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Wang JL, Liu MS, Fu YD, Kan QB, Li CY, Ma R, Fang ZW, Liu HX, Li MX, Lv JL, Sang P, Zhang C, Li HW. Exploring the conformational dynamics and thermodynamics of EGFR S768I and G719X + S768I mutations in non-small cell lung cancer: An in silico approaches. Open Life Sci 2023; 18:20220768. [PMID: 38035047 PMCID: PMC10685407 DOI: 10.1515/biol-2022-0768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 12/02/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is often driven by mutations in the epidermal growth factor receptor (EGFR) gene. However, rare mutations such as G719X and S768I lack standard anti-EGFR targeted therapies. Understanding the structural differences between wild-type EGFR and these rare mutants is crucial for developing EGFR-targeted drugs. We performed a systematic analysis using molecular dynamics simulations, essential dynamics (ED), molecular mechanics Poisson-Boltzmann surface area, and free energy calculation methods to compare the kinetic properties, molecular motion, and free energy distribution between wild-type EGFR and the rare mutants' structures G719X-EGFR, S768I-EGFR, and G719X + S768I-EGFR. Our results showed that S768I-EGFR and G719X + S768I-EGFR have higher global and local conformational flexibility and lower thermal and global structural stability than WT-EGFR. ED analysis revealed different molecular motion patterns between S768I-EGFR, G719X + S768I-EGFR, and WT-EGFR. The A-loop and αC-helix, crucial structural elements related to the active state, showed a tendency toward active state development, providing a molecular mechanism explanation for NSCLC caused by EGFR S768I and EGFR G719C + S768I mutations. The present study may be helpful in the development of new EGFR-targeted drugs based on the structure of rare mutations. Our findings may aid in developing new targeted treatments for patients with EGFR S768I and EGFR G719X + S768I mutations.
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Affiliation(s)
- Jun-Ling Wang
- Clinical Laboratory, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Ming-Sheng Liu
- Department of Urological Surgery, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Yu-Dong Fu
- Department of Thoracic Surgery, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Qiang-Bo Kan
- Department of Thoracic Surgery, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Chun-Yan Li
- Department of Oncology, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Rong Ma
- Clinical Laboratory, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Zhe-Wei Fang
- Clinical Laboratory, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Hong-Xia Liu
- Clinical Laboratory, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Meng-Xian Li
- Clinical Laboratory, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Jia-Ling Lv
- Department of Oncology, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Peng Sang
- School of Life Science, Dali University, Dali671003, China
| | - Chao Zhang
- Department of Oncology, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Hong-Wei Li
- Clinical Laboratory, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
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Wang JL, Fu YD, Gao YH, Li XP, Xiong Q, Li R, Hou B, Huang RS, Wang JF, Zhang JK, Lv JL, Zhang C, Li HW. Unique characteristics of G719X and S768I compound double mutations of epidermal growth factor receptor (EGFR) gene in lung cancer of coal-producing areas of East Yunnan in Southwestern China. Genes Environ 2022; 44:17. [PMID: 35606799 PMCID: PMC9125819 DOI: 10.1186/s41021-022-00248-z] [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: 02/11/2022] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
Background The principal objective of this project was to investigate the Epidermal Growth Factor Receptor (EGFR) gene mutation characteristics of lung cancer patients, which can provide a molecular basis for explaining the clinicopathological features, epidemiology and use of targeted therapy in lung cancer patients in the coal-producing areas of East Yunnan. Methodology We collected 864 pathologically confirmed lung cancer patients’ specimens in First People’s Hospital of Qujing City of Yunnan Province from September 2016 to September 2021. We thereafter employed Next Generation Sequencing (NGS) technology to detect all exons present in the EGFR gene. Results The overall mutation frequency of the EGFR gene was 47.22%. The frequency of EGFR gene mutations in the tissue, plasma, and cytology samples were found to be 53.40%, 23.33%, and 62.50%, respectively. Univariate analysis indicated that the coal-producing areas and Fuyuan county origin were significantly associated with relatively low EGFR gene mutation frequency. Female, non-smoking history, adenocarcinoma, non-brain metastasis, and tissue specimens were found to be related to high EGFR gene mutation frequency. Multivariate logistic regression analysis suggested the lung cancer patients in the central area of Qujing City, stage Ia, non-coal-producing areas, non-Fuyuan origin, and non-Xuanwei origin were more likely to develop EGFR gene mutations. The most common mutations were L858R point mutation (33.09%) and exon 19 deletion (19-del) (21.32%). Interestingly, the mutation frequency of G719X (p = 0.001) and G719X + S768I (p = 0.000) in the coal-producing areas were noted to be more significant than those in non-coal-producing regions. Conclusion This findings of this study might be important in establishing the correlation between routine using NGS for EGFR gene mutation diagnosis and clinical practice in the lung cancer patients. Supplementary Information The online version contains supplementary material available at 10.1186/s41021-022-00248-z.
