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Research Articles

In silico assessment of DNA damage response gene variants associated with head and neck cancer

ORCID Icon, ORCID Icon, , &
Pages 2090-2107 | Received 31 Oct 2020, Accepted 05 Jan 2022, Published online: 17 Jan 2022

References

  • Aboonabi, A., Singh, I., & Rose' Meyer, R. (2020). Cytoprotective effects of berry anthocyanins against induced oxidative stress and inflammation in primary human diabetic aortic endothelial cells. Chemico-Biological Interactions, 317, 108940. https://doi.org/10.1016/j.cbi.2020.108940
  • Abreu Velez, A. M., & Howard, M. S. (2015). Tumor-suppressor genes, cell cycle regulatory checkpoints, and the skin. North American Journal of Medical Sciences, 7(5), 176–188. https://doi.org/10.4103/1947-2714.157476
  • Adzhubei, I., Jordan, D. M., & Sunyaev, S. R. (2013). Predicting functional effect of human missense mutations using PolyPhen-2. Current protocols in human genetics. Chapter 7:Unit7 20.
  • Agrahari, A. K., Doss, G. P. C., Siva, R., Magesh, R., & Zayed, H. (2019). Molecular insights of the G2019S substitution in LRRK2 kinase domain associated with Parkinson's disease: A molecular dynamics simulation approach. Journal of Theoretical Biology, 469, 163–171. https://doi.org/10.1016/j.jtbi.2019.03.003
  • Ahn, E. J., Kim, J. H., Kim, T. K., Park, J. H., Lee, D. K., Lee, S., In, J., & Kang, H. (2019). Assessment of P values for demographic data in randomized controlled trials. Korean Journal of Anesthesiology, 72(2), 130–134. https://doi.org/10.4097/kja.d.18.00333
  • Ajayi, B. O., Adedara, I. A., & Farombi, E. O. (2019). 6-Gingerol abates benzo[a]pyrene-induced colonic injury via suppression of oxido-inflammatory stress responses in BALB/c mice. Chemico-Biological Interactions, 307, 1–7. https://doi.org/10.1016/j.cbi.2019.04.026
  • Akbari, E., Taghizadeh, M., & Nemati, F. (2021). Comparative investigation of R213G mutation in DNA-binding domain of P53 protein via molecular dynamics simulation [Original Article]. Journal of Health and Biomedical Informatics, 8(1), 105–116.
  • Baker, C. M. (2015). Polarizable force fields for molecular dynamics simulations of biomolecules. Wiley Interdisciplinary Reviews: Computational Molecular Science, 5(2), 241–254. https://doi.org/10.1002/wcms.1215
  • Barrett, J. C., Fry, B., Maller, J., & Daly, M. J. (2005). Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics (Oxford, England), 21(2), 263–265. https://doi.org/10.1093/bioinformatics/bth457
  • Bhattacharjee, A., Giri, S., Roy, M., & Chakraborty, A. (2018). Correlation of serum lactate dehydrogenase and alkaline phosphatase in different histological grades of head and neck squamous cell carcinoma and premalignant lesions. Journal of Cancer Research and Therapeutics, 14(5), 934–940. https://doi.org/10.4103/0973-1482.172718
  • Borchiellini, D., Etienne-Grimaldi, M. C., Bensadoun, R. J., Benezery, K., Dassonville, O., Poissonnet, G., Llorca, L., Ebran, N., Formento, P., Château, Y., Thariat, J., & Milano, G. (2017). Candidate apoptotic and DNA repair gene approach confirms involvement of ERCC1, ERCC5, TP53 and MDM2 in radiation-induced toxicity in head and neck cancer. Oral Oncology, 67, 70–76. https://doi.org/10.1016/j.oraloncology.2017.02.003
  • Branzei, D., & Foiani, M. (2006). The Rad53 signal transduction pathway: Replication fork stabilization, DNA repair, and adaptation. Experimental Cell Research, 312(14), 2654–2659. https://doi.org/10.1016/j.yexcr.2006.06.012
  • Bray, F., Ferlay, J., Soerjomataram, I., Siegel, R. L., Torre, L. A., & Jemal, A. (2018). Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: a Cancer Journal for Clinicians, 68(6), 394–424. https://doi.org/10.3322/caac.21492
  • Bray, F., Ren, J. S., Masuyer, E., & Ferlay, J. (2013). Global estimates of cancer prevalence for 27 sites in the adult population in 2008. International Journal of Cancer, 132(5), 1133–1145. https://doi.org/10.1002/ijc.27711
  • Burington, B., Barlogie, B., Zhan, F., Crowley, J., & Shaughnessy, J. D. Jr.(2008). Tumor cell gene expression changes following short-term in vivo exposure to single agent chemotherapeutics are related to survival in multiple myeloma. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 14(15), 4821–4829. https://doi.org/10.1158/1078-0432.CCR-07-4568
  • Capriotti, E., Fariselli, P., & Casadio, R. (2005). I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure [Evaluation Studies Research Support, Non-U.S. Gov't]. Nucleic Acids Research, 33(Web Server issue), W306–W310. https://doi.org/10.1093/nar/gki375
  • Carrera-Lasfuentes, P., Lanas, A., Bujanda, L., Strunk, M., Quintero, E., Santolaria, S., Benito, R., Sopeña, F., Piazuelo, E., Thomson, C., Pérez-Aisa, A., Nicolás-Pérez, D., Hijona, E., Espinel, J., Campo, R., Manzano, M., Geijo, F., Pellise, M., Zaballa, M., … García-González, M. A. (2017). Relevance of DNA repair gene polymorphisms to gastric cancer risk and phenotype. Oncotarget, 8(22), 35848–35862. https://doi.org/10.18632/oncotarget.16261
