Exploring the role of TLK2 mutation in tropical calcific pancreatitis: an in silico and molecular dynamics simulation study

References

• Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins: Structure, Function, and Bioinformatics, 17(4), 412–425. https://doi.org/10.1002/prot.340170408
   PubMed Web of Science ®Google Scholar
• Arter, C., Trask, L., Ward, S., Yeoh, S., & Bayliss, R. (2022). Structural features of the protein kinase domain and targeted binding by small-molecule inhibitors. Journal of Biological Chemistry. 298(8), 102247. https://doi.org/10.1016/j.jbc.2022.102247
   PubMed Web of Science ®Google Scholar
• Ashkenazy, H., Abadi, S., Martz, E., Chay, O., Mayrose, I., Pupko, T., & Ben-Tal, N. (2016). ConSurf 2016: An improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Research, 44(W1), W344–W350. https://doi.org/10.1093/nar/gkw408
   PubMed Web of Science ®Google Scholar
• Balaji, L. N., Tandon, R. K., Tandon, B. N., & Banks, P. A. (1994). Prevalence and clinical features of chronic pancreatitis in southern India. International Journal of Pancreatology: Official Journal of the International Association of Pancreatology, 15(1), 29–34. https://doi.org/10.1007/bf02924385
   PubMedGoogle Scholar
• Barman, K. K., Premalatha, G., & Mohan, V. (2003). Tropical chronic pancreatitis. Postgraduate Medical Journal, 79(937), 606–615. https://doi.org/10.1136/pmj.79.937.606
   PubMed Web of Science ®Google Scholar
• Basit, A., Cho, M.-G., Kim, E.-Y., Kwon, D., Kang, S.-J., & Lee, J.-H. (2020). The cGAS/STING/TBK1/IRF3 innate immunity pathway maintains chromosomal stability through regulation of p21 levels. Experimental & Molecular Medicine, 52(4), 643–657. https://doi.org/10.1038/s12276-020-0416-y
   PubMed Web of Science ®Google Scholar
• Bhattacharya, R., Rose, P. W., Burley, S. K., & Prlić, A. (2017). Impact of genetic variation on three-dimensional structure and function of proteins. PloS One, 12(3), e0171355. https://doi.org/10.1371/journal.pone.0171355
   PubMed Web of Science ®Google Scholar
• Bruinsma, W., van den Berg, J., Aprelia, M., & Medema, R. H. (2016). Tousled-like kinase 2 regulates recovery from a DNA damage-induced G2 arrest. EMBO Reports, 17(5), 659–670. https://doi.org/10.15252/embr.201540767
   PubMed Web of Science ®Google Scholar
• Capriotti, E., Fariselli, P., & Casadio, R. (2005). I-Mutant2.0: Predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Research, 33(Web Server), W306–W310. https://doi.org/10.1093/nar/gki375
   PubMed Web of Science ®Google Scholar
• Chari, S. T., Mohan, V., Pitchumoni, C. S., Viswanathan, M., Madanagopalan, N., & Lowenfels, A. B. (1994). Risk of pancreatic carcinoma in tropical calcifying pancreatitis: An epidemiologic study. Pancreas, 9(1), 62–66. https://doi.org/10.1097/00006676-199401000-00009
   PubMed Web of Science ®Google Scholar
• Chen, J., Aronow, B. J., & Jegga, A. G. (2009). Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics, 10(1), 73. https://doi.org/10.1186/1471-2105-10-73
   PubMedGoogle Scholar
• Chen, J., Bardes, E. E., Aronow, B. J., & Jegga, A. G. (2009). ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Research, 37(Web Server), W305–W311. a https://doi.org/10.1093/nar/gkp427
   PubMedGoogle Scholar
• Cingolani, P., Platts, A., Wang, L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., & Ruden, D. M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 6(2), 80–92. https://doi.org/10.4161/fly.19695
   PubMed Web of Science ®Google Scholar
• Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., McVean, G., & Durbin, R. (2011). The variant call format and VCFtools. Bioinformatics (Oxford, England), 27(15), 2156–2158. https://doi.org/10.1093/bioinformatics/btr330
   PubMed Web of Science ®Google Scholar
