Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype

Research output: Contribution to journalArticlepeer-review

Abstract

IPF is a progressive fibrotic lung disease whose pathogenesis remains incompletely understood. We have previously discovered pathologic mesenchymal progenitor cells (MPCs) in the lungs of IPF patients. IPF MPCs display a distinct transcriptome and create sustained interstitial fibrosis in immune deficient mice. However, the precise pathologic alterations responsible for this fibrotic phenotype remain to be uncovered. Quantitative mass spectrometry and interactomics is a powerful tool that can define protein alterations in specific subcellular compartments that can be implemented to understand disease pathogenesis. We employed quantitative mass spectrometry and interactomics to define protein alterations in the nuclear compartment of IPF MPCs compared to control MPCs. We identified increased nuclear levels of PARP1, CDK1, and BACH1. Interactomics implicated PARP1, CDK1, and BACH1 as key hub proteins in the DNA damage/repair, differentiation, and apoptosis signaling pathways respectively. Loss of function and inhibitor studies demonstrated important roles for PARP1 in DNA damage/repair, CDK1 in regulating IPF MPC stemness and self-renewal, and BACH1 in regulating IPF MPC viability. Our quantitative mass spectrometry studies combined with interactomic analysis uncovered key roles for nuclear PARP1, CDK1, and BACH1 in regulating IPF MPC fibrogenicity.

Original languageEnglish (US)
Article number2200018
JournalProteomics
Volume22
Issue number13-14
DOIs
StatePublished - Jul 2022

Bibliographical note

Funding Information:
The proteomics sample preparation, mass spectrometry analysis and database searching was performed at the Center for Mass Spectrometry and Proteomics in the department of Biochemistry, Molecular Biology and Biophysics at the University of Minnesota; supporting agencies are listed here: https://cbs.umn.edu/cmsp/about This work was supported by National Institutes of Health grants R01 HL125227 to C.A.H. and funds provided by the O'Brien and Witowski families.

Funding Information:
This work was supported by National Institutes of Health grants R01 HL125227 to C.A.H. and funds provided by the O'Brien and Witowski families.

Publisher Copyright:
© 2022 Wiley-VCH GmbH.

Keywords

  • DNA damage
  • apoptosis
  • differentiation
  • idiopathic pulmonary fibrosis (IPF)
  • ingenuity pathway analysis
  • mesenchymal progenitor cells (MPCs)
  • nuclear fraction
  • quantitative mass spectrometry

PubMed: MeSH publication types

  • Journal Article

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