Transcriptomic analysis reveals that combinations of vitamins A, D2, and D3 have synergistic effects in HCT-116 colon cancer cells by altering the expression of genes involved in multiple canonical pathways including apoptosis, regulation of the epithelial mesenchymal transition and immunity

Integrated systems biology approaches suggest that combinations of nutrients may be more effective against cancer due to the large number of signaling pathways associated with cancer initiation and promotion. In a previous work, we have reported that combinations of vitamins A (as all trans-retinoic acid, ATRA), D2, and D3 act synergistically to induce apoptosis in colon and gastric cancer cells. In this work, we use whole-genome transcriptomic profiling to detect gene expression changes using RNA-seq to more comprehensively investigate the biological pathways affected by the combination of vitamin D2, D3 and ATRA. HCT-116 colon cancer cells were harvested, RNA was isolated and RNA-seq libraries were prepared using a Universal Plus mRNASeq kit. Sequencing was carried out on NovaSeq 6000. General quality-control metrics were obtained using FastQC and raw reads were aligned to human reference genome hg38 using STAR and BWA MEM. ENSEMBL genes were quantified using FeatureCounts, and differential expression statistics were computed using EdgeR. Specific gene expression was validated using qPCR. Transcriptomic analysis showed that of 26,313 genes analyzed, the expression of 8,402 genes was significantly altered (4030 up-regulated and 4373 down-regulated, FDR<0.05) in the treated cells, of which, 3,621 genes were differentially expressed (fold change <-1 or >+1 and an FDR <0.05). IngenuityÒ Pathway analysis revealed the involvement of 97 canonical pathways, with the top pathways including: mechanisms of cancer, apoptosis, myc-mediated apoptosis, regulation of the epithelial mesenchymal transition, and immunity.