Additional file 1 of DNA damage response signatures are associated with frontline chemotherapy response and routes of tumor evolution in extensive stage small cell lung cancer

Additional file 1: Supplementary Figure 1: DDR subtyping analysis overview. A. DDR network overview. HR: Homologous recombination. MMEJ: microhomology-mediated end-joining. NHEJ: Non-homologous end-joining. BER: Base excision repair. NER: Nucleotide excision repair. MMR: Mismatch repair. DR: Direct reversal repair. TLS: Translesion synthesis. Checkpoint: Damage sensing and signaling. FA: Fanconi Anemia. Numbers in parentheses indicate number of pathway genes analyzed by our method. B. WE score formula and Essentiality Scaling Factor (ESF) criteria. Supplementary Figure 2: DDR cluster prevalence and DDR pathway single gene heatmaps. A. DDR cluster prevalence in GEMINI cohort. B. DDR cluster prevalence in IMPOWER133 cohort. C. GEMINI DDR pathway single gene expression heatmap. D. IMPOWER133 DDR pathway single gene expression heatmap. Supplementary Figure 3: IMpower133 DDR cluster differential gene expression and quantitative set analysis (QuSAGE) BG signature results. Supplementary Figure 4: SCLC CellMiner cell line DDR optimal number of k clusters elbow plot. Supplementary Figure 5: SCLC CellMiner cell line DDR cluster prevalence and marker expression. A. DDR cluster prevalence in SCLC cell line models. B. DNA damage responsive transcription factors, intra-S cell cycle checkpoint, and G2/M cell cycle checkpoint machinery expression across SCLC cell line DDR clusters. C. SLFN11 protein expression in SCLC cell line DDR clusters. D. Total RB1 and RB1-S807.S811 phospho protein expression across SCLC cell line DDR clusters. E. Cell line DDR cluster MYC family gene expression. Supplementary Figure 6: SCLC cell line DDR cluster mutation profiling. Oncoprints for TP53, RB1, and DDR gene mutations in DDR Low, Intermediate, and High clusters. Mutation data is from CCLE whole exome sequencing [17]. Supplementary Figure 7: SCLC cell line DDR cluster nonsynonymous tumor mutational burden (TMB). TMB data is from CCLE whole exome sequencing [17]. Supplementary Figure 8: SCLC/hgNEC PDX/CDX DDR gene expression and cell cycle state distribution. A. Expression of DNA damage responsive transcription factors, intra-S, and G2/M cell cycle checkpoint effectors in PDX/CDX DDR clusters. B. PDX/CDX DDR cluster scRNAseq cell cycle state distributions. Supplementary Figure 9: IMpower133 subtyping method comparison. A. Three way alluvial plot demonstrating assignment overlap between MDACC SCLC subtypes [5], Genentech (GNE) subtypes [7], and DDR status. B. IMpower133 DDR cluster and GNE subtype assignment table. Values listed represent the number of samples in each assignment category. The corresponding X2 Pearson residual dot plot comparing DDR cluster and GNE subtype assignments is shown on the right. Supplementary Figure 10: GEMINI and IMpower133 DDR cluster neuroendocrine score single gene heatmaps. A. GEMINI DDR cluster neuroendocrine score single gene expression heatmap. B. IMpower133 DDR cluster neuroendocrine score single gene expression heatmap. Supplementary Figure 11: SCLC CellMiner DDR cluster neuroendocrine features. A. SCLC cell line DDR cluster NE scores. B. SCLC cell line DDR cluster neuroendocrine status as reported by Tlemsani et al. C. SCLC PDX/CDX DDR cluster NE scores. Supplementary Figure 12: IMpower133 SCLC-A only immune checkpoint marker expression. Boxplots depict mRNA expression of CD274/PD1, CTLA4, and HAVCR2/TIM3 in SCLC-A tumors, split by their DDR status. Supplementary Figure 13: SCLC/hgNEC PDX/CDX DDR cluster MHC Class I scRNAseq expression. Supplementary Figure 14: IMpower133 DDR cluster chemotherapy response analysis. A. RECIST Best Overall Response (BOR) for IMpower133 DDR clusters following frontline EP chemotherapy. PD: Progressive disease. SD: Stable disease. PR: Partial response. CR: Complete response. B. Progression free survival Kaplan Meier plot for SCLC-A DDR clusters following frontline EP chemotherapy. C. Forest plot for progression free survival for SCLC-A DDR clusters following frontline EP chemotherapy. Supplementary Figure 15: IMpower133 DDR cluster all subtypes chemotherapy response analysis. A. Overall survival (OS) Kaplan Meier plot for all subtypes DDR clusters following frontline EP chemotherapy. B. Progression free survival (PFS) Kaplan Meier plot for all subtypes DDR clusters following frontline EP chemotherapy. C. Forrest plots for all subtype DDR cluster OS and PFS outcomes following frontline EP chemotherapy. Supplementary Figure 16: MDACC GEMINI subtype switching plots. Subtype space and SCLC-DMC subtype calls for MDACC GEMINI subtype switching patients. Supplementary Figure 17: MDACC GEMINI subtype switching patient outcomes following frontline chemoimmunotherapy. A. Overall survival outcomes following frontline chemoimmunotherapy. B. Progression free survival following frontline chemoimmunotherapy. Supplementary Figure 18: Promoter methylation changes for MDACC GEMINI subtype switching patients from baseline to progression following frontline chemoimmunotherapy. For all panels, data presented is RRBS methylation data previously published by Heeke et al [14]. Supplementary Figure 19: Circulating tumor DNA fraction for subtype switching tumors at baseline and progression following frontline chemoimmunotherapy. Supplementary Figure 20: SC53 Leiden cluster specific top drivers of plasticity. scRNAseq data for SC53 is from Gay et al. [5]. Supplementary Figure 21: WebGestalt over-representation analysis of SC53 Leiden Cluster 8 marker genes. Supplementary Figure 22: SC53 Leiden cluster specific random walk simulations. scRNAseq data for SC53 is from Gay et al. [5]. Supplementary Table 1: WE score individual DDR gene Essentiality Scaling Factor (ESF) assignments and example raw WE score generation. Supplementary Table 2: SCLC cell line whole exome sequencing mutation enrichment statistics by DDR cluster. Genes not listed in Supplementary Table 2 were not mutated in any DDR Low, DDR Intermediate, or DDR High cell line models. Supplementary Table 3: SC53 dynamic genes by Leiden cluster.