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Heriyanto DS, Laiman V, Limantara NV, Anantawikrama WP, Yuliani FS, Cempaka R, Anwar SL. High frequency of KRAS and EGFR mutation profiles in BRAF-negative thyroid carcinomas in Indonesia. BMC Res Notes 2022; 15:369. [PMID: 36510281 PMCID: PMC9743704 DOI: 10.1186/s13104-022-06260-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Thyroid cancer incidence has steadily increased in Indonesia. However, data on Kirsten rat sarcoma virus (KRAS) and EGFR mutations in thyroid cancer in Indonesia remain unavailable, except for BRAF-V600E, the most common BRAF gene mutation. This study aimed to analyze KRAS and EGFR mutation profiles in BRAF-V600E negative thyroid cancer samples. RESULTS BRAF-V600E mutations were found in papillary thyroid carcinomas in 40.3% patients with mean age of 53 years old. In BRAF-V600E-negative samples, 41.3% had KRAS mutations with mean age of 55.5 years old. KRAS mutation was found in 52.6% of follicular carcinomas and 47.4% of papillary thyroid carcinomas. Additionally, 45.7% had EGFR mutations in patients with mean age of 50.5 years old. EGFR mutation was found in 71.4% of papillary thyroid carcinoma and 28.6% of follicular carcinoma. Nearly half of the BRAF-V600E negative thyroid carcinoma samples harbored either KRAS or EGFR mutations. This finding suggests that in BRAF-V600E negative thyroid carcinoma samples, testing for RAS and EGFR mutation may be warranted for further therapeutic consideration.
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Affiliation(s)
- Didik Setyo Heriyanto
- grid.8570.a0000 0001 2152 4506Department of Anatomical Pathology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada-Dr. Sardjito Hospital, Farmako Street, Yogyakarta, 55281 Indonesia
| | - Vincent Laiman
- grid.8570.a0000 0001 2152 4506Department of Anatomical Pathology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada-Dr. Sardjito Hospital, Farmako Street, Yogyakarta, 55281 Indonesia
| | - Nikko Vanda Limantara
- grid.8570.a0000 0001 2152 4506Department of Anatomical Pathology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada-Dr. Sardjito Hospital, Farmako Street, Yogyakarta, 55281 Indonesia
| | - Widyan Putra Anantawikrama
- grid.8570.a0000 0001 2152 4506Department of Anatomical Pathology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada-Dr. Sardjito Hospital, Farmako Street, Yogyakarta, 55281 Indonesia
| | - Fara Silvia Yuliani
- grid.8570.a0000 0001 2152 4506Department of Pharmacology and Therapy, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281 Indonesia
| | - Rita Cempaka
- grid.8570.a0000 0001 2152 4506Department of Anatomical Pathology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada-Dr. Sardjito Hospital, Farmako Street, Yogyakarta, 55281 Indonesia
| | - Sumadi Lukman Anwar
- grid.8570.a0000 0001 2152 4506Department of Surgery, Subdivision of Oncology Surgery; Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada-Dr. Sardjito Hospital, Yogyakarta, 55281 Indonesia
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Xie F, Yan L, Li YM, Lan Y, Xiao J, Zhang MB, Jin Z, Zhang Y, Tian XQ, Zhu YQ, Li ZP, Luo YK. Targeting Diagnosis of High-Risk Papillary Thyroid Carcinoma Using Ultrasound Contrast Agent With the BRAF V600E Mutation: An Experimental Study. JOURNAL OF ULTRASOUND IN MEDICINE : OFFICIAL JOURNAL OF THE AMERICAN INSTITUTE OF ULTRASOUND IN MEDICINE 2022; 41:2789-2802. [PMID: 35229905 DOI: 10.1002/jum.15967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/14/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
