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Series GSE142310 Query DataSets for GSE142310
Status Public on Mar 30, 2020
Title LY75 ablation mediates mesenchymal-epithelial transition (MET) in epithelial ovarian cancer (EOC) cells associated with aberrant DNA methylation alterations implicated in EOC dissemination
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary In epithelial ovarian cancer (EOC), acquisition of invasiveness is accompanied by the loss of the epithelial features and the gain of a mesenchymal phenotype, a process known as epithelial-mesenchymal transition (EMT). Understanding the regulation of cell behavior during EMT is crucial for identifying the molecular mechanisms of EOC dissemination. Previously we identified the mannose receptor LY75 as the cellular phenotype modulator. LY75 suppression induces the mesenchymal to epithelial transition (MET) in EOC cell lines with mesenchymal phenotype. In this study, we used the Reduced Representation Bisulfite Sequencing (RRBS) technology for a comprehensive analysis of DNA methylation alterations during LY75-mediated EMT in EOC cells. Three different comparison (M vs E) combinations were used for RRBS analysis, as further analysis of the sequencing data based on differentially methylated regions (DMRs) covering genes’ exons and promoter regions was indicative for about 10,000 genes displaying DMRs for each of the three experimental combinations. Consecutive Venn diagram analysis of the DMRs data from the of the three experimental combinations revealed 6666 genes, displaying common altered DMRs in their exons/promoter regions, following LY75-mediated EMT alterations in EOC cells. Based on the 6666 gene list, we further proceeded with a more stringent selection of genes displaying rather high degree (>70%) of methylation in their promoter regions and previously shown to be implicated in cancer-related EMT signaling. Our stringent selection retained 45 genes (see Supplemental Table 1E), as the DNA methylation status of the promoter regions of most of these genes was further validated by an alternative approach (BSP sequencing). Ten genes were finally selected, whose promoter DNA methylation pattern coincided with their mRNA and protein expression levels. Further in vitro and in vivo studies are warranted to more completely elucidate the functional implications of these 10 genes in ovarian tumorigenesis.
Overall design Examination and comparison of DNA methylation profiles in SKOV3 cells with mesenchymal phenotype (M) (sh-control) versus SKOV3 cells with epithelial phenotype (E) (following LY75 gene ablation)
Contributor(s) Bachvarov D
Citation(s) 32156068
Submission date Dec 18, 2019
Last update date Mar 30, 2020
Contact name Clémence Belleannee
Organization name CHU de Québec-Université Laval Research Center
Street address 2705 Bd Laurier
City Québec
ZIP/Postal code G1V 4G2
Country Canada
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (4)
GSM4225036 ShLy75-S
GSM4225037 Ly75-KO-S
GSM4225038 Ly75-OV-S
BioProject PRJNA596535
SRA SRP238112

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE142310_Ly75-KO-S-vs-Ly75-OV-S_diff_meth_tiles_1000bp_25p_q_0_01.csv.gz 913.5 Kb (ftp)(http) CSV
GSE142310_Sh-vs-Ly75_diff_meth_tiles_1000bp_25p_q_0_01.csv.gz 723.1 Kb (ftp)(http) CSV
GSE142310_ShC-S-vs-ShLy75-S_diff_meth_tiles_1000bp_25p_q_0_01.csv.gz 1.6 Mb (ftp)(http) CSV
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