A detailed understanding of the COL10A1 and SOX9 genes interaction based on potentially damaging mutations in gastric cancer using computational techniques

References

• Accelrys Software Inc. Discovery Studio Modeling Environment. (2012). Release 3.5. Accelrys Software Inc.
   Google Scholar
• Adzhubei, I., Jordan, D. M., & Sunyaev, S. R. (2013). Predicting functional effect of human missense mutations using PolyPhen-2. Current Protocols in Human Genetics, 76, 7–20. https://doi.org/10.1002/0471142905.hg0720s76
   Google Scholar
• Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S., & Sunyaev, S. R. (2010). A method and server for predicting damaging missense mutations. Nature Methods, 7(4), 248–249. https://doi.org/10.1038/nmeth0410-248
   PubMed Web of Science ®Google Scholar
• Ain, N. U., Makitie, O., & Naz, S. (2018). Autosomal recessive chondrodysplasia with severe short stature caused by a biallelic COL10A1 variant. Journal of Medical Genetics, 55(6), 403–407. https://doi.org/10.1136/jmedgenet-2017-104885
   PubMed Web of Science ®Google Scholar
• Al-Khafaji, K., Al-Duhaidahawi, D., & Taskin Tok, T. (2021). Using integrated computational approaches to identify safe and rapid treatment for SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 39(9), 3387–3395. https://doi.org/10.1080/07391102.2020.1764392
   PubMed Web of Science ®Google Scholar
• Bastide, P., Darido, C., Pannequin, J., Kist, R., Robine, S., Marty-Double, C., Bibeau, F., Scherer, G., Joubert, D., Hollande, F., Blache, P., & Jay, P. (2007). Sox9 regulates cell proliferation and is required for Paneth cell differentiation in the intestinal epithelium. The Journal of Cell Biology, 178(4), 635–648. 13https://doi.org/10.1083/jcb.200704152
   PubMed Web of Science ®Google Scholar
• Bateman, J. F., Wilson, R., Freddi, S., Lamandé, S. R., & Savarirayan, R. (2005). Mutations of COL10A1 in Schmid metaphyseal chondrodysplasia. Human Mutation, 25(6), 525–534. https://doi.org/10.1002/humu.20183
   PubMed Web of Science ®Google Scholar
• Belo, J., Krishnamurthy, M., Oakie, A., & Wang, R. (2013). The role of SOX9 transcription factor in pancreatic and duodenal development. Stem Cells and Development, 22(22), 2935–2943. 15https://doi.org/10.1089/scd.2013.0106
   PubMed Web of Science ®Google Scholar
• Benkert, P., Biasini, M., & Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (Oxford, England), 27(3), 343–350. https://doi.org/10.1093/bioinformatics/btq662
   PubMed Web of Science ®Google Scholar
• Bhowmik, A., Biswas, S., Hajra, S., & Saha, P. (2021). In silico validation of potent phytochemical orientin as inhibitor of SARS-CoV-2 spike and host cell receptor GRP78 binding. Heliyon, 7(1), e05923 https://doi.org/10.1016/j.heliyon.2021.e05923
   PubMed Web of Science ®Google Scholar
• Bonaventure, J., Chaminade, F., & Maroteaux, P. (1995). Mutations in three subdomains of the carboxy-terminal region of collagen type X account for most of the Schmid metaphyseal dysplasias. Human Genetics, 96(1), 58–64. https://doi.org/10.1007/BF00214187
   PubMed Web of Science ®Google Scholar
• Bromberg, Y., & Rost, B. (2007). SNAP: Predict effect of non-synonymous polymorphisms on function. Nucleic Acids Research, 35(11), 3823–3835. https://doi.org/10.1093/nar/gkm238
   PubMed Web of Science ®Google Scholar
• Cancer Genome Atlas Research Network. (2014). Comprehensive molecular characterization of gastric adenocarcinoma. Nature, 513(7517), 202–209. https://doi.org/10.1038/nature13480
   PubMed Web of Science ®Google Scholar
