title: [Target-resequencing to identify microRNA-associated SNP and predict the effect of SNP on microRNA function in colorectal cancer patients].
abstract: OBJECTIVE
  To identify SNPs in the miRNA genes in colorectal cancer (CRC) patients and to investigate their association with CRC.
  
  
  METHODS
  DNAs were isolated from 30 CRC tumor tissues and 30 tumor-adjacent tissues, and subjected to target capture using a custom miRNA chip covering 685 miRNA genes from NimbleGen. The captured DNAs were then sequenced using the Illumina's sequencing technology, and the data were analyzed.
  
  
  RESULTS
  We identified 64 SNPs in 43 miRNA genes and most of these SNPs are novel SNPs not reported previously. Prediction of functional consequences of the SNPs using TargetScan and miRSNP showed that SNPs of hsa-mir-1273-G/A, hsa-mir-548h-3-C/U, hsa-mir-1290-A/G, and hsa-mir-1273-C/U resulted in reduction of their mature miRNA abundance. SNPs of hsa-mir-376b-C/G, hsa-mir-604-T/C, hsa-mir-1268-T/G and hsa-mir-146a-C/G resulted in changes in their targeted genes. Finally, we focused on the analysis of SNPs in mir-146a and we found that mir-146a rs1052918 C>G was predicted to promote tumorigenesis via the Wnt signaling pathway.
  
  
  CONCLUSIONS
  SNPs in the miRNA genes are important for tumorigenesis. The changes by hsa-mir-146a rs1052918 C>G may result in loss of Wnt, constant activation of the Wnt signaling pathway, and uncontrolled cell proliferation and tumor progression.
authors.affiliation: Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou 310000, China.
authors.forename: Qingchong
authors.initials: Q
authors.lastname: Qiu
authors.affiliation: Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou 310000, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Liu
authors.affiliation: Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou 310000, China.
authors.forename: Jiaofang
authors.initials: J
authors.lastname: Shao
authors.affiliation: Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou 310000, China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Lou
authors.affiliation: Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou 310000, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Chen
authors.affiliation: Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou 310000, China; Email: biaoylin@gmail.com.
authors.forename: Biaoyang
authors.initials: B
authors.lastname: Lin
mesh_terms: D001483:Base Sequence; D049109:Cell Proliferation; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000473:pathology; D006801:Humans; D035683:MicroRNAs / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: C574604:MIRN1290 microRNA, human; C542542:MIRN146 microRNA, human; D035683:MicroRNAs