Role of different epigenetic drugs in reshaping murine melanoma tumor microenvironment [Array]
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PROVIDER: PRJNA1068512 | ENA |
REPOSITORIES: ENA
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Project description:Role of different epigenetic drugs in reshaping murine melanoma tumor microenvironment
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Project description:To highlight the role of epigenetics in immune responses, we exploited a model of melanoma using B16F10 injected subcutaneously in syngeneic C57black6j mice and studied the effect of inhibitors of (i) BET bromodomain (OTX-015) (ii) DNA methyltransferase (DNMT) (guadecitabine) on in vivo tumour growth. OTX-015 showed significant in vivo effects in reducing tumour growth in our setting. Guadecitabine induced MHC class I expression on tumour cells, but the latter also increased immune checkpoint expression on cancer cells. Each epigenetic agent altered the tumour microenvironment (TME), mostly by reducing immune suppression, particularly of Tregs or MDSC, or both. OTX-015 and guadecitabine had strong effects, but in opposite ways. OTX-015 downmodulated antitumour responses, whereas guadecitabine remodeled the TME to be more immune-responsive. Epigenetic therapy may enhance immunotherapy, but specific schedules for treatments need to be studied for each drug. Among the drugs tested, guadecitabine seems to be the most promising drug for successful combination immunotherapy.
2025-01-31 | GSE254073 | GEO
Project description:To highlight the role of epigenetics in immune responses, we exploited a model of melanoma using B16F10 injected subcutaneously in syngeneic C57black6j mice and studied the effect of inhibitors of (i) BET bromodomain (OTX-015) (ii) DNA methyltransferase (DNMT) (guadecitabine) on in vivo tumour growth. OTX-015 showed significant in vivo effects in reducing tumour growth in our setting. Guadecitabine induced MHC class I expression on tumour cells, but the latter also increased immune checkpoint expression on cancer cells. Each epigenetic agent altered the tumour microenvironment (TME), mostly by reducing immune suppression, particularly of Tregs or MDSC, or both. OTX-015 and guadecitabine had strong effects, but in opposite ways. OTX-015 downmodulated antitumour responses, whereas guadecitabine remodeled the TME to be more immune-responsive. Epigenetic therapy may enhance immunotherapy, but specific schedules for treatments need to be studied for each drug. Among the drugs tested, guadecitabine seems to be the most promising drug for successful combination immunotherapy.
2025-01-31 | GSE254070 | GEO
Project description:2D culture as a model for drug testing often turns to be clinically futile. Therefore, 3D cultures (3Ds) show potential to better model responses to drugs observed in vivo. In preliminary studies, using melanoma (B16F10) and renal (RenCa) cancer, we confirmed that 3Ds better mimics the tumor microenvironment. Here, we evaluate how the proposed 3D mode of culture affects tumor cell susceptibility to anti-cancer drugs, which have distinct mechanisms of action (everolimus, doxorubicin, cisplatin). Melanoma spheroids show higher resistance to all used drugs, as compared to 2D. In RCC model, such modulation was only observed for doxorubicin treatment. As drug distribution was not affected by the 3D shape, we assessed the expression of MDR1 and mTor. Upregulation of MDR1 in RCC spheroids was observed, in contrast to melanoma. In both models mTor expression was not affected by the 3D cultures. By NGS, 10 genes related with metabolism of xenobiotics by cytochrome p450 were deregulated in renal cancer spheroids; 9 of them were later confirmed in melanoma model. The differences between 3D models and classical 2D cultures point to the potential to uncover new non canonical mechanisms to explain drug resistance set by the tumor in its microenvironment.
