Correlation of MLH1 polymorphisms, survival statistics, in silico assessment and gene downregulation with clinical outcomes among breast cancer cases

  • Saima Shakil MalikEmail author
  • Ayisha Zia
  • Sumaira Mubarik
  • Nosheen Masood
  • Sajid Rashid
  • Alice Sherrard
  • Muhammad Bilal Khan
  • Muhammad Tahir Khadim
Original Article


This study aimed to investigate the role of MLH1 polymorphisms, respective protein structure prediction, survival analysis, related clinicopathological details and MLH1 expression in breast cancer (BC). Genotyping of selected SNPs in BC patients (493) and age matched controls (387) were performed by Tetra–ARMS PCR. Gene expression among breast tumors (127) and adjacent control tissues were analysed using reverse transcriptase PCR (RT-PCR) and immunohistochemistry. Statistical analysis was performed by SPSS and MedCalc. Conditional logistic regression analysis was applied to compute the odds ratio and confidence interval. Phyre2 and I-TASSER were used to generate MLH1 protein structures and verified by a variety of computational tools. Genotyping illustrated that MLH1 polymorphisms (rs63749795 and rs63749820) were significantly associated (P ≤ 0.05) with risk of developing BC. Down regulation of MLH1 gene expression/loss of the MLH1 protein (OR 12; CI 2.8–53.1) was observed in BC cases, illustrating its potential role in disease development. Moreover, loss of the MLH1 protein was found to be associated with higher grade cancer (P = 0.02) and lymph node positivity (P = 0.03), highlighting its essential role, as a component of the mismatch repair (MMR) machinery. Bioinformatics analysis confirmed that nonsense mutations produce a truncated MLH1 protein, causing a reduction in MMR efficiency. No association between MLH1 polymorphisms and overall and progression free survival statistics was observed among BC cases, possibly due to short follow–up study. Results at DNA, RNA and protein levels, along with in silico analysis, highlights the potential role of MLH1 in DNA repair mechanisms, within BC. Therefore, it was concluded that MLH1 may contribute towards BC development and progression.


MLH1 ARMS PCR Breast cancer Polymorphisms Expression Survival analysis 



We would like to thank all the patients, their family members and colleagues at Armed Forces Institute of Pathology for their kind help and support.


No support or funding is available for this study.

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflict of interest.


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Fatima Jinnah Women UniversityRawalpindiPakistan
  2. 2.National Centre for Bioinformatics, Quaid-i-Azam UniversityIslamabadPakistan
  3. 3.Department of Epidemiology and Biostatistics, School of Health SciencesWuhan UniversityWuhanChina
  4. 4.Department of Cellular and Molecular Medicine, School of Life SciencesBristol UniversityBristolUK
  5. 5.Armed Forces Institute of PathologyRawalpindiPakistan

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