Deciphering the impact of SNAI1 gene on renal tubular cell proteome, nucleolar stress, ribosome biogenesis, senescence, DNA damage response, and focal adhesion dynamics

Abstract

Snail1, encoded by SNAI1 gene, is an essential protein that regulates epithelial–mesenchymal transition, which leads to extracellular matrix accumulation and kidney fibrosis, but with unclear cellular and molecular mechanisms. This study compared the cellular proteome of SNAI1-overexpressed renal tubular cells with that of vector-control cells by label-free quantitative proteomics, followed by functional assessments using various assays. A total of 233 proteins showed significant changes in their levels by ectopic SNAI1 expression. Of these, immunoblotting confirmed the decreases in HSP60 and HSP70 and the increase in DDX1. Bioinformatic analyses revealed the top 10 transcription factors as key upstream regulators of the altered cellular proteome, and translational regulation, ribosome, cell cycle regulation, and cellular senescence were primarily associated with these altered proteins. Gene ontology enrichment showed that focal adhesion, the structure where cells maintain their interior-extracellular matrix interactions, was one of the major affected cellular components. Experimental validations demonstrated that SNAI1-overexpressed cells displayed increases in nucleophosmin, nucleolar organizer regions, cell size, granularity, p21, γH2AX, MMP-9 secretion, and paxillin expression, confirming the bioinformatic predictions. This study has broadened our knowledge of Snail1 functions beyond its established role as the epithelial–mesenchymal transition regulator. In addition to alterations in the cellular proteome, ectopic SNAI1 expression induced nucleolar stress, ribosome biogenesis, senescence, and DNA damage response in renal tubular cells. Moreover, Snail1 also affected the dynamics of focal adhesion, which is imperative for cell migration, by regulating paxillin expression. These findings may offer new therapeutic targets related to Snail1-dependent mechanisms for effective management of kidney fibrosis.