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Affiliation(s)
- Jun-Ling Wang
- Biological Laboratory, First People's Hospital of Qujing, Qujing, 655000, China
| | - Yu-Dong Fu
- Department of Thoracic Surgery, First People's Hospital of Qujing, Qujing, 655000, China
| | - Yan-Hong Gao
- Department of Traditional Chinese Medicine, First People's Hospital of Qujing, Qujing, 655000, China
| | - Xiu-Ping Li
- Biological Laboratory, First People's Hospital of Qujing, Qujing, 655000, China
| | - Qian Xiong
- Biological Laboratory, First People's Hospital of Qujing, Qujing, 655000, China
| | - Rui Li
- Department of Medical Administration, First People's Hospital of Qujing, Qujing, 655000, China
| | - Bo Hou
- Department of Thoracic Surgery, First People's Hospital of Qujing, Qujing, 655000, China
| | - Ruo-Shan Huang
- Department of Thoracic Surgery, First People's Hospital of Qujing, Qujing, 655000, China
| | - Jun-Feng Wang
- Department of Thoracic Surgery, First People's Hospital of Qujing, Qujing, 655000, China
| | - Jian-Kun Zhang
- Department of Pathology, First People's Hospital of Qujing, Qujing, 655000, China
| | - Jia-Ling Lv
- Department of Oncology, First People's Hospital of Qujing, Qujing, 655000, China
| | - Chao Zhang
- Department of Oncology, First People's Hospital of Qujing, Qujing, 655000, China.
| | - Hong-Wei Li
- Biological Laboratory, First People's Hospital of Qujing, Qujing, 655000, China.
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Dhar C. Utilizing Publicly Available Cancer Clinicogenomic Data on CBioPortal to Compare Epidermal Growth Factor Receptor Mutant and Wildtype Non-Small Cell Lung Cancer. Cureus 2021; 13:e14683. [PMID: 34055528 PMCID: PMC8149776 DOI: 10.7759/cureus.14683] [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] [Indexed: 12/05/2022] Open
Abstract
Publicly available clinicogenomic data on platforms such as the cancer BioPortal (cBioPortal.org) allow for efficient analyses by researchers with little or no experience working with Big Data. cBioPortal.org also allows for appropriate statistical testing and downloadable images for easy dissemination of findings. In this study, the cBioPortal.org platform was tested and its utility demonstrated by comparing cases of non-small cell lung cancer (NSCLC) with and without epidermal growth factor receptor gene (EGFR) mutations. Patients with EGFR mutations were more likely to be female, of Asian ethnicity, never-smokers, and be diagnosed with lung adenocarcinoma. Metastasis to the pleura, pleural fluid, and liver was common in patients with EGFR mutant NSCLC. On the other hand, lymph node, brain, and adrenal gland metastases were more common in patients with other mutations. While the median overall survival was about the same in the two groups, progression-free survival was significantly shorter in the EGFR mutant group. The mutational landscape was significantly different in the two groups with EGFR mutant NSCLCs having a lower mutational burden. Differences in copy number alterations between the two groups were also noted. The descriptive data generated from this study such as age, gender, smoking history, and histological subtype recapitulate findings of other studies on EGFR mutant NSCLCs. Further prospective and/or preclinical studies are needed to confirm differences noted in this study. cBioPortal.com queries may be used to supplement clinical/pre-clinical studies or to generate novel hypotheses.
