HDAC1 and HDAC6 are essential for driving growth in IDH1 mutant glioma

Abstract

Introduction: Low-grade and secondary high-grade gliomas frequently contain a mutation in the IDH1 metabolic enzyme that is hypothesized to drive tumorigenesis by inhibiting many of the chromatin-regulating enzymes that regulate DNA structure. Much of the previous research has focused on DNA methylation leaving histone modifications relatively under-studied. Histone deacetylase inhibitors are promising anti-cancer agents and have already been used in clinical trials, however a clear understanding of their mechanism or gene targets is lacking. In this study, the authors genetically dissect patient-derived IDH1 mutant cultures to determine which HDAC enzymes drive growth in IDH1 mutant gliomas and what are the down-stream gene targets. This information will allow clinicians to design more specific HDAC inhibitors as well as monitor for treatment response. Methods: A panel of patient-derived gliomasphere cell lines (2 IDH1 mutant lines, 3 IDH1 wildtype lines) were subjected to a drug-screen of 110 epigenetic modifying drugs from 34 different epigenetic classes. The effect of LBH (Panobinostat) on gene expression and chromatin structure was tested on patient-derived IDH1 mutant lines. The role of each of the highly expressed HDAC enzymes was molecularly dissected using lentiviral RNA interference knock-down vectors and a patient-derived IDH1 mutant in vitro model of glioblastoma (HK252). These results were then confirmed in an in vivo xenotransplant model (BT-142). Results: The IDH1 mutation leads to gene down-regulation, DNA hypermethylation, increased DNA accessibility and H3K27 hypo-acetylation in two distinct IDH1 mutant over-expression models. The drug screen identified histone deacetylase inhibitors (HDACi) and Panobinostat (LBH) more specifically as the most selective compounds to inhibit growth in IDH1 mutant glioma lines. Of the eleven annotated HDAC enzymes (HDAC1-11) only six are expressed in IDH1 mutant glioma tissue samples and patient-derived gliomasphere lines (HDAC1, HDAC2, HDAC3, HDAC4, HDAC6, HDAC9). Lentiviral knock-down experiments revealed that HDAC1 and HDAC6 are the most consistently essential for growth both in vitro and in vivo and target very different gene modules. Knock-down of HDAC1 or HDAC6 in vivo led to a more circumscribed less invasive tumor. Conclusions: The gene dysregulation induced by the IDH1 mutation is wide-spread and only partially reversible by direct IDH1 inhibition. This study reports a previously under-described phenomenon of histone deacetylation induced by the IDH1 mutant enzyme and identifies HDAC1 and HDAC6 as important and drug-targetable enzymes that are necessary for growth and invasiveness in IDH1 mutant gliomas.

A histone deacetylase, FaSRT1‐2, plays multiple roles in regulating fruit ripening, plant growth and stresses resistance of cultivated strawberry

“…Notably, these genes, namely FvH4_3g16760 and FvH4_5g27840, paly crucial roles in the GA metabolic and signalling pathway (Figure 7). One plausible explanation for this finding is that in the knockout mutants, other members of the SRT family compensate for the absence of FvSRT1, as in line with the previous observation (Garrett et al, 2023). In summary, our findings highlight that FaSRT1-2 exerts regulatory control over strawberry plant growth, development, and morphogenesis through its influence on ABA and GA 3 as well as modulation of key genes expression in the signalling pathway.…”

De novo lipogenesis pathway is a vulnerability in IDH1 mutant glioma

“…We next re-analyzed our previously published RNA-seq and ATAC-seq dataset 15 of IDH1 MT and IDH1 WT cell lines treated with 1mM VPA for 5 days and found that similar to the current findings, VPA treatment increased a greater number of genes and downregulated a smaller number of genes in both IDH1 WT and IDH1 MT cell lines (Fig3G). Interestingly, ATAC seq analysis showed that despite of the relatively increased transcription, a greater number of peaks were lost and only a few peaks were gained after VPA treatment (Fig3H), suggesting VPA treatment activates transcription but paradoxically results in chromatin condensation.…”

“…Next, we wondered whether the effect of VPA on lipogenic genes is dependent or independent of HDAC inhibition. We re-analyzed RNA seq data from our recently published work 15 in which shRNAs used to knockdown different HDACs in IDH1 MT cell line HK252 to assess the effects on fatty acid metabolism genes. We found that knockdown of HDAC2,3,4, & 9 increased expression of lipogenic genes such FASN, stearyl coA desaturase (SCD) and HMGCR.…”

“…In recent years several studies have emerged indicating that IDH1 MT gliomas are inhibited by HDACis such as panobinostat 15,21 and belinostat 22 . In our study, we found that IDH1 MT gliomas are more sensitive to VPA when compared to IDH1 WT glioma cell lines.…”

“…ATAC seq data was used from Garrett et al 15 . Alignment of reads was carried out using the Burrows-Wheeler Aligner mem using hg19 assembly.…”