A Genome-Wide Study of Allele-Specific Expression in Colorectal Cancer

Zhi Liu, Xiao Dong, Yixue Li

Research output: Contribution to journalArticlepeer-review

Abstract

Accumulating evidence from small-scale studies has suggested that allele-specific expression (ASE) plays an important role in tumor initiation and progression. However, little is known about genome-wide ASE in tumors. In this study, we conducted a comprehensive analysis of ASE in individuals with colorectal cancer (CRC) on a genome-wide scale. We identified 5.4 thousand genome-wide ASEs of single nucleotide variations (SNVs) from tumor and normal tissues of 59 individuals with CRC. We observed an increased ASE level in tumor samples and the ASEs enriched as hotspots on the genome. Around 63% of the genes located there were previously reported to contain complex regulatory elements, e.g., human leukocyte antigen (HLA), or were implicated in tumor progression. Focussing on the allelic expression of somatic mutations, we found that 37.5% of them exhibited ASE, and genes harboring such somatic mutations, were enriched in important pathways implicated in cancers. In addition, by comparing the expected and observed ASE events in tumor samples, we identified 50 tumor specific ASEs which possibly contributed to the somatic events in the regulatory regions of the genes and significantly enriched known cancer driver genes. By analyzing CRC ASEs from several perspectives, we provided a systematic understanding of how ASE is implicated in both tumor and normal tissues and will be of critical value in guiding ASE studies in cancer.

Original languageEnglish (US)
Article number570
JournalFrontiers in Genetics
Volume9
DOIs
StatePublished - Nov 27 2018
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the National Key R&D Program of China (2016YFC0901704, 2017YFA0505500, 2017YFC0907505, and 2017YFC0908405).

Publisher Copyright:
© Copyright © 2018 Liu, Dong and Li.

Keywords

  • allele-specific expression
  • cis-regulatory variation
  • colorectal cancer
  • somatic mutation
  • tumor

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