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Petrini I, Bruno R, Di Stefano I, Aprile V, Korasidis S, Pardini E, Chella A, Alì G. A patient with a Germline (p.R776H) EGFR Mutation With Multiple Lung Cancers Harboring Different Somatic EGFR Mutations. Clin Lung Cancer 2024; 25:e238-e242. [PMID: 38729783 DOI: 10.1016/j.cllc.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 05/12/2024]
Affiliation(s)
- Iacopo Petrini
- Unit of Medical Oncology, Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Rossella Bruno
- Unit of Pathological Anatomy, University Hospital of Pisa, 56125 Pisa, Italy
| | - Iosè Di Stefano
- Department of Surgical, Medical, and Molecular Pathology and Critical Care Medicine, University of Pisa, 56126 Pisa, Italy
| | - Vittorio Aprile
- Unit of Thoracic Surgery, University Hospital of Pisa, 56125 Pisa, Italy
| | | | - Eleonora Pardini
- Unit of Medical Oncology, Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Antonio Chella
- Unit of Pneumology, University Hospital of Pisa, 56125 Pisa, Italy
| | - Greta Alì
- Department of Surgical, Medical, and Molecular Pathology and Critical Care Medicine, University of Pisa, 56126 Pisa, Italy.
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Wang Y, Hu C, Yu H, Hu J, Zhou Z, Fu N, Huang X, Kong F, Wang W, Liu J. Insensitivity of oncogenic EGFR R776L mutation to EGFR inhibitors in lung cancer. Lung Cancer 2024; 189:107495. [PMID: 38335691 DOI: 10.1016/j.lungcan.2024.107495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/09/2023] [Accepted: 01/27/2024] [Indexed: 02/12/2024]
Abstract
Non-small cell lung cancers (NSCLC) account for 85 % of total lung cancers. Mutation in EGFRdrives the progress of NSCLSs with high mortality rate. Besides the common mutations in EGFR, which together comprise of 85 % of all EGFR mutations and respond to the targeted therapy of EGFR tyrosine kinase inhibitors (TKIs), many other low-frequency mutations of EGFR are existed in patients. The oncogenic roles and sensitivity of these mutations to EGFR TKIs are not fully understood yet. Here we described two cases of lung adenocarcinoma patients harboring EGFR R776L missense mutation, showed PD and SD after treatment with third-generation EGFR inhibitor, Almonertinib. Chemotherapy afterward showed PR effect in one patient with PSF of 10 months. We also explored the oncogenic feature of single R776L mutation by Ba/F3 isogenic cells and found that, EGFR R776L mutation activates EGFR-related survival signaling pathway in Ba/F3 cells, and they are insensitive to gefitinib, afatinib, and Almonertinib, which consistent with our clinical observation.
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Affiliation(s)
- Yun Wang
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China
| | - Chen Hu
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China; Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China
| | - Hongwei Yu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Jie Hu
- University of Science and Technology of China, Hefei, Anhui 230026, PR China; Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui 230088, PR China
| | - Zhiwei Zhou
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China
| | - Ning Fu
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China
| | - Xiang Huang
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China
| | - Fanhao Kong
- The Experimental High School Attached to Beijing Normal University, Beijing, PR China
| | - Wenchao Wang
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China; Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230026, PR China.
| | - Jing Liu
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China; Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230026, PR China.
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Soleymani S, Gravel N, Huang LC, Yeung W, Bozorgi E, Bendzunas NG, Kochut KJ, Kannan N. Dark kinase annotation, mining, and visualization using the Protein Kinase Ontology. PeerJ 2023; 11:e16087. [PMID: 38077442 PMCID: PMC10704995 DOI: 10.7717/peerj.16087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/22/2023] [Indexed: 12/18/2023] Open
Abstract
The Protein Kinase Ontology (ProKinO) is an integrated knowledge graph that conceptualizes the complex relationships among protein kinase sequence, structure, function, and disease in a human and machine-readable format. In this study, we have significantly expanded ProKinO by incorporating additional data on expression patterns and drug interactions. Furthermore, we have developed a completely new browser from the ground up to render the knowledge graph visible and interactive on the web. We have enriched ProKinO with new classes and relationships that capture information on kinase ligand binding sites, expression patterns, and functional features. These additions extend ProKinO's capabilities as a discovery tool, enabling it to uncover novel insights about understudied members of the protein kinase family. We next demonstrate the application of ProKinO. Specifically, through graph mining and aggregate SPARQL queries, we identify the p21-activated protein kinase 5 (PAK5) as one of the most frequently mutated dark kinases in human cancers with abnormal expression in multiple cancers, including a previously unappreciated role in acute myeloid leukemia. We have identified recurrent oncogenic mutations in the PAK5 activation loop predicted to alter substrate binding and phosphorylation. Additionally, we have identified common ligand/drug binding residues in PAK family kinases, underscoring ProKinO's potential application in drug discovery. The updated ontology browser and the addition of a web component, ProtVista, which enables interactive mining of kinase sequence annotations in 3D structures and Alphafold models, provide a valuable resource for the signaling community. The updated ProKinO database is accessible at https://prokino.uga.edu.