  • Cetinbas, N., Daugaard, M., Mullen, A. R., Hajee, S., Rotblat, B., Lopez, A., Li, A., DeBerardinis, R. J., & Sorensen, P. H. (2015). Loss of the tumor suppressor Hace1 leads to ROS-dependent glutamine addiction. Oncogene, 34(30), 4005–4010. https://doi.org/10.1038/onc.2014.316
  • Chang, X., & Wang, K. (2012). wANNOVAR: Annotating genetic variants for personal genomes via the web. Journal of Medical Genetics, 49(7), 433–436. https://doi.org/10.1136/jmedgenet-2012-100918
  • Chatterjee, S., Patra, D., Chakraborti, U., Sengupta, D., Ghosh, P., Basu, A., Sadhukhan, G. C., & Chowdhury, K. D. (2019). Association of p38MAPK-p53-Fas aggregation in S-allyl cysteine mediated regulation of hepatocarcinoma. Environmental Toxicology, 34(8), 928–940. https://doi.org/10.1002/tox.22764
  • Choi, Y., Sims, G. E., Murphy, S., Miller, J. R., & Chan, A. P. (2012). Predicting the functional effect of amino acid substitutions and indels [Research Support, N.I.H., Extramural]. PloS One, 7(10), e46688. https://doi.org/10.1371/journal.pone.0046688
  • Choudhury, J. H., & Ghosh, S. K. (2015). Gene-environment interaction and susceptibility in head and neck cancer patients and in their first-degree relatives: A study of Northeast Indian population. Journal of Oral Pathology & Medicine, 44(7), 495–501. https://doi.org/10.1111/jop.12249
  • Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
  • Courtois, G., & Fauvarque, M.-O. (2018). The many roles of ubiquitin in NF-κB signaling. Biomedicines, 6(2), 43. https://doi.org/10.3390/biomedicines6020043
  • Das, R., & Ghosh, S. K. (2017). Genetic variants of the DNA repair genes from Exome Aggregation Consortium (EXAC) database: Significance in cancer. DNA Repair, 52, 92–102. https://doi.org/10.1016/j.dnarep.2017.02.013
  • Das, R., Kundu, S., Laskar, S., Choudhury, Y., & Ghosh, S. K. (2018). Assessment of DNA repair susceptibility genes identified by whole exome sequencing in head and neck cancer. DNA Repair, 66-67, 50–63. https://doi.org/10.1016/j.dnarep.2018.04.005
  • Datta, S., Chaturvedi, P., Mishra, A., & Pawar, P. (2014). A review of Indian literature for association of smokeless tobacco with malignant and premalignant diseases of head and neck region. Indian Journal of Cancer, 51(3), 200–208. https://doi.org/10.4103/0019-509X.146713
  • Daugaard, M., Nitsch, R., Razaghi, B., McDonald, L., Jarrar, A., Torrino, S., Castillo-Lluva, S., Rotblat, B., Li, L., Malliri, A., Lemichez, E., Mettouchi, A., Berman, J. N., Penninger, J. M., & Sorensen, P. H. (2013). Hace1 controls ROS generation of vertebrate Rac1-dependent NADPH oxidase complexes. Nature Communications, 4, 2180. https://doi.org/10.1038/ncomms3180
  • Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., McMorran, R., Wiegers, J., Wiegers, T. C., & Mattingly, C. J. (2019). The comparative toxicogenomics database: Update 2019. Nucleic Acids Research, 47(D1), D948–D954. https://doi.org/10.1093/nar/gky868
  • De Oliveira, C. C. S., Pereira, G. R. C., De Alcantara, J. Y. S., Antunes, D., Caffarena, E. R., & De Mesquita, J. F. (2019). In silico analysis of the V66M variant of human BDNF in psychiatric disorders: An approach to precision medicine. PloS One, 14(4), e0215508. https://doi.org/10.1371/journal.pone.0215508
  • Desai, M., & Chauhan, J. (2016). In silico analysis of nsSNPs in human methyl CpG binding protein 2. Meta Gene, 10, 1–7. https://doi.org/10.1016/j.mgene.2016.09.004
  • Dhull, A. K., Atri, R., Dhankhar, R., Chauhan, A. K., & Kaushal, V. (2018). Major risk factors in head and neck cancer: A retrospective analysis of 12-year experiences. World Journal of Oncology, 9(3), 80–84. https://doi.org/10.14740/wjon1104w
  • Donner, A. J., Hoover, J. M., Szostek, S. A., & Espinosa, J. M. (2007). Stimulus-specific transcriptional regulation within the p53 network. Cell Cycle (Georgetown, Tex.), 6(21), 2594–2598. https://doi.org/10.4161/cc.6.21.4893
  • Doss, C. G. P., & Zayed, H. (2020). Mutational landscape of K-Ras substitutions at 12th position-a systematic molecular dynamics approach. Journal of Biomolecular Structure and Dynamics, https://doi.org/10.1080/07391102.2020.1830177
  • Dumont, P., Leu, J. I., Della Pietra, A. C., 3rd, George, D. L., & Murphy, M. (2003). The codon 72 polymorphic variants of p53 have markedly different apoptotic potential. Nature Genetics, 33(3), 357–365. https://doi.org/10.1038/ng1093
  • Dylawerska, A., Barczak, W., Wegner, A., Golusinski, W., & Suchorska, W. M. (2017). Association of DNA repair genes polymorphisms and mutations with increased risk of head and neck cancer: A review [Review]. Medical Oncology (Northwood, London, England), 34(12), 197. https://doi.org/10.1007/s12032-017-1057-4
  • El-Hachem, N., & Ballotti, R. (2018). The pro-tumoral function of HACE1. Oncoscience, 5(5–6), 128–129. https://doi.org/10.18632/oncoscience.418
  • Eswar, N., Webb, B., Marti‐Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M‐y., Pieper, U., & Sali, A. (2006). Comparative protein structure modeling using Modeller. Current Protocols in Bioinformatics, 15(1), 5.6. 1–5.6. 30. https://doi.org/10.1002/0471250953.bi0506s15
