Setd4-expressing cells drive regenerative recovery in chronic liver injury

Abstract

Background & aims: Chronic liver injury and its progression to disease often extend beyond exposure to toxic metabolites or xenobiotics. Recovery from chronic injury, when achieved, depends on de novo regeneration, the underlying mechanisms of which remain poorly understood. Herein, we investigate a specific cell population proposed to be fundamental for de novo regeneration and recovery following chronic injury, aiming to elucidate its regulatory mechanisms.

Methods: Setd4-expressing (Setd4⁺) cells were identified in murine liver tissue by single-molecule fluorescence in situ hybridization. These Setd4⁺ cells were labeled and lineage traced in Setd4Cre-ER^T2/+;Rosa26^lsl-tdTomato mice following tamoxifen induction for either 3 days or over 3 weeks. Chronic liver injury was induced by 12 weeks of thioacetamide drinking or 4 weeks of a 3,5-diethoxycarbonyl-1,4-dihydrocollidine diet. Targeted ablation of Setd4⁺ cells was performed in Setd4CreER^T2;Rosa26^DTA/+ mice to assess their functional role. The regulatory mechanisms governing the dormant and active states of Setd4⁺ cells were investigated through analyses of chromatin structure, immunostaining, bulk RNA-seq, and CUT&RUN-seq.

Results: We identified a damage-resistant, dormant population of long-lived Setd4⁺ cells in the murine liver. These cells survived under chronic injury and were then activated to proliferate, facilitating regenerative recovery. Acting as a reserve population, Setd4⁺ cells initiated de novo regeneration upon loss of less resistant proliferative hepatocytes. Mechanistically, dormant Setd4⁺ cells maintained a silenced metabolic state under H4K20me3-mediated heterochromatin, enabling survival during chronic injury. Chromatin remodeling then increased accessibility, triggering activation from dormancy and initiating regeneration.

Conclusions: Dormant Setd4⁺ cells serve as a reserve population that endure chronic injury and, through chromatin remodeling-mediated activation, initiate de novo regeneration, which is fundamental for recovery from chronic liver injury.

Impact and implications: This study identifies dormant Setd4⁺ cells in midlobular zone 2 as a previously unrecognized reserve population crucial for liver regeneration following chronic injury. By uncovering how H4K20me3-mediated heterochromatin maintains their dormancy and how chromatin remodeling triggers their activation, the findings reveal a fundamental mechanism enabling tissue recovery when conventional hepatocytes fail. Understanding this regenerative reserve provides a new framework for therapeutic strategies aimed at enhancing endogenous repair in chronic liver disease.

Keywords: Chromatin remodelling; Chronic liver injury; Damage-resistant hepatocytes; De novo regeneration; Dormant cells; Set domain-containing protein 4.