Fig. 7: Combined analysis of chromatin occupancy and Hi-ChIP profiles identify CDK4/6 as a new potential therapeutic target for DSRCT tumors.

a Hockey plot shows the number of EWS-WT1 associated loops connected to genes transcriptionally down-regulated upon EWS-WT1 knockdown in the JN-DSRCT1 cell line (n = 1000). Out of most connected 1000 promoters, 323 target genes displaying more than 5 EWS-WT1-associated loops were selected for further analysis. H3K27ac Hi-ChIP in JN-DSRCT1 cell line was performed once. Expression profiling was performed four times in shRNA transduced JN-DSRCT1. b Heatmap depicts gene expression levels in primary DSRCT tumors for the 323 genes connected to EWS-WT1 binding sites and whose expression decreases upon the fusion protein knockdown identified in Fig. 3f. Comparison with Dedifferentiated Liposarcoma (DDLPS), Myxofibrosarcoma (MFS), Malignant Peripheral Nerve Sheath Tumor (MPNST), SARC (Sarcoma), Synovial Sarcoma (SS), Leiomyosarcoma arising in gynecologic location (uterine ULMS) and soft tissue (STLMS) sites, and Undifferentiated Pleomorphic Sarcoma (UPS) described in ref. ³¹. c Top 9 target genes that can be targeted by at least 1 clinically-approved compound inhibiting their activity amongst the 323 that are connected to EWS-WT1 sites and show high expression in primary DSRCT tumors (as in Fig. 7a, b). d CCND1 expression levels across a panel of primary sarcoma samples described in ref. ³¹. Number of samples: DDLPS n = 51, MFS n = 17, MPNST n = 5, DSRCT 10, SARC n = 53, SS n = 10, STLMS n = 54, ULMS n = 29, UPS n = 45. Median value is shown as a line within the boxplot, which spans from the 25th to 75th percentiles. Whiskers indicate a 1.5× inter-quartile range. e Left: Example shows marked changes in H3K27ac Hi-ChIP connectivity at the CCND1 locus upon EWS-WT1 knockdown in the JN-DSRCT1 cell line. Right: changes in CCND1 expression levels in JN-DSRCT1 cells upon EWS-WT1 knockdown, as assessed by RNA-seq. f Absolute Palbociclib IC₅₀ value for JN-DSRCT1 cells, as compared to a panel of 492 tumor cell lines described in ref. ⁴¹. g Boxplots show weight of JN-DSRCT1-derived tumors in Palbociclib- or solvent-treated-immunocompromised mice at the end of the treatment. 6 week-old male mice were injected at the beginning of the study. The total number of treated tumors were 15 and 14 respectively. Median value is shown as a line within the boxplot, which spans from the 25th to 75th percentiles. Whiskers indicate minimum to maximum value range. p values were calculated using two-sided t tests. (**) p value = 0.0033. Source data are provided as a Source Data file. h Tumor growth progression over time of patient-derived DSRCT xenografts (SJDSRCT046151_X1 = SJ-PDX1), in solvent and Palbociclib-treated immunocompromised mice. 6 week-old male mice were injected at the beginning of the study. The total number of treated tumors were 16 and 12 respectively. p values were calculated using two-sided t tests. (***) p value at endpoint = 5.7 e-6. Source data are provided as a Source Data file. i Boxplots show weight of SJ-PDX1-derived tumors in solvent- or Palbociclib-treated-immunocompromised mice at the end of the treatment. The total number of treated tumors were 16 and 12, respectively. p values were calculated using two-sided t tests. (***) p value = 3.3 e–6. Median value is shown as a line within the boxplot, which spans from the 25th to 75th percentiles. Whiskers indicate minimum to maximum value range. Source data are provided as a Source Data file.