  • Farre, D., Roset, R., Huerta, M., Adsuara, J. E., Rosello, L., Alba, M. M., & Messeguer, X. (2003). Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN [Research Support, Non-U.S. Nucleic Acids Res, 31(13), 3651–3653. https://doi.org/10.1093/nar/gkg605
  • Fountzilas, G., Psyrri, A., Giannoulatou, E., Tikas, I., Manousou, K., Rontogianni, D., Ciuleanu, E., Ciuleanu, T., Resiga, L., & Zaramboukas, T. (2018). Prevalent somatic BRCA1 mutations shape clinically relevant genomic patterns of nasopharyngeal carcinoma in Southeast Europe. International Journal of Cancer, 142(1), 66–80. https://doi.org/10.1002/ijc.31023
  • Friedman, R., Boye, K., & Flatmark, K. (2013). Molecular modelling and simulations in cancer research. Biochimica et Biophysica Acta (Bba) – Reviews on Cancer, 1836(1), 1–14. https://doi.org/10.1016/j.bbcan.2013.02.001
  • Galot, R., van Marcke, C., Helaers, R., Mendola, A., Goebbels, R.-M., Caignet, X., Ambroise, J., Wittouck, K., Vikkula, M., Limaye, N., & Machiels, J.-P H. (2020). Liquid biopsy for mutational profiling of locoregional recurrent and/or metastatic head and neck squamous cell carcinoma. Oral Oncology, 104, 104631. https://doi.org/10.1016/j.oraloncology.2020.104631
  • Gao, Q., Bi, P., Luo, D., Guan, Y., Zeng, W., Xiang, H., Mi, Q., Yang, G., Li, X., & Yang, B. (2020). Nicotine-induced autophagy via AMPK/mTOR pathway exerts protective effect in colitis mouse model. Chemico-Biological Interactions, 317, 108943. https://doi.org/10.1016/j.cbi.2020.108943
  • Gao, Y., Hayes, R. B., Huang, W. Y., Caporaso, N. E., Burdette, L., Yeager, M., Chanock, S. J., & Berndt, S. I. (2011). DNA repair gene polymorphisms and tobacco smoking in the risk for colorectal adenomas [Comparative Study Randomized Controlled Trial Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural]. Carcinogenesis, 32(6), 882–887. https://doi.org/10.1093/carcin/bgr071
  • Gautam, N., Verma, H., Choudhary, S., Kaur, S., & Silakari, O. (2021). Functional relationship of SNP (Ala490Thr) of an epigenetic gene EZH2 results in the progression and poor survival of ER+/tamoxifen treated breast cancer patients. Journal of Genetics, 100(2), 1–19. https://doi.org/10.1007/s12041-021-01327-w
  • Ge, S. X., Jung, D., & Yao, R. (2020). ShinyGO: A graphical gene-set enrichment tool for animals and plants. Bioinformatics (Oxford, England), 36(8), 2628–2629. https://doi.org/10.1093/bioinformatics/btz931
  • Gomez‐Puerto, M. C., Iyengar, P. V., García de Vinuesa, A., Ten Dijke, P., & Sanchez-Duffhues, G. (2019). Bone morphogenetic protein receptor signal transduction in human disease. The Journal of Pathology, 247(1), 9–20. https://doi.org/10.1002/path.5170
  • Guex, N., & Peitsch, M. C. (1997). SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling . Electrophoresis, 18(15), 2714–2723. https://doi.org/10.1002/elps.1150181505
  • Gunaratna, R. T., Santos, A., Luo, L., Nagi, C., Lambertz, I., Spier, M., Conti, C. J., & Fuchs-Young, R. S. (2019). Dynamic role of the codon 72 p53 single-nucleotide polymorphism in mammary tumorigenesis in a humanized mouse model. Oncogene, 38(18), 3535–3550. https://doi.org/10.1038/s41388-018-0630-4
  • Gupta, S., Gupta, R., Sinha, D. N., & Mehrotra, R. (2018). Relationship between type of smokeless tobacco & risk of cancer: A systematic review. The Indian Journal of Medical Research, 148(1), 56–76. https://doi.org/10.4103/ijmr.IJMR_2023_17
  • Han, J.-H., Kerrison, N., Chothia, C., & Teichmann, S. A. (2006). Divergence of interdomain geometry in two-domain proteins. Structure (London, England: 1993), 14(5), 935–945. https://doi.org/10.1016/j.str.2006.01.016
  • Hecht, M., Bromberg, Y., & Rost, B. (2015). Better prediction of functional effects for sequence variants [Research Support, Non-U.S.]. Bmc Genomics, 16(Suppl 8), S1. https://doi.org/10.1186/1471-2164-16-S8-S1
  • Heo, L., Park, H., & Seok, C. (2013). GalaxyRefine: protein structure refinement driven by side-chain repacking. Nucleic Acids Research, 41(Web Server issue), W384–W388. https://doi.org/10.1093/nar/gkt458
  • Heroiu Cataloiu, A. D., Danciu, C. E., & Popescu, C. R. (2013). Multiple cancers of the head and neck. Maedica, 8(1), 80–85.
  • Higashi, M., Kolla, V., Iyer, R., Naraparaju, K., Zhuang, T., Kolla, S., & Brodeur, G. M. (2015). Retinoic acid-induced CHD5 upregulation and neuronal differentiation of neuroblastoma. Molecular Cancer, 14(1), 1–10. https://doi.org/10.1186/s12943-015-0425-y
  • Hirschhorn, T., Levi-Hofman, M., Danziger, O., Smorodinsky, N. I., & Ehrlich, M. (2017). Differential molecular regulation of processing and membrane expression of Type-I BMP receptors: Implications for signaling. Cellular and Molecular Life Sciences: CMLS, 74(14), 2645–2662. https://doi.org/10.1007/s00018-017-2488-y
  • Hu, Y., McDermott, M. P., & Ahrendt, S. A. (2005). The p53 codon 72 proline allele is associated with p53 gene mutations in non-small cell lung cancer. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 11(7), 2502–2509. https://doi.org/10.1158/1078-0432.CCR-04-1913
  • Huihui, X., Yanli, Q., Song, D., Ying., & Xueshan, Q. (2010). BMP7 Signaling via BMPR1A, BMPR1B Inhibits the Proliferation of Lung Large Carcinoma NCI-H460 Cell. Chinese Journal of Lung Cancer, 13(7), 659–64.
