Howlader N, Forjaz G, Mooradian MJ, Meza R, Kong CY, Cronin KA, et al. The effect of advances in lung-cancer treatment on population mortality. N Engl J Med 2020;383:640–9.
Chapman PB, Hauschild A, Robert C, Haanen JB, Ascierto P, Larkin J, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med 2011;364:2507–16.
Skoulidis F, Li BT, Dy GK, Price TJ, Falchook GS, Wolf J, et al. Sotorasib for lung cancers with KRAS p.G12C mutation. N Engl J Med 2021;384:2371–81.
Maemondo M, Inoue A, Kobayashi K, Sugawara S, Oizumi S, Isobe H, et al. Gefitinib or chemotherapy for non-small-cell lung cancer with mutated EGFR. N Engl J Med 2010;362:2380–8.
Wirth LJ, Sherman E, Robinson B, Solomon B, Kang H, Lorch J, et al. Efficacy of selpercatinib in RET-altered thyroid cancers. N Engl J Med 2020;383:825–35.
Subbiah V, Hu MI, Wirth LJ, Schuler M, Mansfield AS, Curigliano G, et al. Pralsetinib for patients with advanced or metastatic RET-altered thyroid cancer (ARROW): a multi-cohort, open-label, registrational, phase 1/2 study. Lancet Diabetes Endocrinol 2021;9:491–501.
Ikemura S, Yasuda H, Matsumoto S, Kamada M, Hamamoto J, Masuzawa K, et al. Molecular dynamics simulation-guided drug sensitivity prediction for lung cancer with rare EGFR mutations. Proc Nat Acad Sci U S A 2019;116:10025–30.
Foley SB, Rios JJ, Mgbemena VE, Robinson LS, Hampel HL, Toland AE, et al. Use of whole genome sequencing for diagnosis and discovery in the cancer genetics clinic. EBioMedicine 2015;2:74–81.
Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al. Highly accurate protein structure prediction with AlphaFold. Nature 2021;596:583–9.
Buel GR, Walters KJ. Can AlphaFold2 predict the impact of missense mutations on structure? Nat Struct Mol Biol 2022;29:1–2.
Mulligan LM. RET revisited: expanding the oncogenic portfolio. Nat Rev Cancer
2014;14:173–86.
Plaza-Menacho I, Barnouin K, Goodman K, Martinez-Torres RJ, Borg A, Murray-Rust J, et al. Oncogenic RET kinase domain mutations perturb the autophosphorylation trajectory by enhancing substrate presentation in trans. Mol Cell 2014;53:738–51.
Romei C, Ciampi R, Elisei R. A comprehensive overview of the role of the RET proto-oncogene in thyroid carcinoma. Nat Rev Endocrinol 2016;12:192–202.
Arnedo-Pac C, Mularoni L, Muinos F, Gonzalez-Perez A, Lopez-Bigas N. OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers. Bioinformatics 2019;35:4788–90.
Li J, Shang G, Chen YJ, Brautigam CA, Liou J, Zhang X, et al. Cryo-EM analyses reveal the common mechanism and diversification in the activation of RET by different ligands. Elife 2019;8:e47650.
Jung J, Kobayashi C, Kasahara K, Tan C, Kuroda A, Minami K, et al. New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems. J Comput Chem 2021;42:231–41.
Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C, et al. Scalable open science approach for mutation calling of tumor exomes using multiple genomic pipelines. Cell Syst 2018;6:271–81.
Thein KZ, Velcheti V, Mooers BHM, Wu J, Subbiah V. Precision therapy for RET-altered cancers with RET inhibitors. Trends Cancer 2021;7:1074–88.
Kohno T, Tabata J, Nakaoku T. REToma: a cancer subtype with a shared driver
oncogene. Carcinogenesis 2020;41:123–9.
Kohsaka S, Nagano M, Ueno T, Suehara Y, Hayashi T, Shimada N, et al. A method of high-throughput functional evaluation of EGFR gene variants of unknown significance in cancer. Sci Transl Med 2017;9:eaan6566.
Tabata et al.
Jacobson MP, Friesner RA, Xiang Z, Honig B. On the role of the crystal environment in determining protein side-chain conformations. J Mol Biol 2002;320:597–608.
Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, et al. A hierarchical approach to all-atom protein loop prediction. Proteins 2004;55: 351–67.
Li H, Robertson AD, Jensen JH. Very fast empirical prediction and rationali- zation of protein pKa values. Proteins 2005;61:704–21.
Roos K, Wu C, Damm W, Reboul M, Stevenson JM, Lu C, et al. OPLS3e: extending force field coverage for drug-like small molecules. J Chem Theory Comput 2019;15:1863–74.
Berendsen HJC, Grigera JR, Straatsma TP. The missing term in effective pair potentials. J Phys Chem 1987;91:6269–71.
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000;33:889–97.
Abraham MJ, Murtola T, Schulz R, P´all S, Smith JC, Hess B, et al. GROMACS: high-performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 2015;1–2:19–25.
Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 2010;78:1950–8.
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79: 926–35.
Darden T, York D, Pedersen L. Particle mesh Ewald: an Ns_log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089–92.
Feenstra KA, Hess B, Berendsen HJC. Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J Comput Chem 1999;20:786–98.
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM. LINCS: a linear constraint solver for molecular simulations. J Comput Chem 1997;18:1463–72.
Bussi G, Donadio D, Parrinello M. Canonical sampling through velocity rescaling. J Chem Phys 2007;126:014101.