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Affiliation(s)
- Chirag Dhar
- Medicine and Cellular and Molecular Medicine, University of California San Diego, La Jolla, USA
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D'Souza G, Dhar C, Kyalanoor V, Yadav L, Sharma M, Nawaz S M, Srivastava S. High frequency of exon 20 S768I EGFR mutation detected in malignant pleural effusions: A poor prognosticator of NSCLC. Cancer Rep (Hoboken) 2020; 3:e1262. [PMID: 32761886 PMCID: PMC7941414 DOI: 10.1002/cnr2.1262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/26/2020] [Accepted: 06/01/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Lung cancer is the cause of a fourth of all cancer-related deaths. About a third of all lung adenocarcinoma tumours harbour mutations on exons 18 to 21 of the epidermal growth factor receptor (EGFR) gene. Detection of these mutations allows for targeted therapies in the form of EGFR Tyrosine kinase inhibitors. Recently, "liquid biopsies" have emerged as an alternative to conventional tissue mutation detection. AIM In this pilot study, we attempted to optimize EGFR mutation detection from malignant pleural effusions (MPEs) as "liquid biopsies" when tissue biopsies were unavailable. Resulting mutations were then to be mapped on the EGFR gene and explored using cBioPortal, a public cancer genomic database. METHODS AND RESULTS We first attempted a direct sequencing approach and showed that single nucleotide variants (SNVs) were likely to be missed in MPEs. We then switched to and optimized an EGFR mutant-specific quantitative polymerase chain reaction-based assay. This assay was piloted on n = 10 pleural effusion samples (one non-malignant pleural effusion as a negative control). 5/9 (55.55%) samples harboured EGFR mutations with 2/9 (22.22%) being exon 19 deletions and 3/9 (33.33%) the S768I mutation. The frequency of the S768I SNV in our study was significantly higher than that observed in other studies (~0.2%). Utilizing cBioPortal data, we report that patients with S768I have a shorter median survival time (6 months vs 38 months), progression-free survival time (8 months vs 44 months) and lower tumor mutation count compared to patients with other EGFR mutations. CONCLUSIONS The shorter survival of patients with the S768I SNV predicts aggressive disease and poor prognosis as a result of this mutation. Studies in larger cohorts and/or animal models are necessary to confirm these findings.
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Affiliation(s)
- George D'Souza
- St. John's Research InstituteBangaloreIndia
- Department of Pulmonary MedicineSt. John's Medical College and HospitalBangaloreIndia
| | - Chirag Dhar
- St. John's Research InstituteBangaloreIndia
- Department of Pulmonary MedicineSt. John's Medical College and HospitalBangaloreIndia
- School of MedicineUniversity of CaliforniaSan DiegoCaliforniaUSA
| | - Vishal Kyalanoor
- Department of Transfusion Medicine and ImmunohaematologySt. John's Medical College and HospitalBangaloreIndia
| | - Lokendra Yadav
- Department of Transfusion Medicine and ImmunohaematologySt. John's Medical College and HospitalBangaloreIndia
| | - Mugdha Sharma
- St. John's Research InstituteBangaloreIndia
- Department of Transfusion Medicine and ImmunohaematologySt. John's Medical College and HospitalBangaloreIndia
- Department of General MedicineSt. John's Medical College and HospitalBangaloreIndia
| | - Mohammad Nawaz S
- Department of Pulmonary MedicineSt. John's Medical College and HospitalBangaloreIndia
| | - Sweta Srivastava
- Department of Transfusion Medicine and ImmunohaematologySt. John's Medical College and HospitalBangaloreIndia
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