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

Author(s):Show less -

do Canto, Luisa Matos ^{[1, 2]} ; Barros-Filho, Mateus Camargo ^{[1, 3]} ; Rainho, Claudia Aparecida ^[4] ; Marinho, Diogo ^[5] ; Kupper, Bruna Elisa Catin ^[6] ; Begnami, Maria Dirlei Ferreira de Souza ^[7] ; Scapulatempo-Neto, Cristovam ^{[8, 9]} ; Havelund, Birgitte Mayland ^{[10, 11]} ; Lindebjerg, Jan ^{[10, 12]} ; Marchi, Fabio Albuquerque ^[1] ; Baumbach, Jan ^[13] ; Aguiar, Jr., Samuel ^[6] ; Rogatto, Silvia Regina ^{[2, 10, 14]}

Affiliation:Show less -

^[1] AC Camargo Canc Ctr, Int Res Ctr CIPE, BR-04002010 Sao Paulo - Brazil

^[2] Univ Hosp Southern Denmark, Dept Clin Genet, DK-7100 Vejle - Denmark

^[3] HCFMUSP, Hosp Clin, Dept Head & Neck Surg, BR-01246903 Sao Paulo - Brazil

^[4] Sao Paulo State Univ Unesp, Inst Biosci, Dept Chem & Biol Sci, BR-18618689 Botucatu, SP - Brazil

^[5] Psykiatrisk Ctr Sct, Inst Biol Psychiat, DK-4000 Roskilde - Denmark

^[6] AC Camargo Canc Ctr, Colorectal Canc Serv, BR-04002010 Sao Paulo - Brazil

^[7] Sirio Libanes Hosp, Dept Pathol, BR-01308050 Sao Paulo - Brazil

^[8] Mol Oncol Res Ctr, BR-14784400 Barretos - Brazil

^[9] Diagnost Amer DASA, BR-06455010 Barueri - Brazil

^[10] Danish Colorectal Canc Ctr South, DK-7100 Vejle - Denmark

^[11] Univ Hosp Southern Denmark, Dept Oncol, DK-7100 Vejle - Denmark

^[12] Univ Hosp Southern Denmark, Dept Pathol, DK-7100 Vejle - Denmark

^[13] Tech Univ Munich, TUM Sch Life Sci Weihenstephan, D-85354 Freising Weihenstephan - Germany

^[14] Univ Southern Denmark, Inst Reg Hlth Res, Fac Hlth Sci, DK-5000 Odense - Denmark

• Document type: Journal article
• Source: CANCERS; v. 12, n. 11 NOV 2020.
• Web of Science Citations: 0

Abstract

Simple Summary Patients with locally advanced rectal cancer have been treated with chemoradiotherapy followed by surgery, which results in variable therapy response. To date, there is a lack of established predictive biomarkers to distinguish responsive from non-responsive patients. Therefore, patients can be overtreated resulting in unnecessary toxicity, or therapy changes can occur later when the cancer is more aggressive. We used pre-treatment biopsies to evaluate changes in DNA methylation that could predict the chemoradiotherapy response. Data from an external dataset were used to confirm our findings. We identified and validated a classifier, composed of three candidates, that was able to distinguish responders from non-responders. The genomic context of our biomarkers was explored, giving evidence that they play a role in regulating gene expression. The biomarkers herein described can be easily evaluated in the clinical practice and can help to guide rectal cancer patients' treatment by identifying responders and non-responders. 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-naive 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. (AU)

• FAPESP's process: 15/25803-4 - Integrative (genomic, transcriptomic and methylome) analyses of rectal cancer to unravel predictors of neoadjuvant treatment response
• Grantee: Luisa Matos Do Canto Alvim
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)
• FAPESP's process: 08/57887-9 - National Institute of Oncogenomics
• Grantee: Luiz Paulo Kowalski
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 14/06323-9 - Molecular markers identification of neoadjuvant treatment response in rectal adenocarcinoma patients
• Grantee: Luisa Matos Do Canto Alvim
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)