Fig. 2: LOC expression is regulated by IDH-dependent methylation.
a, LOC expression levels in patients with IDH-wild-type (n = 87) and IDH-mutant (n = 141) gliomas (CGGA cohort). Horizontal lines indicate the median value; bottom boundary indicates Q1; top boundary indicates Q3; whiskers extend from the box and show the range of the data. b, Patients (CGGA cohort) were grouped according to tumour source and WHO grading and the LOC expression levels of the IDH-wild-type and IDH-mutant groups were compared. WHO grade II, IDH wild-type (n = 59) and IDH mutant (n = 9); WHO grade III, IDH wild-type (n = 58) and IDH mutant (n = 17); and WHO grade IV, IDH wild-type (n = 24) and IDH mutant (n = 61). Horizontal lines indicate the median value; bottom boundary indicates Q1; top boundary indicates Q3; whiskers extend from the box and show the range of the data. c, Methylation levels of the CpG island (cg23512958) upstream of LOC in IDH-wild-type (n = 64) and IDH-mutant (n = 81) tumour samples (CGGA cohort). ssGSEA, single-sample gene set enrichment analysis. Horizontal lines indicate median value; bottom boundary indicate Q1; top boundary indicates Q3; whiskers extend from the box and show the range of the data. d, Schematic of the process to generate IDH-mutant cells using single-base editing technology. e, Sanger sequencing was used to verify successful base editing of IDH-wild-type LN18 cells to generate the IDH-mutant heterozygotes. f, Protein lysates from LN18 IDH-wild-type and IDH-mutant clones were analysed by western blot using anti-IDH1(R132H). g, LOC expression levels, determined by qPCR, of the LN18 IDH-wild-type and IDH-mutant clones. h, LOC expression levels, determined by qPCR, of LN18 IDH-wild-type and IDH-mutant clones following treatment with or without 10 μM AGI-5198. i, LOC expression levels, determined by qPCR, of IDH-wild-type and IDH-mutant clones following treatment with or without 10 μM 5-AzaC. j, Methylation profiling of the upstream CpG island of LOC of the different clones (determined using digestion with methylation-sensitive restriction enzymes and real-time PCR). g–j, The data represent the mean ± s.e.m. of n = 3 biologically independent samples. k, Kaplan–Meier survival curve of patients in the CGGA cohort with IDH-mutant or IDH-wild-type glioblastomas with high or low LOC expression. l, Kaplan–Meier survival curve of patients in the SMC cohort with glioblastoma, grouped as in k. P values were determined using the Wilcoxon rank-sum test (a–c), a two-tailed Student’s t-test (g–j) or a log-rank test (k,l). Source numerical data and unprocessed blots are provided.
