IDH1 mutant glioma is preferentially sensitive to the HDAC inhibitor panobinostat

Sears, Thomas K.; Horbinski, Craig; Woolard, Kevin D.

doi:10.1007/s11060-021-03829-0

Cited by 10 publications

(11 citation statements)

References 49 publications

(61 reference statements)

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“…ATAC-seq reads in FASTQ format were rst subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7 [32],…”

Section: Atac-seqmentioning

confidence: 99%

“…RNA (≥ 200 nucleotides) was puri ed from cells using the Quick-RNA MiniPrep Plus Kit (Zymo Research, #R1057). The quality control check on RNA-seq reads was performed with FastQC v0.11.7 [32]. Adapter sequences and bad quality segments were trimmed using Trim Galore!…”

Section: Rna-seqmentioning

confidence: 99%

“…Follow-up studies have been encouraging but mixed [25][26][27][28][29][30] . Interestingly three recent studies found that HDAC inhibitors may be speci cally effective in IDH1 mutant gliomas [31][32][33] . Histone deacetylases are ubiquitously expressed in various cell types and regulate multiple cellular processes.…”

Section: Introductionmentioning

confidence: 99%

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

Garrett

Albano

Carnwath

et al. 2022

Preprint

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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.

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Section: Atac-seqmentioning

confidence: 99%

Section: Rna-seqmentioning

confidence: 99%

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

Garrett

Albano

Carnwath

et al. 2022

Preprint

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“…(54,55) Recent studies have demonstrated preferential vulnerability of mIDH1-expressing glioma models to inhibitors targeting HDAC, which is a component of the NuRD complex. (56,57) Interestingly, mIDH1 glioma cells treated with panobinostat displayed increased H3K14ac, which is recognized by ZMYND8. (57) Our current findings provide evidence that ZMYND8 is epigenetically regulated in human mIDH1 GCCs based on the loss of active histone mark H3K4me3 at the ZMYND8 promoter locus following mIDH1 inhibition.…”

Section: Discussionmentioning

confidence: 99%

Zinc Finger MYND-Type Containing 8 (ZMYND8) is epigenetically regulated in mutant Isocitrate Dehydrogenase 1 (IDH1) glioma to promote radioresistance

Carney

Banerjee

Mujeeb

et al. 2022

Preprint

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Mutant isocitrate dehydrogenase 1 (mIDH1) alters the epigenetic regulation of chromatin, leading to a hypermethylation phenotype in adult glioma. Establishment of glioma-specific methylation patterns by mIDH1 reprogramming drives oncogenic features of cancer metabolism, stemness and therapeutic resistance. This work focuses on identifying gene targets epigenetically dysregulated by mIDH1. Treatment of glioma cells with mIDH1 specific inhibitor AGI-5198, upregulated gene networks involved in replication stress. Specifically, we found that the expression of ZMYND8, a regulator of DNA damage response was decreased in three patient-derived glioma cell cultures (GCC) after treatment with AGI-5198. ZMYND8 functions as a chromatin reader to modulate enhancer activity and recruit DNA repair machinery. Knockdown of ZMYND8 expression sensitized mIDH1 GCCs to radiotherapy marked by decreased cellular viability. Following IR, mIDH1 glioma cells with ZMYND8 knockout (KO) exhibit significant phosphorylation of ATM and sustained γH2AX activation. ZMYND8 KO mIDH1 GCCs were further responsive to IR when treated with either BRD4 or HDAC inhibitors. The accumulation of DNA damage in ZMYND8 KO mIDH1 GCCs promoted the phosphorylation of cell cycle checkpoint proteins Chk1 and Chk2. In addition, the recruitment of ZMYND8 to sites of DNA damage has been shown to be PARP-dependent. PARP inhibition further enhanced the efficacy of radiotherapy in ZMYND8 KO mIDH1 glioma cells. These findings indicate the impact of ZMYND8 in the maintenance of genomic integrity and repair of IR-induced DNA damage in mIDH1 glioma. Translational Relevance: Our understanding of radioresistance mechanisms in patient-derived glioma cell cultures (GCC) that endogenously express mIDH1-R132H are limited. We have uncovered a novel gene target Zinc Finger MYND-Type Containing 8 (ZMYND8) that is downregulated following treatment of human mIDH1 GCCs with mIDH1 specific inhibitors. We demonstrate that suppression of ZMYND8 expression by shRNA knockdown or genetic knockout reduces the cellular viability of mIDH1 GCCs to ionizing radiation (IR). Our findings reveal an epigenetic vulnerability of mIDH1 GCCs to ZMYND8 knockout (KO) which results in impaired resolution of IR-induced DNA damage and induction of cell cycle arrest. Additionally, ZMYND8 KO mIDH1 GCCs display increased radiosensitivity to inhibition of epigenetic regulators BRD4, HDAC, and PARP which could be mediated by enhanced replicative stress.