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Affiliation(s)
- Saber Soleymani
- Department of Computer Science, University of Georgia, Athens, GA, United States
| | - Nathan Gravel
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Liang-Chin Huang
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Elika Bozorgi
- Department of Computer Science, University of Georgia, Athens, GA, United States
| | - Nathaniel G. Bendzunas
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Krzysztof J. Kochut
- Department of Computer Science, University of Georgia, Athens, GA, United States
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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Wu Z, Wang Y, Jin L, Wei J, Han L, Su J, Cao S, Liu S, Duan X, Zhao X. Case report: identification of EGFR R776H and FANCE R381H germline mutations in a patient with multiple pulmonary nodules. J Cancer Res Clin Oncol 2023; 149:921-927. [PMID: 36163560 DOI: 10.1007/s00432-022-04290-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/14/2022] [Indexed: 11/30/2022]
Abstract
Pulmonary nodules evaluation is clinically crucial because they may be the early predictors of lung cancer. Except for CT screening and serum tumor biomarkers testing, genetic alteration analysis by next-generation sequencing (NGS) technology can also help to find cancer earlier. In this study, we report a case of multiple pulmonary nodules patient with EGFR R776H and FANCE R381H germline mutations. Her father, paternal aunt, and elder uncle harbored either one or both two mutations and were found with multiple pulmonary ground-glass or sub-solid nodules. Her 7-year-old daughter also inherited the same two mutations.
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Affiliation(s)
- Zhenzhen Wu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanli Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Linling Jin
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Juan Wei
- Department of Respiratory Medicine, Jiangsu Suining People's Hospital, Xuzhou, China
| | - Li Han
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, China
| | - Junyan Su
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, China
| | - Shuliang Cao
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, China
| | - Siyao Liu
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, China
| | - Xiaohong Duan
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, China.
| | - Xin Zhao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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Li D, Liu X, Cui S, Yang D, Zhu Y, Pan E, Yang P, Dai Z. A Primary Lung and Breast Cancer Patient with Germline EGFR R776H Mutation: A Case Report and Literature Review. Onco Targets Ther 2023; 16:17-22. [PMID: 36698436 PMCID: PMC9868143 DOI: 10.2147/ott.s391766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023] Open
Abstract
For advanced non-small cell lung cancer (NSCLC) patients with common epidermal growth factor receptor (EGFR) mutations (exon 19 deletions or the exon 21 L858R mutation), tyrosine kinase inhibitors (TKIs) are the standard therapies. However, EGFR germline mutations are extremely rare in lung cancer, and the effective therapy is unclear. This study reports a patient with primary breast and lung cancer carried rare germline EGFR R776H and somatic L861Q mutation, who benefit from EGFR TKIs. Her family cancer history review demonstrated that her three out of four sisters with lung cancer were positive for EGFR R776H. Interestingly, only her healthy sister had type O blood, different from other sisters with type B blood. Our study provides a meaningful insight into the potential treatment option for patients with germline EGFR R776H and somatic L861Q mutation and highlights the importance of next-generation sequencing (NGS) in discovering rare genetic alterations to guide the prevention of genetic disease.
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Affiliation(s)
- Dan Li
- The Second Department of Thoracic Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
| | - Xin Liu
- The Second Department of Thoracic Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
| | - SaiQiong Cui
- The Second Department of Thoracic Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
| | - DaFu Yang
- The Second Department of Thoracic Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
| | - Yue Zhu
- The Second Department of Thoracic Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China
| | - Evenki Pan
- Nanjing Geneseeq Technology Inc., Nanjing, People’s Republic of China
| | - Peng Yang
- Nanjing Geneseeq Technology Inc., Nanjing, People’s Republic of China
| | - ZhaoXia Dai
- The Second Department of Thoracic Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, People’s Republic of China,Correspondence: ZhaoXia Dai, The Second Department of Thoracic Medical Oncology, The Second Hospital of Dalian Medical University, No. 467, Zhongshan Road, Shahekou District, Dalian, People’s Republic of China, Email
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Ko HW, Shie SS, Wang CW, Chiu CT, Wang CL, Yang TY, Chou SC, Liu CY, Kuo CHS, Lin YC, Li LF, Yang CT, Wang CC. Association of smoking status with non-small cell lung cancer patients harboring uncommon epidermal growth factor receptor mutation. Front Immunol 2022; 13:1011092. [PMID: 36341427 PMCID: PMC9632177 DOI: 10.3389/fimmu.2022.1011092] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/05/2022] [Indexed: 09/10/2023] Open
Abstract
INTRODUCTION Uncommon epidermal growth factor receptor (EGFR) mutations include single and complex mutations. However, the association of the smoking status of patients with uncommon and complex EGFR mutations remains unclear. METHODS This retrospective study evaluates the spectrum of uncommon EGFR mutations and investigates the influence of smoking status on the frequency of various uncommon EGFR mutations using a multi-institutional medical database. RESULTS Between 2010 and 2019, 5,608 non-small cell lung cancer (NSCLC) patients were analyzed. EGFR mutations were detected in 3,155 (56.3%) patients. Among the 399 (12.6%) patients with uncommon mutations, 198 had single uncommon and 201 complex mutations, including 87 exon 20 insertions, 79 de novo T790M, 70 complex common, and 52 complex uncommon mutations. For comparison, we also included 402 patients with common EGFR mutations. The percentage of ever-smokers was significantly higher in patients with uncommon EGFR mutations than in patients with common EGFR mutations (25.8% vs. 17.4%, p = 0.005). Furthermore, the percentage of ever-smokers was higher in those with a complex mutation than in those with a single uncommon mutation (30.3% vs. 21.2%, p = 0.040). Among patients carrying uncommon EGFR mutations, ever-smokers had significantly more complex uncommon EGFR mutations than never-smokers (22.3% vs. 9.8%, p = 0.002). Among patients carrying G719X, L861Q, and S768I, ever-smokers tended to have complex EGFR mutations more frequently than never-smokers (64.7% vs. 28.7%, 50.0% vs. 18.7%, 88.9% vs. 81.2%, respectively). CONCLUSIONS Our study demonstrates not only a comprehensive spectrum of uncommon EGFR mutations, but also a positive relationship between smoking status and uncommon EGFR mutation frequency, especially complex uncommon EGFR mutations. The results suggest that smoking contributes to the development of complex EGFR mutations.