• Dou, Z., Ghosh, K., Vizioli, M. G., Zhu, J., Sen, P., Wangensteen, K. J., Simithy, J., Lan, Y., Lin, Y., Zhou, Z., Capell, B. C., Xu, C., Xu, M., Kieckhaefer, J. E., Jiang, T., Shoshkes-Carmel, M., Tanim, K. M. A. A., Barber, G. N., Seykora, J. T., … Berger, S. L. (2017). Cytoplasmic chromatin triggers inflammation in senescence and cancer. Nature, 550(7676), 402–406. https://doi.org/10.1038/nature24050
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P., & Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. https://doi.org/10.1021/jm0306430
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. https://doi.org/10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Giroux, V., Iovanna, J., & Dagorn, J. C. (2006). Probing the human kinome for kinases involved in pancreatic cancer cell survival and gemcitabine resistance. FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology, 20(12), 1982–1991. https://doi.org/10.1096/fj.06-6239com
   PubMed Web of Science ®Google Scholar
• Groth, A., Lukas, J., Nigg, E. A., Silljé, H. H., Wernstedt, C., Bartek, J., & Hansen, K. (2003). Human Tousled like kinases are targeted by an ATM- and Chk1-dependent DNA damage checkpoint. The EMBO Journal, 22(7), 1676–1687. https://doi.org/10.1093/emboj/cdg151
   PubMed Web of Science ®Google Scholar
• Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry, 47(7), 1750–1759. https://doi.org/10.1021/jm030644s
   PubMed Web of Science ®Google Scholar
• Heidenblad, M., Lindgren, D., Veltman, J. A., Jonson, T., Mahlamäki, E. H., Gorunova, L., van Kessel, A. G., Schoenmakers, E. F. P. M., & Höglund, M. (2005). Microarray analyses reveal strong influence of DNA copy number alterations on the transcriptional patterns in pancreatic cancer: Implications for the interpretation of genomic amplifications. Oncogene, 24(10), 1794–1801. https://doi.org/10.1038/sj.onc.1208383
   PubMed Web of Science ®Google Scholar
• Huang, D., Sherman, B. T., & Lempicki, R. A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 4(1), 44–57. https://doi.org/10.1038/nprot.2008.211
   PubMed Web of Science ®Google Scholar
• Huang, H., Zou, Y., Zhang, H., Li, X., Li, Y., Deng, X., Sun, H., Guo, Z., & Ao, L. (2020). A qualitative transcriptional prognostic signature for patients with stage I-II pancreatic ductal adenocarcinoma. Translational Research: The Journal of Laboratory and Clinical Medicine, 219, 30–44. https://doi.org/10.1016/j.trsl.2020.02.004
   PubMed Web of Science ®Google Scholar
• Ioannidis, N. M., Rothstein, J. H., Pejaver, V., Middha, S., McDonnell, S. K., Baheti, S., Musolf, A., Li, Q., Holzinger, E., Karyadi, D., Cannon-Albright, L. A., Teerlink, C. C., Stanford, J. L., Isaacs, W. B., Xu, J., Cooney, K. A., Lange, E. M., Schleutker, J., Carpten, J. D., … Sieh, W. (2016). REVEL: An ensemble method for predicting the pathogenicity of rare missense variants. American Journal of Human Genetics, 99(4), 877–885. https://doi.org/10.1016/j.ajhg.2016.08.016
   PubMed Web of Science ®Google Scholar
• Jacobson, M. P., Friesner, R. A., Xiang, Z., & Honig, B. (2002). On the role of crystal packing forces in determining protein sidechain conformations. Journal of Molecular Biology. 320(3), 597–608. https://doi.org/10.1007/s10822-018-0162-6
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., & Tirado-Rives, J. (1988). The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. Journal of the American Chemical Society, 110(6), 1657–1666. https://doi.org/10.1021/ja00214a001
   PubMed Web of Science ®Google Scholar
• Kevin, J. B., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., Sacerdoti, F. D., Salmon, J. K., Shan, Y., & Shaw, D. E. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters. In Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), November 11–17.