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
  • Jakubowski, H., F3. Hydrogen Bonding. (2021).
  • Jayaprakash, C., Varghese, V. K., Jayaram, P., Chakrabarty, S., Kudva, A., Ray, S., & Satyamoorthy, K. (2020). Relevance and actionable mutational spectrum in oral squamous cell carcinoma. Journal of Oral Pathology & Medicine: Official Publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology, 49(5), 427–434. https://doi.org/10.1111/jop.12985
  • Jiang, H.-Y., Zeng, Y., Xu, W.-D., Liu, C., Wang, Y.-J., Wang, Y.-D., & Wang, Y. (2015). Genetic association between the XPG Asp1104His polymorphism and head and neck cancer susceptibility: evidence based on a meta-analysis. Asian Pacific Journal of Cancer Prevention: APJCP, 16(9), 3645–3651. https://doi.org/10.7314/apjcp.2015.16.9.3645
  • Jiricny, J. (2006). The multifaceted mismatch-repair system. Nature Reviews. Molecular Cell Biology, 7(5), 335–346. https://doi.org/10.1038/nrm1907
  • Johnson, J. M., Castle, J., Garrett-Engele, P., Kan, Z., Loerch, P. M., Armour, C. D., Santos, R., Schadt, E. E., Stoughton, R., & Shoemaker, D. D. (2003). Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science (New York, N.Y.), 302(5653), 2141–2144. https://doi.org/10.1126/science.1090100
  • Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118(45), 11225–11236. https://doi.org/10.1021/ja9621760
  • Joshi, P., Dutta, S., Chaturvedi, P., & Nair, S. (2014). Head and neck cancers in developing countries. Rambam Maimonides Medical Journal, 5(2), e0009. https://doi.org/10.5041/RMMJ.10143
  • Joyce, C., & Kasi, A. (2019). Cancer, Tumor-Suppressor Genes. StatPearls. Treasure Island (FL).
  • Karn, R., & Emerson, I. A. (2019). Breast cancer mutation in GATA3 zinc finger 1 induces conformational changes leading to the closer binding of ZnFn2 with a wrapping architecture. Journal of Biomolecular Structure and Dynamics, 1–15. https://doi.org/10.1080/07391102.2019.1620635
  • Keijzers, G., Bakula, D., Petr, M. A., Madsen, N. G. K., Teklu, A., Mkrtchyan, G., Osborne, B., & Scheibye-Knudsen, M. (2018). Human exonuclease 1 (EXO1) regulatory functions in DNA replication with putative roles in cancer. International Journal of Molecular Sciences, 20(1), 74. https://doi.org/10.3390/ijms20010074
  • Kel, A. E., Gossling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O. V., & Wingender, E. (2003). MATCH: A tool for searching transcription factor binding sites in DNA sequences [Research Support, Non-U.S. Gov't]. Nucleic Acids Research, 31(13), 3576–3579. https://doi.org/10.1093/nar/gkg585
  • Khongsti, S., Shunyu, B. N., & Ghosh, S. (2019). Promoter-associated DNA methylation & expression profiling of genes (FLT 3, EPB41L3 & SFN) in patients with oral squamous cell carcinoma in the Khasi & Jaintia population of Meghalaya, India. The Indian Journal of Medical Research, 150(6), 584–591. https://doi.org/10.4103/ijmr.IJMR_620_18
  • Kodandaraman, G., Bankoglu, E. E., & Stopper, H. (2020). Overlapping mechanism of the induction of genomic damage by insulin and adrenaline in human promyelocytic HL-60 cells. Toxicology in Vitro: An International Journal Published in Association with BIBRA, 66, 104867. https://doi.org/10.1016/j.tiv.2020.104867
  • Kreuzer, K., Bohmert, L., Alhalabi, D., Buhrke, T., Lampen, A., & Braeuning, A. (2020). Identification of a transcriptomic signature of food-relevant genotoxins in human HepaRG hepatocarcinoma cells. Food and Chemical Toxicology: An International Journal Published for the British Industrial Biological Research Association, 140, 111297. https://doi.org/10.1016/j.fct.2020.111297
  • Kumar, R., Bansal, A., Shukla, R., Raj Singh, T., Wasudeo Ramteke, P., Singh, S., & Gautam, B. (2019). In silico screening of deleterious single nucleotide polymorphisms (SNPs) and molecular dynamics simulation of disease associated mutations in gene responsible for oculocutaneous albinism type 6 (OCA 6) disorder. Journal of Biomolecular Structure & Dynamics, 37(13), 3513–3523. https://doi.org/10.1080/07391102.2018.1520649
  • Kundu, S., Ramshankar, V., Verma, A. K., Thangaraj, S. V., Krishnamurthy, A., Kumar, R., Kannan, R., & Ghosh, S. K. (2018). Association of DFNA5, SYK, and NELL1 variants along with HPV infection in oral cancer among the prolonged tobacco-chewers. Tumor Biology, 40(8), 1010428318793023. https://doi.org/10.1177/1010428318793023
  • Lacko, M., Ophuis, M. B. O., Peters, W. H., & Manni, J. J. (2009). Genetic polymorphisms of smoking-related carcinogen detoxifying enzymes and head and neck cancer susceptibility. Anticancer Research, 29(2), 753–761.
