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Roa P, Foglizzo V, Harada G, Repetto M, Kulick A, de Stanchina E, de Marchena M, Auwardt S, Sayed Ahmed S, Bremer NV, Yang SR, Feng Y, Zhou C, Kong N, Liang R, Xu H, Zhang B, Bardelli A, Toska E, Ventura A, Drilon A, Cocco E. Zurletrectinib is a next-generation TRK inhibitor with strong intracranial activity against NTRK fusion-positive tumours with on-target resistance to first-generation agents. Br J Cancer 2024; 131:601-610. [PMID: 38902532 PMCID: PMC11300601 DOI: 10.1038/s41416-024-02760-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND While NTRK fusion-positive cancers can be exquisitely sensitive to first-generation TRK inhibitors, resistance inevitably occurs, mediated in many cases by acquired NTRK mutations. Next-generation inhibitors (e.g., selitrectinib, repotrectinib) maintain activity against these TRK mutant tumors; however, there are no next-generation TRK inhibitors approved by the FDA and select trials have stopped treating patients. Thus, the identification of novel, potent and specific next-generation TRK inhibitors is a high priority. METHODS In silico modeling and in vitro kinase assays were performed on TRK wild type (WT) and TRK mutant kinases. Cell viability and clonogenic assays as well as western blots were performed on human primary and murine engineered NTRK fusion-positive TRK WT and mutant cell models. Finally, zurletrectinib was tested in vivo in human xenografts and murine orthotopic glioma models harboring TRK-resistant mutations. RESULTS In vitro kinase and in cell-based assays showed that zurletrectinib, while displaying similar potency against TRKA, TRKB, and TRKC WT kinases, was more active than other FDA approved or clinically tested 1st- (larotrectinib) and next-generation (selitrectinib and repotrectinib) TRK inhibitors against most TRK inhibitor resistance mutations (13 out of 18). Similarly, zurletrectinib inhibited tumor growth in vivo in sub-cute xenograft models derived from NTRK fusion-positive cells at a dose 30 times lower when compared to selitrectinib. Computational modeling suggests this stronger activity to be the consequence of augmented binding affinity of zurletrectinib for TRK kinases. When compared to selitrectinib and repotrectinib, zurletrectinib showed increased brain penetration in rats 0.5 and 2 h following a single oral administration. Consistently, zurletrectinib significantly improved the survival of mice harboring orthotopic NTRK fusion-positive, TRK-mutant gliomas (median survival = 41.5, 66.5, and 104 days for selitrectinib, repotrectinib, and zurletrectinib respectively; P < 0.05). CONCLUSION Our data identifies zurletrectinib as a novel, highly potent next-generation TRK inhibitor with stronger in vivo brain penetration and intracranial activity than other next-generation agents.
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MESH Headings
- Humans
- Animals
- Mice
- Protein Kinase Inhibitors/pharmacology
- Receptor, trkA/genetics
- Receptor, trkA/antagonists & inhibitors
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/drug effects
- Receptor, trkB/antagonists & inhibitors
- Receptor, trkB/genetics
- Xenograft Model Antitumor Assays
- Receptor, trkC/genetics
- Receptor, trkC/antagonists & inhibitors
- Cell Line, Tumor
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/antagonists & inhibitors
- Rats
- Brain Neoplasms/drug therapy
- Brain Neoplasms/genetics
- Brain Neoplasms/pathology
- Pyrazoles/pharmacology
- Glioma/drug therapy
- Glioma/genetics
- Glioma/pathology
- Pyrimidines/pharmacology
- Mutation
- Female
- Membrane Glycoproteins
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Affiliation(s)
- Paola Roa
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center (SCCC), Miami, FL, USA
| | - Valentina Foglizzo
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center (SCCC), Miami, FL, USA
| | - Guilherme Harada
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matteo Repetto
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Oncology and Haemato-Oncology, University of Milan, 20133, Milan, Italy
| | - Amanda Kulick
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michelle de Marchena
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center (SCCC), Miami, FL, USA
| | - Supipi Auwardt
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center (SCCC), Miami, FL, USA
| | - Shaza Sayed Ahmed
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center (SCCC), Miami, FL, USA
| | - Nicole Virginia Bremer
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center (SCCC), Miami, FL, USA
| | - Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yangbo Feng
- Sylvester Comprehensive Cancer Center (SCCC), Miami, FL, USA
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Chao Zhou
- InnoCare Pharma Limited, Beijing, China
| | | | | | | | - Bin Zhang
- InnoCare Pharma Limited, Beijing, China
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Eneda Toska
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Emiliano Cocco
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA.
