Novel high-risk missense mutations identification in FAT4 gene causing Hennekam syndrome and Van Maldergem syndrome 2 through molecular dynamics simulation

Informatics in Medicine Unlocked - Tập 37 - Trang 101160 - 2023
Khyber Shinwari1,2, Hafiz Muzzammel Rehman3, Ningkun Xiao4, Liu Guojun5, Muhammad Ajmal Khan6, Mikhail A. Bolkov1,7, Irina A. Tuzankina1,7, Valery A. Chereshnev1,7
1Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
2Faculty of Education, Department of Biology, Nangarhar University, Nangarhar, Afghanistan
3School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
4Department of Psychology, Humanities of Ural Federal University, Yekaterinburg, Russia
5School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
6Division of Life Sciences, Center for Cancer Research and Stat Key Lab for Molecular Neurosciences, Hong Kong University of Sciences and Technology, Hong Kong
7Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia

Tài liệu tham khảo

Hennekam, 1989, Autosomal recessive intestinal lymphangiectasia and lymphedema, with facial anomalies and mental retardation, Am J Med Genet, 34, 593, 10.1002/ajmg.1320340429 Rao, 2015, Hennekam lymphangiectasia syndrome, Int J Res Med Sci, 3, 516, 10.5455/2320-6012.ijrms20150229 Van Balkom, 2002, Lymphedema-lymphangiectasia-mental retardation (Hennekam) syndrome: a review, Am J Med Genet, 112, 412, 10.1002/ajmg.10707 Erkan, 1998, Syndrome de Hennekam [Hennekam syndrome], Arch Pediatr, 5, 1344, 10.1016/S0929-693X(99)80054-2 Cormier-Daire, 1995, Craniosynostosis and kidney malformation in a case of Hennekam syndrome, Am J Med Genet, 57, 66, 10.1002/ajmg.1320570115 Nişli, 2008, Hennekam sendromlu bir olguda başvuru nedeni olarak perikard efüzyonu [A case of Hennekam syndrome presenting with massive pericardial effusion], Turk Kardiyol Dernegi Arsivi, 36, 325 Musumeci, 2006, Cutaneous manifestations and massive genital involvement in Hennekam syndrome, Pediatr Dermatol, 23, 239, 10.1111/j.1525-1470.2006.00225.x Bellini, 2003, Hennekam syndrome presenting as nonimmune hydrops fetalis, congenital chylothorax, and congenital pulmonary lymphangiectasia, Am J Med Genet, 120A, 92, 10.1002/ajmg.a.20180 Rockson, 1999, Lymphoscintigraphic manifestations of Hennekam syndrome--a case report, Angiology, 50, 1017, 10.1177/000331979905001207 Al-Gazali, 2003, Further delineation of Hennekam syndrome, Clin Dysmorphol, 12, 227, 10.1097/00019605-200310000-00003 Huppke, 2000, Two brothers with Hennekam syndrome and cerebral abnormalities, Clin Dysmorphol, 9, 21, 10.1097/00019605-200009010-00004 Al Sinani, 2012, Octreotide in Hennekam syndrome-associated intestinal lymphangiectasia, World J Gastroenterol, 18, 6333, 10.3748/wjg.v18.i43.6333 Bellini, 2003, Hennekam syndrome presenting as nonimmune hydrops fetalis, congenital chylothorax, and congenital pulmonary lymphangiectasia, Am J Med Genet, 120, 92, 10.1002/ajmg.a.20180 VanBalkom, 2002, Lymphedema–lymphangiectasia–mental retardation (Hennekam) syndrome: a review, Am J Med Genet, 112, 412, 10.1002/ajmg.10707 Boopathy, 2019, Role of hippo pathway-YAP/TAZ signaling in angiogenesis, Front Cell Dev Biol, 7, 49, 10.3389/fcell.2019.00049 Cha, 2021, A novel role of Hippo-Yap/TAZ signaling pathway in lymphatic vascular development, BMB Rep, 54, 285, 10.5483/BMBRep.2021.54.6.020 Alders, 2009, Mutations in CCBE1 cause generalized lymph vessel dysplasia in humans, Nat Genet, 41, 1272, 10.1038/ng.484 Alders, 2014, Hennekam syndrome can be caused by FAT4 mutations and be allelic to Van Maldergem syndrome, Hum Genet, 