Figure 1

Cbx7 is methylated and downregulated in GBM.

(A) Beta values of Cbx7 in control brain (lab dataset n = 9, GSE28867 dataset n = 3, lab dataset n = 8), Glioblastoma samples (lab dataset n = 36, GSE28867 dataset n = 55, TCGA dataset n = 295), plotted as box and whisker plots. t-test was performed between control brain and GBM samples, p values are indicated. (B) Beta values of Cbx7 in control brain (n = 9) (lab dataset) and different glioma grades; (Grade II n = 63, Grade III n = 131, GBM n = 143), from TCGA data set, plotted as box and whisker plot. Significance testing was performed using ANOVA (Tukey, post hoc) across different sample groups, overall p value was < 0.0001 and the comparative p values are indicated. (C) Cbx7 transcript levels derived from various datasets in control brain (lab dataset n = 8, GSE28866 dataset n = 6, TCGA dataset n = 10) and Glioblastoma samples (lab dataset n = 82, GSE28866 dataset n = 40, TCGA dataset n = 548), were plotted as scatter plot. t-test was performed between control brain and GBM samples, p values are indicated. (D) Cbx7 transcript levels across different glioma grades (REMBRANDT data set) (control brain n = 28, Grade II n = 65, Grade III n = 58, GBM n = 227), plotted as scatter plot. Significance testing was performed using ANOVA (Tukey, post hoc) across different sample groups, overall p value was < 0.0001 and the comparative p values are indicated. (E) Correlation curve graph, depicting significant negative correlation between Cbx7 methylation and its expression in TCGA dataset; p value and correlation coefficient (R) are indicated. (F) Cbx7 transcript levels in control brain and various glioma cell lines (U87, U138, U251, U343, U373, LN18, LN229 and SVG) and HEK293T using qRT-PCR is plotted. (G) RNA was isolated from LN18, LN229 and U373 after treatment with 5-aza-2-deoxycytidine (DAC) for 3 and 5 days with 10, 20 and 50 μM concentrations. Cbx7 transcript levels were quantified by qRT-PCR. (H) Bisulphite sequencing of Cbx7 promoter region. Each row indicates methylation pattern of one sample. Percentage methylation of promoter was calculated as total percent of methylated cytosines from 10 randomly sequenced colonies. TSS, transcription start site, dashed line represents the CpG island analyzed by sequencing, red box represents CpG corresponding to cg23124451 probe in the Infinium array.