Identification of paired-related Homeobox Protein 1 as a key mesenchymal transcription factor in pulmonary fibrosis
Abstract
Matrix remodeling is a salient feature of idiopathic pulmonary fibrosis (IPF). Targeting cells driving matrix remodeling could be a promising avenue for IPF treatment. Analysis of transcriptomic database identified the mesenchymal transcription factor PRRX1 as upregulated in IPF. PRRX1, strongly expressed by lung fibroblasts, was regulated by a TGF-b/PGE2 balance in vitro in control and IPF human lung fibroblasts, while IPF fibroblast-derived matrix increased PRRX1 expression in a PDGFR dependent manner in control ones. PRRX1 inhibition decreased human lung fibroblast proliferation by downregulating the expression of S phase cyclins. PRRX1 inhibition also impacted TGF-β driven myofibroblastic differentiation by inhibiting SMAD2/3 phosphorylation through phosphatase PPM1A upregulation and TGFBR2 downregulation, leading to TGF-β response global decrease. Finally, targeted inhibition of Prrx1 attenuated fibrotic remodeling in vivo with intra-tracheal antisense oligonucleotides in bleomycin mouse model of lung fibrosis and ex vivo using human and mouse precision-cut lung slices. Our results identified PRRX1 as a key mesenchymal transcription factor during lung fibrogenesis.
Data availability
For gene expression profiling, publicly available datasets were obtained from NCBI Gene Expression Omnibus (GSE2052, GSE24206 and GSE21411) , IPF Cell Atlas (www.ipfcellatlas.com) or FibroXplorer (www.fibroXplorer.com). Newly generated expression dataset has been deposited in the Gene Expression Omnibus GSE161364. All data generated or analyzed during this study are included in the manuscript and supporting files.
-
IPF versus ControlNCBI Gene Expression Omnibus, GSE2052.
-
Validated Gene Expression Signatures of Idiopathic Pulmonary FibrosisNCBI Gene Expression Omnibus, GSE24206.
-
Systems biology of interstitial lung diseasesNCBI Gene Expression Omnibus, GSE21411.
Article and author information
Author details
Funding
Agence Nationale de la Recherche (JCJC ANR-16-CE14-00)
- Arnaud A Mailleux
European Respiratory Society (ERS-LTRF 2015 - 4476)
- Antoine Froidure
Fondation pour la Recherche Médicale (FDT2021060129750)
- Méline Homps-Legrand
Fondation pour la Recherche Médicale (FDM41320)
- Aurélien Justet
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: All animal experiments were conducted in accordance with the Directive 2010/63/EU of the European Parliament and approved by the local Animal ethics committee ("Comité d'éthique Paris Nord 121", APAFiS #4778 Etudedufacteurdetran_2016031617411315).
Human subjects: The study on human material was performed in accordance with the Declaration of Helsinki and approved by the local ethics committee (CPP Ile de France 1, No.0811760). Written informed consent was obtained from all subjects.
Copyright
© 2023, Marchal-Duval et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 1,096
- views
-
- 223
- downloads
-
- 5
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Further reading
-
- Cell Biology
- Immunology and Inflammation
Antibodies are used in many areas of biomedical and clinical research, but many of these antibodies have not been adequately characterized, which casts doubt on the results reported in many scientific papers. This problem is compounded by a lack of suitable control experiments in many studies. In this article we review the history of the ‘antibody characterization crisis’, and we document efforts and initiatives to address the problem, notably for antibodies that target human proteins. We also present recommendations for a range of stakeholders – researchers, universities, journals, antibody vendors and repositories, scientific societies and funders – to increase the reproducibility of studies that rely on antibodies.
-
- Cancer Biology
- Cell Biology
The canonical NF-κB transcription factor RELA is a master regulator of immune and stress responses and is upregulated in PDAC tumours. In this study, we characterised previously unexplored endogenous RELA-GFP dynamics in PDAC cell lines through live single cell imaging. Our observations revealed that TNFα stimulation induces rapid, sustained, and non-oscillatory nuclear translocation of RELA. Through Bayesian analysis of single cell datasets with variation in nuclear RELA, we predicted that RELA heterogeneity in PDAC cell lines is dependent on F-actin dynamics. RNA-seq analysis identified distinct clusters of RELA-regulated gene expression in PDAC cells, including TNFα-induced RELA upregulation of the actin regulators NUAK2 and ARHGAP31. Further, siRNA-mediated depletion of ARHGAP31 and NUAK2 altered TNFα-stimulated nuclear RELA dynamics in PDAC cells, establishing a novel negative feedback loop that regulates RELA activation by TNFα. Additionally, we characterised the NF-κB pathway in PDAC cells, identifying how NF-κB/IκB proteins genetically and physically interact with RELA in the absence or presence of TNFα. Taken together, we provide computational and experimental support for interdependence between the F-actin network and the NF-κB pathway with RELA translocation dynamics in PDAC.