OBJECTIVE High-risk papillary thyroid carcinoma (PTC) patients with BRAF mutation have lymph node and distant metastases and poor prognosis. Therefore, this study aims to develop a targeted ultrasound contrast agent for the BRAFV600E mutation to screen high-risk PTC at early stage. METHODS The targeted lipid nanobubbles carrying BRAFV600E antibody were prepared using thin film hydration-sonication and avidin-biotin binding methods. The physicochemical properties and stability of the targeted nanobubbles were detected by transmission electron microscopy, atomic force microscopy, and confocal laser scanning microscopy. The target binding abilities of the targeted nanobubbles in the PTC cells (B-CPAP) overexpressed mutant BRAFV600E were evaluated by immunofluorescence staining, quantitative real-time polymerase chain reaction, western blot, and fluorescence microscopy. After PTC tumor models overexpressed mutant BRAFV600E were established, the enhanced images of targeted lipid nanobubbles and untargeted lipid nanobubbles on PTC tumors in nude mice were observed using contrast-enhanced ultrasound imaging. RESULTS The targeted lipid nanobubbles revealed uniform, round morphology, and good stability with a nanoscale size. Besides, BRAFV600E monoclonal antibody was observed to be combined on the surface of lipid nanobubbles. Furthermore, the targeted nanobubbles had a good targeting diagnosis ability in PTC cells with BRAFV600E overexpression. Moreover, the targeted nanobubbles had better ultrasound enhancement and peak intensity of the time-intensity curve (P < .001) in PTC tumors with BRAFV600E overexpression as compared to the untargeted lipid nanobubbles. CONCLUSION The targeted lipid nanobubbles carrying BRAFV600E antibody could be regarded as a potential targeted ultrasound contrast agent for the diagnosis of high-risk PTC.
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Affiliation(s)
- Fang Xie
- Department of Ultrasound, The First Medical Center of PLA General Hospital, Beijing, China
| | - Lin Yan
- Department of Ultrasound, The First Medical Center of PLA General Hospital, Beijing, China
| | - Yi-Ming Li
- Department of Ultrasound, The First Medical Center of PLA General Hospital, Beijing, China
| | - Yu Lan
- Department of Ultrasound, The First Medical Center of PLA General Hospital, Beijing, China
| | - Jing Xiao
- Department of Ultrasound, The First Medical Center of PLA General Hospital, Beijing, China
| | - Ming-Bo Zhang
- Department of Ultrasound, The First Medical Center of PLA General Hospital, Beijing, China
| | - Zhuang Jin
- Department of Ultrasound, The First Medical Center of PLA General Hospital, Beijing, China
| | - Ying Zhang
- Department of Ultrasound, The First Medical Center of PLA General Hospital, Beijing, China
| | - Xiao-Qi Tian
- Department of Ultrasound, The First Medical Center of PLA General Hospital, Beijing, China
| | - Ya-Qiong Zhu
- Department of Ultrasound, The First Medical Center of PLA General Hospital, Beijing, China
| | - Zhi-Ping Li
- Pharmacology Research Department, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Yu-Kun Luo
- Department of Ultrasound, The First Medical Center of PLA General Hospital, Beijing, China
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Dain Md Opo FA, Alsaiari AA, Rahman Molla MH, Ahmed Sumon MA, Yaghmour KA, Ahammad F, Mohammad F, Simal-Gandara J. Identification of novel natural drug candidates against BRAF mutated carcinoma; An integrative in-silico structure-based pharmacophore modeling and virtual screening process. Front Chem 2022; 10:986376. [PMID: 36267655 PMCID: PMC9577413 DOI: 10.3389/fchem.2022.986376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/07/2022] [Indexed: 12/30/2022] Open
Abstract
The BRAF gene is responsible for transferring signals from outside of the cell to inside of the nucleus by converting a protein namely B-Raf through the RAS/MAPK pathway. This pathway contribute to cell division, proliferation, migration, and apoptotic cell death of human and animal. Mutation in this gene may cause the development of several cancers, including lung, skin, colon, and neuroblastoma. Currently, a few available drugs are being used that has developed by targeting the BRAF mutated protein, and due to the toxic side effects, patients suffer a lot during their treatment. Therefore this study aimed to identify potentially lead compounds that can target and block the expression of BRAF and subsequently inhibit the cancer. The hits were generated through the pharmacophore model-based virtual screening, molecular docking, pharmacohore model