Figure 3.

TE families are reprogrammed in a subset of patients with prostate cancer. A and B, Heat maps displaying the deviation (Dev) Z-scores of TE families differentially enriched in H3K27ac-positive chromatin between pluripotent stem cells and benign prostate tissue state across H3K27ac profiles of CPC-GENE patients (A; n = 48) or Porto patients (B; n = 92). BCR, biochemical recurrence; NE score, neuroendocrine score; Neg, negative; Pos, positive; REP score, reprogramming score. C and D, Volcano plots showing median difference in deviation Z-scores for each TE family enriched in H3K27ac-positive chromatin between reprogrammed (REP) and constant (CONST) patients (CPC-GENE patients in C, Porto patients in D) vs. the −log₁₀ q-value for that difference. The gray dashed line corresponds to −log₁₀(q-value) = 2 (q-value = 0.01). The number of TE families enriched in reprogrammed or constant patients is reported at the top. n.s., not significant. E, UpSet plot showing the intersection of TE families enriched in reprogrammed CPC-GENE and Porto patients. Note that the vast majority of TE families are commonly enriched. F, UpSet plot showing the intersection of TE families enriched in pluripotent stem cells (PSC), benign prostate, and reprogrammed prostate cancer patients. Note that 164 TE families are commonly enriched in patients with reprogrammed prostate cancer and PSCs, corresponding to reprogrammed TE families, while 22 TE families are shared between patients with prostate cancer and benign prostate. Red font highlights the set of TE families described in the corresponding results section (more precisely, 164 TE families common to prostate cancer patients and pluripotent stem cells and 22 TE families common to prostate cancer patients and benign prostate epithelium). G–I, Box plot displaying the reprogramming score in reprogrammed and constant CPC-GENE (G) and Porto patients [with intermediate (INT) patients; H], and in pluripotent stem cells and benign prostate (I). P value results of Wilcoxon test are showcased on the box plot. J, Breakdown of common prostate cancer genetic aberrations called from whole-genome sequencing data in each of the 48 CPC-GENE samples separated by TE-based clustering (left). Comparison of the frequency of genetic aberrations using Fisher exact test (right). The red dashed line corresponds to −log₁₀(P) = 1.3 (P = 0.05) threshold. Note that no genetic aberration tested was found significantly different between reprogrammed and constant patients. NA, not available.