Extended Data Fig. 7: Comparison of ALL patients and cell lines.
From: Acute lymphoblastic leukemia displays a distinct highly methylated genome
a) PCA based on the average methylation of the variable commonly covered CGIs (left) and based on the methylation status of the variable commonly covered CGIs (right) of precursor T cells, T-ALL patients and T-ALL cell lines (n = 7,914 CGIs, n = 10 precursor T cell, 48 T-ALL and 9 cell line samples). b) Violin plot showing the mean methylation of 1-kb tiles separated by HMDs and PMDs (n = 718,674 and n = 716,821 tiles respectively) for each T-ALL and B-ALL cell line as well as ALL subtypes and healthy cells for comparison. Lines denote the median. c) Violin plot showing the mean methylation of variable CGIs (defined across all normal and ALL samples, n = 9,349) for each B-ALL cell line and B-ALL subtypes as well as healthy cells for comparison. White dots denote the median, edges denote the IQR and whiskers denote either 1.5 × IQR or minima/maxima (if no point exceeded 1.5 × IQR; minima/maxima are indicated by the violin plot range). d) Heatmap showing the methylation status of the promoter CGIs of a panel of epigenetic regulators in T-ALL and B-ALL cell lines. Only ARID1B does not have a promoter CGI and instead the mean methylation of the promoter region is shown. SUV39H1 is located on the X chromosome, which is excluded from methylation analysis. e) Jurkat cells were transfected with px458 containing a guide RNA targeting exon 3 of the TET2 gene and expressing a GFP reporter. GFP positive cells were sorted by FACS as single cells and expanded. Images show transfected Jurkat cells in brightfield (left) and the GFP signal (right). The transfection was repeated four times independently leading to one successful knockout. The image is representative of four images taken from one plate. Scale bar = 100 um. f) cDNA genotyping PCR in WT and Jurkat TET2 KO cells. A primer pair (F1, R1) inside exon 3 and flanking the target site of the gRNA yields a 525 bp product in WT Jurkat cells, and no product in the KO when run on a 1% agarose gel with the NEB 2-Log DNA ladder. g) Jurkat TET2 KO shows a 7-kb insertion at the guide RNA cut site in exon 3, which is normally 3,455 bp long in WT cells, resulting in a premature stop codon. h) Expression of epigenetic regulators in Jurkat WT and KO cells. Upon TET2 KO, DNMT3B gets significantly up-regulated.
