Identification of non-synonymous SNPs affecting structure and function of MLH1 and NBN proteins: a computational approach

Adzhubei IA, Schmidt S, Peshkin L et al (2010) A method and server for predicting damaging missense mutations. Nat Methods 7(4):248–249

Article  CAS  PubMed  PubMed Central  Google Scholar 

Andersen SD, Liberti SE, Lützen A, Drost M, Bernstein I, Nilbert M, Dominguez M, Nyström M, Van Overeem Hansen T, Christoffersen JW, Jäger AC, de Wind N, Nielsen FC, Tørring PM, Rasmussen LJ (2012) Functional characterization of MLH1 missense variants identified in Lynch syndrome patients. Hum Mutat 33(12):1647–1655. https://doi.org/10.1002/humu.22153

Berardinelli F, Masi A, Antoccia A (2013) NBN gene polymorphisms and cancer susceptibility: a systemic review. Curr Genomics 14(7):425–440. https://doi.org/10.2174/13892029113146660012

Article  CAS  PubMed  PubMed Central  Google Scholar 

Berger MF, Mardis ER, Garraway LA (2016) The emerging role of precision oncology in cancer treatment. Cancer Cell 29(4):461–472

Google Scholar 

Calabrese R, Capriotti E, Fariselli P et al (2009) Functional annotations improve the predictive capability of the human mutation pathogenicity predictor SNPs&GO. Hum Mutat 30(8):1237–1244

Article  CAS  PubMed  Google Scholar 

Capriotti E, Fariselli P (2017) PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants. Nucleic Acids Res 45(W1):W247–W252

Article  CAS  PubMed  PubMed Central  Google Scholar 

Capriotti E, Calabrese R, Fariselli P, Martelli PL, Altman RB, Casadio R (2013) WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation. BMC Genomics 14:1–7

Article  Google Scholar 

Chen Y, Wang X, Xu Y (2016) Regulatory SNPs in cancer: Mechanisms and implications. J Cancer Res Ther 12(2):313–319

Google Scholar 

D’Andrea AD (2018) Mechanisms of PARP inhibitor sensitivity and resistance in cancer therapy. Nat Rev Cancer 18(12):735–751

Google Scholar 

de Almeida Paiva V, de Souza Gomes I, Monteiro CR, Mendonça MV, Martins PM, Santana CA, ... de Azevedo Silveira S (2022) Protein structural bioinformatics: an overview. Comput Biol Med 147:105695

Deriano L, Roth DB (2013a) Modernizing the nonhomologous end-joining repertoire: alternative and classical NHEJ share the stage. Annu Rev Genet 47:433–455

Article  CAS  PubMed  Google Scholar 

Deriano L, Roth DB (2013b) Modernizing the nonhomologous end-joining repertoire: alternative and classical NHEJ. DNA Rsepair 32:32–40. https://doi.org/10.1016/j.dnarep.2013.04.011

Dienstmann R, Vermeulen L, Guinney J et al (2017) Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer. Nat Rev Cancer 17(2):79–92

Article  CAS  PubMed  Google Scholar 

Domingo J, Bae J, Attardi G (2005) Functional domains of MLH1 and its role in DNA mismatch repair. J Mol Biol 345(3):567–580

Google Scholar 

Domingo E, Niessen RC, Oliveira C, Alhopuro P, Moutinho C, Espín E, ... Hofstra RM (2005) BRAF-V600E is not involved in the colorectal tumorigenesis of HNPCC in patients with functional MLH1 and MSH2 genes. Oncogene 24(24):3995–3998

George DCP, Chakraborty C, Haneef SS, NagaSundaram N, Chen L, Zhu H (2014) Evolution-and structure-based computational strategy reveals the impact of deleterious missense mutations on MODY 2 (maturity-onset diabetes of the young, type 2). Theranostics 4(4):366

Article  PubMed  PubMed Central  Google Scholar 

Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, ... Swanton C (2012) Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. New England J Med 366(10):883–892

Godino J, de la Hoya M, Diaz-Rubio E, Benito M, Caldés T (2001) Eight novel germline MLH1 and MSH2 mutations in hereditary non-polyposis colorectal cancer families from Spain. Hum Mutat 18(6):549–549

Article  CAS  PubMed  Google Scholar 

Green ED, Gunter C, Biesecker LG (2020) Genetics and genomics in personalized medicine: contributions to precision healthcare. Science 367(6482):1403–1410

Google Scholar 

Hampel H, Frankel WL, Martin E, Arnold M, Khanduja K, Kuebler P, ... de la Chapelle A (2008) Screening for Lynch syndrome (hereditary nonpolyposis colorectal cancer) in a cohort of colorectal cancer patients. J Clin Oncol 26(4):578–585

Harkness EF, Barrow E, Newton K, Green K, Clancy T, Lalloo F, ... Evans DG (2015) Lynch syndrome caused by MLH1 mutations is associated with an increased risk of breast cancer: a cohort study. J Med Genet. https://doi.org/10.1136/jmedgenet-2015-103216

Hassan M, Chaudhary S, Ahsan M (2021) Molecular dynamics simulation as a tool for the identification of mutation-induced structural alterations. Comput Biol Chem 91:107348

Google Scholar 

Hecht M, Bromberg Y, Rost B (2015) Better prediction of functional effects for sequence variants. BMC Genomics 16(S8):S1

