Comparative RNA-Seq Analysis of Colon Spheroids and Patient-derived Tissues Identifies Non-Canonical Transcript Isoforms of Protein-Coding Genes Implicated in Colon Carcinogenesis

Abstract

Objectives:This study aimed to identify transcript isoforms of protein-coding genes with potential relevance to the malignant transformation of gut mucosa.Methods:Colon cancer cell lines (HCT116, DLD1, SW620) and immortalized cells derived from healthy gut epithelium (HCEC-1CT) were cultured as spheroids and subjected to RNA sequencing to profile both canonical and non-canonical transcripts. The resulting data were compared with prior bioinformatics study findings that analyzed RNA-seq datasets from 473 patient-derived tumor and 417 non-tumor colon tissue samples.Results:Among 375 transcripts previously reported as significantly dysregulated in colon (39 up-regulated and 336 down-regulated), 32 transcripts displayed expression patterns in colon cell lines consistent with those observed in patient tissues (4 up-regulated and 28 down-regulated). In silico characterization of these molecules revealed that all of them exhibited at least 1 feature commonly associated with RNAs possessing regulatory functions, such as coding truncated protein isoform, exosomal localization, or enrichment in repetitive elements. The most prominently dysregulated transcripts with consistent expression profiles across both datasets were NTMT1-204 (up-regulated in cancer) and BLOC1S6-218 and DCTN1-205 (both down-regulated in cancer). The remaining 343 transcripts did not show consistent expression patterns in the cell lines, suggesting their dysregulation in patient-derived tissues may be due to the stromal or microenvironmental factors absent in vitro.Conclusion:In summary, this comparative transcriptomic analysis identified 32 transcript isoforms, comprising 2 canonical and 30 non-canonical transcripts, that may play regulatory roles in colon carcinogenesis and warrant further investigation in the context of gut epithelial cell biology