  • Landrum, M. J., Lee, J. M., Benson, M., Brown, G., Chao, C., Chitipiralla, S., Gu, B., Hart, J., Hoffman, D., Hoover, J., Jang, W., Katz, K., Ovetsky, M., Riley, G., Sethi, A., Tully, R., Villamarin-Salomon, R., Rubinstein, W., & Maglott, D. R. (2016). ClinVar: Public archive of interpretations of clinically relevant variants. Nucleic Acids Research, 44(D1), D862–D868. https://doi.org/10.1093/nar/gkv1222
  • Lang, J., Tobias, E., & Mackie, R. (2011). Preliminary evidence for involvement of the tumour suppressor gene CHD5 in a family with cutaneous melanoma. British Journal of Dermatology, 164(5), 1010–1016. https://doi.org/10.1111/j.1365-2133.2011.10223.x
  • Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
  • Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., O'Donnell-Luria, A. H., Ware, J. S., Hill, A. J., Cummings, B. B., Tukiainen, T., Birnbaum, D. P., Kosmicki, J. A., Duncan, L. E., Estrada, K., Zhao, F., Zou, J., Pierce-Hoffman, E., Berghout, J., … MacArthur, D. G., Exome Aggregation Consortium. (2016). Analysis of protein-coding genetic variation in 60,706 humans. Nature, 536(7616), 285–291.
  • Levine, A. J. (2019). The many faces of p53: Something for everyone. Journal of Molecular Cell Biology, 11(7), 524–530. https://doi.org/10.1093/jmcb/mjz026
  • Li, M., Chen, R., Ji, B., Fan, C., Wang, G., Yue, C., & Jin, G. (2020). RAD52 variants influence NSCLC risk in the Chinese population in a high altitude area. Therapeutic Advances in Respiratory Disease, 14, 1753466620918192. https://doi.org/10.1177/1753466620918192
  • Li, W., Wu, J., Kim, S.-Y., Zhao, M., Hearn, S. A., Zhang, M. Q., Meistrich, M. L., & Mills, A. A. (2014). Chd5 orchestrates chromatin remodelling during sperm development. Nature Communications, 5(1), 1–15. https://doi.org/10.1038/ncomms4812
  • Liang, X., Yin, N., Liang, S., Yang, R., Liu, S., Lu, Y., Jiang, L., Zhou, Q., Jiang, G., & Faiola, F. (2020). Bisphenol A and several derivatives exert neural toxicity in human neuron-like cells by decreasing neurite length. Food and Chemical Toxicology: An International Journal Published for the British Industrial Biological Research Association, 135, 111015. https://doi.org/10.1016/j.fct.2019.111015
  • Lieberman, R., Xiong, D., James, M., Han, Y., Amos, C. I., Wang, L., & You, M. (2016). Functional characterization of RAD52 as a lung cancer susceptibility gene in the 12p13.33 locus. Molecular Carcinogenesis, 55(5), 953–963. https://doi.org/10.1002/mc.22334
  • Lin, A., Wang, R. T., Ahn, S., Park, C. C., & Smith, D. J. (2010). A genome-wide map of human genetic interactions inferred from radiation hybrid genotypes. Genome Research, 20(8), 1122–1132. https://doi.org/10.1101/gr.104216.109
  • Lok, B. H., & Powell, S. N. (2012). Molecular pathways: understanding the role of Rad52 in homologous recombination for therapeutic advancement. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 18(23), 6400–6406. https://doi.org/10.1158/1078-0432.CCR-11-3150
  • Lovell, S. C., Davis, I. W., Arendall, I. I W., De Bakker, P. I., Word, J. M., Prisant, M. G., Richardson, J. S., & Richardson, D. C. (2003). Structure validation by Cα geometry: ϕ, ψ and Cβ deviation. Proteins: Structure, Function, and Bioinformatics, 50(3), 437–450. https://doi.org/10.1002/prot.10286
  • Lu, Q., Tan, Y. H., & Luo, R. (2007). Molecular dynamics simulations of p53 DNA-binding domain. The Journal of Physical Chemistry. B, 111(39), 11538–11545. https://doi.org/10.1021/jp0742261
  • Marcelino, A. M., & Gierasch, L. M. (2008). Roles of beta-turns in protein folding: From peptide models to protein engineering. Biopolymers, 89(5), 380–391. https://doi.org/10.1002/bip.20960
  • Messeguer, X., Escudero, R., Farre, D., Nunez, O., Martinez, J., & Alba, M. M. (2002). PROMO: detection of known transcription regulatory elements using species-tailored searches [Research Support, Non-U.S. Bioinformatics (Oxford, England), 18(2), 333–334. https://doi.org/10.1093/bioinformatics/18.2.333
  • Mi, H., Poudel, S., Muruganujan, A., Casagrande, J. T., & Thomas, P. D. (2016). PANTHER version 10: Expanded protein families and functions, and analysis tools. Nucleic Acids Research, 44(D1), D336–D342. https://doi.org/10.1093/nar/gkv1194
  • Mohanty, S., Devi, Y. S., Daniel, N. R., Ponna, D. R., Devi, M., & Singh, L. J. (2020). Clinicopathological association of p16 and its impact on outcome of chemoradiation in head-and-neck squamous cell cancer patients in North-East India. Cancer Translational Medicine, 6(1), 10. https://doi.org/10.4103/ctm.ctm_34_19
  • Mora Lagares, L., Minovski, N., Caballero Alfonso, A. Y., Benfenati, E., Wellens, S., Culot, M., Gosselet, F., & Novic, M. (2020). Homology modeling of the human P-glycoprotein (ABCB1) and insights into ligand binding through molecular docking studies. International Journal of Molecular Sciences, 21(11), 4058. https://doi.org/10.3390/ijms21114058
  • Morin, I., Ngo, H. P., Greenall, A., Zubko, M. K., Morrice, N., & Lydall, D. (2008). Checkpoint-dependent phosphorylation of Exo1 modulates the DNA damage response. The EMBO Journal, 27(18), 2400–2410. https://doi.org/10.1038/emboj.2008.171
  • Murawska, M., & Brehm, A. (2011). CHD chromatin remodelers and the transcription cycle. Transcription, 2(6), 244–253. https://doi.org/10.4161/trns.2.6.17840
  • Ng, P. C., & Henikoff, S. (2003). SIFT: Predicting amino acid changes that affect protein function [Research Support, U.S. Gov't, P.H.S.]. Nucleic Acids Research, 31(13), 3812–3814. https://doi.org/10.1093/nar/gkg509
  • Nogueira, A., Fernandes, M., Catarino, R., & Medeiros, R. (2019). RAD52 functions in homologous recombination and its importance on genomic integrity maintenance and cancer therapy. Cancers, 11(11), 1622. https://doi.org/10.3390/cancers11111622
  • OriginLab, C. (2021). Origin(Pro) 2021b. Northampton, MA, USA; [accessed].