133, 1161, 10.1007/s00439-014-1456-y Brouillard, 2017, Loss of ADAMTS3 activity causes Hennekam lymphangiectasia-lymphedema syndrome 3, Hum Mol Genet, 26, 4095, 10.1093/hmg/ddx297 Shah, 2013, CCBE1 mutation in two siblings, one manifesting lymphedema-cholestasis syndrome, and the other, fetal hydrops, PLoS One, 8, 10.1371/journal.pone.0075770 Hogan, 2009, Ccbe1 is required for embryonic lymphangiogenesis and venous sprouting, Nat Genet, 41, 396, 10.1038/ng.321 Bos, 2011, CCBE1 is essential for mammalian lymphatic vascular development and enhances the lymphangiogenic effect of vascular endothelial growth factor-C in vivo, Circ Res, 109, 486, 10.1161/CIRCRESAHA.111.250738 Sandbank, 2019, Oral and topical sirolimus for vascular anomalies: a multicentre study and review, Acta Derm Venereol, 99, 10.2340/00015555-3262 Mahoney, 1991, The fat tumor suppressor gene in Drosophila encodes a novel member of the cadherin gene superfamily, Cell, 67, 853, 10.1016/0092-8674(91)90359-7 Clark, 1995, Dachsous encodes a member of the cadherin superfamily that controls imaginal disc morphogenesis in Drosophila, Genes Dev, 9, 1530, 10.1101/gad.9.12.1530 Katoh, 2006, Comparative integromics on FAT1, FAT2, FAT3 and FAT4, Int J Mol Med, 18, 523 Tanoue, 2005, New insights into Fat cadherins, J Cell Sci, 118, 2347, 10.1242/jcs.02398 2004, Finishing the euchromatic sequence of the human genome, Nature, 431, 931, 10.1038/nature03001 Dabhi, 2014, In silico analysis of single nucleotide polymorphism (SNP) in human TNF-α gene, Meta Gene, 2, 586, 10.1016/j.mgene.2014.07.005 Barroso, 1999, Dominant negative mutations in human PPARgamma associated with severe insulin resistance, diabetes mellitus and hypertension, Nature, 402, 880, 10.1038/47254 Chasman, 2001, Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation, J Mol Biol, 307, 683, 10.1006/jmbi.2001.4510 Lander, 1996, The new genomics: global views of biology, Science, 274, 536, 10.1126/science.274.5287.536 Smith, 1994, Estrogen resistance caused by a mutation in the estrogen-receptor gene in a man [published correction appears in N Engl J Med 1995 Jan 12;332(2):131], N Engl J Med, 331, 1056, 10.1056/NEJM199410203311604 Sherry, 2001, dbSNP: the NCBI database of genetic variation, Nucleic Acids Res, 29, 308, 10.1093/nar/29.1.308 Stenson, 2017, The human gene mutation database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next generation sequencing studies, Hum Genet, 136, 665, 10.1007/s00439-017-1779-6 Pinero, 2017, DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants, Nucleic Acids Res, 45, 10.1093/nar/gkw943 Ng, 2006, Predicting the effects of amino acid substitutions on protein function, Annu Rev Genom Hum Genet, 7, 61, 10.1146/annurev.genom.7.080505.115630 Adzhubei, 2013, Predicting functional effect of human missense mutations using PolyPhen‐2, Curr Protocols Human Genetics, 76, 7, 10.1002/0471142905.hg0720s76 Kumar, 2009, Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm, Nat Protoc, 4, 1073, 10.1038/nprot.2009.86 Li, 2018, VarCards: an integrated genetic and clinical database for coding variants in the human genome, Nucleic Acids Res, 46, D1039, 10.1093/nar/gkx1039 Choi, 2012, Predicting the functional effect of amino acid substitutions and indels, PLoS One, 7, 10.1371/journal.pone.0046688 Hecht, 2015, Better prediction of functional effects for sequence variants, BMC Genom, 16, 1, 10.1186/1471-2164-16-S8-S1 Niroula, 2015, PON-P2: prediction method for fast and reliable identification of harmful variants, PLoS One, 10, 10.1371/journal.pone.0117380 