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Affiliation(s)
- How-Wen Ko
- Division of Thoracic Oncology, Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shian-Sen Shie
- Department of Internal Medicine, Linkou Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Wei Wang
- Department of Pathology, Linkou Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chi-Tsun Chiu
- Institute of European and American Studies, Academia Sinica, Taipei, Taiwan
| | - Chih-Liang Wang
- Division of Thoracic Oncology, Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tsung-Ying Yang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shou-Chu Chou
- Department of Family Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Chien-Ying Liu
- Division of Thoracic Oncology, Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Hsi Scott Kuo
- Division of Thoracic Oncology, Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Thoracic Medicine, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Yu-Ching Lin
- Department of Pulmonary and Critical Care Medicine, Chiayi Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Puzi, Taiwan
| | - Li-Fu Li
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Keelung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Keelung, Taiwan
| | - Cheng-Ta Yang
- Division of Thoracic Oncology, Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Thoracic Medicine, Taoyuan Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Respiratory Therapy, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chin-Chou Wang
- Divisions of Pulmonary & Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung, Taiwan
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Sovich JL, Dan T, Gemmell A, Clark C, Gagan J, Dowell JE. Lung Adenocarcinoma Associated With Germline EGFR R776H Variant: A Case Report and Review of the Literature. JCO Precis Oncol 2022; 6:e2100559. [PMID: 35862867 DOI: 10.1200/po.21.00559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Justin Lin Sovich
- Department of Hematology & Oncology, University of Texas Southwestern, Dallas, TX.,Parkland Health and Hospital System, Dallas, TX
| | - Tu Dan
- Department of Radiation Oncology, University of Texas Southwestern, Dallas, TX
| | - Amber Gemmell
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern, Dallas, TX
| | - Cheyla Clark
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern, Dallas, TX
| | - Jeffrey Gagan
- Department of Pathology, University of Texas Southwestern, Dallas, TX
| | - Jonathan E Dowell
- Department of Hematology & Oncology, University of Texas Southwestern, Dallas, TX.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern, Dallas, TX
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Novel potential oncogenic and druggable mutations of FGFRs recur in the kinase domain across cancer types. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166313. [PMID: 34826586 DOI: 10.1016/j.bbadis.2021.166313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022]
Abstract
Fibroblast growth factor receptors (FGFRs) are recurrently altered by single nucleotide variants (SNVs) in many human cancers. The prevalence of SNVs in FGFRs depends on the cancer type. In some tumors, such as the urothelial carcinoma, mutations of FGFRs occur at very high frequency (up to 60%). Many characterized mutations occur in the extracellular or transmembrane domains, while fewer known mutations are found in the kinase domain. In this study, we performed a bioinformatics analysis to identify novel putative cancer driver or therapeutically actionable mutations of the kinase domain of FGFRs. To pinpoint those mutations that may be clinically relevant, we exploited the recurrence of alterations on analogous amino acid residues within the kinase domain (PK_Tyr_Ser-Thr) of different kinases as a predictor of functional impact. By exploiting MutationAligner and LowMACA bioinformatics resources, we highlighted novel uncharacterized mutations of FGFRs which recur in other protein kinases. By revealing unanticipated correspondence with known variants, we were able to infer their functional effects, as alterations clustering on similar residues in analogous proteins have a high probability to elicit similar effects. As FGFRs represent an important class of oncogenes and drug targets, our study opens the way for further studies to validate their driver and/or actionable nature and, in the long term, for a more efficacious application of precision oncology.
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Guo T, Zhu L, Li W, Lin R, Ding Y, Kang Q, Shao L, Li C, Pan X. Two cases of non-small cell lung cancer patients with somatic or germline EGFR R776H mutation. Lung Cancer 2021; 161:94-97. [PMID: 34555730 DOI: 10.1016/j.lungcan.2021.05.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/28/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022]
Abstract
The development of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) has revolutionized the treatment for non-small cell lung cancer (NSCLC). Comprehensive genomic profiling for NSCLC enables clinicians to identify more uncommon genetic alterations in EGFR. It remains unclear whether patients with certain rare EGFR mutations can benefit from EGFR inhibitors. On the other hand, emerging evidence has also showed the involvement of inherited factors in lung cancer development. However, only few germline EGFR mutations have been reported, and their association with NSCLC familial risk remains ambiguous. Here, we report two cases of NSCLCs with uncommon EGFR mutation R776H. One patient carrying somatic EGFR R776H and L861Q was treated with afatinib and achieved a durable response. The other patient harbored a germline EGFR R776H and her son inherited the same germline R776H mutation whose CT examination showed multiple ground-glass nodules in both lungs requiring further follow-up and diagnosis. Our study demonstrated the responsiveness of compound R776H-L861Q mutations to afatinib. We also revealed the transmission of EGFR R776H and suggested it may confer the high susceptibility to lung cancer.
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Affiliation(s)
- Tianxing Guo
- Department of Thoracic Surgery, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian Province, 350001
| | - Lihuan Zhu
- Department of Thoracic Surgery, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian Province, 350001
| | - Wujin Li
- Department of Thoracic Surgery, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian Province, 350001
| | - Rongjia Lin
- Department of Thoracic Surgery, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian Province, 350001
| | - Yun Ding
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian Province, 350001
| | | | - Lin Shao
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Chanhe Li
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Xiaojie Pan
- Department of Thoracic Surgery, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian Province, 350001.
