UCA remodels tumor microenvironment(scRNA-Seq)
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE277030 | GEO | 2026/05/07
REPOSITORIES: GEO
Similar Datasets
Project description:In recent years,Bap1 has been reported to be involved in the process of tumorigenesis. Bap1 gene mutations frequently occur in tumors such as uveal melanoma, mesothelioma, and kidney cancer. In our study,we found that Bap1 deletion in MC38 colon carcinoma cells can promote anti-tumor immune response. To investigate how the genetic mutational landscape,whole exome sequencing of MC38 colon carcinoma cells and MC38 Bap1-knockout cells were performed.
2025-06-30 | E-MTAB-10584 | biostudies-arrayexpress
Project description:Urocanic acid (UCA) is a major epidermal chromophore that undergoes trans to cis photoisomerisation following exposure to solar ultraviolet radiation (UVR). Although there is considerable evidence that cis-UCA suppresses cell-mediated immune response in mouse skin, the molecular events are not fully understood. In this study, we examined involvement of gene transcription in the immunomodulatory effects of cis-UCA on primary human keratinocytes. The results showed that about 400 genes were induced by UVR, 16 of which also up-regulated by cis-UCA. In contrast, trans-UCA had no effect on gene expression. The genes up-regulated by both cis-UCA and UVR were associated with apoptosis, cell growth arrest, cytokines and oxidative stress. Experiment Overall Design: RNA was extracted from primary human keratinocytes treated with trans-, cis-UCA (10ug/ml) or solar simulated UVR (12J/cm2 ~ 2-3 minimal erythema doses for fair skin), or untreated. At 24hr, the transcriptional profiles were assessed by Affymetrix HG-U133A microarray.
2008-11-06 | E-GEOD-8760 | biostudies-arrayexpress
Project description:The mechanisms by which Pax7 promotes skeletal muscle stem (satellite) cell identity are not yet understood. We have taken advantage of pluripotent stem cells wherein the induced expression of Pax7 robustly initiates the muscle program and enables the generation of muscle precursors that repopulate the satellite cell compartment upon transplantation. Pax7 binding was excluded from H3K27 tri-methylated regions, suggesting that recruitment of this factor is circumscribed by chromatin state. Further, Pax7 binding provoked localized chromatin remodeling, including the acquisition of enhancer-associated histone marks and induction of chromatin accessibility. Conversely, removal of Pax7 led to rapid reversal of these features on a subset of enhancers. Another cohort of Pax7 binding sites exhibited a durably accessible and remodeled chromatin state after Pax7 removal, and persistent enhancer accessibility was associated with subsequent binding by muscle regulatory factors. Our studies provide new insights into Pax7 and the epigenetic landscape of skeletal muscle stem cells.
2017-04-26 | GSE89977 | GEO
Project description:CircNOP58 was significantly upregulated in MM and was associated with inferior survival outcomes. CircNOP58 encodes a previously uncharacterized 466-amino-acid protein, circNOP58-466aa, that undergoes LLPS through intrinsically disordered regions. CircNOP58-466aa promoted MM progression and remodeled the bone marrow tumor microenvironment by enhancing osteoclast differentiation
2026-06-10 | PXD079547 |
Project description:Urocanic acid (UCA) is a major epidermal chromophore that undergoes trans to cis photoisomerisation following exposure to solar ultraviolet radiation (UVR). Although there is considerable evidence that cis-UCA suppresses cell-mediated immune response in mouse skin, the molecular events are not fully understood. In this study, we examined involvement of gene transcription in the immunomodulatory effects of cis-UCA on primary human keratinocytes. The results showed that about 400 genes were induced by UVR, 16 of which also up-regulated by cis-UCA. In contrast, trans-UCA had no effect on gene expression. The genes up-regulated by both cis-UCA and UVR were associated with apoptosis, cell growth arrest, cytokines and oxidative stress. Keywords: Agent response
2007-08-16 | GSE8760 | GEO
Project description:The long-term survival of advanced urothelial carcinoma (UCa) patients is limited due to an innate resistance to treatment. We identified elevated expression of the histone methyltransferase EZH2 as a hallmark of aggressive UCa, and therefore, hypothesized that EPZ-011989, a small molecule catalytic inhibitor of EZH2, might have anti-tumor effects in UCa. Here we show that in a carcinogen-induced mouse bladder cancer model, EZH2 inhibition results in reduced tumor progression, elevated tumor infiltrating T cells, increased pro-inflammatory cytokine secretion and MHC class II expression on UCa cells. Treatment of mice with EPZ011989 causes increased MHC class II expression on the urothelium, and was able to activate CD4+ T cells, which is completely abrogated with genetic ablation of the acquired immune system. These findings support a unique role for EZH2 catalytic activity in mediating UCa immune evasion and, for the first time, prove the efficacy of EZH2 catalytic inhibitors in a UCa model, a finding that can potentially be expanded to humans with UCa.
2022-08-15 | GSE209852 | GEO
Project description:The long-term survival of advanced urothelial carcinoma (UCa) patients is limited due to an innate resistance to treatment. We identified elevated expression of the histone methyltransferase EZH2 as a hallmark of aggressive UCa, and therefore, hypothesized that EPZ-011989, a small molecule catalytic inhibitor of EZH2, might have anti-tumor effects in UCa. Here we show that in a carcinogen-induced mouse bladder cancer model, EZH2 inhibition results in reduced tumor progression, elevated tumor infiltrating T cells, increased pro-inflammatory cytokine secretion and MHC class II expression on UCa cells. Treatment of mice with EPZ011989 causes increased MHC class II expression on the urothelium, and was able to activate CD4+ T cells, which is completely abrogated with genetic ablation of the acquired immune system. These findings support a unique role for EZH2 catalytic activity in mediating UCa immune evasion and, for the first time, prove the efficacy of EZH2 catalytic inhibitors in a UCa model, a finding that can potentially be expanded to humans with UCa.
2022-08-15 | GSE209851 | GEO
Project description:This study was designed to investigate DNA supercoiling across the human genome and to understand how supercoiling domains impact on higher levels of genome organisation. DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, M-bM-^@M-^\openM-bM-^@M-^] chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes. The gene transcription of 3 independent biological replicates were investigated
2013-02-17 | E-GEOD-43449 | biostudies-arrayexpress
Project description:High-grade serous ovarian, fallopian tube or peritoneal carcinoma is an aggressive subtype that frequently develops resistance to chemotherapy. It remains controversial whether the resistance is caused by the acquisition of new molecular aberrations or alternatively through the selection of rare preexisting tumor clones. To address this question, we applied single cell RNA sequencing to depict the tumor landscape of a single case of advanced high-grade serous fallopian tube carcinoma during neoadjuvant chemotherapy (NACT).
2022-08-16 | GSE191301 | GEO
Project description:This study was designed to investigate DNA supercoiling across the human genome and to understand how supercoiling domains impact on higher levels of genome organisation. DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, M-bM-^@M-^\openM-bM-^@M-^] chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes. The binding of bTMP, as a reporter for DNA supercoiling, was investigated in RPE1 cells. Experiments were biological replicates
2013-02-17 | E-GEOD-43450 | biostudies-arrayexpress