validation, ADME (absorption, distribution, metabolism, and excretion) analysis molecular dynamics (MD) simulation to find more suitable candidate against the overexpress BRAF gene. The pharmacophore based screening initially identified 14 k possible hits from online database which were further screened by ligand scout advance software to get hit compound. Based on molecular docking score of ZINC70454679 (-10.6 kcal/mol), ZINC253500968 (-9.4 kcal/mol), ZINC106887736 (-8.6 kcal/mol), and ZINC107434492 (-8.1 kcal/mol), pharmacophore feature and toxicity evaluation, we selected four possible lead compounds. The dynamic simulation with Schrodinger Maestro software was used to determine the stability of the potential lead candidates with target protein (PDB ID: 5VAM). The results showed that the newly obtained four compounds were more stable than the control ligand (Pub Chem ID: 90408826). The current results showed that the ZINC70454679, ZINC253500968, ZINC106887736, and ZINC107434492 compounds may be able to work against several cancers through targeting the BRAF overexpressed gene. To develop a novel drug candidate, however the evaluation of the web lab based experimental work are necessary to evaluate the efficiency of the each compound against the BRAF target gene.
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Affiliation(s)
- F. A. Dain Md Opo
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Embryonic Stem Cell Research Unit, King Fahd Medical Research Center (KFMRC), KAU, Jeddah, Saudi Arabia
| | - Ahad Amer Alsaiari
- Clinical Laboratories, Science Department, College of Applied Medical Science, Taif University, Taif, Saudi Arabia
| | | | - Md Afsar Ahmed Sumon
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khaled A. Yaghmour
- Family Medicine Department, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Foysal Ahammad
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Division of Biological and Biomedical Sciences (BBS), College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, Qatar
- *Correspondence: Foysal Ahammad, ; Farhan Mohammad, ; Jesus Simal-Gandara,
| | - Farhan Mohammad
- Division of Biological and Biomedical Sciences (BBS), College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, Qatar
- *Correspondence: Foysal Ahammad, ; Farhan Mohammad, ; Jesus Simal-Gandara,
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
- *Correspondence: Foysal Ahammad, ; Farhan Mohammad, ; Jesus Simal-Gandara,
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Pham M, Pham Q, Nguyen U, Nguyen L, Nguyen H, Vu T, Nguyen B, Stenman J, Tho H. Highly sensitive detection of EGFR L858R mutation at the mRNA level. Anal Biochem 2022; 654:114799. [PMID: 35780814 DOI: 10.1016/j.ab.2022.114799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022]
Abstract
The missense mutation EGFR L858R implies increased sensitivity to EGFR tyrosine kinase inhibitor (TKIs) therapy, despite a significant non-response rate. Currently, detection of EGFR L858R mutation is mostly DNA based, therefore, the allele-specific expression level of the mutated gene and its clinical relevance is hidden. Based on the extendable blocking probes and hot-start protocol for reverse transcription, we have developed and validated a novel one-step realtime RT-PCR assay that enables detection of EGFR L858R mutation at the mRNA level. This RNA-based assay was able to detect the EGFR L858R mutation in a 10,000-fold excess of its wildtype counterpart, indicating an analytical sensitivity of 0.01%. In comparison to the reference DNA-based assay, the RNA-based assay further detected the EGFR L858R mutation in significantly additional formalin-fixed paraffin-embedded (FFPE) samples (19.2% vs 15.0%). Interestingly, our data showed that the relative mRNA levels of EGFR L858R mutation varied greatly in tumor tissues (∼4 logs); and the circulating mRNA of EGFR L858R mutation was detectable in plasma of NSCLC patients. This novel RNA-based PCR assay provides a simple and ultrasensitive tool for detection of EGFR L858R mutation at the mRNA level as a new class of biomarkers.
