Received: 28 June 2018 | Accepted: 31 October 2018 DOI: 10.1002/jso.25304 RESEARCH ARTICLE Hypomethylation of mismatch repair genes MLH1 and MSH2 is associated with chemotolerance of breast carcinoma: Clinical significance Hemantika Dasgupta PhD 1 | Saimul Islam MSc 1 | Neyaz Alam MBBS, MS 2 | Anup Roy MD 3 | Susanta Roychoudhury PhD 4 | Chinmay Kumar Panda PhD 1 1 Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India 2 Department of Surgical Oncology, Chittaranjan National Cancer Institute, Kolkata, India 3 Department of Pathology, Nil Ratan Sircar Medical College and Hospital, Kolkata, India 4 Research Divison, Saroj Gupta Cancer Center and Research Institute, Kolkata, India Correspondence Chinmay Kumar Panda, Department of Oncogene Regulation, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata 700026, West Bengal, India. Email: ckpanda.cnci@gmail.com Funding information UGC NET Fellowship, Grant/Award Numbers: F.2‐3/2000 (SA‐I), 2061030813 Background and Objectives: The aim of the study was to understand the importance of mismatch repair genes MLH1 and MSH2 in chemotolerance and prognosis of breast carcinoma (BC). Methods: First, the alterations (deletion/methylation/expression) of MLH1 and MSH2 were analyzed in 45 neoadjuvant chemotherapy (NACT)‐treated and 133 pretherapeutic BC samples. The chemotolerant BC cells were characterized by treating two BC cell lines MCF‐7 and MDA MB 231 with two anthracycline antitumor antibiotics, doxorubicin and nogalamycin. Results: The deletion frequencies were 32% to 38% in MLH1/MSH2 genes and promoter methylation frequencies were 49% to 62% in MLH1 and 41% to 51% in MSH2 in both NACT‐treated and pretherapeutic samples. The overall alteration of MLH1 and MSH2 was 58% to 71% in the samples. Reduced messenger RNA (mRNA) and protein expression were found in both the genes and it showed concordance with the molecular alterations. NACT‐treated patients showed better prognosis. The chemotherapeutic drug induced increased mRNA/protein expression of the genes in BC cell lines was due to their promoter hypomethylation, as analyzed by quantitative methylation assay. This phenomenon was also evident in NACT‐treated BC samples. Conclusion: MLH1/MSH2 genes play a critical role in the development of BC. Hypomethylation of MLH1/MSH2 genes might be important in chemotolerance of the disease. KEYWORDS breast carcinoma, doxorubicin/nogalamycin, MLH1/MSH2, neoadjuvant chemotherapy, promo- ter hypomethylation 1 | INTRODUCTION Breast carcinoma (BC) is the most common cancer among women worldwide. 1 It accounts for 25% of the cancer burden in Eastern Indian population. 2 Some of the etiological factors of BC are a genetic predisposition, exposure to ionization radiation, HPV infection, hormo- nal exposures, and obesity. 3-6 The early‐onset BC (age of onset below 40 years) is more aggressive and shows lower survival rates compared J Surg Oncol. 2018;1-13. wileyonlinelibrary.com/journal/jso © 2018 Wiley Periodicals, Inc. | 1 Abbreviations: 5‐aza‐dC, 5‐aza‐2′‐deoxycytidine; BC, breast carcinoma; ER, estrogen receptor; HER2, human epidermal growth factor receptor 2; HRP, horseradish peroxidase; MAI, microsatellite size alterations of one allele; MAII, microsatellite size alterations of two alleles; MMR, mismatch repair; MSRA, methylation sensitive restriction analysis; NACT, neoadjuvant chemotherapy; PR, progesterone receptor; qRT‐PCR, real‐time PCR quantification; TNM, tumor size, lymph node, metastasis; UICC, International Union Against Cancer.