methylation   304

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MethylMix 2.0: an R package for identifying DNA methylation genes | Bioinformatics | Oxford Academic
DNA methylation is an important mechanism regulating gene transcription, and its role in carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is a major mechanism of gene expression deregulation in a wide range of diseases. At the same time, high-throughput DNA methylation assays have been developed generating vast amounts of genome wide DNA methylation measurements. We developed MethylMix, an algorithm implemented in R to identify disease specific hyper and hypomethylated genes. Here we present a new version of MethylMix that automates the construction of DNA-methylation and gene expression datasets from The Cancer Genome Atlas (TCGA). More precisely, MethylMix 2.0 incorporates two major updates: the automated downloading of DNA methylation and gene expression datasets from TCGA and the automated preprocessing of such datasets: value imputation, batch correction and CpG sites clustering within each gene. The resulting datasets can subsequently be analyzed with MethylMix to identify transcriptionally predictive methylation states. We show that the Differential Methylation Values created by MethylMix can be used for cancer subtyping.
DNA  methylation  tcga 
august 2018 by Segalllab
Tumour spheres with inverted polarity drive the formation of peritoneal metastases in patients with hypermethylated colorectal carcinomas | Nature Cell Biology
Quite remarkable indication of apical out spheroids being mechanisms for tumor cell survival and metastasis in CRC that is CIMP.

"Metastases account for 90% of cancer-related deaths; thus, it is vital to understand the biology of tumour dissemination. Here, we collected and monitored >50 patient specimens ex vivo to investigate the cell biology of colorectal cancer (CRC) metastatic spread to the peritoneum. This reveals an unpredicted mode of dissemination. Large clusters of cancer epithelial cells displaying a robust outward apical pole, which we termed tumour spheres with inverted polarity (TSIPs), were observed throughout the process of dissemination. TSIPs form and propagate through the collective apical budding of hypermethylated CRCs downstream of canonical and non-canonical transforming growth factor-β signalling. TSIPs maintain their apical-out topology and use actomyosin contractility to collectively invade three-dimensional extracellular matrices. TSIPs invade paired patient peritoneum explants, initiate metastases in mice xenograft models and correlate with adverse patient prognosis. Thus, despite their epithelial architecture and inverted topology TSIPs seem to drive the metastatic spread of hypermethylated CRCs.
apical_out_spheroid  crc  Metastasis  methylation  inverted_polarity 
july 2018 by Segalllab
Non-coding RNAs, epigenetics, and cancer: tying it all together | SpringerLink
good reference regarding methylation of miRNA promoters - have one mir375 exampl
miR-375  methylation 
june 2018 by Segalllab
Early-Life Gene Expression in Neurons Modulates Lasting Epigenetic States - ScienceDirect
reference to DNMT3A as initiator of methylaiton and also CA methylation. Idea that the longer the gene has low transcription, the larger the probability of methylation
methylation  dnmt3a 
december 2017 by Segalllab

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