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“…Glioma cell culture 0827, 0923, and 0905 GBM stem-like cells were previously isolated by Dr. Howard Fine's lab and have been previously characterized for GBM stem-like properties and genomic alterations (Toledo et (Sears et al 2021). All cell lines were grown in de ned neurobasal cell culture medium that includes B-27 and N2 supplements along with EGF and FGF growth factors (NBE).…”

Section: Methodsmentioning

confidence: 99%

R132H IDH1 sensitizes glioma to the antiproliferative and cytotoxic effects of BET inhibition

Sears

Woolard

2022

Preprint

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IntroductionMutations in isocitrate dehydrogenase 1/2 (IDHmut) identify a subset of gliomas that exhibit epigenetic dysregulation via aberrant DNA methylation. These tumors are ultimately fatal and lack effective therapeutic strategies. Considering the epigenetic dysregulation of IDHmut gliomas, we hypothesized that epigenetic-targeting drugs may yield therapeutic benefits in gliomas bearing IDHmut. One set of targets includes the Bromodomain and Extraterminal (BET) family of transcriptional coactivators.MethodsWe used TCGA data from glioma patients to determine whether BET proteins affect patient survival differently based on IDH status. Follow-up experiments using a set of IDH wildtype/mutant glioma cultures, as well as an IDH wildtype glioblastoma cell line expressing exogenous R132H IDH1, focused on cell health assays to investigate whether IDHmut was associated with increased sensitivity to the BET inhibitor JQ1. Immunoblots were used to evaluate the molecular response to JQ1 in these cultures.ResultsWe identified that high BRD4 expression associated with decreased survival only in IDHmut glioma patients. Cell viability analysis showed that IDHmut sensitized glioma cells to delayed cytotoxicity (10 days) in response to JQ1. Early effects of JQ1 (3 days) were primarily antiproliferative, with IDHmut glioma exhibiting a modest increase in sensitivity. Finally, exogenous R132H IDH1 expression in a resistant IDH wildtype cell line recapitulated the JQ1-mediated delayed cytotoxicity seen in our endogenous IDHmut glioma cells.ConclusionOverall, these data suggest that BRD4 enhances malignancy primarily in gliomas bearing IDHmut and is associated with greater sensitivity to BET inhibition. The finding that BET inhibition primarily exhibits delayed cytotoxicity may be overlooked in conventional short endpoint dose-response assays. Follow-up mechanistic and animal studies will help address the translational potential of these findings.

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IDH1 mutant glioma is preferentially sensitive to the HDAC inhibitor panobinostat

Cited by 10 publications

References 49 publications

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

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

Zinc Finger MYND-Type Containing 8 (ZMYND8) is epigenetically regulated in mutant Isocitrate Dehydrogenase 1 (IDH1) glioma to promote radioresistance

R132H IDH1 sensitizes glioma to the antiproliferative and cytotoxic effects of BET inhibition

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