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P16 epimutation modulates the tumor microenvironment and promotes malignancy of Apc-mutant colon cancer (RNA-Seq)

ABSTRACT: Using a mouse model of engineered p16 promoter hypermethylation (p16cis/cis), we found that p16 epimutation cooperates with mutant Apc to promote colon cancer development. Therefore, we performed RNA-seq analysis to identify genes regulated by p16 epimutation that contribute to intestinal carcinogenesis.

ORGANISM(S): Mus musculus

PROVIDER: GSE213566 | GEO | 2023/08/02

REPOSITORIES: GEO

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p16 epimutation modulates the tumor microenvironment and promotes malignancy of Apc-mutant colon cancer (scRNA-Seq)

Project description:Methylation of p16 promoter resulting in epigenetic gene silencing- known as p16 epimutation- is common in human colorectal cancer (CRC). Using mouse models, we demonstrated that p16 epimutation cooperates with mutant Apc to promote colon cancer development. To comprehensively characterize immune function within the tumor microenvironment (TME), we performed single-cell RNA sequencing (scRNA-seq) of colon tumors in these animals.

2023-08-02 | GSE213567 | GEO

p16 epimutation modulates the tumor microenvironment and promotes malignancy of Apc-mutant colon cancer

Project description:We previously generated a mouse model of p16 epimutation (named as p16cis/cis) through targeted knock-in of a 140-bp Alu-related DNA sequence (cis-element) that facilitates the spread of DNA methylation at promoter CpG islands (CGIs) in cis (Yu et al. JCI, 2014). We generated primary mouse embryonic fibroblasts (MEFs) from p16cis/cis and control mice. By whole genome bisulfite sequencing (WGBS) for comprehensive DNA methylation profiling, we showed that cis-element-mediated approach specifically induces p16 promoter hypermethylation.

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p16 epimutation modulates the tumor microenvironment and promotes malignancy of Apc-mutant colon cancer

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-08-02 | GSE213568 | GEO

Molecular properties of epimutation hotspots

Project description:Mistakes in the maintenance of CG methylation is a source of heritable epimutations in plants. Multigenerational surveys indicate that the rate of these stochastic events varies substantially across the genome, with some regions harboring localized “epimutation hotspots”. Using Arabidopsis as a model, we show that epimutation hotspots are indexed by a specific set of chromatin states (CS) that map to sub-regions of gene body methylation genes. Although these regions comprise only ~12% of all CGs in the genome, they account for ~63% of all epimutation events per unit time. Molecular profiling revealed that these regions contain unique sequence features, harbor steady-state intermediate methylation levels, and act as putative targets of antagonistic DNA methylation pathways. We further demonstrate that experimentally-induced shifts in steady-state methylation in these hotspot regions are sufficient to significantly alter local epimutation intensities. Our work thus lays foundation for dissecting the molecular mechanisms of epimutation hotspots in plants.

2021-12-02 | GSE178684 | GEO

Expression data from RCAS PDGFB/Nestin tv-A glioma cells within Ptprd+/+p16-/- (n=2), Ptprd+/-p16-/- (n=2), and Ptrpd-/-p16-/- (n=3) mice.

Project description:PTPRD is a tumor suppressor of glioma that is frequently co-deleted with CDKN2A/p16. We show that Ptprd and p16 cooperate to promote gliomagenesis in the RCAS PDGFB / Nestin tv-A glioma mouse model. We found unique gene expression changes within tumor cells of Ptprd+/-p16-/- vs. Ptprd+/+p16-/- and Ptprd-/-p16-/- tumor cells. Neonatal mice were injected with RCAS PDGFB GFP. At symptoms, or at 12 weeks post injection, GFP+DAPI- tumor cells were sorted for RNA extraction and hybridization on Affymetrix microarrays. The mouse strain used was a mixed background of C57/BL6 and FVB/N. Ptprd mice were from Uetani et al. 2000 and p16/Nestin-tvA mice were from Tchouganouva et al. 2007.

2014-06-02 | E-GEOD-55061 | biostudies-arrayexpress

Comparison between HPV+ / p16+ versus the HPV-/p16- from HNSCC patients

Project description:Head and neck squamous cell carcinomas are heterogeneous neoplasms that show clinical and biological differences in association with the human papillomavirus (HPV). To provide adequate therapeutic strategies, biological and clinical characterization is essential to stratify patients based on prognostic and predictive factors. Reports on HNSCC are scarce in Mexico, thus in the present study, we analyze 414 cases of HNSCC, including those of the oropharynx (OPSCC), larynx (LASCC), and oral cavity (OCSCC). We determined the presence of HPV and p16 expression. Global expression profiles were analyzed with Affymetrix HTA 2.0 microarray in 25 selected cases HPV+/p16+ versus HPV-/p16-. In our study we analyze 25 samples derived from HNSCC patients. 18 samples were HPV-/p16- and 7 HPV+/p16+. We compared the HPV-/p16- versus the HPV+/p16+ and identified differentially expressed RNAs with a fold change greater than 1.5 or less than -1.5. These data were used to obtain 98 genes that are differentially expressed in absence of HPV. The present study offers information regarding clinical and molecular characteristics of HNSCC, both associated and unassociated with HPV, in Mexican patients.

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Expression data from RCAS PDGFB/Nestin tv-A glioma cells within Ptprd+/+p16-/- (n=2), Ptprd+/-p16-/- (n=2), and Ptrpd-/-p16-/- (n=3) mice.

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Paradoxical mitotic exit induced by a small molecule inhibitor of APC/C Cdc20

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2020-01-07 | PXD013786 | Pride

Molecular properties of epimutation hotspots

Project description:Molecular properties of epimutation hotspots

| PRJNA740019 | ENA

Gene expression profile of p16-induced senescence in normal human diploid fibroblasts.

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