   Google Scholar
• Kim, S. T., Ahn, T. J., Lee, E., Do, I. G., Lee, S. J., Park, S. H., Park, J. O., Park, Y. S., Lim, H. Y., Kang, W. K., Kim, S. H., Lee, J., & Kim, H. C. (2015). Exploratory biomarker analysis for treatment response in KRAS wild-type metastatic colorectal cancer patients who received cetuximab plus irinotecan. BMC Cancer, 15(1), 747. https://doi.org/10.1186/s12885-015-1759-y
   PubMedGoogle Scholar
• Kim, J. A., Anurag, M., Veeraraghavan, J., Schiff, R., Li, K., & Wang, X. S. (2016). Amplification of TLK2 induces genomic instability via impairing the G2-M checkpoint. Molecular Cancer Research: MCR, 14(10), 920–927. a https://doi.org/10.1158/1541-7786.MCR-16-0161
   PubMed Web of Science ®Google Scholar
• Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology, 37(8), 907–915. https://doi.org/10.1038/s41587-019-0201-4
   PubMed Web of Science ®Google Scholar
• Kim, J. A., Tan, Y., Wang, X., Cao, X., Veeraraghavan, J., Liang, Y., Edwards, D. P., Huang, S., Pan, X., Li, K., Schiff, R., & Wang, X. S. (2016). Comprehensive functional analysis of the tousled-like kinase 2 frequently amplified in aggressive luminal breast cancers. Nature Communications, 7(1), 12991. b https://doi.org/10.1038/ncomms12991
   PubMedGoogle Scholar
• Klimovskaia, I. M., Young, C., Strømme, C. B., Menard, P., Jasencakova, Z., Mejlvang, J., Ask, K., Ploug, M., Nielsen, M. L., Jensen, O. N., & Groth, A. (2014). Tousled-like kinases phosphorylate Asf1 to promote histone supply during DNA replication. Nature Communications, 5(1), 3394. https://doi.org/10.1038/ncomms4394
   PubMedGoogle Scholar
• Krause, D. R., Jonnalagadda, J. C., Gatei, M. H., Sillje, H. H., Zhou, B. B., Nigg, E. A., & Khanna, K. (2003). Suppression of Tousled-like kinase activity after DNA damage or replication block requires ATM, NBS1 and Chk1. Oncogene, 22(38), 5927–5937. https://doi.org/10.1038/sj.onc.1206691
   PubMed Web of Science ®Google Scholar
• Lelieveld, S. H., Reijnders, M. R. F., Pfundt, R., Yntema, H. G., Kamsteeg, E.-J., de Vries, P., de Vries, B. B. A., Willemsen, M. H., Kleefstra, T., Löhner, K., Vreeburg, M., Stevens, S. J. C., van der Burgt, I., Bongers, E. M. H. F., Stegmann, A. P. A., Rump, P., Rinne, T., Nelen, M. R., Veltman, J. A., … Gilissen, C. (2016). Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Nature Neuroscience, 19(9), 1194–1196. https://doi.org/10.1038/nn.4352
   PubMed Web of Science ®Google Scholar
• Lenkiewicz, E., Malasi, S., Hogenson, T. L., Flores, L. F., Barham, W., Phillips, W. J., Roesler, A. S., Chambers, K. R., Rajbhandari, N., Hayashi, A., Antal, C. E., Downes, M., Grandgenett, P. M., Hollingsworth, M. A., Cridebring, D., Xiong, Y., Lee, J.-H., Ye, Z., Yan, H., … Barrett, M. T. (2020). Genomic and epigenomic landscaping defines new therapeutic targets for adenosquamous carcinoma of the pancreastargeting adenosquamous carcinoma of the pancreas. Cancer Research, 80(20), 4324–4334. https://doi.org/10.1158/0008-5472.CAN-20-0078
   PubMed Web of Science ®Google Scholar
• Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., & Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics (Oxford, England), 25(16), 2078–2079. https://doi.org/10.1093/bioinformatics/btp352
   PubMed Web of Science ®Google Scholar
• Lin, M., Yao, Z., Zhao, N., & Zhang, C. (2019). TLK2 enhances aggressive phenotypes of glioblastoma cells through the activation of SRC signaling pathway. Cancer Biology & Therapy, 20(1), 101–108. https://doi.org/10.1080/15384047.2018.1507257
   PubMed Web of Science ®Google Scholar