- Sylvester Comprehensive Cancer Center (SCCC), Miami, FL, USA.
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2
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Zhang Q, Chen K, Yu X, Fan Y. Spotlight on the treatment of non-small cell lung cancer with rare genetic alterations and brain metastasis: Current status and future perspectives. Int J Cancer 2024. [PMID: 38958227 DOI: 10.1002/ijc.35070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024]
Abstract
In patients with non-small cell lung cancer (NSCLC), oncogenic variants present in <5% of cases are considered rare, the predominant of which include human epidermal growth factor receptor 2 (HER2) mutations, mesenchymal-epithelial transition (MET) alterations, c-ros oncogene 1 (ROS1) rearrangements, rearrangement during transfection (RET) fusions, v-raf mouse sarcoma virus oncogene homolog B1 (BRAF) mutations, and neurotrophic troponin receptor kinase (NTRK) fusions. Brain metastases (BMs) occur in approximately 10%-50% of patients with NSCLC harboring rare genetic variants. The recent advent of small-molecule tyrosine kinase inhibitors and macromolecular antibody-drug conjugates (ADCs) has conferred marked survival benefits to patients with NSCLC harboring rare driver alterations. Despite effective brain lesion control for most targeted agents and promising reports of intracranial remission associated with novel ADCs, BM continues to be a major therapeutic challenge. This review discusses the recent advances in the treatment of NSCLC with rare genetic variants and BM, with a particular focus on intracranial efficacy, and explores future perspectives on how best to treat these patients.
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Affiliation(s)
- Qian Zhang
- Department of Oncology, The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Kaiyan Chen
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Xiaoqing Yu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- Department of Clinical Trial, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Yun Fan
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
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3
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Dong K, Zhu Y, Liu X, Sun W, Yang X, Chi K, Jia L, Diao X, Huang X, Zhou L, Lin D. Feasibility of two-step approach for screening NTRK fusion in two major subtypes of non-small cell lung cancer within a large cohort. Hum Pathol 2024; 149:39-47. [PMID: 38866255 DOI: 10.1016/j.humpath.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/23/2024] [Accepted: 06/08/2024] [Indexed: 06/14/2024]
Abstract
Our objective is to investigate a cost-effective approach to screen for NTRK fusion in the major subtypes of non-small cell lung cancer (NSCLC). Evaluate the concordance between immunohistochemistry (IHC) and next-generation sequencing (NGS), as well as between fluorescence in situ hybridization (FISH) and NGS, to detect any discrepancies in methodological consistency between lung adenocarcinoma (LADC) and lung squamous cell carcinoma (LSCC). Analyze the factors influencing IHC results. A cohort of 1654 patients with NSCLC underwent screening for NTRK fusion using whole slide IHC. The positive cases were analyzed by both FISH and NGS. Totally, 57 tested positive for pan-TRK, with positivity rates of 0.68% (10/1467) for LADC and 29.01% (47/162) for LSCC. FISH showed separate NTRK1 and NTRK3 rearrangements in two pan-TRK-positive LADCs, while all LSCCs tested negative. NGS confirmed functional NTRK fusion in two FISH-positive cases: one involving TPM3-NTRK1 and the other involving SQSTM1-NTRK3. A non-functional fusion of NTRK2-XRCC1 was detected in LSCC, while FISH was negative. According to our approach, the prevalence of NTRK fusion in NSCLC is 0.12%. The concordance rate between IHC and RNA-based NGS was 20% (2/10) in LADC and 0% (0/162) in LSCC. When the positive criteria increased over 50% of tumor cells showing strong staining, the concordance would be 100% (2/2). A concordance rate of 100% (2/2) was observed between FISH and RNA-based NGS in LADC. The expression of pan-TRK was significantly correlated with the tumor proportion score (TPS) of PD-L1 (p < 0.05) and transcript per million (TPM) values of NTRK2 (p < 0.05). We recommend using IHC with strict criteria to screen NTRK fusion in LADC rather than LSCC, confirmed by RNA-based NGS directly. When the NGS results are inconclusive, FISH validation is necessary.
