Comprehensive Analysis of DNA Methylation and Prediction of Response to NeoadjuvantTherapy in Locally Advanced Rectal Cancer

Abstract

The treatment for locally advanced rectal carcinomas (LARC) is based on neoadjuvant chemoradiotherapy (nCRT) and surgery, which results in pathological complete response (pCR) in up to 30% of patients. Since epigenetic changes may influence response to therapy, we aimed to identify DNA methylation markers predictive of pCR in LARC patients treated with nCRT. We used high-throughput DNA methylation analysis of 32 treatment-naïve LARC biopsies and five normal rectal tissues to explore the predictive value of differentially methylated (DM) CpGs. External validation was carried out with The Cancer Genome Atlas-Rectal Adenocarcinoma (TCGA-READ 99 cases). A classifier based on three-CpGs DM (linked to OBSL1, GPR1, and INSIG1 genes) was able to discriminate pCR from incomplete responders with high sensitivity and specificity. The methylation levels of the selected CpGs confirmed the predictive value of our classifier in 77 LARCs evaluated by bisulfite pyrosequencing. Evaluation of external datasets (TCGA-READ, GSE81006, GSE75546, and GSE39958) reproduced our results. As the three CpGs were mapped near to regulatory elements, we performed an integrative analysis in regions associated with predicted cis-regulatory elements. A positive and inverse correlation between DNA methylation and gene expression was found in two CpGs. We propose a novel predictive tool based on three CpGs potentially useful for pretreatment screening of LARC patients and guide the selection of treatment modality.

Predicting response to neoadjuvant chemoradiotherapy in rectal cancer: from biomarkers to tumor models

“… 162 This classifier was shown to discriminate between complete and incomplete responders with 100% sensitivity and 90% specificity, and this predictive value was further verified in an independent cohort of 77 LARC patients. 162 …”

Validation of Gene Expression-Based Predictive Biomarkers for Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer

“…DNA-based molecular markers, including mutations in KRAS or TP53 and microsatellite instability (MSI), may also be associated with responses to neoadjuvant treatment in LARC [ 41 , 42 , 43 ]. Other promising tissue-based predictive biomarkers, including the expression of microRNAs [ 38 ], differentially methylated CpGs [ 44 ], immune profiles [ 45 , 46 ], multi-protein expression assays by immunohistochemistry [ 47 ], are necessary to be validated on large, retrospective, and prospective cohorts of pre-treatment LARC biopsies, although the translation of biomarkers into clinical practice remains challenging. In addition, integrative approaches that include not only tissue-based biomarkers but also liquid-based molecular assays and imaging modalities may contribute to more sensitive stratification of patients with LARC receiving nCRT [ 2 , 38 ].…”

Biomarkers and cell-based models to predict the outcome of neoadjuvant therapy for rectal cancer patients

“…From these, they proposed a classifier based on three sites with differentially methylated CpGs (linked to OBSL1, GPR1, and INSIG1). The classifier was then validated with pyrosequencing in a mixed cohort of 77 LARCs and showed 93.8% sensitivity and 67.3% specificity [71].…”