American Association for Cancer Research
15417786mcr190309-sup-219410_2_supp_5601136_pttf9z.xlsx (4.51 MB)

Table S2 from CRISPR Editing of Mutant IDH1 R132H Induces a CpG Methylation-Low State in Patient-Derived Glioma Models of G-CIMP

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posted on 2023-04-03, 16:48 authored by Casey J. Moure, Bill H. Diplas, Lee H. Chen, Rui Yang, Christopher J. Pirozzi, Zhaohui Wang, Ivan Spasojevic, Matthew S. Waitkus, Yiping He, Hai Yan

Differentially Methylated Probes Parental vs. Edited Clones or Parental vs. Unedited Clones







Mutations in isocitrate dehydrogenases 1 and 2 (IDH) occur in the majority of World Health Organization grade II and III gliomas. IDH1/2 active site mutations confer a neomorphic enzyme activity producing the oncometabolite D-2-hydroxyglutarate (D-2HG), which generates the glioma CpG island methylation phenotype (G-CIMP). While IDH1/2 mutations and G-CIMP are commonly retained during tumor recurrence, recent work has uncovered losses of the IDH1 mutation in a subset of secondary glioblastomas. Cooccurrence of the loss of the mutant allele with extensive methylation changes suggests a possible link between the two phenomena. Here, we utilize patient-derived IDH1R132H/WT glioma cell lines and CRISPR-Cas9–mediated gene knockout to model the genetic loss of IDH1R132H, and characterize the effects of this deletion on DNA methylation. After D-2HG production has been abolished by deletions within the IDH1 alleles, these models show persistent DNA hypermethylation at seven CpG sites previously used to define G-CIMP–positivity in patient tumor samples. Despite these defining G-CIMP sites showing persistent hypermethylation, we observed a genome-wide pattern of DNA demethylation, enriched for CpG sites located within open sea regions of the genome, as well as in CpG-island shores of transcription start sites, after loss of D-2HG production. These results suggest that inhibition of D-2HG from genetic deletion of IDH alleles is not sufficient to reverse hypermethylation of all G-CIMP–defining CpG sites, but does result in more demethylation globally and may contribute to the formation of a G-CIMP-low–like phenotype. These findings show that loss of the IDH1 mutation in malignant glioma cells leads to a pattern of DNA methylation alterations, and shows plausibility of IDH1 mutation loss being causally related to the gain of a G-CIMP-low–like phenotype.