Additional file 2 of Landscape of immune-related signatures induced by targeting of different epigenetic regulators in melanoma: implications for immunotherapy
Creators: name: Anichini, Andrea
name: Molla, Alessandra
name: Nicolini, Gabriella
name: Perotti, Valentina Eleonora
name: Sgambelluri, Francesco
name: Covre, Alessia
name: Fazio, Carolina
name: Lofiego, Maria Fortunata
name: Di Giacomo, Anna Maria
name: Coral, Sandra
name: Manca, Antonella
name: Sini, Maria Cristina
name: Pisano, Marina
name: Noviello, Teresa
name: Caruso, Francesca
name: Brich, Silvia
name: Pruneri, Giancarlo
name: Maurichi, Andrea
name: Santinami, Mario
name: Ceccarelli, Michele
name: Palmieri, Giuseppe
name: Maio, Michele
name: Mortarini, Roberta
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Supplementary Figs. S1 to S21. Supplementary Fig. S1. Expression in ten melanoma cell lines of genes and gene families targeted by epigenetic drugs. Supplementary Fig. S2. Differentiation profile of melanoma cell lines. Supplementary Fig. S3. Susceptibility of ten melanoma cell lines to the anti-proliferative effects of epigenetic drugs. Supplementary Fig. S4. Methylation status of LINE-1, MAGE-A1 and NY-ESO-1 in 9 melanoma cell lines treated with guadecitabine. Supplementary Fig. S5. Volcano plot of differentially expressed genes in VRG100 and CST30 cell lines. Supplementary FigureS6. Whole genome gene modulation analysis by 4 epigenetic drugs in two melanoma cell lines. Supplementary Fig. S7. Edwards-VENN diagram analysis of significantly modulated genes by epigenetic drugs. Supplementary Fig. S8. Original and revised gene classification of the NanoString nCounter PanCancer Immune Profiling panel. Supplementary Fig. S9. Quantitative analysis of Nanostring data in ten melanoma cell lines treated with epigenetic drugs. Supplementary Fig. S10. Modulation of immune-related genes in melanoma cell lines by epigenetic drugs. Supplementary Fig. S11. Comparison of immune-related gene modulation by BET inhibitors JQ1 and OTX-015. Supplementary Fig. S12. Immune-related signature of epigenetic drugs in melanoma. Supplementary Fig. S13. Outline of the strategy for quantitative analysis and visualization of western blot data. Supplementary Fig. S14. Quantitative western blot analysis and visualization of the modulation of LMP7 by epigenetic drugs in 11 melanoma cell lines. Supplementary Fig. S15. Pipeline of data analysis based on Upstream Regulators (UR) identified by IPA. Supplementary Fig. S16. Classification of URs significantly modulated by at least two different drugs in melanoma cell line VRG100. Supplementary Fig. S17. Classification of URs significantly modulated by at least two different drugs in melanoma cell line CST30. Supplementary Fig. S18. Summary of the major functional networks linking relevant URs emerging from IPA Core Analysis in melanoma cell line VRG100. Supplementary Fig. S19. Comparison of URs activated by guadecitabine in-vitro and in-vivo. Supplementary Fig. S20. Comparison of URs activated by guadecitabine in melanoma cell line VRG100 vs a mesothelioma cell line vs hepatocarcinoma cell lines. Supplementary Fig. S21. Prognostic significance of selected genes in the guadecitabine signatures in 41 TCGA tumor types.