• Chan, D., Cole, W. G., Rogers, J. G., & Bateman, J. F. (1995). Type X collagen multimer assembly in vitro is prevented by a Gly618 to Val mutation in the alpha 1(X) NC1 domain resulting in Schmid metaphyseal chondrodysplasia. The Journal of Biological Chemistry, 270(9), 4558–4562. https://doi.org/10.1074/jbc.270.9.4558
   PubMed Web of Science ®Google Scholar
• Chen, Q., Wu, S. N., Chen, Y. X., C, S. K., Zhang, L., Wei, H. Y., & Kumar, S. A. (2020). A novel missense COL10A1 mutation: C.2020G > A; p. Gly674Arg linked with the bowed legs stature in the Schmid metaphyseal chondrodysplasia-affected Chinese lineage. Bone Rep, 12, 100240. https://doi.org/10.1016/j.bonr.2019.100240
   PubMedGoogle Scholar
• Choudhary, M. I., Shaikh, M., Tul-Wahab, A., & Ur-Rahman, A. (2020). In silico identification of potential inhibitors of key SARS-CoV-2 3CL hydrolase (Mpro) via molecular docking, MMGBSA predictive binding energy calculations, and molecular dynamics simulation. PLoS One, 15(7), e0235030 https://doi.org/10.1371/journal.pone.0235030
   PubMed Web of Science ®Google Scholar
• Cordovil, K. (2018). Sickle cell disease: A genetic disorder of beta-globin. In Thalassemia and Other Hemolytic Anemias (pp. 89–113). https://doi.org/10.5772/intechopen.74778
   Google Scholar
• de Vries, S. J., van Dijk, M., & Bonvin, A. M. (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5(5), 883–897. https://doi.org/10.1038/nprot.2010.32
   PubMed Web of Science ®Google Scholar
• Grimm, D., Bauer, J., Wise, P., Krüger, M., Simonsen, U., Wehland, M., Infanger, M., & Corydon, T. J. (2020). The role of SOX family members in solid tumours and metastasis. Seminars in Cancer Biology, 67(Pt 1), 122–153. https://doi.org/10.1016/j.semcancer.2019.03.004
   PubMed Web of Science ®Google Scholar
• Haseeb, A., & Lefebvre, V. (2019). The SOXE transcription factors-SOX8, SOX9 and SOX10-share a bi-partite transactivation mechanism . Nucleic Acids Research, 47(13), 6917–6931. https://doi.org/10.1093/nar/gkz523
   PubMed Web of Science ®Google Scholar
• Fitzsimmons, R., Amin, N., Uversky, V. N. (2016). Understanding the roles of intrinsic disorder in subunits of hemoglobin and the disease process of sickle cell anemia. Intrinsically disordered proteins, 4(1), e1248273. https://doi.org/10.1080/21690707.2016.1248273
   Google Scholar
• Higuchi, S., Takagi, M., Shimomura, S., Nishimura, G., & Hasegawa, Y. (2016). A Japanese familial case of Schmid metaphyseal chondrodysplasia with a novel mutation in COL10A1. Clinical Pediatric Endocrinology: Case Reports and Clinical Investigations: Official Journal of the Japanese Society for Pediatric Endocrinology, 25(3), 107–110. https://doi.org/10.1297/cpe.25.107
   PubMedGoogle Scholar
• Hofmann, M. J., Bracamonte, S. E., Eizaguirre, C., & Barluenga, M. (2017). Molecular characterization of MHC class IIB genes of sympatric Neotropical cichlids. BMC Genetics, 18(1), 15 https://doi.org/10.1186/s12863-017-0474-x
   PubMedGoogle Scholar
• Hossain, R., Islam, M. T., Ray, P., Jain, D., Saikat, A. S., & Nahar, L. (2021). Amentoflavone, New Hope against SARS-CoV-2: An Outlook through its Scientific Records and an in silico Study. Pharmacognosy Research, 13(3), 149–157.
   Web of Science ®Google Scholar
• Ingram, V. M. (1959). Abnormal human haemoglobins. III the chemical difference between normal and sickle cell haemoglobins. Biochimica et Biophysica Acta, 36(2), 402–411. https://doi.org/10.1016/0006-3002(59)90183-0
   PubMedGoogle Scholar
• Jabeen, A., Mohamedali, A., & Ranganathan, S. (2019). Protocol for protein structure modelling. In Encyclopedia of bioinformatics and computational biology: ABC of Bioinformatics (pp. 252–272). Elsevier.
