Downregulation of HDAC9 Alleviates Autophagy Dysfunction by Inducing Acetylation of ATG4B in Metabolic Dysfunction‐Associated Steatotic Liver Disease

Sep 1, 2025FASEB journal : official publication of the Federation of American Societies for Experimental Biology

Lowering HDAC9 improves cell cleanup by changing ATG4B in fatty liver disease linked to metabolism problems

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Abstract

A total of 91 candidate genes related to metabolic dysfunction-associated steatotic liver disease (MASLD) were identified through the analysis of two datasets.

Epigenetic modifications, including methylation and acetylation, play critical roles in MASLD.
HDAC9 was identified as a key gene associated with MASLD through protein-protein interaction network analysis and machine learning.
High levels of HDAC9 expression correlate with increased liver enzymes and serum lipids in patients with MASLD.
Loss-of-function experiments indicated that silencing HDAC9 reduces fibrosis and inflammation in both mouse models and human liver cells.
HDAC9 may impair autophagy by decreasing acetylation of H3K9 at the ATG4B promoter, thus inhibiting its transcription.

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Metabolic dysfunction-associated steatotic liver disease (MASLD) is a prevalent hepatic metabolic disorder with a rising global incidence. Epigenetic modifications-such as methylation, acetylation, phosphorylation, and ubiquitination-play critical roles in the initiation and progression of MASLD. This study utilized two datasets, GSE89632 and GSE202379. By intersecting 2602 differentially expressed genes (DEGs) with 720 epigenetic factor-related genes (EF-RGs), 91 candidate genes were identified. Protein-protein interaction (PPI) network analysis, machine learning, and single-cell sequencing collectively identified HDAC9 as the hub gene. HDAC9 was found to be highly expressed in db/db mice and patients with MASLD and positively correlated with liver enzymes and serum lipids in patients with MASLD. Loss-of-function experiments confirmed its pathogenic role in MASLD in both in vitro and in vivo models. Silencing HDAC9 reduced the severity of fibrosis and inflammation, while also alleviating autophagy dysfunction in db/db mice and palmitic acid-treated human liver sinusoidal endothelial cells (hLSECs). Mechanistically, HDAC9 was shown to decrease H3K9 acetylation at the promoter region of ATG4B, a key autophagy regulator, thereby suppressing ATG4B transcription and impairing autophagy in MASLD. In conclusion, this study demonstrates that HDAC9 expression increases alongside clinical indicators of MASLD, and HDAC9 knockdown alleviates fibrosis and inflammation and restores autophagy by enhancing ATG4B acetylation. Therefore, HDAC9 may serve as a potential biomarker for the prevention and treatment of MASLD.

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Downregulation of HDAC9 Alleviates Autophagy Dysfunction by Inducing Acetylation of ATG4B in Metabolic Dysfunction‐Associated Steatotic Liver Disease

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