Additional file 1 of Modulation of SLFN11 induces changes in DNA Damage response in breast cancer

Additional file 1: gRNA location and CRISPR modification. (Fig. S1A) The predicted promoter region of SLFN11 (in green) is surrounding the gene’s exon1 and CpG island (in red) analysis show its location in the center of the promoter area. gRNAs were therefore designed along the central region of the promoter of SLFN11 (N1 to N10). (Fig. S1B) Schematic representation of the strategy adopted to respectively increase SLFN11 expression using UNISAM system and decrease SLFN11 expression using KRAB system. After insertion of the gRNA into the respective plasmids, cells were transformed with the integrative plasmids using electroporation and selected for the expression of respectively mCherry or GFP reporter genes. Cells were then analyzed for SLFN11 expression by westernblot and by Q-RT-PCR. Additional file 2: Screening of gRNA efficiency at upregulating or downregulating SLFN11 using UNISAM or KRAB systems. (Fig. S2A–Fig. S2D) Relative mRNA expression of SLFN11 analyzed by Q-RT-PCR (N = 3, technical replicates) (Fig. S2A–Fig. S2C) and relative SLFN11 protein expression analyzed by CWB (N = 2, technical replicates) (Fig. S2B–Fig. S2D) in BT-549 cancer cell lines modified with each gRNA for CRISPR-dCas9-UNISAM (Fig. S2A, Fig. S2B) or CRISPR-dCas9-KRAB (Fig. S2C, Fig. S2D) relative to non-modified cell line. (Fig. S2E–Fig. S2H) Relative mRNA expression of SLFN11 analyzed by Q-RT-PCR (N = 3, technical replicates) (Fig. S2E–Fig. S2G) and relative SLFN11 protein expression analyzed by CWB (N = 2, technical replicates) (Fig. S2F–Fig. S2H) in T47D cancer cell lines modified with each gRNA for CRISPR-dCas9-UNISAM (Fig. S2E–Fig. S2F) or 5 (N1, N2, N6, N7 and N10) of the 7 gRNA for CRISPR-dCas9-KRAB (Fig. S2G, Fig. S2H) relative to non-modified cell line. (Fig. S2I) Relative mRNA expression of SLFN11 analyzed by Q-RT-PCR in MDA-MB-231 cancer cell lines modified with each gRNA for CRISPR-dCas9-UNISAM relative to non-modified cell line. Additional file 3: Representative CWB results. (Fig. S3A) Representative CWB results of the analysis of SLFN11 protein expression in the 8 tested unmodified breast cancer cell lines compared to HFF. (Fig. S3B) Representative SLFN11 protein expression in BT-549, T47D and MDA-MB-231 analyzed by CWB after treatment with 5uM of DAC for 72 h compared to the expression level in untreated HFF. (Fig. S3C) Representative SLFN11 protein expression in BT-549, T47D and MDA-MB-231 analyzed by CWB after treatment with 5 nM of IFN-γ for 24 h compared to the expression level in untreated HFF. (Fig. S3D–Fig. S3E) Representative SLFN11 protein expression in BT-549 (D) or T47D (Fig. S3E) modified with UNISAM and each of the 7 gRNA compared to the respective unmodified cells. (Fig. S3F-Fig. S3G) Representative SLFN11 protein expression in BT-549 (Fig. S3F) or T47D (Fig. S3G) modified with KRAB and each of the 7 gRNA compared to the respective unmodified cells. (Fig. S3H-Fig. S3I) Representative SLFN11 protein expression level analyzed by CWB in BT-549 (Fig. S3H) or T47D (Fig. S3I) after modification with UNISAM (gRNA 7 or gRNA SCR) or KRAB (gRNA 7 or gRNA SCR) compared to respective unmodified cells and HFF. (Fig. S3J) Representative SLFN11 protein expression level analyzed by CWB in MDA-MB-231 after modification with UNISAM (gRNA 7) compared to respective unmodified cells and HFF. Additional file 4: Fig. S4. Principal component analysis pre and post-combat. Principal component analysis based on gene expression for all samples (baseline and cisplatin-treated samples) pre and post performing combat on samples to remove batch effect for BT-549 and T47D cell lines. Additional file 5: Fig. S5 Pathway enrichment analysis. Enriched pathways associated with DEG (n = 181, FDR   = 1) from limma analysis in UNISAM up/KRAB down and UNISAM down/KRAB up, using Ingenuity Pathway Analysis (IPA)

Additional file 7 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Additional file 7: Akaike information criterion (AIC), delta AIC, and HRs for death (overall survival) and corresponding 95%-confidence interval for ICR and 3 ir-lncRNA signature in 18 solid cancer TCGA datasets and RAQA cohort

Additional file 9 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Additional file 9: Correlation of 3 ir-lncRNA signature with immune subpopulations across tumor types. Pearson correlation heatmap between immune cell subpopulation enrichment scores and 3 ir-lncRNA scores