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Additional file 1. Supplementary Methods.

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.

Despite decreased postoperative mortality, pancreatic resections continue to be associated with high morbidity rates. Vascular complications and, in particular, erosive bleeding from the large retroperitoneal vasculature are particularly difficult to treat and account for a large percentage of the residual postoperative mortality of pancreatic resections. We herein analyze the pathogenesis, diagnosis, preventive measures and possible remedies of either hemorrhagic or occlusive complications of pancreatic resections through a review of the literature and of our institutional experience consisting of 818 pancreatectomies.

Background Improvement of efficacy of immune checkpoint blockade (ICB) remains a major clinical goal. Association of ICB with immunomodulatory epigenetic drugs is an option. However, epigenetic inhibitors show a heterogeneous landscape of activities. Analysis of transcriptional programs induced in neoplastic cells by distinct classes of epigenetic drugs may foster identification of the most promising agents. Methods Melanoma cell lines, characterized for mutational and differentiation profile, were treated with inhibitors of DNA methyltransferases (guadecitabine), histone deacetylases (givinostat), BET proteins (JQ1 and OTX-015), and enhancer of zeste homolog 2 (GSK126). Modulatory effects of epigenetic drugs were evaluated at the gene and protein levels. Master molecules explaining changes in gene expression were identified by Upstream Regulator (UR) analysis. Gene set enrichment and IPA were used respectively to test modulation of guadecitabine-specific gene and UR signatures in baseline and on-treatment tumor biopsies from melanoma patients in the Phase Ib NIBIT-M4 Guadecitabine + Ipilimumab Trial. Prognostic significance of drug-specific immune-related genes was tested with Timer 2.0 in TCGA tumor datasets. Results Epigenetic drugs induced different profiles of gene expression in melanoma cell lines. Immune-related genes were frequently upregulated by guadecitabine, irrespective of the mutational and differentiation profiles of the melanoma cell lines, to a lesser extent by givinostat, but mostly downregulated by JQ1 and OTX-015. GSK126 was the least active drug. Quantitative western blot analysis confirmed drug-specific modulatory profiles. Most of the guadecitabine-specific signature genes were upregulated in on-treatment NIBIT-M4 tumor biopsies, but not in on-treatment lesions of patients treated only with ipilimumab. A guadecitabine-specific UR signature, containing activated molecules of the TLR, NF-kB, and IFN innate immunity pathways, was induced in drug-treated melanoma, mesothelioma and hepatocarcinoma cell lines and in a human melanoma xenograft model. Activation of guadecitabine-specific UR signature molecules in on-treatment tumor biopsies discriminated responding from non-responding NIBIT-M4 patients. Sixty-five % of the immune-related genes upregulated by guadecitabine were prognostically significant and conferred a reduced risk in the TCGA cutaneous melanoma dataset. Conclusions The DNMT inhibitor guadecitabine emerged as the most promising immunomodulatory agent among those tested, supporting the rationale for usage of this class of epigenetic drugs in combinatorial immunotherapy approaches.