Parrinello M, Rahman A. Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys 1981;52:7182–90.
Doerr S, Harvey MJ, No´e F, De Fabritiis G. HTMD: high-throughput molecular dynamics for molecular discovery. J Chem Theory Comput 2016;12:1845–52.
AACR Project GENIE Consortium. AACR project GENIE: powering precision medicine through an international consortium. Cancer Discov 2017;7:818–31.
Chakravarty D, Gao J, Phillips SM, Kundra R, Zhang H, Wang J, et al. OncoKB: a precision oncology knowledge base. JCO Precis Oncol 2017;2017:PO.17.00011.
Wang K, Holt C, Lu J, Brohus M, Larsen KT, Overgaard MT, et al. Arrhythmia mutations in calmodulin cause conformational changes that affect interactions with the cardiac voltage-gated calcium channel. Proc Natl Acad Sci U S A 2018; 115:E10556–E65.
Priori SG, Napolitano C, Memmi M, Colombi B, Drago F, Gasparini M, et al. Clinical and molecular characterization of patients with catecholaminergic polymorphic ventricular tachycardia. Circulation 2002;106:69–74.
Bigalke JM, Aibara S, Roth R, Dahl G, Gordon E, Dorbeus S, et al. Cryo-EM structure of the activated RET signaling complex reveals the importance of its cysteine-rich domain. Sci Adv 2019;5:eaau4202.
Dixon AS, Schwinn MK, Hall MP, Zimmerman K, Otto P, Lubben TH, et al. NanoLuc complementation reporter optimized for accurate measurement of protein interactions in cells. ACS Chem Biol 2016;11:400–8.
Subbiah V, Yang D, Velcheti V, Drilon A, Meric-Bernstam F. State-of- the-art strategies for targeting RET-dependent cancers. J Clin Oncol 2020; 38:1209–21.
Kohno T, Ichikawa H, Totoki Y, Yasuda K, Hiramoto M, Nammo T, et al. KIF5B-RET fusions in lung adenocarcinoma. Nat Med 2012;18:375–7.
Gainor JF, Curigliano G, Kim DW, Lee DH, Besse B, Baik CS, et al. Pralsetinib for RET fusion-positive non-small-cell lung cancer (ARROW): a multi-cohort, open-label, phase 1/2 study. Lancet Oncol 2021;22:959–69.
Drilon A, Oxnard GR, Tan DSW, Loong HHF, Johnson M, Gainor J, et al. Efficacy of selpercatinib in RET fusion-positive non-small-cell lung cancer. N Engl J Med 2020;383:813–24.
Rich TA, Reckamp KL, Chae YK, Doebele RC, Iams WT, Oh MS, et al. Analysis of cell-free DNA from 32,989 advanced cancers reveals novel co-occurring activating RET alterations and oncogenic signaling pathway aberrations. Clin Cancer Res 2019;25:5832–42.
Watanabe S, Takeda M, Otani T, Yoshida T, Sakai K, Olek E, et al. Complete response to selective RET inhibition with selpercatinib (LOXO-292) in a patient with RET fusion-positive breast cancer. JCO Precis Oncol 2021;5: PO.20.00282.
Tsui DCC, Kavanagh BD, Honce JM, Rossi C, Patil T, Camidge DR. Central nervous system response to selpercartinib in patient with RET-rearranged non- small cell lung cancer after developing leptomeningeal disease on pralsetinib. Clin Lung Cancer 2021;23:e5–e8.
Ortiz MV, Gerdemann U, Raju SG, Henry D, Smith S, Rothenberg SM, et al. Activity of the highly specific RET inhibitor selpercatinib (LOXO-292) in pediatric patients with tumors harboring RET gene alterations. JCO Precis Oncol 2020;4:PO.19.00401.
Yoshizawa T, Uchibori K, Araki M, Matsumoto S, Ma B, Kanada R, et al. Microsecond-timescale MD simulation of EGFR minor mutation predicts the structural flexibility of EGFR kinase core that reflects EGFR inhibitor sensitivity. NPJ Precis Oncol 2021;5:32.
Assadollahi V, Rashidieh B, Alasvand M, Abdolahi A, Lopez JA. Interaction and molecular dynamics simulation study of Osimertinib (AstraZeneca 9291) anti- cancer drug with the EGFR kinase domain in native protein and mutated L844V and C797S. J Cell Biochem 2019;120:13046–55.
Zabriskie MS, Eide CA, Tantravahi SK, Vellore NA, Estrada J, Nicolini FE, et al. BCR-ABL1 compound mutations combining key kinase domain positions confer clinical resistance to ponatinib in Ph chromosome-positive leukemia. Cancer Cell 2014;26:428–42.
Eide CA, Zabriskie MS, Savage Stevens SL, Antelope O, Vellore NA, Than H, et al. Combining the allosteric inhibitor asciminib with ponatinib suppresses emer- gence of and restores efficacy against highly resistant BCR-ABL1 mutants. Cancer Cell 2019;36:431–43.
Nakaoku T, Kohno T, Araki M, Niho S, Chauhan R, Knowles PP, et al. A secondary RET mutation in the activation loop conferring resistance to vande- tanib. Nat Commun 2018;9:625.
Lourenco C, Resetca D, Redel C, Lin P, MacDonald AS, Ciaccio R, et al. MYC protein interactors in gene transcription and cancer. Nat Rev Cancer 2021;21: 579–91.
論文の公開元へ
