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Characterization of Wild-Type and Mutated RET Proto-Oncogene Associated with Familial Medullary Thyroid Cancer

  • Masbi, Mohammad Hosein ;
  • Mohammadiasl, Javad ;
  • Galehdari, Hamid ;
  • Ahmadzadeh, Ahmad ;
  • Tabatabaiefar, Mohammad Amin ;
  • Golchin, Neda ;
  • Haghpanah, Vahid ;
  • Rahim, Fakher
  • Published : 2014.03.01

Abstract

Background: We aimed to assess RET proto-oncogene polymorphisms in three different Iranian families with medullary thyroid cancer (MTC), and performed molecular dynamics simulations and free energy stability analysis of these mutations. Materials and Methods: This study consisted of 48 patients and their first-degree relatives with MTC confirmed by pathologic diagnosis and surgery. We performed molecular dynamics simulations and free energy stability analysis of mutations, and docking evaluation of known RET proto-oncogene inhibitors, including ZD-6474 and ponatinib, with wild-type and mutant forms. Results: The first family consisted of 27 people from four generations, in which nine had the C.G2901A (P.C634Y) mutation; the second family consisted of six people, of whom three had the C.G2901T (P.C634F) mutation, and the third family, who included 12 individuals from three generations, three having the C.G2251A (P.G691S) mutation. The automated 3D structure of RET protein was predicted using I-TASSER, and validated by various protein model verification programs that showed more than 96.3% of the residues in favored and allowed regions. The predicted instability indices of the mutated structures were greater than 40, which reveals that mutated RET protein is less thermo-stable compared to the wild-type form (35.4). Conclusions: Simultaneous study of the cancer mutations using both in silico and medical genetic procedures, as well as onco-protein inhibitor binding considering mutation-induced drug resistance, may help in better overcoming chemotherapy resistance and designing innovative drugs.

