BER genes expression in oral and pre-oral cancer: Combinatorial approach to propose potential biomarker

Kumud Nigam; Yogendra Verma; Manish Dwivedi; Somali Sanyal

doi:10.1016/j.currproblcancer.2024.101104

BER genes expression in oral and pre-oral cancer: Combinatorial approach to propose potential biomarker

Curr Probl Cancer. 2024 May 7:50:101104. doi: 10.1016/j.currproblcancer.2024.101104. Online ahead of print.

Authors

Kumud Nigam¹, Yogendra Verma², Manish Dwivedi¹, Somali Sanyal³

Affiliations

¹ Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, Gomti Nagar Ext. Lucknow-226028, India.
² Department of Oral Pathology, King George's Medical University, Lucknow, India.
³ Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, Gomti Nagar Ext. Lucknow-226028, India. Electronic address: ssanyal@lko.amity.edu.

PMID: 38718710
DOI: 10.1016/j.currproblcancer.2024.101104

Abstract

Objective: DNA repair genes and their variants have been found to alter the risk of oral cancer.

Method: The level of expression of XRCC3, NBS1, and OGG1 genes among 20 cases of oral cancer, 6 pre-oral cancer, and 50 healthy control subjects was measured with RT-PCR. All the subjects were also genotyped for XRCC3 rs861539 C>T, NBS1 rs1805794 C>G, and OGG1 rs1052133 C>G polymorphisms by the PCR-RFLP method; their genotypes were correlated with their level of expression. Further, a localized fold structure analysis of the mRNA sequence surrounding the studied SNPs was performed with RNAfold.

Results: Results showed increased expression of XRCC3, NBS1, and OGG1 transcripts among oral cancer (4.49 fold, 3.45 fold, and 3.27 fold) as well as pre-oral cancer (3.04 fold, 5.32 fold, and 1.74 fold) as compared to control subjects. The transcript level of OGG1 was found to be significantly increased (6.68 fold, p-value 0.009) with the GG genotype compared to the CC genotype. The C>T polymorphism of XRCC3 and the C>G polymorphism of OGG1 result in an apparent change in its mRNA secondary structure. Folding energy with the C allele for XRCC3 C>T polymorphism was lower than that of the T allele (MFE C vs T: -50.20 kcal/mol vs -48.70 kcal/mol). In the case of OGG1 C>G polymorphism MFE for the C allele was higher (-23.30 kcal/mole) than with the G allele (-24.80 kcal/mol).

Conclusion: Our results showed elevated levels of XRCC3, NBS1, and OGG1 both in oral cancer and pre-oral cancer conditions, which indicates their role as prospective biomarkers of oral cancer and pre-cancerous lesions. SNPs in these genes alter their level of expression, possibly by altering the secondary structure of their transcript. However, due to the small sample size our study can only provide a suggestive conclusion and warned future study with large sample size to verify our findings.

Keywords: DNA repair genes; Gene expression; Oral cancer; Polymorphism; Pre-oral cancer; RNAfold.