Crosstalk between DNA methylation and gene expression in colorectal cancer, a potential plasma biomarker for tracing this tumor

Mohammad Amin Kerachian,Afsaneh Mojtabanezhad Shariatpanahi,Marjan Azghandi,Kamran Ghaffarzadegan,Ghodratollah Soltani,Ali Javadmanesh,Maryam Yassi,Fatemeh Khadangi,Abdorasool Hayatbakhsh,Ehsan Shams Davodly,Amin Talebi

doi:10.1038/s41598-020-59690-0

Abstract

Colorectal cancer (CRC), the second leading cause of cancer mortality, constitutes a significant global health burden. An accurate, noninvasive detection method for CRC as complement to colonoscopy could improve the effectiveness of treatment. In the present study, SureSelectXT Methyl-Seq was performed on cancerous and normal colon tissues and CLDN1, INHBA and SLC30A10 were found as candidate methylated genes. MethyLight assay was run on formalin-fixed paraffin-embedded (FFPE) and fresh case and control tissues to validate the methylation of the selected gene. The methylation was significantly different (p-values < 2.2e-16) with a sensitivity of 87.17%; at a specificity cut-off of 100% in FFPE tissues. Methylation studies on fresh tissues, indicated a sensitivity of 82.14% and a specificity cut-off of 92% (p-values = 1.163e-07). The biomarker performance was robust since, normal tissues indicated a significant 22.1-fold over-expression of the selected gene as compared to the corresponding CRC tissues (p-value < 2.2e-16) in the FFPE expression assay. In our plasma pilot study, evaluation of the tissue methylation marker in the circulating cell-free DNA, demonstrated that 9 out of 22 CRC samples and 20 out of 20 normal samples were identified correctly. In summary, there is a clinical feasibility that the offered methylated gene could serve as a candidate biomarker for CRC diagnostic purpose, although further exploration of our candidate gene is warranted.

Highlights

Colorectal cancer (CRC) constitutes a significant global health burden, leading to over 862,000 deaths globally in 2018
DNA methylation is negatively correlated with gene expression but so far this association can only be detected for hundreds of genes, and the correlation direction is both positive and negative[22]
We investigated the interplay between CpG methylation and gene expression

Summary

Introduction

Colorectal cancer (CRC) constitutes a significant global health burden, leading to over 862,000 deaths globally in 2018. An ideal screening tool should be inexpensive, noninvasive, easy to perform, and accurate with high sensitivity for advanced adenomas or early cancer It should be widely available and specific enough to avoid unnecessary second level tests. The fecal occult blood test (FOBT), used in population-based screening, was the first and cheapest noninvasive option, which is widely available now. The fecal occult blood test (FOBT), used in population-based screening, was the first and cheapest noninvasive option, which is widely available This method requires several attempts and has a low sensitivity (59.7%). Epi proColon 2.0 CE is based on methylated septin 9 (SEPT9) gene from the circulating cell-free DNA (cfDNA) in the blood It is accessible in Europe and different nations such as China[10,11]. A variety of biomarkers such as diagnostic, preventive and prognostic has been offered for CRC based the cellular and molecular tumorigenesis

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