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Soyer SM, Ozbek P, Kasavi C. Lung Adenocarcinoma Systems Biomarker and Drug Candidates Identified by Machine Learning, Gene Expression Data, and Integrative Bioinformatics Pipeline. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024. [PMID: 38979602 DOI: 10.1089/omi.2024.0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Lung adenocarcinoma (LUAD) is a significant planetary health challenge with its high morbidity and mortality rate, not to mention the marked interindividual variability in treatment outcomes and side effects. There is an urgent need for robust systems biomarkers that can help with early cancer diagnosis, prediction of treatment outcomes, and design of precision/personalized medicines for LUAD. The present study aimed at systems biomarkers of LUAD and deployed integrative bioinformatics and machine learning tools to harness gene expression data. Predictive models were developed to stratify patients based on prognostic outcomes. Importantly, we report here several potential key genes, for example, PMEL and BRIP1, and pathways implicated in the progression and prognosis of LUAD that could potentially be targeted for precision/personalized medicine in the future. Our drug repurposing analysis and molecular docking simulations suggested eight drug candidates for LUAD such as heat shock protein 90 inhibitors, cardiac glycosides, an antipsychotic agent (trifluoperazine), and a calcium ionophore (ionomycin). In summary, this study identifies several promising leads on systems biomarkers and drug candidates for LUAD. The findings also attest to the importance of integrative bioinformatics, structural biology and machine learning techniques in biomarker discovery, and precision oncology research and development.
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Affiliation(s)
- Semra Melis Soyer
- Department of Bioengineering, Faculty of Engineering, Marmara University, İstanbul, Türkiye
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, İstanbul, Türkiye
| | - Ceyda Kasavi
- Department of Bioengineering, Faculty of Engineering, Marmara University, İstanbul, Türkiye
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Imyanitov EN, Mitiushkina NV, Kuligina ES, Tiurin VI, Venina AR. Pathways and targeting avenues of BRAF in non-small cell lung cancer. Expert Opin Ther Targets 2024:1-10. [PMID: 38941191 DOI: 10.1080/14728222.2024.2374742] [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: 03/10/2024] [Accepted: 06/27/2024] [Indexed: 06/30/2024]
Abstract
INTRODUCTION BRAF is a serine-threonine kinase implicated in the regulation of MAPK signaling cascade. BRAF mutation-driven activation occurs in approximately 2-4% of treatment-naive non-small cell carcinomas (NSCLCs). BRAF upregulation is also often observed in tumors with acquired resistance to receptor tyrosine kinase inhibitors (TKIs). AREAS COVERED This review describes the spectrum of BRAF mutations and their functional roles, discusses treatment options available for BRAF p.V600 and non-V600 mutated NSCLCs, and identifies some gaps in the current knowledge. EXPERT OPINION Administration of combined BRAF/MEK inhibitors usually produces significant, although often a short-term, benefit to NSCLC patients with BRAF V600 (class 1) mutations. There are no established treatments for BRAF class 2 (L597, K601, G464, G469A/V/R/S, fusions, etc.) and class 3 (D594, G596, G466, etc.) mutants, which account for up to two-thirds of BRAF-driven NSCLCs. Many important issues related to the use of immune therapy for the management of BRAF-mutated NSCLC deserve further investigation. The rare occurrence of BRAF mutations in NSCLC is compensated by high overall incidence of lung cancer disease; therefore, clinical studies on BRAF-associated NSCLC are feasible.
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Affiliation(s)
- Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg, Russia
| | - Natalia V Mitiushkina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Ekatherina Sh Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Vladislav I Tiurin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Aigul R Venina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
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Imyanitov EN, Preobrazhenskaya EV, Orlov SV. Current status of molecular diagnostics for lung cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:742-765. [PMID: 38966170 PMCID: PMC11220319 DOI: 10.37349/etat.2024.00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/08/2024] [Indexed: 07/06/2024] Open
Abstract
The management of lung cancer (LC) requires the analysis of a diverse spectrum of molecular targets, including kinase activating mutations in EGFR, ERBB2 (HER2), BRAF and MET oncogenes, KRAS G12C substitutions, and ALK, ROS1, RET and NTRK1-3 gene fusions. Administration of immune checkpoint inhibitors (ICIs) is based on the immunohistochemical (IHC) analysis of PD-L1 expression and determination of tumor mutation burden (TMB). Clinical characteristics of the patients, particularly age, gender and smoking history, significantly influence the probability of finding the above targets: for example, LC in young patients is characterized by high frequency of kinase gene rearrangements, while heavy smokers often have KRAS G12C mutations and/or high TMB. Proper selection of first-line therapy influences overall treatment outcomes, therefore, the majority of these tests need to be completed within no more than 10 working days. Activating events in MAPK signaling pathway are mutually exclusive, hence, fast single-gene testing remains an option for some laboratories. RNA next-generation sequencing (NGS) is capable of detecting the entire repertoire of druggable gene alterations, therefore it is gradually becoming a dominating technology in LC molecular diagnosis.