Ferrer-Costa, 2005, PMUT: a web-based tool for the annotation of pathological mutations on proteins, Bioinformatics, 21, 3176, 10.1093/bioinformatics/bti486 Calabrese, 2009, Functional annotations improve the predictive score of human disease-related mutations in proteins, Hum Mutat, 30, 1237, 10.1002/humu.21047 Tang, 2016, PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation, Bioinformatics, 32, 2230, 10.1093/bioinformatics/btw222 Bendl, 2014, PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations, PLoS Comput Biol, 10, 10.1371/journal.pcbi.1003440 Apweiler, 2001, The InterPro database, an integrated documentation resource for protein families, domains and functional sites, Nucleic Acids Res, 29, 37, 10.1093/nar/29.1.37 Warde-Farley, 2010, The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function, Nucleic Acids Res, 38, W214, 10.1093/nar/gkq537 Capriotti, 2005, I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure, Nucleic Acids Res, 33, 10.1093/nar/gki375 Cheng, 2006, Prediction of protein stability changes for single-site mutations using support vector machines, Proteins, 62, 1125, 10.1002/prot.20810 Källberg, 2012, Template-based protein structure modeling using the RaptorX web server, Nat Protoc, 7, 1511, 10.1038/nprot.2012.085 Yang, 2013, Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment, Bioinformatics, 29, 2588, 10.1093/bioinformatics/btt447 Yang, 2013, BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions, Nucleic Acids Res, 41, D1096 Ashkenazy, 2016, Ben-Tal N. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules, Nucleic Acids Res, 44, W344, 10.1093/nar/gkw408 Venselaar, 2010, Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces, BMC Bioinf, 11, 548, 10.1186/1471-2105-11-548 Geourjon, 1995, SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments, Comput Appl Biosci, 11, 681 Deng, 2017, Computational prediction of methylation types of covalently modified lysine and arginine residues in proteins, Briefings Bioinf, 18, 647 Blom, 1999, Sequence and structure-based prediction of eukaryotic protein phosphorylation sites, J Mol Biol, 294, 1351, 10.1006/jmbi.1999.3310 Radivojac, 2010, Identification, analysis, and prediction of protein ubiquitination sites, Proteins, 78, 365, 10.1002/prot.22555 Zhao, 2014, GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs, Nucleic Acids Res, 42, W325, 10.1093/nar/gku383 Kelley, 2015, The Phyre2 web portal for protein modeling, prediction and analysis, Nat Protoc, 10, 845, 10.1038/nprot.2015.053 Wang, 2016, RaptorX-Property: a web server for protein structure property prediction, Nucleic Acids Res, 44, W430, 10.1093/nar/gkw306 Yang, 2015, Protein structure and function prediction using I-TASSER, Curr Protoc Bioinformatics, 52 Benkert, 2011, Toward the estimation of the absolute quality of individual protein structure models, Bioinformatics, 27, 343, 10.1093/bioinformatics/btq662 Wiederstein, 2007, ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins, Nucleic Acids Res, 35, 10.1093/nar/gkm290 Laskowski, 1993, Procheck - a program to check the stereochemical quality of protein structures, J. App. Cryst., 26, 283, 10.1107/S0021889892009944 Bowers, 2006 Ferreira, 2015, Molecular docking and structure-based drug design strategies, Molecules, 20, 13384, 10.3390/molecules200713384 Hildebrand, 2019, Bringing molecular dynamics simulation data into view, Trends Biochem Sci, 44, 902, 10.1016/j.tibs.2019.06.004 Rasheed, 2021, Identification of lead compounds against Scm (fms10) in Enterococcus faecium using computer