title: A systematic analysis on DNA methylation and the expression of both mRNA and microRNA in bladder cancer.
abstract: BACKGROUND
  DNA methylation aberration and microRNA (miRNA) deregulation have been observed in many types of cancers. A systematic study of methylome and transcriptome in bladder urothelial carcinoma has never been reported.
  
  
  RESULTS
  The DNA methylation was profiled by modified methylation-specific digital karyotyping (MMSDK) and the expression of mRNAs and miRNAs was analyzed by digital gene expression (DGE) sequencing in tumors and matched normal adjacent tissues obtained from 9 bladder urothelial carcinoma patients. We found that a set of significantly enriched pathways disrupted in bladder urothelial carcinoma primarily related to "neurogenesis" and "cell differentiation" by integrated analysis of -omics data. Furthermore, we identified an intriguing collection of cancer-related genes that were deregulated at the levels of DNA methylation and mRNA expression, and we validated several of these genes (HIC1, SLIT2, RASAL1, and KRT17) by Bisulfite Sequencing PCR and Reverse Transcription qPCR in a panel of 33 bladder cancer samples.
  
  
  CONCLUSIONS
  We characterized the profiles between methylome and transcriptome in bladder urothelial carcinoma, identified a set of significantly enriched key pathways, and screened four aberrantly methylated and expressed genes. Conclusively, our findings shed light on a new avenue for basic bladder cancer research.
authors.affiliation: Beijing Genomics Institute at Shenzhen, Shenzhen, China.
authors.forename: Jialou
authors.initials: J
authors.lastname: Zhu
authors.forename: Zhimao
authors.initials: Z
authors.lastname: Jiang
authors.forename: Fei
authors.initials: F
authors.lastname: Gao
authors.forename: Xueda
authors.initials: X
authors.lastname: Hu
authors.forename: Liang
authors.initials: L
authors.lastname: Zhou
authors.forename: Jiahao
authors.initials: J
authors.lastname: Chen
authors.forename: Huijuan
authors.initials: H
authors.lastname: Luo
authors.forename: Jihua
authors.initials: J
authors.lastname: Sun
authors.forename: Song
authors.initials: S
authors.lastname: Wu
authors.forename: Yonghua
authors.initials: Y
authors.lastname: Han
authors.forename: Guangliang
authors.initials: G
authors.lastname: Yin
authors.forename: Maoshan
authors.initials: M
authors.lastname: Chen
authors.forename: Zujing
authors.initials: Z
authors.lastname: Han
authors.forename: Xianxin
authors.initials: X
authors.lastname: Li
authors.forename: Yi
authors.initials: Y
authors.lastname: Huang
authors.forename: Weixing
authors.initials: W
authors.lastname: Zhang
authors.forename: Fangjian
authors.initials: F
authors.lastname: Zhou
authors.forename: Tong
authors.initials: T
authors.lastname: Chen
authors.forename: Pingping
authors.initials: P
authors.lastname: Fa
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.forename: Liang
authors.initials: L
authors.lastname: Sun
authors.forename: Huimin
authors.initials: H
authors.lastname: Leng
authors.forename: Fenghao
authors.initials: F
authors.lastname: Sun
authors.forename: Yuchen
authors.initials: Y
authors.lastname: Liu
authors.forename: Mingzhi
authors.initials: M
authors.lastname: Ye
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Cai
authors.forename: Yaoting
authors.initials: Y
authors.lastname: Gui
authors.forename: Xiuqing
authors.initials: X
authors.lastname: Zhang
mesh_terms: D019175:DNA Methylation / Q000235:genetics*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome / Q000235:genetics; D001749:Urinary Bladder Neoplasms / Q000235:genetics*; D019459:Urothelium / Q000473:pathology
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger