fibroblast heterogeneity of skin fibrotic diseases remains unknown.In this study, we performed single-cell RNA-seq in keloid, a paradigm of skin fibrotic diseases, andnormal scardermis tissues.Our results indicate that keloid and normal scar fibroblasts could be divided into 4 subpopulations: secretory-papillary, secretory-reticular, mesenchymal and pro-inflammatory.The percentage of mesenchymal fibroblast subpopulationincreased significantly in keloid compared to normal scar. Interestingly, we also found increasing mesenchymal fibroblast subpopulation in scleroderma, another skin fibrotic disease.Function studies showed that the mesenchymal fibroblasts promoted collagen synthesis of the other fibroblasts in keloid partiallythrough secreting POSTN. These findings will help us understandskin fibroticpathogenesis in depth,and provided potential target cells for fibrotic diseases therapies.
2021-05-23 | GSE163973 | GEO
Project description:Skin fibrotic disease representsa major global healthcare burden, characterized by fibroblast hyperproliferation and excessive accumulation of extracellular matrix.Fibroblasts are found to be heterogeneous in multiple fibrotic diseases,but the fibroblast heterogeneity of skin fibrotic diseases remains unknown.In this study, we performed single-cell RNA-seq in keloid, a paradigm of skin fibrotic diseases, andnormal scardermis tissues.Our results indicate thatkeloid and normal scar fibroblasts could be divided into 4 subpopulations: secretory-papillary, secretory-reticular, mesenchymal and pro-inflammatory.The percentage of mesenchymal fibroblast subpopulationincreased significantly in keloid compared to normal scar. Interestingly, we also found increasing mesenchymal fibroblast subpopulation in scleroderma, another skin fibrotic disease.Function studies showed that the mesenchymal fibroblasts promoted collagen synthesis of the other fibroblasts in keloid partiallythrough secreting POSTN. These findings will help us understandskin fibroticpathogenesis in depth,and provided potential target cells for fibrotic diseases therapies.
2021-06-01 | GSE175866 | GEO
Project description:Idiopathic pulmonary fibrosis (IPF) is the prototypic progressive fibrotic lung disease with a median survival of 2-4 years. Injury to and/or dysfunction of alveolar epithelium are strongly implicated in IPF disease initiation, but what factors determine why fibrosis progresses rather than normal tissue repair occurs remain poorly understood. We previously demonstrated that ZEB1-mediated epithelial-mesenchymal transition (EMT) in human alveolar epithelial type II (ATII) cells augments TGF-β-induced profibrogenic responses in underlying lung fibroblasts by paracrine signalling. Here we investigated bi-directional epithelial-mesenchymal crosstalk and its potential to drive fibrosis progression. RNA sequencing (RNA-seq) of lung fibroblasts exposed to conditioned media from ATII cells undergoing RAS-induced EMT identified many differentially expressed genes including those involved in cell migration and extracellular matrix (ECM) regulation. We confirmed that paracrine signalling between AS-activated ATII cells and fibroblasts augmented fibroblast recruitment and demonstrated that this involved a ZEB1-tissue plasminogen activator (tPA) axis. In a reciprocal fashion, paracrine signalling from TGF-β-activated lung fibroblasts or IPF fibroblasts induced RAS activation in ATII cells, at least partially via the secreted protein, SPARC. Together these data identify that aberrant bi-directional epithelial-mesenchymal crosstalk in IPF drives a chronic feedback loop that maintains a wound-healing phenotype and provides self-sustaining pro-fibrotic signals.
2021-08-19 | PXD025821 | Pride
Project description:Rationale: Fibrotic hypersensitivity pneumonitis is a debilitating interstitial lung disease driven by incompletely understood immune mechanisms. Objectives: To elucidate immune aberrations in fibrotic hypersensitivity pneumonitis in single-cell resolution. Methods: Single-cell 5’ RNA sequencing was conducted on peripheral blood mononuclear cells and bronchoalveolar lavage cells obtained from 45 patients with fibrotic hypersensitivity pneumonitis, 63 idiopathic pulmonary fibrosis, 4 non-fibrotic hypersensitivity pneumonitis, and 36 healthy controls in the United States and Mexico. Analyses included differential gene expression (Seurat), transcription factor activity imputation (DoRothEA-VIPER), and trajectory analyses (Monocle3/Velocyto-scVelo-CellRank). Measurements and Main Results: Overall, 501,534 peripheral blood mononuclear cells from 110 patients and controls and 88,336 bronchoalveolar lavage cells from 19 patients were profiled. Compared to controls, fibrotic hypersensitivity pneumonitis has elevated classical monocytes (adjusted-p=2.5e-3) and are enriched in CCL3hi/CCL4hi and S100Ahi classical monocytes (adjusted-p<2.2e-16). Trajectory analyses demonstrate that S100Ahi classical monocytes differentiate into SPP1hi lung macrophages associated with fibrosis. Compared to both controls and idiopathic pulmonary fibrosis, fibrotic hypersensitivity pneumonitis patient cells are significantly enriched in GZMhi cytotoxic T cells. These cells exhibit transcription factor activities indicative of TGFb and TNFa/NFkB pathways. These results are publicly available at https://ildimmunecellatlas.org. Conclusions: Single-cell transcriptomics of fibrotic hypersensitivity pneumonitis patients uncovered novel immune perturbations, including previously undescribed increases in GZMhi cytotoxic CD4+ and CD8+ T cells – reflecting this disease’s unique inflammatory T-cell driven nature – as well as increased S100Ahi and CCL3hi/CCL4hi classical monocytes also observed in idiopathic pulmonary fibrosis. Both cell populations may guide the development of new biomarkers and therapeutic interventions.
2024-07-09 | GSE271789 | GEO
Project description:The activated fibroblast is the central effector cell for the progressive fibrotic process that characterizes idiopathic pulmonary fibrosis (IPF). An understanding of the genomic phenotype of this cell in isolation is essential to the understanding of disease pathogenesis and is integral to strategizing therapeutic trials. Employing a unique technique that minimizes cellular phenotypic alterations, we characterized the genomic phenotype of non-cultured pulmonary fibroblasts from the lungs of patients with advanced IPF. This approach revealed several novel genes and pathways previously unreported in IPF fibroblasts. Specifically, we demonstrate altered expression in proteasomal constituents, ubiquitination mediators, the Wnt pathway and several cell cycle regulators suggestive of loss of normal cell cycle controls. The pro-inflammatory cytokine CXCL12 was also up-regulated which may provide a mechanism for fibrocytes’ recruitment, while up-regulated oncogenic KIT may promote fibroblast over proliferation. Paradoxically, pro-apoptotic inducers such as death inducing ligand TRAIL (TNFSF10) and pro-apoptotic Bax were also up-regulated. This comprehensive description of altered gene expression within IPF fibroblasts sheds further light on the complex interactions that characterize IPF. Further studies including therapeutic interventions directed at these pathways hold promise for the treatment of this devastating disease.
2010-05-19 | GSE17978 | GEO