• Liu, S., & Guan, W. (2018). STING signaling promotes apoptosis, necrosis, and cell death: An overview and update. Mediators of Inflammation, 2018, 1202797–1202794. https://doi.org/10.1155/2018/1202797
   PubMed Web of Science ®Google Scholar
• Li, J., Abel, R., Zhu, K., Cao, Y., Zhao, S., & Friesner, R. A. (2011). The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling. Proteins: Structure, Function, and Bioinformatics, 79(10), 2794–2812. https://doi.org/10.1002/prot.23106
   PubMed Web of Science ®Google Scholar
• Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), 10–12. https://doi.org/10.14806/ej.17.1.200
   Google Scholar
• McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R., Thormann, A., Flicek, P., & Cunningham, F. (2016). The ensembl variant effect predictor. Genome Biology, 17(1), 122. https://doi.org/10.1186/s13059-016-0974-4
   PubMed Web of Science ®Google Scholar
• Mohan, V., Nagalotimath, S. J., Yajnik, C. S., & Tripathy, B. B. (1998). Fibrocalculous pancreatic diabetes. Diabetes / Metabolism Reviews, 14(2), 153–170. https://doi.org/10.1002/(SICI)1099-0895(199806)14:2%3C153::AID-DMR212%3E3.0.CO;2-Q
   PubMedGoogle Scholar
• Mortuza, G. B., Hermida, D., Pedersen, A. K., Segura-Bayona, S., López-Méndez, B., Redondo, P., Rüther, P., Pozdnyakova, I., Garrote, A. M., Muñoz, I. G., Villamor-Payà, M., Jauset, C., Olsen, J. V., Stracker, T. H., & Montoya, G. (2018). Molecular basis of tousled-like kinase 2 activation. Nature Communications, 9(1), 2535. https://doi.org/10.1038/s41467-018-04941-y
   PubMedGoogle Scholar
• Oshi, M., Patel, A., Le, L., Tokumaru, Y., Yan, L., Matsuyama, R., Endo, I., & Takabe, K. (2021). G2M checkpoint pathway alone is associated with drug response and survival among cell proliferation-related pathways in pancreatic cancer. American Journal of Cancer Research, 11(6), 3070–3084.
   PubMed Web of Science ®Google Scholar
• Paliwal, S., Bhaskar, S., & Chandak, G. R. (2014). Genetic and phenotypic heterogeneity in tropical calcific pancreatitis. World Journal of Gastroenterology, 20(46), 17314–17323. https://doi.org/10.3748/wjg.v20.i46.17314
   PubMed Web of Science ®Google Scholar
• Pejaver, V., Urresti, J., Lugo-Martinez, J., Pagel, K. A., Lin, G. N., Nam, H. J., Mort, M., Cooper, D. N., Sebat, J., Iakoucheva, L. M., Mooney, S. D., & Radivojac, P. (2020). Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. Nature Communications, 11(1), 5918. https://doi.org/10.1038/s41467-020-19669-x
   PubMed Web of Science ®Google Scholar
• Peng, Y.-H., Shiao, H.-Y., Tu, C.-H., Liu, P.-M., Hsu, J. T.-A., Amancha, P. K., Wu, J.-S., Coumar, M. S., Chen, C.-H., Wang, S.-Y., Lin, W.-H., Sun, H.-Y., Chao, Y.-S., Lyu, P.-C., Hsieh, H.-P., & Wu, S.-Y. (2013). Protein kinase inhibitor design by targeting the Asp-Phe-Gly (DFG) motif: The role of the DFG motif in the design of epidermal growth factor receptor inhibitors. Journal of Medicinal Chemistry, 56(10), 3889–3903. https://doi.org/10.1021/jm400072p
   PubMed Web of Science ®Google Scholar
• Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. 50. ()., (), –. https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Segura-Bayona, S., & Stracker, T. H. (2019). The Tousled-like kinases regulate genome and epigenome stability: Implications in development and disease. Cellular and Molecular Life Sciences: CMLS, 76(19), 3827–3841. https://doi.org/10.1007/s00018-019-03208-z
   PubMed Web of Science ®Google Scholar
• Segura-Bayona, S., Villamor-Payà, M., Attolini, C. S., Koenig, L. M., Sanchiz-Calvo, M., Boulton, S. J., & Stracker, T. H. (2020). Tousled-like kinases suppress innate immune signaling triggered by alternative lengthening of telomeres. Cell Reports, 32(5), 107983. https://doi.org/10.1016/j.celrep.2020.107983
