Integration of transcriptomes of senescent cell models with multi-tissue patient samples reveals reduced COL6A3 as an inducer of senescence

Radoslav Savić, Jialiang Yang, Simon Koplev, Mahru C. An, Priyanka L. Patel, Robert N. O'Brien, Brittany N. Dubose, Tetyana Dodatko, Eduard Rogatsky, Katyayani Sukhavasi, Raili Ermel, Arno Ruusalepp, Sander M. Houten, Jason C. Kovacic, Andrew F. Stewart, Christopher B. Yohn, Eric E. Schadt, Remi Martin Laberge, Johan L.M. Björkegren, Zhidong TuCarmen Argmann

Research output: Contribution to journalArticlepeer-review

Abstract

Senescent cells are a major contributor to age-dependent cardiovascular tissue dysfunction, but knowledge of their in vivo cell markers and tissue context is lacking. To reveal tissue-relevant senescence biology, we integrate the transcriptomes of 10 experimental senescence cell models with a 224 multi-tissue gene co-expression network based on RNA-seq data of seven tissues biopsies from ∼600 coronary artery disease (CAD) patients. We identify 56 senescence-associated modules, many enriched in CAD GWAS genes and correlated with cardiometabolic traits—which supports universality of senescence gene programs across tissues and in CAD. Cross-tissue network analyses reveal 86 candidate senescence-associated secretory phenotype (SASP) factors, including COL6A3. Experimental knockdown of COL6A3 induces transcriptional changes that overlap the majority of the experimental senescence models, with cell-cycle arrest linked to modulation of DREAM complex-targeted genes. We provide a transcriptomic resource for cellular senescence and identify candidate biomarkers, SASP factors, and potential drivers of senescence in human tissues.

Original languageEnglish
Article number113371
JournalCell Reports
Volume42
Issue number11
DOIs
StatePublished - 28 Nov 2023

Keywords

  • COL6A3
  • CP: Cell biology
  • cellular senescence
  • collagen
  • disease
  • human
  • integration
  • network
  • transcriptomic

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