   Google Scholar
• Jagga, B., Edwards, M., Pagin, M., Wagstaff, K. M., Aragão, D., Roman, N., Nanson, J. D., Raidal, S. R., Dominado, N., Stewart, M., Jans, D. A., Hime, G. R., Nicolis, S. K., Basler, C. F., & Forwood, J. K. (2021). Structural basis for nuclear import selectivity of pioneer transcription factor SOX2. Nature Communications, 12(1), 28 https://doi.org/10.1038/s41467-020-20194-0
   PubMed Web of Science ®Google Scholar
• Jo, A., Denduluri, S., Zhang, B., Wang, Z., Yin, L., Yan, Z., Kang, R., Shi, L. L., Mok, J., Lee, M. J., & Haydon, R. C. (2014). The versatile functions of Sox9 in development, stem cells, and human diseases. Genes & Diseases, 1(2), 149–161. https://doi.org/10.1016/j.gendis.2014.09.004
   PubMedGoogle Scholar
• Kong, L., Shi, L., Wang, W., Zuo, R., Wang, M., & Kang, Q. (2019). Identification of two novel COL10A1 heterozygous mutations in two Chinese pedigrees with Schmid-type metaphyseal chondrodysplasia. BMC Medical Genetics, 20(1), 200 https://doi.org/10.1186/s12881-019-0937-1
   PubMed Web of Science ®Google Scholar
• Li, T., Huang, H., Shi, G., Zhao, L., Li, T., Zhang, Z., Liu, R., Hu, Y., Liu, H., Yu, J., & Li, G. (2018). TGF-β1-SOX9 axis-inducible COL10A1 promotes invasion and metastasis in gastric cancer via epithelial-to-mesenchymal transition. Cell Death & Disease, 9(9), 849 https://doi.org/10.1038/s41419-018-0877-2
   PubMedGoogle Scholar
• McDowall, S., Argentaro, A., Ranganathan, S., Weller, P., Mertin, S., Mansour, S., Tolmie, J., & Harley, V. (1999). Functional and structural studies of wild type SOX9 and mutations causing campomelic dysplasia. The Journal of Biological Chemistry, 274(34), 24023–24030. 20https://doi.org/10.1074/jbc.274.34.24023
   PubMed Web of Science ®Google Scholar
• Molecular Biology of the Cell., et al. (2002). 4th edition. Alberts B, Johnson A, Lewis J,. Garland Science.
   Google Scholar
• Necula, L., Matei, L., Dragu, D., Pitica, I., Neagu, A. I., Bleotu, C., Dima, S., Popescu, I., Diaconu, C. C., & Chivu-Economescu, M. (2020). High plasma levels of COL10A1 are associated with advanced tumor stage in gastric cancer patients. World Journal of Gastroenterology, 26(22), 3024–3033. https://doi.org/10.3748/wjg.v26.i22.3024
   PubMed Web of Science ®Google Scholar
• Pan, Z., Wang, Y., Gu, X., Wang, J., & Cheng, M. (2020). Refined homology model of cytochrome bcc complex B subunit for virtual screening of potential anti-tuberculosis agents. Journal of Biomolecular Structure and Dynamics, 38(16), 4733–4745. https://doi.org/10.1080/07391102.2019.1688196
   PubMed Web of Science ®Google Scholar
• Rosati, R., Horan, G. S., Pinero, G. J., Garofalo, S., Keene, D. R., Horton, W. A., Vuorio, E., de Crombrugghe, B., & Behringer, R. R. (1994). Normal long bone growth and development in type X collagen-null mice. Nature Genetics, 8(2), 129–135. https://doi.org/10.1038/ng1094-129
   PubMed Web of Science ®Google Scholar
• Tan, J. T., Kremer, F., Freddi, S., Bell, K. M., Baker, N. L., Lamandé, S. R., & Bateman, J. F. (2008). Competency for nonsense-mediated reduction in collagen X mRNA is specified by the 3' UTR and corresponds to the position of mutations in Schmid metaphyseal chondrodysplasia. American Journal of Human Genetics, 82(3), 786–793. https://doi.org/10.1016/j.ajhg.2008.01.006
   PubMed Web of Science ®Google Scholar
• Tate, J. G., Bamford, S., & Jubb, H. C. (2019). COSMIC: The catalogue of somatic mutations in cancer. Nucleic Acids Research, 47(1), 941–947. https://doi.org/10.1093/nar/gky1015
   PubMed Web of Science ®Google Scholar