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Research Paper|Volume 11, Issue 16|pp 6089—6108

Copy number variations primed lncRNAs deregulation contribute to poor prognosis in colorectal cancer

Huimin Liu1,2, Xiaoyu Gu1,2, Guihua Wang1, Ying Huang1, Shaoqing Ju1, Jianfei Huang2, Xudong Wang1,2
  • 1Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
  • 2Clinical Biobank, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
* Equal contribution
Received: May 5, 2019Accepted: August 5, 2019Published: August 22, 2019
https://doi.org/10.18632/aging.102168

Copyright © 2019 Liu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution (CC BY) 3.0 License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Abstract

Copy number variations (CNVs) are crucial genetic change elements in malignancies, and lncRNAs deregulation induced by genomic and epigenomic aberrations plays key driving role in tumorigenesis, including colorectal cancer (CRC). However, effects of CNVs associated with lncRNAs in CRC is largely unknown. Here, we perform integrative analysis considering messenger RNA expression levels, DNA methylation and DNA copy numbers from 289 cases of CRC specimens. There are five prognostic subtypes of CRC determined by multi-omics integration, and differentially expressed lncRNAs (DE-lncRNAs) are acquired among five subtypes and normal cases. Finally, CNVs pattern matched with DE-lncRNAs reveals a signature including 10 lncRNAs (LOC101927604, LOC105377267, CASC15, LINC-PINT, CLDN10-AS1, C14orf132, LMF1, LINC00675, CCDC144NL-AS1, LOC284454), conspicuously contributing to poor prognosis in CRC, which can be validated in another independent dataset. Together, our research is interested in copy number changes relevant with lncRNAs, not only expending the spectrum of CNVs, but also perfecting the regulation network of lncRNAs in CRC. The main purpose is to provide novel biomarkers for prognostic managements of CRC patients.