Fig. 6: Methylation and Expression changes at Transposable Elements (TE) in CD34+ HSPCs following AZA treatment.
From: Clinical response to azacitidine in MDS is associated with distinct DNA methylation changes in HSPCs
a–c n = 18, responder: 10, non-responder: 8. a Methylation proportion (beta value) of CpGs mapping to TEs belonging to LINE, LTR, or SINE families in responders and non-responders. Left: at C1D1. Right: At C1D8. P values are indicated, statistical comparison used is two-sided Wilcoxon Rank-Sum test. Boxplots in (a, d) show centre = median, box = interquartile range (IQR), whiskers = furthest point within 1.5xIQR, outliers = not shown. b Average methylation proportion per patient in responders and non-responders at C1D1 and C1D8. P values are indicated, statistical comparison used is two-sided Wilcoxon Rank-Sum test. Boxplots in (b, c, e, f) show centre = median, box = interquartile range (IQR), whiskers = furthest point within 1.5xIQR, outliers = points >1.5xIQR. c Expression (average logCPM) for TEs belonging to LINE, LTR, or SINE families in responders and non-responders after one cycle of injected AZA (C1D8), statistics refer to two-sided student t-test ns indicates P > 0.05. d–f n = 8 patients, responder: 5, non-responder: 3. d Methylation proportion (beta value) of CpGs mapping to TEs belonging to LINE, LTR, or SINE families in responders and non-responders after one cycle of oral AZA. Left: at C7D1. Right: At C7D22. Statistical comparison used is two-sided Wilcoxon Rank-Sum test. e Average methylation proportion per patient in responders and non-responders at C7D1 and C7D22. Statistical comparison used is two-sided Wilcoxon Rank-Sum test, ns indicates P > 0.05. f Expression (average logCPM) for TEs belonging to LINE, LTR, or SINE families in responders and non-responders after one cycle of oral AZA (C7D22), statistics refer to two-sided student t test, ns indicates P > 0.05. g Per-patient expression of 12 TEs differentially expressed at C7D22 compared to C7D1. Differentially expressed TEs included evolutionarily young (PA1-PA6)71,116 members of the L1PA# subfamily. h Summed enrichment scores for six hallmark inflammatory pathways in responders compared to non-responders.