Article  PubMed  PubMed Central  Google Scholar 

Hortobagyi GN (2020) Precision oncology: the next wave of cancer treatment. Lancet Oncol 21(4):e175–e185

Google Scholar 

Huang L, Guo Z, Wang F, Fu L (2018) The potential role of multi-omics data integration in cancer genomics research. Mol Oncol 12(4):561–576

Google Scholar 

Jiricny J (2013) Postreplicative mismatch repair. Cold Spring Harb Perspect Biol 5(4):a012633

Article  PubMed  PubMed Central  Google Scholar 

Kadyrov FA, Dzantiev L, Constantin N, Modrich P (2006) Endonucleolytic function of MutLα in human mismatch repair. Cell 126(2):297–308

Article  CAS  PubMed  Google Scholar 

Kadyrova LY, Gujar V, Burdett V, Modrich PL, Kadyrov FA (2020) Human MutLγ, the MLH1–MLH3 heterodimer, is an endonuclease that promotes DNA expansion. Proc Natl Acad Sci 117(7):3535–3542

Article  CAS  PubMed  PubMed Central  Google Scholar 

Karakoc E, Kim N, Patel K (2019) Structural biology and computational modeling for drug discovery in oncology. Curr Opin Struct Biol 57:1–10

Google Scholar 

Karimi S et al (2022) Impact of SNPs, of-targets, and passive permeability on efcacy of BCL6 degrading drugs assigned by virtual screening and 3D-QSAR approach. Sci Rep 12:21091

Article  CAS  PubMed  PubMed Central  Google Scholar 

Khalid Z, Almaghrabi O (2020) Mutational analysis on predicting the impact of high-risk SNPs in human secretary phospholipase A2 receptor (PLA2R1). Sci Rep 10(1):11750

Article  CAS  PubMed  PubMed Central  Google Scholar 

Khan N, Khan K, Badshah Y, Trembley JH, Ashraf NM, Shabbir M, ... Razak S (2023) Investigating pathogenic SNP of PKCι in HCV-induced hepatocellular carcinoma. Sci Rep 13(1):12504

Kozakov D, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Vajda S (2013) How good is automated protein docking? Proteins Struct Funct Bioinf 81(12):2159–2166

Article  CAS  Google Scholar 

Kozakov D, Hall DR, Xia B et al (2017) The ClusPro web server for protein-protein docking. Nat Protoc 12(2):255–278

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kumar DT, Emerald LJ, Doss CGP, Sneha P, Siva R, Jebaraj WCE, Zayed H (2018a) Computational approach to unravel the impact of missense mutations of proteins (D2HGDH and IDH2) causing D-2-hydroxyglutaric aciduria 2. Metab Brain Dis 33(5):1699–1710

Article  Google Scholar 

Kumar P, Henikoff S, Ng PC (2018b) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4(7):1073–1081

Article  Google Scholar 

Li B, Krishnan VG, Mort ME et al (2009) Automated inference of molecular mechanisms of disease from amino acid substitutions. Genome Res 19(9):1533–1541

CAS  Google Scholar 

Lo YL, Hsiao CF, Jou YS, Chang GC, Tsai YH, Su WC, ... Hsiung CA (2011) Polymorphisms of MLH1 and MSH2 genes and the risk of lung cancer among never smokers. Lung Cancer 72(3):280–286

Mahdouani M, Ben Ahmed S, Hmila F, Rais H, Ben Sghaier R, Saad H, ... Plotz G (2022) Functional characterization of MLH1 missense variants unveils mechanisms of pathogenicity and clarifies role in cancer. PloS One 17(12):e0278283

Mi H, Ebert D, Muruganujan A, Mills C, Albou LP, Mushayamaha T, Thomas PD (2021) PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. Nucleic Acids Res 49(D1):D394–D403

Article  CAS  PubMed  Google Scholar 

Müller-Koch Y, Kopp R, Lohse P, Baretton G, Stoetzer A, Aust D, ... Holinski-Feder E (2001) Sixteen rare sequence variants of the hMLH1 and hMSH2 genes found in a cohort of 254 suspected HNPCC (hereditary non-polyposis colorectal cancer) patients: mutations or polymorphisms? Eur J Med Res 6(11):473–482

Ng PC, Henikoff S (2001) Predicting deleterious amino acid substitutions. Genome Res 11(5):863–874

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ng PC, Henikoff S (2003) SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31(13):3812–3814

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nithya P, ChandraSekar A (2019) NBN gene analysis and it’s impact on breast cancer. J Med Syst 43(8). https://doi.org/10.1007/s10916-019-1328-z

Otahalova B, Volkova Z, Soukupova J, Kleiblova P, Janatova M, Vocka M, Macurek L, Kleibl Z (2023) Importance of germline and somatic alterations in human MRE11, RAD50, and NBN genes coding for MRN complex. Int J Mol Sci 24(6):5612. https://doi.org/10.3390/ijms24065612

Article  CAS  PubMed  PubMed Central  Google Scholar 

Raevaara TE, Gerdes AM, Lönnqvist KE, Tybjærg‐Hansen A, Abdel‐Rahman WM, Kariola R, ... Nyström‐Lahti M (2004) HNPCC mutation MLH1 P648S makes the functional protein unstable, and homozygosity predisposes to mild neurofibromatosis type 1. Genes Chromosome Cancer 40(3):261–265

Šali A, Blundell TL (1993) Comparative protein modelling by satis

Comments (0)

No login
gif