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MESH Headings
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- In Situ Hybridization, Fluorescence
- Female
- Male
- Middle Aged
- High-Throughput Nucleotide Sequencing
- Receptor, trkA/genetics
- Immunohistochemistry
- Feasibility Studies
- Aged
- Oncogene Proteins, Fusion/genetics
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/analysis
- Receptor, trkC/genetics
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Adult
- Adenocarcinoma of Lung/genetics
- Adenocarcinoma of Lung/pathology
- Reproducibility of Results
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Affiliation(s)
- Kun Dong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, No.52, Fu-Cheng Road, Beijing, 100142, China
| | - Yanli Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, No.52, Fu-Cheng Road, Beijing, 100142, China
| | - Xinying Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, No.52, Fu-Cheng Road, Beijing, 100142, China
| | - Wei Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, No.52, Fu-Cheng Road, Beijing, 100142, China
| | - Xin Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, No.52, Fu-Cheng Road, Beijing, 100142, China
| | - Kaiwen Chi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, No.52, Fu-Cheng Road, Beijing, 100142, China
| | - Ling Jia
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, No.52, Fu-Cheng Road, Beijing, 100142, China
| | - Xinting Diao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, No.52, Fu-Cheng Road, Beijing, 100142, China
| | - Xiaozheng Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, No.52, Fu-Cheng Road, Beijing, 100142, China
| | - Lixin Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, No.52, Fu-Cheng Road, Beijing, 100142, China
| | - Dongmei Lin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, No.52, Fu-Cheng Road, Beijing, 100142, China.
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4
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Malapelle U, Leighl N, Addeo A, Hershkovitz D, Hochmair MJ, Khorshid O, Länger F, de Marinis F, Peled N, Sheffield BS, Smit EF, Viteri S, Wolf J, Venturini F, O'Hara RM, Rolfo C. Recommendations for reporting tissue and circulating tumour (ct)DNA next-generation sequencing results in non-small cell lung cancer. Br J Cancer 2024; 131:212-219. [PMID: 38750115 PMCID: PMC11263606 DOI: 10.1038/s41416-024-02709-4] [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: 01/04/2024] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 07/24/2024] Open
Abstract
Non-small cell lung cancer is a heterogeneous disease and molecular characterisation plays an important role in its clinical management. Next-generation sequencing-based panel testing enables many molecular alterations to be interrogated simultaneously, allowing for comprehensive identification of actionable oncogenic drivers (and co-mutations) and appropriate matching of patients with targeted therapies. Despite consensus in international guidelines on the importance of broad molecular profiling, adoption of next-generation sequencing varies globally. One of the barriers to its successful implementation is a lack of accepted standards and guidelines specifically for the reporting and clinical annotation of next-generation sequencing results. Based on roundtable discussions between pathologists and oncologists, we provide best practice recommendations for the reporting of next-generation sequencing results in non-small cell lung cancer to facilitate its use and enable easy interpretation for physicians. These are intended to complement existing guidelines related to the use of next-generation sequencing (solid and liquid). Here, we discuss next-generation sequencing workflows, the structure of next-generation sequencing reports, and our recommendations for best practice thereof. The aim of these recommendations and considerations is ultimately to ensure that reports are fully interpretable, and that the most appropriate treatment options are selected based on robust molecular profiles in well-defined reports.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Natasha Leighl
- Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Alfredo Addeo
- Oncology Unit, Geneva University Hospital, Geneva, Switzerland
| | | | - Maximilian J Hochmair
- Department of Respiratory & Critical Care Medicine, Karl Landsteiner Institute of Lung Research & Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
| | - Ola Khorshid
- National Cancer Institute, Cairo University, Cairo, Egypt
| | - Florian Länger
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Filippo de Marinis
- Division of Thoracic Oncology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Nir Peled
- Helmesely Cancer Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Brandon S Sheffield
- Division of Advanced Diagnostics, William Osler Health System, Brampton, ON, Canada
| | - Egbert F Smit
- Department of Pulmonary Diseases, Leiden University Medical Centre, Leiden, The Netherlands
| | - Santiago Viteri
- UOMI Cancer Center, Clínica Mi Tres Torres, Barcelona, Spain
| | - Jürgen Wolf
- Lung Cancer Group Cologne, Center for Integrated Oncology, University Hospital of Cologne, Cologne, Germany
| | | | | | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA.