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Galdadas I, Carlino L, Ward RA, Hughes SJ, Haider S, Gervasio FL. Structural basis of the effect of activating mutations on the EGF receptor. eLife 2021; 10:e65824. [PMID: 34319231 PMCID: PMC8318590 DOI: 10.7554/elife.65824] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 07/05/2021] [Indexed: 01/03/2023] Open
Abstract
Mutations within the kinase domain of the epidermal growth factor receptor (EGFR) are common oncogenic driver events in non-small cell lung cancer. Although the activation of EGFR in normal cells is primarily driven by growth-factor-binding-induced dimerization, mutations on different exons of the kinase domain of the receptor have been found to affect the equilibrium between its active and inactive conformations giving rise to growth-factor-independent kinase activation. Using molecular dynamics simulations combined with enhanced sampling techniques, we compare here the conformational landscape of the monomers and homodimers of the wild-type and mutated forms of EGFR ΔELREA and L858R, as well as of two exon 20 insertions, D770-N771insNPG, and A763-Y764insFQEA. The differences in the conformational energy landscapes are consistent with multiple mechanisms of action including the regulation of the hinge motion, the stabilization of the dimeric interface, and local unfolding transitions. Overall, a combination of different effects is caused by the mutations and leads to the observed aberrant signaling.
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Affiliation(s)
- Ioannis Galdadas
- Department of Chemistry, University College LondonLondonUnited Kingdom
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
| | - Luca Carlino
- Oncology R&D, AstraZenecaCambridgeUnited Kingdom
| | | | | | - Shozeb Haider
- UCL School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Francesco Luigi Gervasio
- Department of Chemistry, University College LondonLondonUnited Kingdom
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
- Institute of Structural and Molecular Biology, University College LondonLondonUnited Kingdom
- Pharmaceutical Sciences, University of GenevaGenevaSwitzerland
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11
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Tamirat MZ, Kurppa KJ, Elenius K, Johnson MS. Structural Basis for the Functional Changes by EGFR Exon 20 Insertion Mutations. Cancers (Basel) 2021; 13:1120. [PMID: 33807850 PMCID: PMC7961794 DOI: 10.3390/cancers13051120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 11/21/2022] Open
Abstract
Activating somatic mutations of the epidermal growth factor receptor (EGFR) are frequently implicated in non-small cell lung cancer (NSCLC). While L858R and exon 19 deletion mutations are most prevalent, exon 20 insertions are often observed in NSCLC. Here, we investigated the structural implications of two common EGFR exon 20 insertions in NSCLC, V769insASV and D770insNPG. The active and inactive conformations of wild-type, D770insNPG and V769insASV EGFRs were probed with molecular dynamics simulations to identify local and global alterations that the mutations exert on the EGFR kinase domain, highlighting mechanisms for increased enzymatic activity. In the active conformation, the mutations increase interactions that stabilize the αC helix that is essential for EGFR activity. Moreover, the key Lys745-Glu762 salt bridge was more conserved in the insertion mutations. The mutants also preserved the state of the structurally critical aspartate-phenylalanine-glycine (DFG)-motif and regulatory spine (R-spine), which were altered in wild-type EGFR. The insertions altered the structure near the ATP-binding pocket, e.g., the P-loop, which may be a factor for the clinically observed tyrosine kinase inhibitor (TKI) insensitivity by the insertion mutants. The inactive state simulations also showed that the insertions disrupt the Ala767-Arg776 interaction that is key for maintaining the "αC-out" inactive conformation, which could consequently fuel the transition from the inactive towards the active EGFR state.
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Affiliation(s)
- Mahlet Z. Tamirat
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
| | - Kari J. Kurppa
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20520 Turku, Finland; (K.J.K.); (K.E.)
| | - Klaus Elenius
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20520 Turku, Finland; (K.J.K.); (K.E.)
- Department of Oncology, Turku University Hospital, 20521 Turku, Finland
- Turku Bioscience Center, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
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Yeung W, Ruan Z, Kannan N. Emerging roles of the αC-β4 loop in protein kinase structure, function, evolution, and disease. IUBMB Life 2020; 72:1189-1202. [PMID: 32101380 DOI: 10.1002/iub.2253] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/07/2020] [Indexed: 12/11/2022]
Abstract
The faithful propagation of cellular signals in most organisms relies on the coordinated functions of a large family of protein kinases that share a conserved catalytic domain. The catalytic domain is a dynamic scaffold that undergoes large conformational changes upon activation. Most of these conformational changes, such as movement of the regulatory αC-helix from an "out" to "in" conformation, hinge on a conserved, but understudied, loop termed the αC-β4 loop, which mediates conserved interactions to tether flexible structural elements to the kinase core. We previously showed that the αC-β4 loop is a unique feature of eukaryotic protein kinases. Here, we review the emerging roles of this loop in kinase structure, function, regulation, and diseases. Through a kinome-wide analysis, we define the boundaries of the loop for the first time and show that sequence and structural variation in the loop correlate with conformational and regulatory variation. Many recurrent disease mutations map to the αC-β4 loop and contribute to drug resistance and abnormal kinase activation by relieving key auto-inhibitory interactions associated with αC-helix and inter-lobe movement. The αC-β4 loop is a hotspot for post-translational modifications, protein-protein interaction, and Hsp90 mediated folding. Our kinome-wide analysis provides insights for hypothesis-driven characterization of understudied kinases and the development of allosteric protein kinase inhibitors.