  • Petersen, B., Petersen, T. N., Andersen, P., Nielsen, M., & Lundegaard, C. (2009). A generic method for assignment of reliability scores applied to solvent accessibility predictions [Research Support, Non-U.S. Gov't]. BMC Structural Biology, 9, 51. https://doi.org/10.1186/1472-6807-9-51
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera – A visualization system for exploratory research and analysis. J Comput Chem, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
  • Pickup, M. W., Hover, L. D., Guo, Y., Gorska, A. E., Chytil, A., Novitskiy, S. V., Moses, H. L., & Owens, P. (2015). Deletion of the BMP receptor BMPR1a impairs mammary tumor formation and metastasis. Oncotarget, 6(26), 22890–22904. https://doi.org/10.18632/oncotarget.4413
  • Priya Doss, C. G., Chakraborty, C., Chen, L., & Zhu, H. (2014). Integrating in silico prediction methods, molecular docking, and molecular dynamics simulation to predict the impact of ALK missense mutations in structural perspective. BioMed Research International, 2014, 1–14. https://doi.org/10.1155/2014/895831
  • Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., & Sham, P. C. (2007). PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics, 81(3), 559–575. https://doi.org/10.1086/519795
  • Qin, B., Minter-Dykhouse, K., Yu, J., Zhang, J., Liu, T., Zhang, H., Lee, S., Kim, J., Wang, L., & Lou, Z. (2015). DBC1 functions as a tumor suppressor by regulating p53 stability [Research Support, N.I.H., Extramural]. Cell Reports, 10(8), 1324–1334. https://doi.org/10.1016/j.celrep.2015.01.066
  • Rajasekaran, R., & Sethumadhavan, R. (2010). In silico identification of significant detrimental missense mutations of EGFR and their effect with 4-anilinoquinazoline-based drugs. Applied Biochemistry and Biotechnology, 160(6), 1723–1733. https://doi.org/10.1007/s12010-009-8662-4
  • Ramaswamy, S., Tamayo, P., Rifkin, R., Mukherjee, S., Yeang, C. H., Angelo, M., Ladd, C., Reich, M., Latulippe, E., Mesirov, J. P., Poggio, T., Gerald, W., Loda, M., Lander, E. S., & Golub, T. R. (2001). Multiclass cancer diagnosis using tumor gene expression signatures. Proceedings of the National Academy of Sciences of the United States of America, 98(26), 15149–15154. https://doi.org/10.1073/pnas.211566398
  • Ramireddy, S., Raghuraman, P., Khandelwal, P., Abraham, J., & Sudandiradoss, C. (2018). A molecular simulation analysis of vitamin D targets interleukin 13 (IL13) as an alternative to mometasone in asthma. 3 Biotech, 8(8), 373. https://doi.org/10.1007/s13205-018-1394-9
  • Rao, A. K. D. M., Manikandan, M., Arunkumar, G., Revathidevi, S., Vinothkumar, V., Arun, K., Tiwary, B. K., Rajkumar, K. S., Rajaraman, R., & Munirajan, A. K. (2017). Prevalence of p53 codon 72, p73 G4C14-A4T14 and MDM2 T309G polymorphisms and its association with the risk of oral cancer in South Indians. Gene Reports, 7, 106–112. https://doi.org/10.1016/j.genrep.2017.03.003
  • Reva, B., Antipin, Y., & Sander, C. (2011). Predicting the functional impact of protein mutations: Application to cancer genomics [Research Support, N.I.H., Extramural Validation Studies]. Nucleic Acids Research, 39(17), e118. https://doi.org/10.1093/nar/gkr407
  • Rotblat, B., Southwell, A. L., Ehrnhoefer, D. E., Skotte, N. H., Metzler, M., Franciosi, S., Leprivier, G., Somasekharan, S. P., Barokas, A., Deng, Y., Tang, T., Mathers, J., Cetinbas, N., Daugaard, M., Kwok, B., Li, L., Carnie, C. J., Fink, D., Nitsch, R., … Sorensen, P. H. (2014). HACE1 reduces oxidative stress and mutant Huntingtin toxicity by promoting the NRF2 response. Proceedings of the National Academy of Sciences of the United States of America, 111(8), 3032–3037. https://doi.org/10.1073/pnas.1314421111
  • Saeed, S., Mahjabeen, I., Sarwar, R., Bashir, K., & Kayani, M. A. (2017). Haplotype analysis of XRCC2 gene polymorphisms and association with increased risk of head and neck cancer. Scientific Reports, 7(1), 13210. https://doi.org/10.1038/s41598-017-13461-6
  • Sahu, S. K., Chakrabarti, S., Roy, S. D., Baishya, N., Reddy, R. R., Suklabaidya, S., Kumar, A., Mohanty, S., Maji, S., & Suryanwanshi, A. (2016). Association of p53 codon72 Arg > Pro polymorphism with susceptibility to nasopharyngeal carcinoma: Evidence from a case-control study and meta-analysis. Oncogenesis, 5, e225. https://doi.org/10.1038/oncsis.2016.31
  • Schrodinger, L. L. C., Forthcoming. (2015). November. The PyMOL Molecular Graphics System, Version 1.8.