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5
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Tóth LJ, Mokánszki A, Méhes G. The rapidly changing field of predictive biomarkers of non-small cell lung cancer. Pathol Oncol Res 2024; 30:1611733. [PMID: 38953007 PMCID: PMC11215025 DOI: 10.3389/pore.2024.1611733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/04/2024] [Indexed: 07/03/2024]
Abstract
Lung cancer is a leading cause of cancer-related death worldwide in both men and women, however mortality in the US and EU are recently declining in parallel with the gradual cut of smoking prevalence. Consequently, the relative frequency of adenocarcinoma increased while that of squamous and small cell carcinomas declined. During the last two decades a plethora of targeted drug therapies have appeared for the treatment of metastasizing non-small cell lung carcinomas (NSCLC). Personalized oncology aims to precisely match patients to treatments with the highest potential of success. Extensive research is done to introduce biomarkers which can predict the effectiveness of a specific targeted therapeutic approach. The EGFR signaling pathway includes several sufficient targets for the treatment of human cancers including NSCLC. Lung adenocarcinoma may harbor both activating and resistance mutations of the EGFR gene, and further, mutations of KRAS and BRAF oncogenes. Less frequent but targetable genetic alterations include ALK, ROS1, RET gene rearrangements, and various alterations of MET proto-oncogene. In addition, the importance of anti-tumor immunity and of tumor microenvironment has become evident recently. Accumulation of mutations generally trigger tumor specific immune defense, but immune protection may be upregulated as an aggressive feature. The blockade of immune checkpoints results in potential reactivation of tumor cell killing and induces significant tumor regression in various tumor types, such as lung carcinoma. Therapeutic responses to anti PD1-PD-L1 treatment may correlate with the expression of PD-L1 by tumor cells. Due to the wide range of diagnostic and predictive features in lung cancer a plenty of tests are required from a single small biopsy or cytology specimen, which is challenged by major issues of sample quantity and quality. Thus, the efficacy of biomarker testing should be warranted by standardized policy and optimal material usage. In this review we aim to discuss major targeted therapy-related biomarkers in NSCLC and testing possibilities comprehensively.
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Affiliation(s)
- László József Tóth
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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6
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Repetto M, Chiara Garassino M, Loong HH, Lopez-Rios F, Mok T, Peters S, Planchard D, Popat S, Rudzinski ER, Drilon A, Zhou C. NTRK gene fusion testing and management in lung cancer. Cancer Treat Rev 2024; 127:102733. [PMID: 38733648 DOI: 10.1016/j.ctrv.2024.102733] [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: 02/08/2024] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 05/13/2024]
Abstract
Neurotrophic tyrosine receptor kinase (NTRK) gene fusions are recurrent oncogenic drivers found in a variety of solid tumours, including lung cancer. Several tropomyosin receptor kinase (TRK) inhibitors have been developed to treat tumours with NTRK gene fusions. Larotrectinib and entrectinib are first-generation TRK inhibitors that have demonstrated efficacy in patients with TRK fusion lung cancers. Genomic testing is recommended for all patients with metastatic non-small cell lung cancer for optimal drug therapy selection. Multiple testing methods can be employed to identify NTRK gene fusions in the clinic and each has its own advantages and limitations. Among these assays, RNA-based next-generation sequencing (NGS) can be considered a gold standard for detecting NTRK gene fusions; however, several alternatives with minimally acceptable sensitivity and specificity are also available in areas where widespread access to NGS is unfeasible. This review highlights the importance of testing for NTRK gene fusions in lung cancer, ideally using the gold-standard method of RNA-based NGS, the various assays that are available, and treatment algorithms for patients.
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Affiliation(s)
- Matteo Repetto
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA.
