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Long non-coding RNAs (lncRNAs) emerged as key regulators of diverse roles during colorectal cancer (CRC) carcinogenesis, but their specific function still remains to be explored. The present study aimed to re-annotate the Affymetrix Human Exon 1.0 ST Array for defining differential lncRNAs in CRC. Their prognostic relevance was also developed for screening key regulators in CRC. The CRC datasets E-GEOD-31737, E-MATB-829, Affymetrix colon cancer dataset and E-GEOD-24550 were re-purposed for searching differential lncRNAs and exploring their association with overall survival (OS). The identified lncRNAs were validated in CRC tissues or cell lines. As a result, 462, 286 and 166 differential lncRNAs were identified, respectively, in three predictive datasets. Among them, 48 lncRNAs were commonly observed to exhibit differential expression in the three datasets. Notably, the overexpression of family with sequence similarity 83 member H (FAM83H)-antisense (AS) 1 (P=0.038) and VPS9 domain containing 1 (VPS9D1)-AS1 (P=0.020) indicated shorter OS time than lower expression. The overexpression of FAM83H-AS1 (P=0.033) and VPS9D1-AS1 (P=0.011) was validated in cancerous tissues. Thus, FAM83H-AS1 and VPS9D1-AS1 may potentially enhance carcinogenesis or may be developed as prognostic biomarkers for CRC. In conclusion, a total of 48 CRC-related lncRNAs were identified, the majority of which were confirmed to exhibit dysregulation. FAM83H-AS1 and VPS9D1-AS1 could have a potential use as prognostic biomarkers for CRC patients.

Dysregulation of long non-coding RNA profiles in human colorectal cancer and its association with overall survival