  • Seo, H., Park, Y., Min, B. J., Seo, M. E., & Kim, J. H. (2017). Evaluation of exome variants using the ion proton platform to sequence error-prone regions. PloS One, 12(7), e0181304. https://doi.org/10.1371/journal.pone.0181304
  • Sever, R., & Brugge, J. S. (2015). Signal transduction in cancer. Cold Spring Harbor Perspectives in Medicine, 5(4), a006098. https://doi.org/10.1101/cshperspect.a006098
  • Sharma, V., Nandan, A., Singh, H., Agarwal, S., Tripathi, R., Sinha, D. N., & Mehrotra, R. (2019). Events of alternative splicing in head and neck cancer via RNA sequencing – An update. BMC Genomics, 20(1), 442. https://doi.org/10.1186/s12864-019-5794-y
  • Sherry, S. T., Ward, M. H., Kholodov, M., Baker, J., Phan, L., Smigielski, E. M., & Sirotkin, K. (2001). dbSNP: The NCBI database of genetic variation. Nucleic Acids Research, 29(1), 308–311. https://doi.org/10.1093/nar/29.1.308
  • Singh, S., Yennamalli, R. M., Gupta, M., & Changotra, H. (2020). Identification of nsSNPs of transcription factor E2F1 predisposing individuals to lung cancer and head and neck cancer. Mutation Research, 821, 111704. https://doi.org/10.1016/j.mrfmmm.2020.111704
  • Slade, I., Stephens, P., Douglas, J., Barker, K., Stebbings, L., Abbaszadeh, F., Pritchard-Jones, K., Cole, R., Pizer, B., Stiller, C., Vujanic, G., Scott, R. H., Stratton, M. R., & Rahman, N., FACT oration. (2010). Constitutional translocation breakpoint mapping by genome-wide paired-end sequencing identifies HACE1 as a putative Wilms tumour susceptibility gene. Journal of Medical Genetics, 47(5), 342–347. https://doi.org/10.1136/jmg.2009.072983
  • Stanley, F. K., Moore, S., & Goodarzi, A. A. (2013). CHD chromatin remodelling enzymes and the DNA damage response. Mutation Research/Fundamental and Molecular Mechanisms of Mutation Research, 750(1-2), 31–44. https://doi.org/10.1016/j.mrfmmm.2013.07.008
  • Stenson, P. D., Mort, M., Ball, E. V., Evans, K., Hayden, M., Heywood, S., Hussain, M., Phillips, A. D., & Cooper, D. N. (2017). The human gene mutation database: Towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Human Genetics, 136(6), 665–677. https://doi.org/10.1007/s00439-017-1779-6
  • Stirewalt, D. L., & Radich, J. P. (2003). The role of FLT3 in haematopoietic malignancies. Nature Reviews. Cancer, 3(9), 650–665. https://doi.org/10.1038/nrc1169
  • Sturgis, E. M., & Cinciripini, P. M. (2007). Trends in head and neck cancer incidence in relation to smoking prevalence: An emerging epidemic of human papillomavirus-associated cancers? Cancer, 110(7), 1429–1435. https://doi.org/10.1002/cncr.22963
  • Su, L., Sai, Y., Fan, R., Thurston, S. W., Miller, D. P., Zhou, W., Wain, J. C., Lynch, T. J., Liu, G., & Christiani, D. C. (2003). P53 (codon 72) and P21 (codon 31) polymorphisms alter in vivo mRNA expression of p21. Lung Cancer, 40(3), 259–266. https://doi.org/10.1016/S0169-5002(03)00081-3
  • Takahashi, S. (2011). Downstream molecular pathways of FLT3 in the pathogenesis of acute myeloid leukemia: Biology and therapeutic implications. Journal of Hematology & Oncology, 4(1), 13. https://doi.org/10.1186/1756-8722-4-13
  • Takahashi, S. (2020). Mutations of FLT3 receptor affect its surface glycosylation, intracellular localization, and downstream signaling. Leukemia Research Reports, 13, 100187. https://doi.org/10.1016/j.lrr.2019.100187
  • Tanikawa, M., Wada-Hiraike, O., Nakagawa, S., Shirane, A., Hiraike, H., Koyama, S., Miyamoto, Y., Sone, K., Tsuruga, T., Nagasaka, K., Matsumoto, Y., Ikeda, Y., Shoji, K., Oda, K., Fukuhara, H., Nakagawa, K., Kato, S., Yano, T., & Taketani, Y. (2011). Multifunctional transcription factor TFII-I is an activator of BRCA1 function. British Journal of Cancer, 104(8), 1349–1355. https://doi.org/10.1038/bjc.2011.75
  • Thomas, M., Kalita, A., Labrecque, S., Pim, D., Banks, L., & Matlashewski, G. (1999). Two polymorphic variants of wild-type p53 differ biochemically and biologically. Molecular and Cellular Biology, 19(2), 1092–1100. https://doi.org/10.1128/MCB.19.2.1092
  • Tinhofer, I., Budach, V., Saki, M., Konschak, R., Niehr, F., Jöhrens, K., Weichert, W., Linge, A., Lohaus, F., Krause, M., Neumann, K., Endris, V., Sak, A., Stuschke, M., Balermpas, P., Rödel, C., Avlar, M., Grosu, A. L., Abdollahi, A., … Baumann, M., DKTK-ROG. (2016). Targeted next-generation sequencing of locally advanced squamous cell carcinomas of the head and neck reveals druggable targets for improving adjuvant chemoradiation [Multicenter Study Research Support, Non-U.S. Gov't]. European Journal of Cancer (Oxford, England : 1990), 57, 78–86. https://doi.org/10.1016/j.ejca.2016.01.003
  • Torgovnick, A., & Schumacher, B. (2015). DNA repair mechanisms in cancer development and therapy. Frontiers in Genetics, 6, 157. https://doi.org/10.3389/fgene.2015.00157
