Investigation of promoter methylation of MCPH1 gene in circulating cell-free DNA of brain tumor patients

Abstract

Introduction

Despite advanced diagnostic and therapeutic techniques, many brain tumors are still diagnosed at high grades and, therefore finding novel molecular markers may assist in early detection and reducing brain tumors-related mortality rate. Owing to the previous reports on the importance of MCPH1 gene in tumorigenesis, the present study was aimed to study the promoter methylation of MCPH1 gene in paired circulating cell-free DNA (cfDNA) and tumor tissues of brain tumor patients.

Materials and methods

Fourteen fresh paired serum and tumor tissue samples in addition to 18 isolated serum samples were collected from patients affected by different grades of brain tumor. Genomic DNA and cfDNA was isolated from tissue and serum samples using QIAamp DNA Mini Kit Norgen Bioteck Kit, respectively. Methylation DNA immunoprecipitation Real-time polymerization chain reaction (MeDIP-Real-time PCR) was performed on isolated DNA samples using EpiQuik MeDIP Ultra Kit and specific primer pairs. cfDNA quantity was determined through Real-time PCR analysis using specific primer pairs designed for GAPDH gene.

Results

MCPH1 was methylated in 54% of cfDNA samples which was significantly associated with tumor grade, as well (P-value = 0.02). The methylation rate of MCPH1 was found as 78% in the tissue samples which was meaningfully associated with tumor grade (P-value = 0.03). Moreover, methylation of the MCPH1 gene was consistent in 57% of the same cfDNA and tissue samples. Methylation of MCPH1 gene in neither tumor tissues nor cfDNA was not correlated with age and sex of the patients.

Discussion and conclusion

Due to the conformity of methylation of MCPH1 gene in cfDNA and tissue samples in more than half of the enrolled patients, especially in higher grades of tumors, it seems that MCPH1 promoter methylation could be a potential epimarker in not only detection of brain tumors but also in response to chemo- and radiotherapy which warranted further assessment.

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Acknowledgments

Special thanks to the attending neurosurgeons, nurses and medical staffs of Shohada Tajrish Hospital for providing patients' samples and information.

Funding

This study was funded by personal fund.

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Correspondence to Mohammad Hossein Modarressi or Fatemeh Karami.

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Communicated by Sreedharan Sajikumar.

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Ghodsi, M., Shahmohammadi, M., Modarressi, M.H. et al. Investigation of promoter methylation of MCPH1 gene in circulating cell-free DNA of brain tumor patients. Exp Brain Res (2020). https://doi.org/10.1007/s00221-020-05848-1

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Keywords

  • Brain tumor
  • Cell-free DNA
  • MeDIP-real-time PCR
  • MCPH1
  • Promoter methylation