Transcriptomic and epigenetic profiling of fibroblasts in Idiopathic Pulmonary Fibrosis (IPF) [RNA-seq]
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE180415 | GEO | 2021/07/20
REPOSITORIES: GEO
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Project description:Idiopathic pulmonary fibrosis (IPF) is a disease related to AT2 cell. We used flow cytometry to analyze the epithelial component of donor and IPF lungs. From the live cells, we first excluded the CD31PosCD45Pos and then selected the EPCAMPos cells for further analysis using the human AT2 cell marker HTll-280 and the surface marker PD-L1. Our data indicate that, the bona fide differentiated AT2 cells (HTll-280High PD-L1Neg), were drastically reduced in the context of IPF. More interestingly, the number of HTll-280Low/Neg PD-L1High was drastically increased, suggesting that HTll-280Low PD-L1High epithelial cells could represent a pool of progenitors linked to the deficient AT2 lineage. The aim of this experiment is further characterization of AT2 and PDL1+ cells in donor and IPF.
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Project description:Idiopathic pulmonary fibrosis (IPF) is a lethal fibrotic lung disease characterized by enhanced fibroblast proliferation, collagen synthesis, extracellular matrix deposition. We obtained 28 IPF patient lung tissue samples from the Lung Tissue Research Consortium (LTRC). Here we determined the miRNA expression profiles in these IPF lung samples.
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Project description:Transcriptomic and epigenetic profiling of fibroblasts in Idiopathic Pulmonary Fibrosis (IPF)
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Project description:RNA sequencing has been performed to investigate the transcriptomic profile of fibroblasts derived from apical and basal regions of idiopathic pulmonary fibrosis (IPF) and control (CTR) lungs. Lung fibroblasts were cultured onto T25 flasks until full confluence was reached. Fibroblasts were then harvested by trypsinization using 0.05% trypsin-EDTA and washed in Phosphate Buffered Saline (PBS). RNA was extracted using the RNeasy Mini kit protocol. Samples were then sent to the Australian Genome Research Facility (AGRF) where 1μg of RNA was submitted for next-generation sequencing. Once raw data returned, bioinformatics analysis was conducted. Results revealed little difference at the transcriptomic level between apical lung fibroblasts isolated from IPF and CTR donors. In contrast, there was a significant difference in gene expression between IPF and CTR lung basal fibroblasts with 90 differentially expressed genes (DEGs) identified in IPF basal fibroblasts. Gene ontology analysis of these 90 DEGs suggested that the most important functions were associated with receptor ligand activity, cell adhesion molecule binding, and integrin binding. Furthermore, fibroblasts isolated from the basal and apical sites of control lung were not significantly different. Interestingly, the lung basal fibroblasts from IPF patients were significantly different in their transcriptomic profile to that of apical fibroblasts from the same patients. 303 DEGs were identified in IPF basal fibroblasts compared with IPF apical fibroblasts. According to the GO analysis on these 303 DEGs, the most important function of the identified dysregulated genes was associated with the composition and function of the extracellular (ECM). Further pathway analysis identified 4 signaling pathways, namely arrhythmogenic right ventricular cardiomyopathy, calcium signaling pathway, dilated cardiomyopathy, and hematopoietic cell lineage. An interesting finding was that these IPF basal fibroblasts were clustered into two groups (Group 1 and Group 2). Analysis on these two groups found 3594 DEGs in Group 1 compared to Group 2. Go analysis suggested most of the identified dysregulated genes was involved in the composition and function of the ECM. Pathway analysis identified 28 dysregulated signaling pathways, including PI3K-Akt signaling pathway, TGF-β signaling pathway and Wnt signaling pathway. The results of the transcriptome analysis intimate that the IPF is more predominant in the basal lungs and the fibroblast-derived from the basal region of the fibrotic lungs may serve as a central role in IPF. Moreover, the dramatic difference between two groups of IPF basal fibroblasts might be linked to the differential response to the same drug occurred in IPF patients.
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Project description:Transcriptomic and epigenetic profiling of fibroblasts in Idiopathic Pulmonary Fibrosis (IPF) [RNA-seq]
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Project description:In this study we have focused on the biomechanical properties of scaffolds (decellularized lung tissue) derived from healthy individuals and IPF patients. The longitudinal cellular response of scaffold repopulation with healthy fibroblasts has been quantified using SILAC-MS. Increased scaffold density and stiffness along with differential expressions of proteins clearly separated and defined ECM proteins descriptive for IPF respective healthy scaffolds. Our study aim to understand the role of the ECM in the development of IPF. We have used proteomics to define intrinsic scaffold ECM proteins descriptive for healthy respective IPF scaffolds. To evaluate whether these mediators directs or rejects profibrotic responses fibroblasts repopulated on healthy and IPF derived scaffolds were cultured in heavy labeled medie (SILAC) to differentiate between preexisting scaffold proteins and newly synthesized proteins. The spatial distribution of unique ECM proteins characteristic for healthy fibroblasts on IPF scaffolds were verified with histological staining.
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Project description:Visium (10x Genomics) spatially resolved transcriptomics data generated from normal and Idiopathic Pulmonary Fibrosis (IPF) lung parenchyma tissues collected from human donors. The fresh-frozen tissues that were analyzed were from four healthy control (HC) subjects and from four IPF patients. For each IPF patient, three different tissues were selected representing areas of mild (“B1”), moderate (“B2\") or severe (“B3”) fibrosis within the same donor, as determined by histological inspection of Hematoxylin and Eosin (H&E)-stained samples. Data from a total of 25 tissue sections, from 16 unique lung tissue blocks. The lung tissues were collected post-mortem (HC donors) or during lung transplant/resection (IPF patients) after obtaining informed consent. The study protocols were approved by the local human research ethics committee (HC: Lund, permit number Dnr 2016/317; IPF: Gothenburg, permit number 1026-15) and the samples are anonymized and cannot/should not be traced back to individual donors.
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