Improved microsatellite instability detection in colorectal cancer patients by a combination of fourteen markers especially DNMT3a, DCD, and MT1X

Article type: Research Article

Authors: Khaligh, Ali^a | Fazeli, Mohammad Sadegh^b | Mahmoodzadeh, Habibollah^c | Mehrtash, Amirhosein^a | Kompanian, Setareh^a | Zeinali, Sirous^a | Teimoori-Toolabi, Ladan^{a; *}

Affiliations: [a] Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran | [b] Department of Surgery, Division of Colo-Rectal Surgery, Imam Khomeini Medical Complex, Tehran University of Medical Sciences, Tehran, Iran | [c] Cancer Institute of Iran, Imam Khomeini Medical Complex, Tehran University of Medical Sciences, Tehran, Iran

Correspondence: [*] Corresponding author: Ladan Teimoori-Toolabi, Molecular Medicine Department, Pasteur Institute of Iran, 69 th Pasteur Street, Kargar Avenue, Tehran, Iran. Tel.: +98 21 64112455; Fax: +98 21 66480780; P.O box: 1316943551; E-mail: lteimoori@pasteur.ac.ir.

Abstract: BACKGROUND: Microsatellite instability (MSI) results from genetic and epigenetic changes. Studying Microsatellite instability can help in treatment and categorization of colorectal cancer (CRC) patients. OBJECTIVES: We aimed to investigate whether 14 genomic markers consisting of BAT-62, BAT-60, BAT-59a, BAT-56a, BAT-56b, DCD, RIOX, RNF, FOXP, ACVR, CASP2, HSP110, MT1X, and DNMT3a can increase the detection rate of MSI in CRC. METHODS: Samples were stratified by pentaplex panel (Promega) and 14 markers using multiplex PCR and fragment analysis. In MSI+ samples, to identify the pattern of BRAF V600E mutation and MLH1 promoter methylation, ARMS-scorpion, and Methylation-Specific High-Resolution Melting Curve analysis, were applied respectively. RESULTS: Totally, 35 MSI+ cases identified by 14 marker panel. Only 18 cases of them were detected by both panels which are pentaplex and 14 marker. On the other hand, 17 new MSI+ cases just were identified by 14 markers panel. The highest diagnostic value among 14 markers is related to three makers, namely DCD, MT1X, and DNMT3a. In MSI+ cases, the rate of MLH1 promoter methylation was insignificant, (P value = 0.3979) while the rate of observed BRAFV600E mutation was significantly higher (P value = 0.0002). CONCLUSION: Fourteen marker panel showed higher sensitivity in comparison with the pentaplex panel increasing the detection rate of MSI+ cases up to 1.94 fold. Three markers namely DNMT3a, DCD, and MT1X of 14 marker panel were the best among them showing excellent diagnostic value. A combination of these markers showed 100% sensitivity and specificity in the studied group. In contrary to the markers in the pentaplex panel, these markers had the ability to detect MSI without any bias for the clinicopathological features. These markers will help to identify more end-stage MSI+ tumors which are located distal colon.

Keywords: Colorectal Neoplasm, Microsatellite Instability, Biomarker, tumor, DNA methyltransferase 3A

DOI: 10.3233/CBM-203226

Journal: Cancer Biomarkers, vol. 31, no. 4, pp. 385-397, 2021