Long Noncoding RNA Alternations with APC Mutation and Clinical Diagnostic Value in Colorectal Cancer

Abstract

Colorectal cancer (CRC) is one of the most common malignancies. The mutation of adenomatous polyposis coli (APC) gene has been confirmed as the initiating event for CRC. This study aims to explore differential long noncoding RNA (lncRNA) profiles associated with APC mutation, and further identify potential biomarkers for CRC diagnosis. We performed a comparative analysis of the lncRNAs expression patterns in SW480 cells and SW480APC (restored with full-length APC) cells by Ribo-Zero RNA-Seq and validated by quantitative real-time polymerase chain reaction (RT-qPCR). The candidate lncRNAs were then detected in cell lines and different cohorts of tissue or serum samples of CRC patients. The most up/down regulated lncRNAs were selected to further elucidate the potential role and clinical significance in CRC. The relationships between candidate lncRNAs levels and clinicopathological features of CRC were analyzed. Receiver operating characteristic (ROC) curves were employed to assess the diagnostic efficiency of candidate lncRNAs. The lncRNA deep sequencing results indicated that 11 lncRNAs were up-regulated and 44 lncRNAs were down-regulated and in SW480APC cell compared with SW480 cell. Seven of them (NR_015377, NR_073080, ENS0524987.1, NR_002819, ENS0418393.1, ENS0433753.1, ENS0444286.1) were validated significantly dysregulated. However, only three lncRNAs (ENS0524987.1, NR_002819, ENS0444286.1) were finally identified to be significantly dysregulated with consistent pattern among cell lines, tissue and serum samples. Higher levels of serum ENS0524987.1, NR_002819 and lower levels of ENS0444286.1 were significantly correlated with lymph node metastasis (P=0.000, P=0.011, P=0.002, respectively) and advanced TNM stage (P=0.000, P=0.007, P=0.012, respectively). In addition, we also found the relationship of ENS0524987.1 expression with tumor local invasion (P=0.009). The corresponding area under curve (AUC) of the detection combined with the three lncRNA and CEA were 0.881 (95% CI: 0.838-0.924), significantly higher than that of alone. This finding provides the potential evidence with lncRNAs alterations associated with APC mutation, which could open new insight for novel predictor in future diagnosis and treatment target of CRC. Funding Statement: This work was supported by National Natural Science Foundation of China (No. 81501819 and 81702815), Shandong Key Research and Development Program (2015GSF118167, GG201809250137), Outstanding young scientist research award fund of Shandong Province (BS2014YY002), and Taishan Scholar Program of Shandong Province. Declaration of Interests: The authors report no conflicts of interest in this work. Ethics Approval Statement: The study was approved by the ethics committee of Qilu Hospital of Shandong University.