Keywords

Hereditary MTC;mutation;RET proto-oncogene;in silico;inhibitor binding

References

  1. Wiederstein M, Sippl MJ (2007). ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res, 35, 407-10.
  2. Verkhivker GM, Bouzida D, Gehlhaar DK, et al (2002). Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: the energy landscape analysis of a hot spot at the intermolecular interface. Proteins, 48, 539-57. https://doi.org/10.1002/prot.10164
  3. Wang DD, Zhou W, Yan H, Wong M, Lee V (2013). Personalized prediction of EGFR mutation-induced drug resistance in lung cancer. Sci Rep, 3, 2855.
  4. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004). Development and testing of a general amber force field. J Comput Chem, 25, 1157-74. https://doi.org/10.1002/jcc.20035
  5. Worth CL, Preissner R, Blundell TL (2011). SDM-a server for predicting effects of mutations on protein stability and malfunction. Nucleic Acids Res, 39, 215-22. https://doi.org/10.1093/nar/gkr363
  6. Zedenius J, Wallin G, Hamberger B, et al (1994). Somatic and MEN 2A de novo mutations identified in the RET protooncogene by screening of sporadic MTC:s. Hum Mol Genet, 3, 1259-62. https://doi.org/10.1093/hmg/3.8.1259
  7. Zhang Y (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9 40. https://doi.org/10.1186/1471-2105-9-40
  8. Zhou Y, Zhao Y, Cui B, et al (2007). RET proto-oncogene mutations are restricted to codons 634 and 918 in mainland Chinese families with MEN2A and MEN2B. Clin Endocrinol, 67, 570-6.
  9. Santoro M, Carlomagno F, Melillo RM, Fusco A (2004). Dysfunction of the RET receptor in human cancer. Cell Mol Life Sci, 61, 2954-64. https://doi.org/10.1007/s00018-004-4276-8
  10. Robledo M, Gil L, Pollan M, et al (2003). Polymorphisms G691S/S904S of RET as genetic modifiers of MEN 2A. Cancer Res, 63, 1814-7.
  11. Saggiorato E, Rapa I, Garino F, et al (2007). Absence of RET gene point mutations in sporadic thyroid C-cell hyperplasia. J Mol Diagn, 9, 214-9. https://doi.org/10.2353/jmoldx.2007.060166
  12. Sali A, Blundell TL (1993). Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol, 234, 779-815. https://doi.org/10.1006/jmbi.1993.1626
  13. Schuffenecker I, Virally-Monod M, Brohet R, et al (1998). Risk and penetrance of primary hyperparathyroidism in multiple endocrine neoplasia type 2A families with mutations at codon 634 of the RET proto-oncogene. Groupe D'etude des tumeurs a calcitonine. J Clin Endocrinol Metab, 83, 487-91.
  14. Schymkowitz J, Borg J, Stricher F, et al (2005). The FOLDX web server: an online force field. Nucleic Acids Res, 33 382-8. https://doi.org/10.1093/nar/gki387
  15. Segbena AY, Kueviakoe IM, Agbetiafa K, et al (2012). Chronic myeloid leukemia and imatinib: experience at the lome campus teaching hospital (Togo). Med Sante Trop, 22, 307-11.
  16. Srinivasan J, Miller J, Kollman PA, Case DA (1998). Continuum solvent studies of the stability of RNA hairpin loops and helices. J Biomol Struct Dyn, 16, 671-82. https://doi.org/10.1080/07391102.1998.10508279
  17. Ton GN, Banaszynski ME, Kolesar JM (2013). Vandetanib: a novel targeted therapy for the treatment of metastatic or locally advanced medullary thyroid cancer. Am J Health Syst Pharm, 70, 849-55. https://doi.org/10.2146/ajhp120253
  18. Verkhivker GM, Bouzida D, Gehlhaar DK, et al (2003). Computational detection of the binding-site hot spot at the remodeled human growth hormone-receptor interface. Proteins, 53, 201-19. https://doi.org/10.1002/prot.10456
  19. Othman NH, Omar E, Naing NN (2009). Spectrum of thyroid lesions in hospital Universiti Sains Malaysia over 11years and a review of thyroid cancers in Malaysia. Asian Pac J Cancer Prev, 10, 87-90.
  20. Moura MM, Cavaco BM, Pinto AE, Domingues R, Santos JR, Cid MO, et al (2009). Correlation of RET somatic mutations with clinicopathological features in sporadic medullary thyroid carcinomas. Br J Cancer, 100, 1777-83. https://doi.org/10.1038/sj.bjc.6605056
  21. Mulligan LM, Marsh DJ, Robinson BG, et al (1995). Genotypephenotype correlation in multiple endocrine neoplasia type 2: report of the International RET Mutation Consortium. J Intern Med, 238, 343-6. https://doi.org/10.1111/j.1365-2796.1995.tb01208.x
  22. Nikiforova MN, Nikiforov YE (2008). Molecular genetics of thyroid cancer: implications for diagnosis, treatment and prognosis. Expert Rev Mol Diagn, 8, 83-95. https://doi.org/10.1586/14737159.8.1.83
  23. Parthiban V, Gromiha MM, Schomburg D (2006). CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Res, 34, 239-42. https://doi.org/10.1093/nar/gkl190
