Naeem, W., Nawab, F., Sarwar, M.T. et al. (10 more authors) (2025) Profiling genetic mutations in the DNA damage repair genes of oral squamous cell carcinoma patients from Pakistan. Scientific Reports, 15 (1). 7896. ISSN 2045-2322
Abstract
Herein, we reported mutations in five DNA Damage Repair (DDR) i.e., TP53, ATR, ATM, CHEK1 and CHEK2 involved in OSCC using NG-WES and their analysis using bioinformatics tools. Out of 42 identified mutations, 16.7% are reported for the 1st time. A total of 28 nonsynonymous SNVs are identified. TP53 harbored the highest number of mutations followed by ATM, ATR, CHEK1 and CHEK2. Nine mutations (TP53p.R43H, TP53p.L125Q, TP53p.R116Q, TP53p.C110Y, TP53p.L62F, ATRp.H120Y, ATMp.P1054R, ATMp.D1853V, ATMp.T2934N) were predicted highly pathogenic. SAAFEQ-SEQ predicted destabilizing effects for all mutations, while ISPRED-SEQ identified 09 IS mutations, 07 on TP53, 01 in ATR and 01 in CHEK1 with no IS mutations predicted for ATM and CHEK2. Among the IS mutations, only SNVs were used in MDS simulations. The gyration radius for all IS SNVs was larger for mutant as compared to the wild type indicating perturbed folding behavior of the mutant proteins. Structural deviations across the carbon back bone were noted by RMSD for mutant and wild type. The TP53 IS mutations include TP53p.R116Q, TP53 p.C110Y, TP53p.R43H, TP53p.E214X, TP53p.R210X, TP53 p.C110Afs*5 and TP53 p,S108Ffs*23 whereas ATR and CHEK1 IS mutations consist of ATRp.M1932T and CHEK1p.E76Kfs*21. ConSurf analysis revealed four SNVs with a high conservation score (9) on TP53 and ATM. TP53p.P33R was predominantly associated with moderately differentiated tumors (84.60%), naswar users (86.60%) and positive family history of cancer (91.60%). The TP53p.P33R, ATRp.M211T and CHEK1p.I437V mutations were found recurrently in 21/27 (77.7%), 20/27 (74.04%), and 27/27 (100%) patients, suggesting its potential biomarker applications in local screening.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © The Author(s) 2025. This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/. |
Keywords: | Oral cancer; Oncogenomics; NGS; Biomarker; Bioinformatics; Pashtun; Cancer; Cancer genomics; Molecular biology; Oncology; Oral cancer |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Medicine, Dentistry and Health (Sheffield) > School of Clinical Dentistry (Sheffield) |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 10 Mar 2025 15:56 |
Last Modified: | 10 Mar 2025 15:56 |
Status: | Published |
Publisher: | Springer Science and Business Media LLC |
Refereed: | Yes |
Identification Number: | 10.1038/s41598-025-91700-x |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:224279 |