PhD Scientific Days 2022

Molecular Sciences V.

Folic Acid Treatment Influences the Genome, Epigenome, and Transcriptome of Colorectal Cancer Cells

Text of the abstract

Folic acid (FA) is widely used as a food supplement and an adjunctive medication in cancer therapy. Beyond its several vital metabolic functions, FA is an important epigenetic regulator by being involved in DNA methylation via the synthesis of the main methyl donor molecule, S-adenosylmethionine.
Our aim was to comprehensively investigate DNA methylation alterations induced by FA supplementation on human colorectal cancer cell lines (HT-29 and SW480). Additionally, we aimed to perform in silico analyses to establish relationships between the epigenetic or genetic patterns and the consequent gene expression changes.
Cells were exposed to different FA concentrations (0; 100; 10000 ng/mL) for 72 hours, then DNA methylation level was detected either with next-generation sequencing (RRBS) or with immunocytochemistry (anti-5-methylcytosine/DAPI). DAVID and PANTHER annotation tools were used for the enrichment analysis of cell and SW480 xenograft mice transcriptomic data, while the genetic background of the cell lines was determined with in silico analysis of our previous whole-exome sequencing results.
FA equally caused DNA hyper- and hypomethylation, which mainly affected carcinogenesis-related processes (such as PI3K-Akt, MAPK, and Rap2 signaling pathways). This approximate balance eventually resulted in similar staining intensity of all cell samples with the fluorescent determination of global DNA methylation. We observed that following FA treatment the downregulated genes (HT-29: 78.82%; SW480: 60.60%) outnumbered the upregulated ones (HT-29: 21.18%; SW480: 39.40%) in the cells, as opposed to SCID mice (down: 35.38%; up: 64.62%). However, in the case of SW480 cells and xenografts, the pathways in which most of the analyzed transcripts participated were similar. DNA methylation level of the cell lines was in accordance with the expression alteration of 27 genes, and the different mutation profiles of FA metabolizing genes (i.e., MTHFR) influenced our results.
This study reveals new aspects of FA in the epigenetic regulation and the consequent functional changes of colorectal cancer cells that are important to be considered in patient care when tumor heterogeneity is present.
Supported by the ÚNKP-21-4-I-SE-20 New National Excellence Program of the Ministry for Innovation and Technology from the Source of the National Research, Development and Innovation Fund.