2022-01-20 | GSE190296 | GEO
Project description:Cancer is a disease of aging, and incidence and mortality from all cancers increase logarithmically after the age of 45. Older patients have a much poorer prognosis for melanomas of equal stage, compared to younger individuals. The role of the tumor microenvironment in modulating cancer behavior is widely recognized. We hypothesized that age-related changes in the tumor microenvironment could affect the progression of melanoma. We demonstrate that the aging microenvironment increases the invasion of melanoma cells. Using skin fibroblasts isolated from healthy donors, we have built artificial skin and demonstrate that melanoma cells invade more rapidly when exposed to aged fibroblasts. In a mouse model of melanoma (YUMM1.7, BrafV600E/Cdkn2a-/-/Pten-/-), congeneic to C57/BL6 mice, melanomas invade faster in aged mice. Gene expression analyses suggest that melanoma cells are undergoing DNA damage when exposed to an aged microenvironment, and we confirm this in cellular assays. Proteomics analysis of aging fibroblasts suggest that fibroblasts secrete molecules (laminin b2, Wnt inhibitors) associated with increased resistance to targeted therapy. Indeed, melanoma cells injected into aged mice respond less well to PLX4720 than those injected into young mice. This suggests that exciting new drugs targeting the BRAF pathway may be less effective in aging patients.
2016-04-08 | GSE57445 | GEO
Project description:Eliminating B cells through anti-CD20 antibody led to a drastic reshaping of the inflammatory tumor microenvironment. This included a profound reduction of T cells, endothelial cells, monocytes and fibroblasts. The results of this study are therefore the first evidence in human that B cells are required to sustain the inflammatory tumor microenvironment.
2019-08-14 | E-MTAB-7473 | biostudies-arrayexpress
Project description:Increased MITF expression contributes to melanoma progression and resistance to BRAF pathway inhibition. We show that, unexpectedly, lack of MITF is associated with more severe resistance to a range of inhibitors. Indeed, the presence of endogenous MITF was essential for robust drug responses. Both in primary and acquired resistance, MITF levels inversely correlated with expression of several activated receptor tyrosine kinases, most commonly AXL. The MITF-low/AXL-high/drug resistance phenotype was seen in roughly half of BRAF mutant and the majority of NRAS mutant melanoma cell lines. The dichotomous behavior of MITF in drug response was corroborated in vemurafenib-resistant biopsies, including MITF high and low clones in a relapsed patient. Drug cocktails containing AXL inhibitor enhanced melanoma cell elimination by BRAF or ERK inhibition. Our results demonstrate that a low MITF/AXL ratio predicts early resistance to multiple targeted drugs, and warrant clinical validation of AXL inhibitors to combat resistance of BRAF and NRAS mutant MITF-low melanomas. Experssion analysis by RNAseq of 14 melanoma cell lines.
2014-09-19 | E-GEOD-61544 | biostudies-arrayexpress
Project description:Increased genomic instability and reshaping of tissue microenvironment underlie oncogenic properties of Arid1a mutations
| PRJNA878530 | ENA
Project description:Mutations in the NRAS oncogene are present in up to 20% of melanoma. Here, we show that interferon alpha-inducible protein 6 (IFI6) is necessary for NRASQ61K-induced transformation and melanoma growth. IFI6 was transcriptionally upregulated by NRASQ61K, and knockdown of IFI6 resulted in DNA replication stress due to dysregulated DNA replication via E2F2. This stress consequentially inhibited cellular transformation and melanoma growth via senescence or apoptosis induction depending on the RB and p53 pathway status of the cells. NRAS-mutant melanoma were significantly more resistant to the cytotoxic effects of DNA replication stress-inducing drugs, and knockdown of IFI6 increased sensitivity to these drugs. Pharmacological inhibition of IFI6 expression by the MEK inhibitor trametinib, when combined with DNA replication stress-inducing drugs, blocked NRAS-mutant melanoma growth. Collectively, we demonstrate that IFI6, via E2F2 regulates DNA replication and melanoma development and growth, and this pathway can be pharmacologically targeted to inhibit NRAS-mutant melanoma. YUGASP cells stably expressing a non-silencing shRNA or two individual shRNAs against IFI6 were used to prepare the total RNA, which was then used to analyze for gene expression using Illumina expression array.
2016-09-08 | E-GEOD-69933 | biostudies-arrayexpress
Project description:We subjected 196 melanoma tumors to genome-wide methylation analysis using the Illumina Infinium MethylationEPIC BeadChip array.
2020-03-25 | GSE144487 | GEO