Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Jan;76(1):73-82.
doi: 10.1136/thoraxjnl-2020-214902. Epub 2020 Nov 19.

Transcriptome analysis of IPF fibroblastic foci identifies key pathways involved in fibrogenesis

Delphine Guillotin #  1 , Adam R Taylor #  2 , Manuela Platé #  1 , Paul F Mercer  1 , Lindsay M Edwards  2 , Ross Haggart  3 , Gino Miele  3 , Robin J McAnulty  1 , Toby M Maher  4 , Robert E Hynds  5 , Mariam Jamal-Hanjani  5 , Richard P Marshall  2 , Andrew J Fisher  6   7 , Andy D Blanchard #  2 , Rachel C Chambers #  8
Affiliations

Transcriptome analysis of IPF fibroblastic foci identifies key pathways involved in fibrogenesis

Delphine Guillotin et al. Thorax. 2021 Jan.

Abstract

Introduction: Fibroblastic foci represent the cardinal pathogenic lesion in idiopathic pulmonary fibrosis (IPF) and comprise activated fibroblasts and myofibroblasts, the key effector cells responsible for dysregulated extracellular matrix deposition in multiple fibrotic conditions. The aim of this study was to define the major transcriptional programmes involved in fibrogenesis in IPF by profiling unmanipulated myofibroblasts within fibrotic foci in situ by laser capture microdissection.

Methods: The challenges associated with deriving gene calls from low amounts of RNA and the absence of a meaningful comparator cell type were overcome by adopting novel data mining strategies and by using weighted gene co-expression network analysis (WGCNA), as well as an eigengene-based approach to identify transcriptional signatures, which correlate with fibrillar collagen gene expression.

Results: WGCNA identified prominent clusters of genes associated with cell cycle, inflammation/differentiation, translation and cytoskeleton/cell adhesion. Collagen eigengene analysis revealed that transforming growth factor β1 (TGF-β1), RhoA kinase and the TSC2/RHEB axis formed major signalling clusters associated with collagen gene expression. Functional studies using CRISPR-Cas9 gene-edited cells demonstrated a key role for the TSC2/RHEB axis in regulating TGF-β1-induced mechanistic target of rapamycin complex 1 activation and collagen I deposition in mesenchymal cells reflecting IPF and other disease settings, including cancer-associated fibroblasts.

Conclusion: These data provide strong support for the human tissue-based and bioinformatics approaches adopted to identify critical transcriptional nodes associated with the key pathogenic cell responsible for fibrogenesis in situ and further identify the TSC2/RHEB axis as a potential novel target for interfering with excessive matrix deposition in IPF and other fibrotic conditions.

Keywords: idiopathic pulmonary fibrosis.

PubMed Disclaimer

Conflict of interest statement

Competing interests: RCC received grants from GSK via her institution during the conduct of the study; consultancy fees from Pieris Pharmaceuticals, consultancy fees from Chiesi, consultancy fees from Theravance Biopharma outside the submitted work; and RCC spouse was an employee of GSK during the time this work was conducted. This potential COI was managed by a research framework agreement between UCL and GSK. DG and PFM received salary from this research framework agreement. RM, AT, LME and AB were employees of GlaxoSmithKline during the time this work was performed and hold GSK shares. AJF has received a research grant from GSK to support work contained in this manuscript. RH and GM were employees of Epistem with a commercial interest in the provision of services in the area of investigation. TMM has, via his institution, received industry-academic funding from GSK, R&D and UCB and has received consultancy or speakers fees from Apellis, AstraZeneca, Bayer, Blade Therapeutics, Boehringer Ingelheim, Bristol-Myers Squibb, Galapagos, GlaxoSmithKline R&D, Indalo, Novartis, Pliant, ProMetic, Respivnat, Roche, Samumed and UCB. MJH reports non-financial support from Achilles Therapeutics outside the submitted work. MP, RJM and REH have nothing to disclose.

Publication types