Fig. 2: Genomic mutation signatures in LMS and functional evaluation of defects in the DNA damage response.

a Non-negative matrix factorization (NMF)-extracted and decomposed single-substitution (SBS), indel (ID) and double-nucleotide signatures (DBS) are illustrated in the heatmaps. Common substitution signatures include SBS1, SBS5, SBS8, and SBS40. SBS3 and ID6 (HR-deficiency) are found in 64% of samples. SBS2, SBS13, and DBS11 reflect localized hypermutation events, also called ‘kataegis’. ID8 represents a radiation signature, commonly seen in patients treated with radiation therapy. ‘Other’ substitution signatures, present in less than 5% of samples, can be found in Supplementary Fig. 13. Color refers to signature activity. b Evaluation of sensitivity to DNA damage response pathway, including PARPi, in soft tissue (ST) LMS cell lines (STS39, STS54, STS137, STS210, and STS551) and gynecological LMS cell lines (SKLMS-1, SK-UT-1 and SK-UT-1B). c Representative boxplots of EC₅₀ from LMS (n = 8) and UPS (n = 5) cell lines treated with the PARP inhibitors, talazoparib, and olaparib. The boxes represent the 25th and 75th percentile (bottom and top of box), and median value (horizontal band). The whiskers indicate the variability outside the upper and lower quartiles. For olaparib treatment, boxplots were generated for seven LMS and three UPS cell lines only, as growth suppression failed to occur in the remaining one LMS and two UPS cell lines along with the RPEΔp53 control. In contrast, all LMS cell lines are responsive to talazoparib (median EC₅₀ 0.37 µM) compared to UPS cell lines (median EC₅₀ 6.26 µM, p = 0.072, one-sided Welch’s t-test). Detailed information for all patient derived cell lines (LMS and UPS) can be found in Supplementary Data 8 and 9. d The Traffic Light Reporter (TLR) assay uses a fluorescent-based system (GFP and mCherry) to determine Homologous Recombination (HR) and Non-homologous End Joining (NHEJ) efficiencies, upon induction of a double-strand break (DSB). Stable LMS-TLR (STS39-TLR, STS137-TLR, and STS210-TLR) and control cell lines (RPEΔp53-TLR and RPEΔp53ΔBRCA1-TLR) containing a single copy of the TLR I-SceI target site were generated. An I-SceI tagged with BFP was introduced to evaluate repair efficiencies. Repair of the DSB by HR generates distinct fluorescent signals (GFP⁺), compared to NHEJ (mCherry⁺). LMS cell lines demonstrate HR-deficiency comparable with the RPEΔp53ΔBRCA1 control cell line. In contrast, GFP⁺ cells were detected in the HR proficient RPEΔp53 cell line. e The bar plot illustrates quantification of GFP to mCherry signal in each LMS cell line and controls. Intact HR (GFP⁺) is 6X higher in RPEΔp53, compared to LMS cell lines or the RPEΔp53ΔBRCA1 control. Data are derived from eight cell lines examined over three independent experiments and the error bars represent the standard deviation. Source data are provided as a Source Data file.