| | - Marina Chiara Garassino
- Department of Medicine, Thoracic Oncology Program, The University of Chicago, Chicago, IL, USA
| | | | | | - Tony Mok
- The Chinese University of Hong Kong, Hong Kong, China
| | - Solange Peters
- Centre Hospitalier Universitaire Vaudois, Lausanne University, Lausanne, Switzerland
| | | | - Sanjay Popat
- Royal Marsden NHS Foundation Trust, London, UK; Institute of Cancer Research, London, UK
| | - Erin R Rudzinski
- Seattle Children's Hospital and University of Washington Medical Center, Seattle, WA, USA
| | - Alexander Drilon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | - Caicun Zhou
- Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
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7
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Lasala R, Romagnoli A, Santoleri F, Isgrò V, Confalonieri C, Costantini A, Enrico F, Russo G, Polidori P, Di Paolo A, Malorgio F, Beretta G, Musicco F. The lack of head-to-head randomised trials and the consequences for patients and national health service: The case of non-small cell lung cancer. Eur J Clin Pharmacol 2024; 80:519-527. [PMID: 38244052 DOI: 10.1007/s00228-024-03628-2] [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: 08/29/2023] [Accepted: 01/13/2024] [Indexed: 01/22/2024]
Abstract
INTRODUCTION To introduce a drug to the market, it's not mandatory for it to be more effective and safer than the current treatment for the same condition. Consequently, head-to-head studies between the two best treatments for the same condition are not required, and this could result in a lack of information for patients, clinicians, and decision-makers. This study aims to evaluate the presence of head-to-head studies among the drugs used for the treatment of non-small cell lung cancer (NSCLC). METHODS Taking into account the National Comprehensive Cancer Network (NCCN) guidelines updated to 2022, which list all available treatments for each NSCLC subtype, the search engine Pubmed and the platform clinicaltrials.gov were consulted to find all completed and ongoing head-to-head studies among various treatments for NSCLC. RESULTS Among the anti-EGFR (epidermal growth factor receptor) drugs, 7 studies were found, with 6 completed and 5 registrational for drug commercialisation. No completed study to date has compared osimertinib and afatinib. For anti-ALK (anaplastic lymphoma kinase) drugs, 7 studies were found, with 5 completed. Alectinib, brigatinib, and lorlatinib have no completed comparison studies, but all were compared with crizotinib. Among various immunotherapy-based regimens, 5 studies were found, with only 1 completed. Therapeutic regimens based on pembrolizumab, atezolizumab, or the combination of nivolumab/ipilimumab have not been compared in studies published to date. CONCLUSION There are few head-to-head studies comparing treatments for NSCLC; there are no such studies between the latest generation of drugs. Consequently, ambiguous areas exist due to the lack of comparative studies among the available evidence, preventing the clinician's choice of the most effective treatment and risking the patient receiving suboptimal therapy. Simultaneously, the price of the drug cannot be determined correctly, relying only on indirect evaluations from different trials. To dispel this uncertainty, it would be desirable to initiate a process that brings together the demands derived from clinical practice and clinical research to provide clinicians and patients with the best possible evidence.
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Affiliation(s)
- Ruggero Lasala
- Hospital Pharmacy of Corato, Local Health Unit of Bari, Corato, Italy.
| | - Alessia Romagnoli
- Territorial Pharmaceutical Service, Local Health Unit of Lanciano Vasto Chieti, Chieti, Italy
| | | | - Valentina Isgrò
- Hospital Pharmacy Complex Operational Unit, Azienda Ospedaliera Ospedali Riuniti Villa Sofia Cervello, Palermo, Italy
| | - Corrado Confalonieri
- UOC Farmacia Ospedaliera, Direzione Tecnica Farmacia, AUSL Piacenza, Piacenza, Italy
| | | | - Fiorenza Enrico
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia - IRCCS, Candiolo, Italy
| | - Gianluca Russo
- Medical Oncology, Santo Spirito Hospital, Pescara, Italy
| | - Piera Polidori
- Hospital Pharmacy Complex Operational Unit, Azienda Ospedaliera Ospedali Riuniti Villa Sofia Cervello, Palermo, Italy
| | | | | | | | - Felice Musicco
- Hospital Pharmacy, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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8
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Li W, Huang X, Patel R, Schleifman E, Fu S, Shames DS, Zhang J. Analytical evaluation of circulating tumor DNA sequencing assays. Sci Rep 2024; 14:4973. [PMID: 38424110 PMCID: PMC10904763 DOI: 10.1038/s41598-024-54361-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
In China, circulating tumor DNA analysis is widely used and numerous assays are available. Systematic evaluation to help users make informed selections is needed. Nine circulating tumor DNA assays, including one benchmark assay, were evaluated using 23 contrived reference samples. There were two sample types (cell-free DNA and plasma samples), three circulating tumor DNA inputs (low, < 20 ng; medium, 20-50 ng; high, > 50 ng), two variant allele frequency ranges (low, 0.1-0.5%; intermediate, 0.5-2.5%), and four variant types (single nucleotide, insertion/deletion, structural, and copy number). Sensitivity, specificity, reproducibility, and all processes from cell-free DNA extraction to bioinformatics analysis were assessed. The test assays were generally comparable or superior to the benchmark assay, demonstrating high analytical sensitivity. Variations in circulating tumor DNA extraction and quantification efficiency, sensitivity, and reproducibility were observed, particularly at lower inputs. These findings will guide circulating tumor DNA assay choice for research and clinical studies, allowing consideration of multiple technical parameters.
