Abstract
Despite numerous observations regarding the relationship between DNA methylation changes and cancer progression, only a few genes have been verified as diagnostic biomarkers of colorectal cancer (CRC). To more practically detect methylation changes, we performed targeted bisulfite sequencing. Through co-analysis of RNA-seq, we identified cohort-specific DNA methylation markers: CpG islands of the intragenic regions of PDX1, EN2, and MSX1. We validated that these genes have oncogenic features in CRC and that their expression levels are increased in correlation with the hypermethylation of intragenic regions. The reliable depth of the targeted bisulfite sequencing data enabled us to design highly optimized quantitative methylation-specific PCR primer sets that can successfully detect subtle changes in the methylation levels of candidate regions. Furthermore, these methylation levels can divide CRC patients into two groups denoting good and poor prognoses. In this study, we present a streamlined workflow for screening clinically significant differentially methylated regions. Our discovery of methylation markers in the PDX1, EN2, and MSX1 genes suggests their promising performance as prognostic markers and their clinical application in CRC patients.
Highlights
Colorectal cancer (CRC) is the third most common cancer worldwide, accounting for the second-highest mortality in 20201.CRC is widely known to occur due to the accumulation of genetic and epigenetic alterations
The serrated neoplasia pathway develops via KRAS and BRAF mutations, and epigenetic dysregulation is uniquely distinguished by the CpG island methylator phenotype (CIMP)
The methylation levels of Pancreatic and duodenal homeobox 1 (PDX1), EN2, and Msh homeobox 1 (MSX1) predict CRC metastasis we examined whether the methylation levels of the intragenic CpG regions of PDX1, EN2, and MSX1 have clinical implications
Summary
Colorectal cancer (CRC) is the third most common cancer worldwide, accounting for the second-highest mortality in 20201. CRC is widely known to occur due to the accumulation of genetic and epigenetic alterations. Several molecular pathways involved in the onset and development of CRC have been identified, including the adenoma–carcinoma pathway ( called the chromosomal instability sequence), the serrated neoplasia pathway, and microsatellite instability (MSI)[2,3]. The adenoma–carcinoma pathway accounts for 70–90% of CRC cases and is generally initiated by APC mutations, followed by KRAS activation or loss of TP53 function. The serrated neoplasia pathway develops via KRAS and BRAF mutations, and epigenetic dysregulation is uniquely distinguished by the CpG island methylator phenotype (CIMP). MSI typically occurs with Lynch syndrome, mainly due to mismatch repair (MMR) gene inactivation[4,5,6,7]
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