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Affiliation(s)
- Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia.,Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia
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13
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Rutkowska A, Stoczyńska-Fidelus E, Janik K, Włodarczyk A, Rieske P. EGFR vIII: An Oncogene with Ambiguous Role. JOURNAL OF ONCOLOGY 2019; 2019:1092587. [PMID: 32089685 PMCID: PMC7024087 DOI: 10.1155/2019/1092587] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/22/2019] [Indexed: 12/21/2022]
Abstract
Epidermal growth factor receptor variant III (EGFRvIII) seems to constitute the perfect therapeutic target for glioblastoma (GB), as it is specifically present on up to 28-30% of GB cells. In case of other tumor types, expression and possible role of this oncogene still remain controversial. In spite of EGFRvIII mechanism of action being crucial for the design of small active anticancer molecules and immunotherapies, i.e., CAR-T technology, it is yet to be precisely defined. EGFRvIII is known to be resistant to degradation, but it is still unclear whether it heterodimerizes with EGF-activated wild-type EGFR (EGFRWT) or homodimerizes (including covalent homodimerization). Constitutive kinase activity of this mutated receptor is relatively low, and some researchers even claim that a nuclear, but not a membrane function, is crucial for its activity. Based on the analyses of recurrent tumors that are often lacking EGFRvIII expression despite its initial presence in corresponding primary foci, this oncogene is suggested to play a marginal role during later stages of carcinogenesis, while even in primary tumors EGFRvIII expression is detected only in a small percentage of tumor cells, undermining the rationality of EGFRvIII-targeting therapies. On the other hand, EGFRvIII-positive cells are resistant to apoptosis, more invasive, and characterized with enhanced proliferation rate. Moreover, expression of this oncogenic receptor was also postulated to be a marker of cancer stem cells. Opinions regarding the role that EGFRvIII plays in tumorigenesis and for tumor aggressiveness are clearly contradictory and, therefore, it is crucial not only to determine its mechanism of action, but also to unambiguously define its role at early and advanced cancer stages.
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Affiliation(s)
- Adrianna Rutkowska
- Department of Tumor Biology, Medical University of Lodz, Zeligowskiego 7/9, 90-752 Lodz, Poland
| | - Ewelina Stoczyńska-Fidelus
- Department of Tumor Biology, Medical University of Lodz, Zeligowskiego 7/9, 90-752 Lodz, Poland
- Department of Research and Development, Celther Polska Ltd., Milionowa 23, 93-193 Lodz, Poland
- Department of Research and Development, Personather Ltd., Milionowa 23, 93-193 Lodz, Poland
| | - Karolina Janik
- Department of Tumor Biology, Medical University of Lodz, Zeligowskiego 7/9, 90-752 Lodz, Poland
| | - Aneta Włodarczyk
- Department of Tumor Biology, Medical University of Lodz, Zeligowskiego 7/9, 90-752 Lodz, Poland
| | - Piotr Rieske
- Department of Tumor Biology, Medical University of Lodz, Zeligowskiego 7/9, 90-752 Lodz, Poland
- Department of Research and Development, Celther Polska Ltd., Milionowa 23, 93-193 Lodz, Poland
- Department of Research and Development, Personather Ltd., Milionowa 23, 93-193 Lodz, Poland
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14
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Rich TA, Reckamp KL, Chae YK, Doebele RC, Iams WT, Oh M, Raymond VM, Lanman RB, Riess JW, Stinchcombe TE, Subbiah V, Trevarthen DR, Fairclough S, Yen J, Gautschi O. 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; 25:5832-5842. [PMID: 31300450 DOI: 10.1158/1078-0432.ccr-18-4049] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 05/06/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
PURPOSE RET is an emerging oncogenic target showing promise in phase I/II clinical trials. An understudied aspect of RET-driven cancers is the extent to which co-occurring genomic alterations exist and how they may impact prognosis or therapeutic response. EXPERIMENTAL DESIGN Somatic activating RET alterations were identified among 32,989 consecutive patients with metastatic solid tumors tested with a clinical cell-free circulating tumor DNA (cfDNA) assay. This comprehensive next-generation sequencing (NGS) assay evaluates single-nucleotide variants, and select indels, fusions, and copy number gains in 68-73 clinically relevant cancer genes. RESULTS A total of 176 somatic activating RET alterations were detected in 170 patients (143 fusions and 33 missense mutations). Patients had non-small cell lung (NSCLC, n = 125), colorectal (n = 15), breast (n = 8), thyroid (n = 8), or other (n = 14) cancers. Alterations in other oncogenic signaling pathway genes were frequently identified in RET-positive samples and varied by specific RET fusion gene partner. RET fusions involving partners other than KIF5B were enriched for alterations in MAPK pathway genes and other bona fide oncogenic drivers of NSCLC, particularly EGFR. Molecular and clinical data revealed that these variants emerged later in the genomic evolution of the tumor as mechanisms of resistance to EGFR tyrosine kinase inhibitors. CONCLUSIONS In the largest cancer cohort with somatic activating RET alterations, we describe novel co-occurrences of oncogenic signaling pathway aberrations. We find that KIF5B-RET fusions are highly specific for NSCLC. In our study, only non-KIF5B-RET fusions contributed to anti-EGFR therapy resistance. Knowledge of specific RET fusion gene partner may have clinical significance.
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Affiliation(s)
| | - Karen L Reckamp
- Department of Medical Oncology & Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Young Kwang Chae
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Robert C Doebele
- Medical Oncology/Department of Medicine, University of Colorado Cancer Center, Aurora, Colorado
| | - Wade T Iams
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Michael Oh
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | | | | | - Jonathan W Riess
- Division of Hematology/Oncology, University of California Davis Comprehensive Cancer Center, Sacramento, California
| | | | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David R Trevarthen
- Department of Hematology/Oncology, Comprehensive Cancer Care and Research Institute of Colorado, Englewood, Colorado
| | | | | | - Oliver Gautschi
- University of Berne and Department of Medicine, Cantonal Hospital Lucerne, Lucerne, Switzerland
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15
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Oscorbin IP, Shadrina AS, Kozlov VV, Voitsitsky VE, Filipenko ML. Absence of EGFR C797S Mutation in Tyrosine Kinase Inhibitor-Naïve Non-Small Cell Lung Cancer Tissues. Pathol Oncol Res 2019; 26:1229-1234. [PMID: 31243697 DOI: 10.1007/s12253-019-00683-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/05/2019] [Indexed: 01/03/2023]
Abstract
EGFR tyrosine-kinase inhibitors (TKIs) are used as targeted therapeutics for the treatment of advanced non-small cell lung cancer (NSCLC) with EGFR-activating mutations. EGFR C797S is common causes of acquired resistance to third-generation TKIs. There is wide-spread opinion that resistance-conferring mutation present even in a small proportion of cancer cells before the start of therapy could potentially predict poor response to a targeted drug. In our study, we tested whether C797S can be found in previously untreated NSCLCs. We analyzed DNA samples extracted from formalin-fixed paraffin-embedded (FFPE) tumor tissue sections of 470 lung adenocarcinoma patients, including 235 samples with activating EGFR mutations. Screening was performed using highly sensitive droplet digital PCR assay. No tumor samples with baseline C797S were identified. C797S does not occur in TKI-naïve NSCLCs and provide evidence that screening for this mutation before TKIs administration may not be necessary.