aided drug designing, Life, 11, 10.3390/life11020077 Shivakumar, 2010, Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field, J Chem Theor Comput, 6, 1509, 10.1021/ct900587b Maiorov, 1994, Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins, J Mol Biol, 235, 625, 10.1006/jmbi.1994.1017 El Khatabi, 2022 Shinwari, 2022, Novel disease-associated missense single-nucleotide polymorphisms variants predication by algorithms tools and molecular dynamics simulation of human TCIRG1 gene causing congenital neutropenia and osteopetrosis, Front Mol Biosci, 9, 10.3389/fmolb.2022.879875 Pedersen, 2021, Effective variant filtering and expected candidate variant yield in studies of rare human disease, NPJ Genomic Med, 6, 60, 10.1038/s41525-021-00227-3 Venselaar, 2010, Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces, BMC Bioinf, 11, 548, 10.1186/1471-2105-11-548 AbdulAzeez, 2016, In-silico computing of the most deleterious nsSNPs in HBA1 gene, PLoS One, 11, 10.1371/journal.pone.0147702 Abdulazeez, 2019, The rs61742690 (S783N) single nucleotide polymorphism is a suitable target for disrupting BCL11A-mediated foetal-to-adult globin switching, PLoS One, 14, 10.1371/journal.pone.0212492 Khafizov, 2015, Computational approaches to study the effects of small genomic variations, J Mol Model, 21, 251, 10.1007/s00894-015-2794-y Kucukkal, 2015, Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins, Curr Opin Struct Biol, 32, 18, 10.1016/j.sbi.2015.01.003 Takano, 2012, An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity, Hum Mol Genet, 21, 4497, 10.1093/hmg/dds292 Hsu, 2008, Two distinct Omp85 paralogs in the chloroplast outer envelope membrane are essential for embryogenesis in Arabidopsis thaliana, Plant Signal Behav, 3, 1134, 10.4161/psb.3.12.7095 Vihinen, 1987, Relationship of protein flexibility to thermostability, Protein Eng, 1, 477, 10.1093/protein/1.6.477 Bond, 2010, Gene repression by minimal lac loops in vivo, Nucleic Acids Res, 38, 8072, 10.1093/nar/gkq755 Dai, 2010, p53 post-translational modification: deregulated in tumorigenesis, Trends Mol Med, 16, 528, 10.1016/j.molmed.2010.09.002 Shiloh, 2013, The ATM protein kinase: regulating the cellular response to genotoxic stress, and more, Nat Rev Mol Cell Biol, 14, 197, 10.1038/nrm3546 Deutscher, 2005, Ser/Thr/Tyr protein phosphorylation in bacteria - for long time neglected, now well established, J Mol Microbiol Biotechnol, 9, 125 Puttick, 2008, Histidine phosphorylation in biological systems, Biochim Biophys Acta, 1784, 100, 10.1016/j.bbapap.2007.07.008 Cieśla, 2011, Phosphorylation of basic amino acid residues in proteins: important but easily missed, Acta Biochim Pol, 58, 137, 10.18388/abp.2011_2258 Sawicka, 2014, Sensing core histone phosphorylation - a matter of perfect timing, Biochim Biophys Acta, 1839, 711, 10.1016/j.bbagrm.2014.04.013 Gallo, 2017, The importance of regulatory ubiquitination in cancer and metastasis, Cell Cycle, 16, 634, 10.1080/15384101.2017.1288326 Essadssi, 2019, Computational analysis of nsSNPs of ADA gene in severe combined immunodeficiency using molecular modeling and dynamics simulation, J Immunol Res, 10.1155/2019/5902391 Zhang, 2020, In silico analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in the human GJA3 gene associated with congenital cataract, BMC Mol Cell Biol, 21, 12, 10.1186/s12860-020-00252-7 Shinwari, 2021, Predicting the most deleterious missense nonsynonymous single-nucleotide polymorphisms of Hennekam syndrome-causing CCBE1 gene, in silico analysis, Sci World J, 10.1155/2021/6642626