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Affiliation(s)
- Evgeny N. Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
- Department of Clinical Genetics, St.-Petersburg State Pediatric Medical University, 194100 St.-Petersburg, Russia
- I.V. Kurchatov Complex for Medical Primatology, National Research Centre “Kurchatov Institute”, 354376 Sochi, Russia
| | - Elena V. Preobrazhenskaya
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
- Department of Clinical Genetics, St.-Petersburg State Pediatric Medical University, 194100 St.-Petersburg, Russia
| | - Sergey V. Orlov
- I.V. Kurchatov Complex for Medical Primatology, National Research Centre “Kurchatov Institute”, 354376 Sochi, Russia
- Department of Oncology, I.P. Pavlov St.-Petersburg State Medical University, 197022 St.-Petersburg, Russia
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Xu J, Tian L, Qi W, Lv Q, Wang T. Advancements in NSCLC: From Pathophysiological Insights to Targeted Treatments. Am J Clin Oncol 2024; 47:291-303. [PMID: 38375734 PMCID: PMC11107893 DOI: 10.1097/coc.0000000000001088] [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] [Indexed: 02/21/2024]
Abstract
With the global incidence of non-small cell lung cancer (NSCLC) on the rise, the development of innovative treatment strategies is increasingly vital. This review underscores the pivotal role of precision medicine in transforming NSCLC management, particularly through the integration of genomic and epigenomic insights to enhance treatment outcomes for patients. We focus on the identification of key gene mutations and examine the evolution and impact of targeted therapies. These therapies have shown encouraging results in improving survival rates and quality of life. Despite numerous gene mutations being identified in association with NSCLC, targeted treatments are available for only a select few. This paper offers an exhaustive analysis of the pathogenesis of NSCLC and reviews the latest advancements in targeted therapeutic approaches. It emphasizes the ongoing necessity for research and development in this domain. In addition, we discuss the current challenges faced in the clinical application of these therapies and the potential directions for future research, including the identification of novel targets and the development of new treatment modalities.
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Affiliation(s)
- Jianan Xu
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine
| | - Lin Tian
- Pulmonology Department, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, P.R. China
| | - Wenlong Qi
- Pulmonology Department, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, P.R. China
| | - Qingguo Lv
- Pulmonology Department, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, P.R. China
| | - Tan Wang
- Pulmonology Department, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, P.R. China
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Dankner M, Maxwell J, Rose AAN. The evolving treatment landscape for BRAF-mutated non-small cell lung cancer. Transl Lung Cancer Res 2024; 13:930-935. [PMID: 38736490 PMCID: PMC11082716 DOI: 10.21037/tlcr-24-117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/20/2024] [Indexed: 05/14/2024]
Affiliation(s)
- Matthew Dankner
- Department of Medicine, McGill University, Montréal, Québec, Canada
- Lady Davis Institute for Medical Research & Segal Cancer Centre, Jewish General Hospital, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Institute, Montréal, Québec, Canada
| | - Jennifer Maxwell
- Lady Davis Institute for Medical Research & Segal Cancer Centre, Jewish General Hospital, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - April A. N. Rose
- Department of Medicine, McGill University, Montréal, Québec, Canada
- Lady Davis Institute for Medical Research & Segal Cancer Centre, Jewish General Hospital, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
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Shan KS, Rehman TU, Ivanov S, Domingo G, Raez LE. Molecular Targeting of the BRAF Proto-Oncogene/Mitogen-Activated Protein Kinase (MAPK) Pathway across Cancers. Int J Mol Sci 2024; 25:624. [PMID: 38203795 PMCID: PMC10779188 DOI: 10.3390/ijms25010624] [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: 12/04/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The mitogen-activated protein kinase (MAPK) pathway is essential for cellular proliferation, growth, and survival. Constitutive activation of this pathway by BRAF mutations can cause downstream activation of kinases, leading to uncontrolled cellular growth and carcinogenesis. Therefore, inhibition of BRAF and the downstream substrate MEK has been shown to be effective in controlling tumor growth and proliferation. Over the last decade, several BRAF and MEK inhibitors have been investigated, ranging from primarily melanoma to various cancer types with BRAF alterations. This subsequently led to several Food and Drug Administration (FDA) approvals for BRAF/MEK inhibitors for melanoma, non-small cell lung cancer, anaplastic thyroid cancer, colorectal cancer, histiocytosis neoplasms, and finally, tumor-agnostic indications. Here, this comprehensive review will cover the developments of BRAF and MEK inhibitors from melanomas to tumor-agnostic indications, novel drugs, challenges, future directions, and the importance of those drugs in personalized medicine.
