genome-wide methylation patterns in androgen-independent prostate cancer cells: a comprehensive analysis combining medip-bisulfite, rna, and microrna sequencing data

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ID: 177136
2018
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Abstract
This study aimed to investigate the mechanisms underlying the development of the androgen-independent phenotype in prostate cancer. Methylation patterns were detected in androgen-independent and androgen-dependent lymph node carcinoma of the prostate (LNCaP) prostate carcinoma cells based on methylated DNA immunoprecipitation-bisulfite sequencing data and differentially methylated regions (DMRs) were identified. Differentially expressed genes (DEGs) and micro RNAs (miRNAs) with DMRs (named MDEGs and MDEmiRNAs) were identified by combining transcriptome and methylation data, and transcription factor (TF)-DEGs with DMRs in promoter (PMDEGs) and MDEmiRNA-MDEGs networks were constructed. Furthermore, a time-course analysis of gene transcription during androgen deprivation was performed based on microarray data and DMRs, MDEGs, and DEmiRNAs were validated. In total, 18,447 DMRs, 3369 MDEGs, 850 PMDEGs, and 1 MDEmiRNA (miR-429) were identified. A TF-target network (94 PMDEGs and 5 TFs) and a miRNA–target network (172 MDEGs and miR-429) were constructed. Based on the time-course analysis of genes in the networks, NEDD4L and PBX3 were targeted by SOX5, while GNAQ, ANLN, and KIF11 were targeted by miR-429. The expression levels of these genes and miR-429 were confirmed by quantitative real-time polymerase chain reaction. Additionally, 109 DMRs were confirmed using additional public datasets. The regulatory pathways SOX5-NEDD4L/PBX3, miR429-GNAQ/ANLN—RHOA, and miR429-ANLN—KIF11 may participate in the progression of the androgen-independent phenotype in prostate cancer.
Reference Key
wang2018genesgenome-wide Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Yumin Wang;Tingting Qin;Wangqiang Hu;Binghua Chen;Meijie Dai;Gang Xu
Journal thermal science and engineering progress
Year 2018
DOI
10.3390/genes9010032
URL
http://www.mdpi.com/2073-4425/9/1/32
Keywords
gene expression microrna drought stress prostate cancer abiotic stress lncrna phylogenetic potato genome-wide identificationgenetics

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