   PubMed Web of Science ®Google Scholar
• Sherman, B. T., Hao, M., Qiu, J., Jiao, X., Baseler, M. W., Lane, H. C., Imamichi, T., & Chang, W. (2022). DAVID: A web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Research, 50(W1), W216–W221. https://doi.org/10.1093/nar/gkac194
   PubMed Web of Science ®Google Scholar
• Shrivastava, A., Mathur, K., Verma, R. K., Jayadev Magani, S. K., Vyas, D. K., & Singh, A. (2022). Molecular dynamics study of tropical calcific pancreatitis (TCP) associated calcium-sensing receptor single nucleotide variation. Frontiers in Molecular Biosciences, 9, 982831. https://doi.org/10.3389/fmolb.2022.982831
   PubMed Web of Science ®Google Scholar
• Silljé, H. H., & Nigg, E. A. (2001). Identification of human Asf1 chromatin assembly factors as substrates of Tousled-like kinases. Current Biology: CB, 11(13), 1068–1073. https://doi.org/10.1016/s0960-9822(01)00298-6
   PubMed Web of Science ®Google Scholar
• Simon, B., Lou, H. J., Huet-Calderwood, C., Shi, G., Boggon, T. J., Turk, B. E., & Calderwood, D. A. (2022). Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry. Nature Communications, 13(1), 749. https://doi.org/10.1038/s41467-022-28427-0
   PubMed Web of Science ®Google Scholar
• Singh, G., Bhat, B., Jayadev, M. S. K., Madhusudhan, C., & Singh, A. (2018). mutTCPdb: A comprehensive database for genomic variants of a tropical country neglected disease-tropical calcific pancreatitis. Database: The Journal of Biological Databases and Curation, 2018, bay043. https://doi.org/10.1093/database/bay043
   PubMedGoogle Scholar
• Singh, G., Jayadev Magani, S. K., Sharma, R., Bhat, B., Shrivastava, A., Chinthakindi, M., & Singh, A. (2019). Structural, functional and molecular dynamics analysis of cathepsin B gene SNPs associated with tropical calcific pancreatitis, a rare disease of tropics. PeerJ, 7, e7425. https://doi.org/10.7717/peerj.7425
   PubMed Web of Science ®Google Scholar
• Strohecker, A. M., Joshi, S., Possemato, R., Abraham, R. T., Sabatini, D. M., & White, E. (2015). Identification of 6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase as a novel autophagy regulator by high content shRNA screening. Oncogene, 34(45), 5662–5676. https://doi.org/10.1038/onc.2015.23
   PubMed Web of Science ®Google Scholar
• Tortora, G. J., & Derrickson, B. (2009). Principles of anatomy & physiology (pp. 942–944). Wiley.
   Google Scholar
• Watanabe, T., Kudo, M., & Strober, W. (2017). Immunopathogenesis of pancreatitis. Mucosal Immunology, 10(2), 283–298. https://doi.org/10.1038/mi.2016.101
   PubMed Web of Science ®Google Scholar
• Whitcomb, D. C., Applebaum, S., & Martin, S. P. (1999). Hereditary pancreatitis and pancreatic carcinoma. Annals of the New York Academy of Sciences, 880(1), 201–209. https://doi.org/10.1111/j.1749-6632.1999.tb09524.x
   PubMedGoogle Scholar
• Yang, Y., Muzny, D. M., Reid, J. G., Bainbridge, M. N., Willis, A., Ward, P. A., Braxton, A., Beuten, J., Xia, F., Niu, Z., Hardison, M., Person, R., Bekheirnia, M. R., Leduc, M. S., Kirby, A., Pham, P., Scull, J., Wang, M., Ding, Y., … Eng, C. M. (2013). Clinical whole-exome sequencing for the diagnosis of mendelian disorders. The New England Journal of Medicine, 369(16), 1502–1511. https://doi.org/10.1056/NEJMoa1306555
   PubMed Web of Science ®Google Scholar
• Yang, H., Robinson, P. N., & Wang, K. (2015). Phenolyzer: Phenotype-based prioritization of candidate genes for human diseases. Nature Methods, 12(9), 841–843. https://doi.org/10.1038/nmeth.3484
   PubMed Web of Science ®Google Scholar