Biomarker Discovery for the Carcinogenic Heterogeneity Between Colon and Rectal Cancers Based on lncRNA-Associated ceRNA Network Analysis

Frontiers in Oncology
Xin QiBairong Shen

Abstract

Colorectal cancer (CRC) is one of the leading causes of cancer death worldwide. Emerging evidence has revealed that risk factors and metastatic patterns differ greatly between colon and rectal cancers. However, the molecular mechanism underlying their pathogenic differences remains unclear. Therefore, we here aimed to identify non-coding RNA biomarkers based on lncRNA-associated ceRNA network (LceNET) to elucidate the carcinogenic heterogeneity between colon and rectal cancers. A global LceNET in human was constructed by employing experimental evidence-based miRNA-mRNA and miRNA-lncRNA interactions. Then, four context-specific ceRNA networks related to cancer initiation and metastasis were extracted by mapping differentially expressed lncRNAs, miRNAs and mRNAs to the global LceNET. Notably, a novel network-based bioinformatics model was proposed and applied to identify lncRNA/miRNA biomarkers and critical ceRNA triplets for understanding the carcinogenic heterogeneity between colon and rectal cancers. Moreover, the identified biomarkers were further validated by their diagnostic/prognostic performance, expression pattern and correlation analysis. Based on network modeling, lncRNA KCNQ1OT1 (AUC>0.85) and SNHG1 (AUC>0.94) were un...Continue Reading

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Datasets Mentioned

BETA
GSE9348

Methods Mentioned

BETA
RNA-seq
HITS-CLIP

Software Mentioned

survival
GOplot
LncBase
LceNET
OncoLnc
Cytoscape
GENCODE
ClusterProfiler
ggplot2
ggalluvial

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