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Spatial transcriptomics of the distal lung bronchioles unravel the mechanisms underlying epithelial desquamation in idiopathic pulmonary fibrosis (IPF)

ABSTRACT: Spatial transcriptomics of the distal lung bronchioles unravel the mechanisms underlying epithelial desquamation in idiopathic pulmonary fibrosis (IPF)

PROVIDER: PRJNA1119042 | ENA |

REPOSITORIES: ENA

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Spatial transcriptomics of the distal lung bronchioles unravel the mechanisms underlying epithelial desquamation in idiopathic pulmonary fibrosis (IPF)

Project description:One histopathological hallmark seen in end-stage IPF within the distal bronchioles is epithelial desquamation, a process in which the epithelial cells detach from their basement membrane. We performed spatial transcriptomics to profile the distal bronchiolar epithelium of the IPF lung and compared it to healthy lung bronchiolar epithelium. Our analysis has revealed crucial pathways leading to epithelial desquamation.

2025-09-01 | GSE268850 | GEO

Effect of knockdown of junctional genes JUP and PLEC on Small Airway Epithelial Cells (SAECs) in the context of epithelial desquamation in distal bronchioles of Idiopathic Pulmonary fibrosis (IPF) patients

Project description:JUP and PLEC are downregulated in the distal bronchioles of IPF patients. To understand the relevance of this in the epithelial sloughing (desquamation) phenotype observed in distal bronchioles of IPF patients, we knockeddown JUP and PLEC in small airway epithelial cells thats are isolated from distal bronchioles of human airway epithelium (Lonza). Bulk RNA sequencing of JUP vs Scrambled and PLEC vs Scrambled were performed. The transriptomic data suggests that JUP transcriptionally regulates the matrix synthesis and the transcription of other junctional genes in SAECs. However, no significant effect of PLEC knockdown on transcription of matrix genes, a significant reduction in junctional gene transcripts were observed in PLEC knockdown. These findings suggest that JUP and PLEC may play key roles in the regulation of epithelial integrity during homeostasis, and when desrupted can lead to epithelial desquamation.

2025-09-01 | GSE267943 | GEO

Idiopathic pulmonary fibrosis (IPF)

Project description:Idiopathic pulmonary fibrosis (IPF)

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Single cell RNA Sequencing Identifies G-protein Coupled Receptor 87 as a Basal Cell Marker Expressed in Distal Honeycomb Cysts in Idiopathic Pulmonary Fibrosis

Project description:Idiopathic Pulmonary Fibrosis (IPF) is a devastating and life-threatening lung disease characterized by epithelial reprogramming and increased extracellular matrix deposition leading to loss of lung function. A prominent histopathological structure in the IPF lung are aberrant bronchioles filled with mucus, referred to as honeycomb cysts. These heterogeneous bronchiolized areas feature clusters of simple epithelium with Keratin (KRT)5+ basal-like cells interspersed with pseudostratified epithelium containing differentiated, hyperplastic epithelial cells as well as aberrant ciliated cells. Recent single-cell RNA sequencing studies of the lung epithelium shed further light into cellular subtypes unique to IPF, including basaloid KRT5-/KRT17+ cells present in the distal lung. However, IPF distal bronchiole cell subtypes still remain poorly characterized and their disease contribution remains underinvestigated. Using single-cell RNA sequencing of enriched EpCAM+ lung cells of the distal IPF lung, we identified G-protein coupled receptor (GPR) 87, as a marker of distal bronchioles and KRT5+ IPF basal cells contributing to impaired airway differentiation and honeycombing.

2022-05-01 | GSE190889 | GEO

microRNA expression profiles in Idiopathic Pulmonary Fibrosis (IPF)

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.

2019-04-02 | GSE129126 | GEO

Idiopathic pulmonary fibrosis (IPF)

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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Generation of expandable multipotential distal lung progenitors from human pluripotent stem cells that model idiopathic pulmonary fibrosis [scRNA-Seq]

Project description:Human lungs contain unique cell populations in distal respiratory airways and terminal bronchioles (RA/TRB) that accumulate in patients with lung injury and idiopathic pulmonary fibrosis (IPF), a lethal lung disease. As these populations are absent in rodents, deeper understanding requires a human in vitro model. Here we convert human pluripotent stem cells into expandable spheres, called induced respiratory airway progenitors (iRAPs), consisting of ~99% RA/TRB-associated cell types. One hPSC can give rise to 1010 iRAP cells. We differentiate iRAPs through a stage consistent with transitional AT2 like cells into a population corresponding to mature AT1 cells with 95% purity. iRAPs with deletion of HPS1, which causes pulmonary fibrosis in humans, replicate the aberrant differentiation and recruitment of profibrotic fibroblasts observed in IPF, indicating that intrinsic dysfunction of RA/TRB-associated alveolar progenitors contributes to HPS1-related IPF. iRAPs may provide a system suitable for IPF drug discovery and validation.

2025-01-13 | GSE245722 | GEO

IPF AEx Series

Project description:Viruses in acute exacerbations of idiopathic pulmonary fibrosis Keywords: viral detection BAL from patients with acute exacerbations of IPF and stable IPF were hybridized to a pan-viral cDNA microarray to evaluate the presence of virus during these episodes

2011-03-03 | E-GEOD-27578 | biostudies-arrayexpress

microRNA expression profiles in Idiopathic Pulmonary Fibrosis (IPF)

Project description:microRNA expression profiles in Idiopathic Pulmonary Fibrosis (IPF)

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Spatial transcriptomics (Visium, 10x Genomics) data for human Idiopathic Pulmonary Fibrosis (IPF) and control lung tissue

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.

2024-05-28 | E-MTAB-14121 | biostudies-arrayexpress

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