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Affiliation(s)
- Wenjin Li
- Oncology Biomarker Development, Roche (China) Holding Ltd, Pudong, Shanghai, China
| | - Xiayu Huang
- Oncology Biomarker Development, Roche (China) Holding Ltd, Pudong, Shanghai, China
| | - Rajesh Patel
- Oncology Biomarker Development, Genentech, Ltd, South San Francisco, USA
| | - Erica Schleifman
- Oncology Biomarker Development, Genentech, Ltd, South San Francisco, USA
| | - Shijing Fu
- Oncology Biomarker Development, Roche (China) Holding Ltd, Pudong, Shanghai, China
| | - David S Shames
- Oncology Biomarker Development, Genentech, Ltd, South San Francisco, USA.
| | - Jingyu Zhang
- Oncology Biomarker Development, Roche (China) Holding Ltd, Pudong, Shanghai, China.
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9
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Zheng X, Song X, Zhu G, Pan D, Li H, Hu J, Xiao K, Gong Q, Gu Z, Luo K, Li W. Nanomedicine Combats Drug Resistance in Lung Cancer. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308977. [PMID: 37968865 DOI: 10.1002/adma.202308977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/03/2023] [Indexed: 11/17/2023]
Abstract
Lung cancer is the second most prevalent cancer and the leading cause of cancer-related death worldwide. Surgery, chemotherapy, molecular targeted therapy, immunotherapy, and radiotherapy are currently available as treatment methods. However, drug resistance is a significant factor in the failure of lung cancer treatments. Novel therapeutics have been exploited to address complicated resistance mechanisms of lung cancer and the advancement of nanomedicine is extremely promising in terms of overcoming drug resistance. Nanomedicine equipped with multifunctional and tunable physiochemical properties in alignment with tumor genetic profiles can achieve precise, safe, and effective treatment while minimizing or eradicating drug resistance in cancer. Here, this work reviews the discovered resistance mechanisms for lung cancer chemotherapy, molecular targeted therapy, immunotherapy, and radiotherapy, and outlines novel strategies for the development of nanomedicine against drug resistance. This work focuses on engineering design, customized delivery, current challenges, and clinical translation of nanomedicine in the application of resistant lung cancer.
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Affiliation(s)
- Xiuli Zheng
- Department of Radiology, Department of Respiratory, Huaxi MR Research Center (HMRRC) and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, China
| | - Xiaohai Song
- Department of General Surgery, Gastric Cancer Center and Laboratory of Gastric Cancer, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, China
| | - Guonian Zhu
- Department of Radiology, Department of Respiratory, Huaxi MR Research Center (HMRRC) and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, China
| | - Dayi Pan
- Department of Radiology, Department of Respiratory, Huaxi MR Research Center (HMRRC) and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, China
| | - Haonan Li
- Department of Radiology, Department of Respiratory, Huaxi MR Research Center (HMRRC) and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, China
| | - Jiankun Hu
- Department of General Surgery, Gastric Cancer Center and Laboratory of Gastric Cancer, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, China
| | - Kai Xiao
- Department of Radiology, Department of Respiratory, Huaxi MR Research Center (HMRRC) and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, China
| | - Qiyong Gong
- Department of Radiology, Department of Respiratory, Huaxi MR Research Center (HMRRC) and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, China
- Precision Medicine Key Laboratory of Sichuan Province, Functional and Molecular Imaging Key Laboratory of Sichuan Province, and Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, 610041, China
- Department of Radiology, West China Xiamen Hospital of Sichuan University, Xiamen, Fujian, 361000, China
| | - Zhongwei Gu
- Department of Radiology, Department of Respiratory, Huaxi MR Research Center (HMRRC) and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, China
| | - Kui Luo
- Department of Radiology, Department of Respiratory, Huaxi MR Research Center (HMRRC) and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, China
- Precision Medicine Key Laboratory of Sichuan Province, Functional and Molecular Imaging Key Laboratory of Sichuan Province, and Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, 610041, China