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Affiliation(s)
- Igor P Oscorbin
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentiev Avenue, Novosibirsk, 630090, Russia. .,Novosibirsk State University, 2 Pirogova Street, Novosibirsk, 630090, Russia.
| | - Alexandra S Shadrina
- Novosibirsk State University, 2 Pirogova Street, Novosibirsk, 630090, Russia.,Institute of Cytology and Genetics, 10 Lavrentiev Avenue, Novosibirsk, 630090, Russia
| | - Vadim V Kozlov
- Institute of Cytology and Genetics, 10 Lavrentiev Avenue, Novosibirsk, 630090, Russia.,Novosibirsk Regional Clinical Oncological Center, 2 Plakhotnogo Street, Novosibirsk, 630108, Russia
| | - Vladimir E Voitsitsky
- Institute of Cytology and Genetics, 10 Lavrentiev Avenue, Novosibirsk, 630090, Russia.,Novosibirsk Regional Clinical Oncological Center, 2 Plakhotnogo Street, Novosibirsk, 630108, Russia
| | - Maxim L Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentiev Avenue, Novosibirsk, 630090, Russia.,Novosibirsk State University, 2 Pirogova Street, Novosibirsk, 630090, Russia
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16
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Altered conformational landscape and dimerization dependency underpins the activation of EGFR by αC- β4 loop insertion mutations. Proc Natl Acad Sci U S A 2018; 115:E8162-E8171. [PMID: 30104348 DOI: 10.1073/pnas.1803152115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mutational activation of epidermal growth factor receptor (EGFR) in human cancers involves both point mutations and complex mutations (insertions and deletions). In particular, short in-frame insertion mutations within a conserved αC-β4 loop in the EGFR kinase domain are frequently observed in tumor samples and patients harboring these mutations are insensitive to first-generation EGFR inhibitors. Despite the prevalence and clinical relevance of insertion mutations, the mechanisms by which these mutations regulate EGFR activity and contribute to drug sensitivity are poorly understood. Using cell-based mutation screening, we find that the precise location, length, and sequence of the inserted segment are critical for ligand-independent EGFR activation and downstream signaling. We identify three insertion mutations (N771_P772insN, D770_N771insG, and D770>GY) that activate EGFR in a unique way by relying more on the "acceptor" interface for kinase activation. Our drug inhibition studies indicate that these activating insertion mutations respond more favorably to osimertinib, a recently Food and Drug Administration-approved EGFR inhibitor for T790M-positive patients with lung cancer. Molecular dynamics simulations and umbrella sampling of WT and mutant EGFR suggest a model in which activating insertion mutations increase catalytic activity by relieving key autoinhibitory interactions associated with αC-helix movement and by lowering the transition free energy ([Formula: see text]) between active and inactive states. Our studies also identify a transition state sampled by activating insertion mutations that can be exploited in the design of mutant-selective EGFR inhibitors.
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17
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Sturm N, Tinivella A, Rastelli G. Exploration and Comparison of the Geometrical and Physicochemical Properties of an αC Allosteric Pocket in the Structural Kinome. J Chem Inf Model 2018; 58:1094-1103. [DOI: 10.1021/acs.jcim.7b00735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Noé Sturm
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Annachiara Tinivella
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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18
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Huang LC, Ross KE, Baffi TR, Drabkin H, Kochut KJ, Ruan Z, D'Eustachio P, McSkimming D, Arighi C, Chen C, Natale DA, Smith C, Gaudet P, Newton AC, Wu C, Kannan N. Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources. Sci Rep 2018; 8:6518. [PMID: 29695735 PMCID: PMC5916945 DOI: 10.1038/s41598-018-24457-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 03/23/2018] [Indexed: 11/09/2022] Open
Abstract
Many bioinformatics resources with unique perspectives on the protein landscape are currently available. However, generating new knowledge from these resources requires interoperable workflows that support cross-resource queries. In this study, we employ federated queries linking information from the Protein Kinase Ontology, iPTMnet, Protein Ontology, neXtProt, and the Mouse Genome Informatics to identify key knowledge gaps in the functional coverage of the human kinome and prioritize understudied kinases, cancer variants and post-translational modifications (PTMs) for functional studies. We identify 32 functional domains enriched in cancer variants and PTMs and generate mechanistic hypotheses on overlapping variant and PTM sites by aggregating information at the residue, protein, pathway and species level from these resources. We experimentally test the hypothesis that S768 phosphorylation in the C-helix of EGFR is inhibitory by showing that oncogenic variants altering S768 phosphorylation increase basal EGFR activity. In contrast, oncogenic variants altering conserved phosphorylation sites in the ‘hydrophobic motif’ of PKCβII (S660F and S660C) are loss-of-function in that they reduce kinase activity and enhance membrane translocation. Our studies provide a framework for integrative, consistent, and reproducible annotation of the cancer kinomes.
