Supplementary Figure S1 from Best Overall Response–Associated Signature to Doxorubicin in Soft Tissue Sarcomas: A Transcriptomic Analysis from ANNOUNCE

Identification of three soft tissue sarcoma subtypes. (A) REMARK (Reporting Recommendation for Tumor Marker Prognostic Studies) diagram for patients in the ANNOUNCE trial. (B) Consensus clustering matrix of 259 samples for k = 2 to k = 5 after clustering showed three robust clusters with limited overlap between clusters. (C) Consensus clustering CDF for k = 2 to k = 8. The greatest increase in the area under the CDF curve was seen when three molecular subtypes were assumed. (D) Sankey diagram showing the association of three molecular subtypes vs. tumor subtype in the ANNOUNCE cohort. (E) Gene set enrichment analysis showing signatures of cancer hallmarks (Liberzon et al., 2015) of special interest in soft tissue sarcoma, including immune signatures (Guinney et al., 2015) and canonical pathways (Carter et al., 2006; Guinney et al., 2015). CC1 samples showed a distinguished immune/inflammation profile, CC3 samples showed a strong cell proliferation and CIN pattern, and CC2 samples were under enriched from immune/inflammation and cell proliferation. Kaplan-Meier plots of PFS (F, H, J) and OS (G, I, K) stratified by three subtypes. Patients with the CC3 subtype were associated with better PFS (J) with placebo + doxorubicin compared with olaratumab + doxorubicin in ANNOUNCE. (L) Sankey diagrams showing high concordances between the TCGA molecular subtypes using SSP with the centroids from ANNOUNCE and published TCGA mRNA clusters (left plot), and subtype–tumor type association (right plot). Abbreviations: CDF, cumulative distribution function; CIN, chromosomal instability; CTL, cytotoxic T lymphocyte; Dox, doxorubicin; EMT, epithelial–mesenchymal transition; IL, interleukin; JAK, Janus kinase; MDSC, myeloid-derived suppressor cell; MPNST, malignant peripheral nerve sheath tumor; N, number of patients in the population; n, number of patients in the specified category; NA, not available; NKC, natural killer cell; Olara, olaratumab; PD1, programmed cell death 1; STAT, signal transducer and activator of transcription; TFH, T-follicular helper cell; TH1, T helper cell 1; TNFA, tumor necrosis factor-alpha; TREG, regulatory T cell; VEGF, vascular endothelial growth factor; VEGFR, vascular endothelial growth factor receptor.