  • Tortola, L., Nitsch, R., Bertrand, M. J. M., Kogler, M., Redouane, Y., Kozieradzki, I., Uribesalgo, I., Fennell, L. M., Daugaard, M., Klug, H., Wirnsberger, G., Wimmer, R., Perlot, T., Sarao, R., Rao, S., Hanada, T., Takahashi, N., Kernbauer, E., Demiröz, D., … Penninger, J. M. (2016). The tumor suppressor hace1 is a critical regulator of TNFR1-mediated cell fate. Cell Reports, 15(7), 1481–1492. https://doi.org/10.1016/j.celrep.2016.04.032
  • Tumban, E. (2019). A current update on human papillomavirus-associated head and neck cancers. Viruses, 11(10), 922. https://doi.org/10.3390/v11100922
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
  • Venselaar, H., Te Beek, T. A., Kuipers, R. K., Hekkelman, M. L., & Vriend, G. (2010). Protein structure analysis of mutations causing inheritable diseases. An e-science approach with life scientist friendly interfaces [Research Support, Non-U.S. Gov't]. BMC Bioinformatics, 11, 548. https://doi.org/10.1186/1471-2105-11-548
  • Vigneswaran, N., & Williams, M. D. (2014). Epidemiologic trends in head and neck cancer and aids in diagnosis. Oral and Maxillofacial Surgery Clinics of North America, 26(2), 123–141. https://doi.org/10.1016/j.coms.2014.01.001
  • Volodko, N., Salla, M., Eksteen, B., Fedorak, R. N., Huynh, H. Q., & Baksh, S. (2015). TP53 codon 72 Arg/Arg polymorphism is associated with a higher risk for inflammatory bowel disease development. World Journal of Gastroenterology, 21(36), 10358–10366. https://doi.org/10.3748/wjg.v21.i36.10358
  • Walsh, R., Thomson, K. L., Ware, J. S., Funke, B. H., Woodley, J., McGuire, K. J., Mazzarotto, F., Blair, E., Seller, A., & Taylor, J. C. (2017). Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. Genetics in Medicine: Official Journal of the American College of Medical Genetics, 19(2), 192–203. https://doi.org/10.1038/gim.2016.90
  • Wang, J., Chen, H., Fu, S., Xu, Z. M., Sun, K. L., & Fu, W. N. (2011). The involvement of CHD5 hypermethylation in laryngeal squamous cell carcinoma. Oral Oncology, 47(7), 601–608. https://doi.org/10.1016/j.oraloncology.2011.05.003
  • Wang, Q., Mehmood, A., Wang, H., Xu, Q., Xiong, Y., & Wei, D.-Q. (2019). Computational screening and analysis of lung cancer related non-synonymous single nucleotide polymorphisms on the human kirsten rat sarcoma gene. Molecules, 24(10), 1951. https://doi.org/10.3390/molecules24101951
  • Wang, I. X., Ramrattan, G., & Cheung, V. G. (2015). Genetic variation in insulin-induced kinase signaling. Molecular Systems Biology, 11(7), 820. https://doi.org/10.15252/msb.20156250
  • Warde-Farley, D., Donaldson, S. L., Comes, O., Zuberi, K., Badrawi, R., Chao, P., Franz, M., Grouios, C., Kazi, F., Lopes, C. T., Maitland, A., Mostafavi, S., Montojo, J., Shao, Q., Wright, G., Bader, G. D., & Morris, Q. (2010). The GeneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function. Nucleic Acids Research, 38(Web Server issue), W214–W220. https://doi.org/10.1093/nar/gkq537
  • Wawryk-Gawda, E., Chylińska-Wrzos, P., Lis-Sochocka, M., Chłapek, K., Bulak, K., Jędrych, M., & Jodłowska-Jędrych, B. (2014). P53 protein in proliferation, repair and apoptosis of cells. Protoplasma, 251(3), 525–533. https://doi.org/10.1007/s00709-013-0548-1
  • Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue), W407–W410. https://doi.org/10.1093/nar/gkm290
  • Williams, A. B., & Schumacher, B. (2016). p53 in the DNA-damage-repair process. Cold Spring Harbor Perspectives in Medicine, 6(5), a026070. https://doi.org/10.1101/cshperspect.a026070
  • Wu, X., Zhu, Z., Li, W., Fu, X., Su, D., Fu, L., Zhang, Z., Luo, A., Sun, X., Fu, L., & Dong, J.-T. (2012). Chromodomain helicase DNA binding protein 5 plays a tumor suppressor role in human breast cancer. Breast Cancer Research : BCR, 14(3), R73. https://doi.org/10.1186/bcr3182
  • Xu, D., & Zhang, Y. (2011). Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical Journal, 101(10), 2525–2534. https://doi.org/10.1016/j.bpj.2011.10.024
  • Yuan, L. L., Green, A., David, L., Dozier, C., Récher, C., Didier, C., Tamburini, J., & Manenti, S. (2014). Targeting CHK1 inhibits cell proliferation in FLT3-ITD positive acute myeloid leukemia. Leukemia Research, 38(11), 1342–1349. https://doi.org/10.1016/j.leukres.2014.08.020
  • Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9(1), 40. https://doi.org/10.1186/1471-2105-9-40
  • Zhao, M., Kim, P., Mitra, R., Zhao, J., & Zhao, Z. (2016). TSGene 2.0: An updated literature-based knowledgebase for tumor suppressor genes. Nucleic Acids Research, 44(D1), D1023–1031. https://doi.org/10.1093/nar/gkv1268

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