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Affiliation(s)
- Liang-Chin Huang
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Karen E Ross
- Protein Information Resource (PIR), Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA
| | - Timothy R Baffi
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Krzysztof J Kochut
- Department of Computer Science, University of Georgia, Athens, GA, 30602, USA
| | - Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Peter D'Eustachio
- Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY, 10016, USA
| | - Daniel McSkimming
- Genome, Environment, and Microbiome (GEM) Center of Excellence, University at Buffalo, Buffalo, NY, 14203, USA
| | - Cecilia Arighi
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Chuming Chen
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Darren A Natale
- Protein Information Resource (PIR), Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA
| | | | - Pascale Gaudet
- SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Alexandra C Newton
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Cathy Wu
- Protein Information Resource (PIR), Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
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19
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Su K, Gao S, Ying J, Zou S, He J. Sequencing a super multiple synchronous lung cancer reveals a novel variant in driver gene ARID1B. J Thorac Cardiovasc Surg 2018; 155:e185-e191. [PMID: 29576263 DOI: 10.1016/j.jtcvs.2018.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/19/2017] [Accepted: 01/07/2018] [Indexed: 10/17/2022]
Affiliation(s)
- Kai Su
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Shuangmei Zou
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China.
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20
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Zhou HX, Pang X. Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. Chem Rev 2018; 118:1691-1741. [PMID: 29319301 DOI: 10.1021/acs.chemrev.7b00305] [Citation(s) in RCA: 454] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago , Chicago, Illinois 60607, United States.,Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| | - Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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21
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White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL. Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Sci Signal 2017; 10:10/495/eaam9931. [PMID: 28874603 DOI: 10.1126/scisignal.aam9931] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The intracellular pH (pHi) of most cancers is constitutively higher than that of normal cells and enhances proliferation and cell survival. We found that increased pHi enabled the tumorigenic behaviors caused by somatic arginine-to-histidine mutations, which are frequent in cancer and confer pH sensing not seen with wild-type proteins. Experimentally raising the pHi increased the activity of R776H mutant epidermal growth factor receptor (EGFR-R776H), thereby increasing proliferation and causing transformation in fibroblasts. An Arg-to-Gly mutation did not confer these effects. Molecular dynamics simulations of EGFR suggested that decreased protonation of His776 at high pH causes conformational changes in the αC helix that may stabilize the active form of the kinase. An Arg-to-His, but not Arg-to-Lys, mutation in the transcription factor p53 (p53-R273H) decreased its transcriptional activity and attenuated the DNA damage response in fibroblasts and breast cancer cells with high pHi. Lowering pHi attenuated the tumorigenic effects of both EGFR-R776H and p53-R273H. Our data suggest that some somatic mutations may confer a fitness advantage to the higher pHi of cancer cells.
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Affiliation(s)
- Katharine A White
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nicolas B Strauli
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.,Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.
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22
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Activation of the EGF Receptor by Ligand Binding and Oncogenic Mutations: The "Rotation Model". Cells 2017; 6:cells6020013. [PMID: 28574446 PMCID: PMC5492017 DOI: 10.3390/cells6020013] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/17/2017] [Accepted: 05/31/2017] [Indexed: 01/17/2023] Open
Abstract
The epidermal growth factor receptor (EGFR) plays vital roles in cellular processes including cell proliferation, survival, motility, and differentiation. The dysregulated activation of the receptor is often implicated in human cancers. EGFR is synthesized as a single-pass transmembrane protein, which consists of an extracellular ligand-binding domain and an intracellular kinase domain separated by a single transmembrane domain. The receptor is activated by a variety of polypeptide ligands such as epidermal growth factor and transforming growth factor α. It has long been thought that EGFR is activated by ligand-induced dimerization of the receptor monomer, which brings intracellular kinase domains into close proximity for trans-autophosphorylation. An increasing number of diverse studies, however, demonstrate that EGFR is present as a pre-formed, yet inactive, dimer prior to ligand binding. Furthermore, recent progress in structural studies has provided insight into conformational changes during the activation of a pre-formed EGFR dimer. Upon ligand binding to the extracellular domain of EGFR, its transmembrane domains rotate or twist parallel to the plane of the cell membrane, resulting in the reorientation of the intracellular kinase domain dimer from a symmetric inactive configuration to an asymmetric active form (the “rotation model”). This model is also able to explain how oncogenic mutations activate the receptor in the absence of the ligand, without assuming that the mutations induce receptor dimerization. In this review, we discuss the mechanisms underlying the ligand-induced activation of the preformed EGFR dimer, as well as how oncogenic mutations constitutively activate the receptor dimer, based on the rotation model.
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23
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Martínez-Jiménez F, Overington JP, Al-Lazikani B, Marti-Renom MA. Rational design of non-resistant targeted cancer therapies. Sci Rep 2017; 7:46632. [PMID: 28436422 PMCID: PMC5402386 DOI: 10.1038/srep46632] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/22/2017] [Indexed: 12/29/2022] Open
Abstract
Drug resistance is one of the major problems in targeted cancer therapy. A major cause of resistance is changes in the amino acids that form the drug-target binding site. Despite of the numerous efforts made to individually understand and overcome these mutations, there is a lack of comprehensive analysis of the mutational landscape that can prospectively estimate drug-resistance mutations. Here we describe and computationally validate a framework that combines the cancer-specific likelihood with the resistance impact to enable the detection of single point mutations with the highest chance to be responsible of resistance to a particular targeted cancer therapy. Moreover, for these treatment-threatening mutations, the model proposes alternative therapies overcoming the resistance. We exemplified the applicability of the model using EGFR-gefitinib treatment for Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Cancer (LSCC) and the ERK2-VTX11e treatment for melanoma and colorectal cancer. Our model correctly identified the phenotype known resistance mutations, including the classic EGFR-T790M and the ERK2-P58L/S/T mutations. Moreover, the model predicted new previously undescribed mutations as potentially responsible of drug resistance. Finally, we provided a map of the predicted sensitivity of alternative ERK2 and EGFR inhibitors, with a particular highlight of two molecules with a low predicted resistance impact.
