HDAC4 influences the DNA damage response and counteracts senescence by assembling with HDAC1/HDAC2 to control H2BK120 acetylation and homology-directed repair

Abstract

Access to DNA is the first level of control in regulating gene transcription, a control that is also critical for maintaining DNA integrity. Cellular senescence is characterized by profound transcriptional rearrangements and accumulation of DNA lesions. Here, we discovered an epigenetic complex between HDAC4 and HDAC1/HDAC2 that is involved in the erase of H2BK120 acetylation. The HDAC4/HDAC1/HDAC2 complex modulates the efficiency of DNA repair by homologous recombination, through dynamic deacetylation of H2BK120. Deficiency of HDAC4 leads to accumulation of H2BK120ac, impaired recruitment of BRCA1 and CtIP to the site of lesions, accumulation of damaged DNA and senescence. In senescent cells this complex is disassembled because of increased proteasomal degradation of HDAC4. Forced expression of HDAC4 during RAS-induced senescence reduces the genomic spread of γH2AX. It also affects H2BK120ac levels, which are increased in DNA-damaged regions that accumulate during RAS-induced senescence. In summary, degradation of HDAC4 during senescence causes the accumulation of damaged DNA and contributes to the activation of the transcriptional program controlled by super-enhancers that maintains senescence.

Super-enhancers reorganization controls re-sensitization of oxaliplatin-resistant FBXW7-mutated colorectal cancer

“…Here, the good overlap between the epigenetic perturbation by HDAC4 silencing and its degradation with the PROTAC compound suggests that any off-target effects of #11 do not play a key role in controlling this important re-sensitization phenotype. The most plausible explanation for the different effects of Tsq and #11 is that Tsq displaces only a portion of the heterogeneous protein complexes reported to be assembled by HDAC4 35,67 and which recent biochemical characterizations have shown to be very dynamic 80,81 .…”

“…Importantly, HDAC4 has been reported to be proteasomal degraded under impaired HRR cellular conditions, such as cellular quiescence 34 and senescence 13 . We therefore decided to investigate the effects of homologous recombination inhibition on the expression of HDAC4 and of class I HDACs able to form complexes with HDAC4 (HDAC1/2/3) 35 . We confirmed that the protein level of HDAC4 (Fig.…”

“…Integration of transcriptomic and epigenomic profiling in CRC has been shown to be effective in establishing predictive models for clonal evolution 22 and sensitivity and resistance to chemotherapy treatments 56 . Class IIa HDACs control the cellular epigenetic state by organizing SEs under stress conditions, such as cellular senescence, and supporting the transcriptional response to counteract cell death stimuli 13,35 . To obtain a picture of the epigenetic state of the response to OxPt, we profiled H3K27ac genome-wide in HCT-116 WT and FBXW7 -/cells treated or not treated with OxPt and in which HDAC4 expression was repressed or not with esiRNAs (characterized in Fig.…”

“…HDAC4 acts as an epigenetic modulator by assembling high-molecular weight protein complexes 35,67,68 , some of which have not been fully characterized yet. Tasquinimod (Tsq) is a small molecule effective in locking the regulatory Zn 2+ binding domain of HDAC4 thus preventing its interaction with NCoR/SMRT/HDAC3 69 (Supplementary Fig.…”

“…RNA extraction and quantitative qRT-PCR were performed as previously described 35 . Data were analyzed by comparative threshold cycle (delta delta Ct) using HPRT and GAPDH as normalizer.…”