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Affiliation(s)
- Mai Pham
- Department of Oncology, 103 Military Hospital, Vietnam Military Medical University, 100000, Hanoi, Viet Nam; Department of Oncology, Hanoi Medical University, 100000, Hanoi, Viet Nam
| | - Quynh Pham
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, 222 Phung Hung Street, Ha Dong District, 100000, Hanoi, Viet Nam
| | - Ung Nguyen
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, 222 Phung Hung Street, Ha Dong District, 100000, Hanoi, Viet Nam
| | - Lanh Nguyen
- Department of Pathology, Viet Duc Hospital, 40 Trang Thi, Hoan Kiem, 100000, Hanoi, Viet Nam
| | - Hoa Nguyen
- Medical Department 2, National Cancer Hospital, 100000, Hanoi, Viet Nam
| | - Thang Vu
- Medical Department 4, National Cancer Hospital, 100000, Hanoi, Viet Nam
| | - Ba Nguyen
- Department of Oncology, 103 Military Hospital, Vietnam Military Medical University, 100000, Hanoi, Viet Nam
| | - Jakob Stenman
- Department of Women's and Children's Health, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Ho Tho
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, 222 Phung Hung Street, Ha Dong District, 100000, Hanoi, Viet Nam; Department of Medical Microbiology, 103 Military Hospital, Vietnam Medical University, 100000, Hanoi, Viet Nam.
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Ye P, Cai P, Xie J, Zhang J. Reliability of BRAF mutation detection using plasma sample: A systematic review and meta-analysis. Medicine (Baltimore) 2021; 100:e28382. [PMID: 34941166 PMCID: PMC8701458 DOI: 10.1097/md.0000000000028382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/10/2021] [Accepted: 12/01/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Testing of B-Raf proto-oncogene (BRAF) mutation in tumor is necessary before targeted therapies are given. When tumor samples are not available, plasma samples are commonly used for the testing of BRAF mutation. The aim of this study was to investigate the diagnostic accuracy of BRAF mutation testing using plasma sample of cancer patients. METHODS Databases of Pubmed, Embase, and Cochrane Library were searched for eligible studies investigating BRAF mutation in paired tissue and plasma samples of cancer patients. A total of 798 publications were identified after database searching. After removing 229 duplicated publications, 569 studies were screened using the following exclusion criteria: (1) BRAF mutation not measured in plasma or in tumor sample; (2) lacking BRAF-wildtype or BRAF-mutated samples; (3) tissue and plasma samples not paired; (4) lacking tumor or plasma samples; (5) not plasma sample; (6) not cancer; (7) un-interpretable data. Accuracy data and relevant information were extracted from each eligible study by 2 independent researchers and analyzed using statistical software. RESULTS After pooling the accuracy data from 3943 patients of the 53 eligible studies, the pooled sensitivity, specificity, and diagnostic odds ratio of BRAF mutation testing using plasma sample were 69%, 98%, and 55.78, respectively. Area under curve of summary receiver operating characteristic curve was 0.9435. Subgroup analysis indicated that BRAF mutation testing using plasma had overall higher accuracy (diagnostic odds ratio of 89.17) in colorectal cancer, compared to melanoma and thyroid carcinoma. In addition, next-generation sequencing had an overall higher accuracy in detecting BRAF mutation using plasma sample (diagnostic odds ratio of 63.90), compared to digital polymerase chain reaction (PCR) and conventional PCR, while digital PCR showed the highest sensitivity (74%) among the 3 techniques. CONCLUSION BRAF testing using plasma sample showed an overall high accuracy compared to paired tumor tissue sample, which could be used for cancer genotyping when tissue sample is not available. Large prospective studies are needed to further investigate the accuracy of BRAF mutation testing in plasma sample.
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Affiliation(s)
- Peng Ye
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, P.R. China
| | - Peiling Cai
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, P.R. China
| | - Jing Xie
- Department of Pathology and Clinical Laboratory, Sichuan Provincial Fourth People's Hospital, Chengdu, P.R. China
| | - Jie Zhang
- Adverse Drug Reaction Monitoring Center, Chengdu, P.R. China
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