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Affiliation(s)
- Francisco Martínez-Jiménez
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - John P. Overington
- Medicines Discovery Catapult Block 35, Mereside, Alderley Park, Alderley Edge, Cheshire, SK10 4TG, UK
| | | | - Marc A. Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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24
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Ruan Z, Katiyar S, Kannan N. Computational and Experimental Characterization of Patient Derived Mutations Reveal an Unusual Mode of Regulatory Spine Assembly and Drug Sensitivity in EGFR Kinase. Biochemistry 2017; 56:22-32. [PMID: 27936599 PMCID: PMC5508873 DOI: 10.1021/acs.biochem.6b00572] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The catalytic activation of protein kinases requires precise positioning of key conserved catalytic and regulatory motifs in the kinase core. The Regulatory Spine (RS) is one such structural motif that is dynamically assembled upon kinase activation. The RS is also a mutational hotspot in cancers; however, the mechanisms by which cancer mutations impact RS assembly and kinase activity are not fully understood. In this study, through mutational analysis of patient derived mutations in the RS of EGFR kinase, we identify an activating mutation, M766T, at the RS3 position. RS3 is located in the regulatory αC-helix, and a series of mutations at the RS3 position suggest a strong correlation between the amino acid type present at the RS3 position and ligand (EGF) independent EGFR activation. Small polar amino acids increase ligand independent activity, while large aromatic amino acids decrease kinase activity. M766T relies on the canonical asymmetric dimer for full activation. Molecular modeling and molecular dynamics simulations of WT and mutant EGFR suggest a model in which M766T activates the kinase domain by disrupting conserved autoinhibitory interactions between M766 and hydrophobic residues in the activation segment. In addition, a water mediated hydrogen bond network between T766, the conserved K745-E762 salt bridge, and the backbone amide of the DFG motif is identified as a key determinant of M766T-mediated activation. M766T is resistant to FDA approved EGFR inhibitors such as gefitinib and erlotinib, and computational estimation of ligand binding free energy identifies key residues associated with drug sensitivity. In sum, our studies suggest an unusual mode of RS assembly and oncogenic EGFR activation, and provide new clues for the design of allosteric protein kinase inhibitors.
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Affiliation(s)
- Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Samiksha Katiyar
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
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25
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Modeling the effect of pathogenic mutations on the conformational landscape of protein kinases. Curr Opin Struct Biol 2016; 37:108-14. [DOI: 10.1016/j.sbi.2016.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 12/13/2022]
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26
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Huang Y, Bharill S, Karandur D, Peterson SM, Marita M, Shi X, Kaliszewski MJ, Smith AW, Isacoff EY, Kuriyan J. Molecular basis for multimerization in the activation of the epidermal growth factor receptor. eLife 2016; 5. [PMID: 27017828 PMCID: PMC4902571 DOI: 10.7554/elife.14107] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/27/2016] [Indexed: 12/18/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is activated by dimerization, but activation also generates higher-order multimers, whose nature and function are poorly understood. We have characterized ligand-induced dimerization and multimerization of EGFR using single-molecule analysis, and show that multimerization can be blocked by mutations in a specific region of Domain IV of the extracellular module. These mutations reduce autophosphorylation of the C-terminal tail of EGFR and attenuate phosphorylation of phosphatidyl inositol 3-kinase, which is recruited by EGFR. The catalytic activity of EGFR is switched on through allosteric activation of one kinase domain by another, and we show that if this is restricted to dimers, then sites in the tail that are proximal to the kinase domain are phosphorylated in only one subunit. We propose a structural model for EGFR multimerization through self-association of ligand-bound dimers, in which the majority of kinase domains are activated cooperatively, thereby boosting tail phosphorylation. DOI:http://dx.doi.org/10.7554/eLife.14107.001
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Affiliation(s)
- Yongjian Huang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Shashank Bharill
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Deepti Karandur
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Sean M Peterson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Morgan Marita
- Department of Chemistry, University of Akron, Akron, United States
| | - Xiaojun Shi
- Department of Chemistry, University of Akron, Akron, United States
| | | | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, United States
| | - Ehud Y Isacoff
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, United States
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Chemistry, University of California, Berkeley, Berkeley, United States
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27
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Kornev AP, Taylor SS. Dynamics-Driven Allostery in Protein Kinases. Trends Biochem Sci 2015; 40:628-647. [PMID: 26481499 DOI: 10.1016/j.tibs.2015.09.002] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/27/2015] [Accepted: 09/01/2015] [Indexed: 01/05/2023]
Abstract
Protein kinases have very dynamic structures and their functionality strongly depends on their dynamic state. Active kinases reveal a dynamic pattern with residues clustering into semirigid communities that move in μs-ms timescale. Previously detected hydrophobic spines serve as connectors between communities. Communities do not follow the traditional subdomain structure of the kinase core or its secondary structure elements. Instead they are organized around main functional units. Integration of the communities depends on the assembly of the hydrophobic spine and phosphorylation of the activation loop. Single mutations can significantly disrupt the dynamic infrastructure and thereby interfere with long-distance allosteric signaling that propagates throughout the whole molecule. Dynamics is proposed to be the underlying mechanism for allosteric regulation in protein kinases.
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Affiliation(s)
- Alexandr P Kornev
- Department of Pharmacology, University of California at San Diego, La Jolla, CA, 92093, USA.
| | - Susan S Taylor
- Department of Pharmacology, University of California at San Diego, La Jolla, CA, 92093, USA; Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093, USA.
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