Inhibition of CAF-1 histone chaperone complex triggers cytosolic DNA and dsRNA sensing pathways and induces intrinsic immunity of hepatocellular carcinoma

Abstract

Background & Aims: Chromatin assembly factor 1 (CAF-1) is a replication-dependent epigenetic regulator that controls cell cycle progression and chromatin dynamics. In this study, we aim to investigate the immunomodulatory role and therapeutic potential of the CAF-1 complex in hepatocellular carcinoma (HCC). Methods: CAF-1 complex knockout cell lines were established using the CRISPR/Cas9 system. The effects of CAF-1 in HCC were studied in HCC cell lines, nude mice, and immunocompetent mice. RNA-Seq, ChIP-Seq, and ATAC-Seq were used to explore the changes in the epigenome and transcriptome. Results: CAF-1 complex was significantly upregulated in human and mouse HCCs and was associated with poor prognosis of HCC patients. Knockout of CAF-1 remarkably suppressed HCC growth in both in vitro and in vivo models. Mechanistically, depletion of CAF-1 induced replicative stress and chromatin instability, which eventually led to cytoplasmic DNA leakage as micronuclei. Also, ChIP-Seq analyses revealed a massive H3.3 histone variant replacement upon CAF-1 knockout. Enrichment of euchromatic H3.3 increased chromatin accessibility and activated the expression of endogenous retrovirus elements (ERVs), a phenomenon known as viral mimicry. Altogether, cytosolic micronuclei and ERVs are recognized as ectopic elements by the STING and dsRNA viral sensing pathways, respectively. As a result, knockout of CAF-1 activated inflammatory response and anti-tumor immune surveillance and thereby significantly enhanced the anti-cancer effect of immune checkpoint inhibitor (ICI) in HCC. Conclusion: Our findings suggest that CAF-1 is essential for HCC development, targeting CAF-1 may awaken the anti-cancer immune response and may work cooperatively with ICI treatment in cancer therapy.