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Affiliation(s)
- Khine S. Shan
- Memorial Health Care, Division of Hematology and Oncology, Pembroke Pines, FL 33328, USA; (T.U.R.); (S.I.); (G.D.)
| | - Tauseef U. Rehman
- Memorial Health Care, Division of Hematology and Oncology, Pembroke Pines, FL 33328, USA; (T.U.R.); (S.I.); (G.D.)
| | - Stan Ivanov
- Memorial Health Care, Division of Hematology and Oncology, Pembroke Pines, FL 33328, USA; (T.U.R.); (S.I.); (G.D.)
| | - Gelenis Domingo
- Memorial Health Care, Division of Hematology and Oncology, Pembroke Pines, FL 33328, USA; (T.U.R.); (S.I.); (G.D.)
| | - Luis E. Raez
- Memorial Health Care, Thoracic Oncology Program, Pembroke Pines, FL 33328, USA;
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Ambrosini-Spaltro A, Rengucci C, Capelli L, Chiadini E, Calistri D, Bennati C, Cravero P, Limarzi F, Nosseir S, Panzacchi R, Valli M, Ulivi P, Rossi G. Clinicopathological Features of Non-Small Cell Lung Carcinoma with BRAF Mutation. Curr Oncol 2023; 30:10019-10032. [PMID: 37999148 PMCID: PMC10670100 DOI: 10.3390/curroncol30110728] [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: 10/08/2023] [Revised: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
(1) Background: BRAF mutations affect 4-5% of lung adenocarcinomas. This study aimed to analyze the clinicopathological features of lung carcinomas with BRAF mutations, focusing on V600E vs. non-V600E and the presence of co-mutations. (2) Methods: All BRAF-mutated lung carcinomas were retrieved from a molecular diagnostic unit (the reference unit for four different hospitals). The samples were analyzed using next-generation sequencing. Statistical analyses included log-rank tests for overall survival (OS) and progression-free survival (PFS). (3) Results: In total, 60 BRAF-mutated lung carcinomas were retrieved: 24 (40.0%) with V600E and 36 (60.0%) with non-V600E mutations, and 21 (35.0%) with other co-mutations and 39 (65.0%) with only BRAF mutations. Survival data were available for 54/60 (90.0%) cases. Targeted therapy was documented in 11 cases. Patients with V600E mutations exhibited a better prognosis than patients with non-V600E mutations (p = 0.008 for OS, p = 0.018 for PFS); this was confirmed in PFS (p = 0.036) when considering only patients who received no targeted therapy. Patients with co-mutations displayed no prognostic difference compared to patients carrying only BRAF mutations (p = 0.590 for OS, p = 0.938 for PFS). (4) Conclusions: BRAF-mutated lung carcinomas with V600E (40.0%) had a better prognosis than those without V600E. Concomitant co-mutations (35.0%) did not affect the prognosis.
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Affiliation(s)
| | - Claudia Rengucci
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (C.R.); (L.C.); (E.C.); (D.C.); (P.U.)
| | - Laura Capelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (C.R.); (L.C.); (E.C.); (D.C.); (P.U.)
| | - Elisa Chiadini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (C.R.); (L.C.); (E.C.); (D.C.); (P.U.)
| | - Daniele Calistri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (C.R.); (L.C.); (E.C.); (D.C.); (P.U.)
| | - Chiara Bennati
- Oncology Unit, Santa Maria Delle Croci Hospital, AUSL Romagna, 48121 Ravenna, Italy;
| | - Paola Cravero
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy;
| | - Francesco Limarzi
- Pathology Unit, Morgani-Pierantoni Hospital, AUSL Romagna, 47121 Forlì, Italy;
| | - Sofia Nosseir
- Pathology Unit, Santa Maria Delle Croci Hospital, AUSL Romagna, 48121 Ravenna, Italy;
| | | | - Mirca Valli
- Pathology Unit, Infermi Hospital, AUSL Romagna, 47923 Rimini, Italy;
| | - Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (C.R.); (L.C.); (E.C.); (D.C.); (P.U.)
| | - Giulio Rossi
- Pathology Unit, Department of Oncology, Fondazione Poliambulanza, 25124 Brescia, Italy;
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De Giglio A, Ricciuti B, Metro G. The expanding scenario of advanced non-small-cell lung cancer between emerging evidence and clinical tasks. Drugs Context 2023; 12:dic-2022-11-4. [PMID: 37168875 PMCID: PMC10166260 DOI: 10.7573/dic.2022-11-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 11/13/2022] [Indexed: 05/13/2023] Open
Abstract
This Editorial by De Giglio, Ricciuti and Metro introduces the series Treatment of advanced non-small-cell lung cancer: one size does not fit all: https://www.drugsincontext.com/special_issues/treatment-of-advanced-non-small-cell-lung-cancer-one-size-does-not-fit-all/.
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Affiliation(s)
- Andrea De Giglio
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Giulio Metro
- Medical Oncology, Santa Maria Della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy
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