Joint DNA Methylation and Transcriptomic Analysis of Colorectal Cancer Samples for Biomarker Identification

Colorectal cancer (CRC) is a term that refers to the combination of colon and rectal cancer as they are being treated as a single tumor. In CRC, 72% of tumors are colon cancer while the other 28% represent rectal cancer [1]. CRC is a multifactorial disease caused by both genetic and epigenetic changes in the colon mucosal cells, affecting the oncogenes, DNA repair genes, and tumor suppressor genes [2]. Currently, two DNA methylation based biomarkers for CRC have received FDA approval: SEPT9, used in blood-based screening tests, and a combination of NDRG4 and BMP3 for stool-based tests[3]. Although DNA methylation biomarkers have been explored in colorectal cancer (CRC), the identification of robust and clinically valuable biomarkers remains a challenge, particularly for early-stage detection and precancerous lesions. Patients often receive diagnoses at the locally advanced stage, which limits the potential utility of current biomarkers in clinical settings. This study aims to address this gap by employing a custom bioinformatics pipeline to identify novel DNA methylation-regulated genes associated with CRC. Datasets used in this study were retrieved from GEO Database using the GEOquery package [4]. Specifically, the GSE75548 and GSE75546 datasets, which represent expression profiling by array and methylation profiling by genome tiling array, respectively, were collected from six tissue samples of patients with rectal cancer with paired normal tissues. Differential analysis was used to identify differentially methylated CPG sites (DMCs) and identify differentially expressed genes (DEGs) using the Limma package[5]. From the overlap of DMCs with DEGs in rectal cancer, we identified seven methylation regualetd genes (MRGs)[6] (GNG7, ZCCHC14, HKDC1, AZGP1, ALG1L, PITX2, and PDX1) as biomarkers for CRC. The KEGG pathway enrichment analysis [7] revealed the involvement of these methylation-regulated genes in two distinct pathways, namely Type II Diabetes Mellitus, and the biosynthesis of Neomycin, Kanamycin, and Gentamicin, which are related to human disease, and metabolism, respectively. Additionally, through gene ontology[8], we found the identified MRGs are involved in endocrine system development, intracellular glucose homeostasis, glucose metabolic process, metabolic process, and several other significant biological processes. Our findings highlight the strength of our approach in jointly identifying methylation regulated biomarkers for colorectal cancer.