Fig. 6: Human FN-RMS is dependent on PAX7. | Nature Communications

Fig. 6: Human FN-RMS is dependent on PAX7.

From: Synthetic essentiality between PTEN and core dependency factor PAX7 dictates rhabdomyosarcoma identity

Fig. 6

a PAX7 expression by RNA sequencing (log2(TPM + 1)) from the DepMap (20Q3 release). Red bar indicates sarcoma cell lines. The number of cell lines is indicated along the x axis label for each respective tumor type. b RNA sequencing (FPKM) of PAX7 in human FN-RMS (n = 64), FP-RMS (P3F-RMS n = 29, P7F- RMS n = 10) tumors, and human skeletal muscle (n = 20) (SkM) from the NCI dataset30. (SkM-FN-RMS P < 0.0001, SkM-P7F-RMS P < 0.0001). c CERES gene dependency score for PAX7 in FN-RMS cells (n = 5) compared to all other cell lines in the DepMap, 20Q3 release. (FN-RMS-non-RMS soft-tissue tumors P = 0.0015, FP-RMS-non-RMS soft-tissue tumors P = 0.0450, FN-RMS-others and FP-RMS-others P < 0.0001). d Gene expression by real-time PCR of PAX7 in SMS-CTR, RD, Rh18, SJRHB015721_X1, and SJRHB011_Y1-cultured cells following transduction with PAX7 targeting or scramble shRNA, in triplicate, 5 days post transduction. Normalized to ACTB expression and expressed relative to scramble. (RD Scr-shPAX7-A P = 0.008, RD Scr-shPAX7-D P = 0.0023) (SMS-CTR Scr-shPAX7-A P < 0.0001 Scr-shPAX7-D P = 0.0003) (Rh18 Scr-shPAX7-A P = 0.0013, Scr-shPAX7-D P = 0.0009) (SJRHB015721_X1 Scr-shPAX7-A P = 0.0406, Scr-shPAX7-D P = 0.0092) (SJRHB011_Y1 Scr-shPAX7-A P < 0.0001, Scr-shPAX7-D P = 0.0318). e Cell viability by Cell Titer Glo assay of RD, SMS-CTR, Rh18, SJRHB015721_X1, and SJRHB011_Y cell lines after PAX7 knockdown, in quadruplicate. All P values are <0.0001. f SMS-CTR proliferation assay following PAX7 knockdown, n = 30 images (six wells, five images taken per well). g–i Tumor volume over time (g, P < 0.0001) and final tumor mass (h, P = 0.0003) of orthotopically injected SMS-CTR cells in SCID/Beige mice (n = 10 per group) transduced with PAX7 targeting or scramble shRNAs. i representative histology of tumors from (g), n = 10. j–l Tumor volume over time (i, all P values <0.0001) and final tumor mass (j, Scr-shPAX7-A P = 0.0028, Scr-shPAX7-D P = 0.0006) of orthotopically injected SJRHB015721_X1 cells in SCID/Beige mice transduced with PAX7 targeting or scramble shRNAs, n = 6. l representative histology of tumors from (j), n = 6. All P values in pairwise comparisons were determined by Student’s t test (unpaired, two-tailed); *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. Data represented as mean + SEM. See also Supplementary Fig. 7. Source data are provided as a Source Data file.

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