Transcriptional profiling of PHF19 gene in colon cancer cell lines cultivated in 3D

Abstract

Introduction: A recent comprehensive pan-cancer transcriptome analysis revealed differential activity of two alternative promoters of the gene PHF19 in malignant and non-malignant gut mucosa. Transcription from the promoter which is up-regulated in colorectal cancer results in the synthesis of transcript PHF19-207. This finding indicates that transcript PHF19-207 could potentially be used as a biomarker for this disease. Our study aimed to assess the expression profile of the PHF19 gene in colon cancer. Methods: Immortalized colonic epithelial cell line isolated from healthy tissue (HCEC-1CT) as well as a set of colon cancer cell lines (DLD1, SW620, HCT116) were used for transcriptional profiling of PHF19 in cells cultivated in 3D. The transcriptional profile was obtained using RNA sequencing and the function of transcript PHF19-207 was evaluated using in silico tools. Results: Our analysis confirmed the up-regulation of transcript PHF19-207 in all malignant cell cultures in comparison to the healthy cell line HCEC-1CT. The expression of transcript PHF19-207 was more notable in cell lines that originated from colon cancer in later stages. Coding Potential Calculator tool classifies this transcript as non-coding, with a probability of 0.2. Annolnc tool shows the up-regulation of thistranscript in colorectal cancer cell lines and its down-regulation in healthy samples. Also, thistool predicts that transcript PHF19-207 localizes in the nucleus. Conclusion: We conclude that transcript PHF19-207 could serve as a biomarker for colorectal cancer. Also, we hypothesize that thistranscript is a lncRNA with a role in gene expression regulation and could be linked to oncogenesis.