  24. Pinna G, Orgiana G, Riola A, Ghiani M, Lai ML, Carcassi C, et al (2007). RET proto-oncogene in Sardinia: V804M is the most frequent mutation and may be associated with FMTC/ MEN-2A phenotype. Thyroid, 17, 101-4. https://doi.org/10.1089/thy.2006.0198
  25. Pronk S, Pall S, Schulz R, et al (2013). GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29, 845-54. https://doi.org/10.1093/bioinformatics/btt055
  26. Punales MK, Graf H, Gross JL, Maia AL (2003). RET codon 634 mutations in multiple endocrine neoplasia type 2: variable clinical features and clinical outcome. J Clin Endocrinol Metab, 88, 2644-9. https://doi.org/10.1210/jc.2002-021422
  27. Punales MK, Rocha AP, Gross JL, Maia AL (2004). [Medullary thyroid carcinoma: clinical and oncological features and treatment]. Arq Bras Endocrinol Metabol, 48, 137-46.
  28. Hedayati M, Zarif Yeganeh M, Sheikhol Eslami S, et al (2011). Predominant RET germline mutations in exons 10, 11, and 16 in Iranian patients with hereditary medullary thyroid carcinoma. J Thyroid Res, 2011: 264248.
  29. Dixit A, Torkamani A, Schork NJ, Verkhivker G (2009). Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: the impact on protein structure, dynamics, and stability. Biophys J, 96, 858-74. https://doi.org/10.1016/j.bpj.2008.10.041
  30. Eng C, Clayton D, Schuffenecker I, et al (1996). The relationship between specific RET proto-oncogene mutations and disease phenotype in multiple endocrine neoplasia type 2. International RET mutation consortium analysis. JAMA, 276, 1575-9. https://doi.org/10.1001/jama.1996.03540190047028
  31. Hedayati M, Nabipour I, Rezaei-Ghaleh N, Azizi F (2006). Germline RET mutations in exons 10 and 11: an Iranian survey of 57 medullary thyroid carcinoma cases. Med J Malaysia, 61, 564-9.
  32. Kaplan W, Littlejohn TG (2001). Swiss-PDB Viewer (Deep View). Brief Bioinform, 2, 195-7. https://doi.org/10.1093/bib/2.2.195
  33. Kollman PA, Massova I, Reyes C, et al (2000). Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res, 33, 89-97.
  34. Kouvaraki MA, Shapiro SE, Perrier ND, et al (2005). RET proto-oncogene: a review and update of genotype-phenotype correlations in hereditary medullary thyroid cancer and associated endocrine tumors. Thyroid, 15, 531-544. https://doi.org/10.1089/thy.2005.15.531
  35. Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM (1996). AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR, 4, 477-86.
  36. Matias-Guiu X, De Lellis R (2013). medullary thyroid carcinoma: a 25-year perspective. Endocr Pathol. [Epub ahead of print].
  37. Bowie JU, Luthy R, Eisenberg D (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-70. https://doi.org/10.1126/science.1853201
  38. Anders J, Kjar S, Ibanez CF (2001). Molecular modeling of the extracellular domain of the RET receptor tyrosine kinase reveals multiple cadherin-like domains and a calciumbinding site. J Biol Chem, 276, 35808-17. https://doi.org/10.1074/jbc.M104968200
  39. Asai N, Iwashita T, Matsuyama M, Takahashi M (1995). Mechanism of activation of the RET proto-oncogene by multiple endocrine neoplasia 2A mutations. Mol Cell Biol 15, 1613-9.
  40. Borrello MG, Aiello A, Peissel B, et al (2011). Functional characterization of the MTC-associated germline RETK666E mutation: evidence of oncogenic potential enhanced by the G691S polymorphism. Endocr Relat Cancer, 18, 519-27. https://doi.org/10.1530/ERC-10-0306
  41. Brady SW, Zhang J, Seok D, Wang H, Yu D (2014). Enhanced PI3K p110alpha signaling confers acquired lapatinib resistance that can be effectively reversed by a p110alphaselective PI3K inhibitor. Mol Cancer Ther, 13, 60-7
  42. Cheng J, Randall A, Baldi P (2006). Prediction of protein stability changes for single-site mutations using support vector machines. Proteins, 62, 1125-32.
  43. Colovos C, Yeates TO (1993). Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci, 2, 1511-9. https://doi.org/10.1002/pro.5560020916
  44. Cosconati S, Forli S, Perryman AL, Harris R, Goodsell DS, Olson AJ (2010). Virtual Screening with AutoDock: Theory and Practice. Expert Opin Drug Discov, 5, 597-60. https://doi.org/10.1517/17460441.2010.484460
  45. De Falco V, Buonocore P, Muthu M, Torregrossa L, Basolo F, Billaud M, et al (2013). Ponatinib (AP24534) is a novel potent inhibitor of oncogenic RET mutants associated with thyroid cancer. J Clin Endocrinol Metab, 98, 811-9. https://doi.org/10.1210/jc.2012-3292

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