Detection of methylated BCAT1 and IKZF1 in stage II/III rectal cancer receiving chemoradiation.

Abstract

602 Background: In liquid biopsy, analyses of circulating tumor DNA (ctDNA) in blood have been used as a tool in cancer screening, identifying tumor mutations and monitoring treatment responses/recurrences. Aberrant methylation of some genes have been associated with cancer. Two genes, BCAT1 and IKZF1, are highly methylated and specific to colorectal cancer (CRC) in blood. Detection of these two methylated genes in post-surgery samples also correlates with higher chance of recurrence. Here we investigated the presence of methylated BCAT1 and IKZF1 at multiple time-points for each patient. Methods: Plasma was extracted from blood within 4 hours of the blood collection. ctDNA were extracted from plasma and bisulphite converted using commercially available kits. Real-time qPCR was used to analyze the converted DNA in three replicates and deemed positive if at least one replicate detected either methylated BCAT1 or IKZF1. Quantification of both genes were determined using separate gene-specific standard curves. Results: Nine Stage II/III rectal cancer (RC) patients was enrolled into the study, with one pre-treatment blood draw and several subsequent draws collected throughout the treatment cycles. five patients tested positive for at least one of the methylated genes prior to treatment. Four of these five patients showed an immediate drop in detection for the assayed genes after one cycle of chemotherapy and either remains at low concentration or is undetectable through the rest of the treatment cycles. These patients either have partial or complete response to the treatment regimen. One patient with continuous high levels of methylated BCAT1 and IKZF1 post-treatment have recurred two months after surgery. Conclusions: Methylated BCAT1 and/or IKZF1 were detected in over 50% of the Stage II/III RC patients pre-treatment. This assay is sensitive to the effect of chemotherapy regimen. A significant number of these patients showed a partial/complete response to their treatment regimen and/or reduction in tumor burden, which is reflected in the loss of detection of these two genes. This study shows that this assay may be a viable tool to pair with Imaging for assessment of patient response to treatment regimen.