| | - Weimin Li
- Department of Radiology, Department of Respiratory, Huaxi MR Research Center (HMRRC) and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, China
- Precision Medicine Key Laboratory of Sichuan Province, Functional and Molecular Imaging Key Laboratory of Sichuan Province, and Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, 610041, China
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10
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Conde E, Hernandez S, Alonso M, Lopez-Rios F. Pan-TRK Immunohistochemistry to Optimize the Detection of NTRK Fusions: Removing the Hay When Looking for the Needle. Mod Pathol 2023; 36:100346. [PMID: 37757968 DOI: 10.1016/j.modpat.2023.100346] [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: 06/06/2023] [Revised: 08/17/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023]
Affiliation(s)
- Esther Conde
- Pathology Department, Hospital Universitario 12 de Octubre, Universidad Complutense de Madrid, Research Institute Hospital 12 de Octubre (i+12), CIBERONC, Madrid, Spain
| | - Susana Hernandez
- Pathology Department, Hospital Universitario 12 de Octubre, Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | - Marta Alonso
- Pathology Department, Hospital Universitario 12 de Octubre, Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | - Fernando Lopez-Rios
- Pathology Department, Hospital Universitario 12 de Octubre, Universidad Complutense de Madrid, Research Institute Hospital 12 de Octubre (i+12), CIBERONC, Madrid, Spain.
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11
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Shang X, Zhang W, Han W, Xia H, Liu N, Wang X, Liu Y. Efficacy of immune checkpoint inhibitors in non-small cell lung cancer with NTRK family mutations. BMC Pulm Med 2023; 23:482. [PMID: 38031067 PMCID: PMC10688060 DOI: 10.1186/s12890-023-02707-x] [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: 05/08/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND The efficacy of immune checkpoint inhibitors (ICIs) in non-small cell lung cancer (NSCLC) patients harboring neurotrophin receptor kinase (NTRK) family mutations remains obscure. METHODS The Zehir cohort from cBioPortal was used to analyze the mutations (MT) frequency of NTRK family in patients with NSCLC, and their correlation with clinical characteristics and patient survival. The influence of NTRK MT on ICIs efficacy was evaluated in ICIs-treated patients from Samstein cohort and further validated by use of data from OAK/POPLAR cohort. RESULTS In the Zehir cohort, a significant difference was observed in median overall survival (mOS) between patients with NTRK MT and wild-type (WT) (mOS: 18.97 vs. 21.27 months, HR = 1.34, 95%CI 1.00-1.78; log-rank P = 0.047). In Samstein cohort, the mOS of NTRK mutant patients receiving ICIs has improved compared to WT patients (mOS: 21.00 vs. 11.00 months, log-rank P = 0.103). Notably, in subgroup analysis, ICIs significantly prolonged mOS in patients with NTRK3 MT than in WT patients (mOS: not available vs. 11.00 months, HR = 0.36, 95%CI 0.16-0.81; log-rank P = 0.009). Identical mOS between NTRK MT and WT patients receiving ICIs treatment (mOS: 13.24 vs. 13.50 months, log-rank P = 0.775) was observed in OAK/POPLAR cohort. Moreover, a similar programmed death ligand 1 (PD-L1) expression, but higher tumor mutational burden (TMB), blood TMB (bTMB) and enriched anti-tumor immunity were observed in NTRK MT compared to WT (P < 0.05). CONCLUSION Taking high TMB or bTMB into consideration, patients with NTRK mutant NSCLC could benefit from ICIs treatment.
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Affiliation(s)
- Xiaoling Shang
- Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China
| | - Wengang Zhang
- Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China
| | - Wenfei Han
- Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China
| | - Handai Xia
- Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China
| | - Ni Liu
- Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China
| | - Xiuwen Wang
- Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China.
| | - Yanguo Liu
- Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China.
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12
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Prevost R, Chretien B, Minoc EM, Dolladille C, Da-Silva A, Nehme A, Joly F, Lelong-Boulouard V, Bastien E. Neurocognitive impairment in females with breast cancer treated with endocrine therapy and CDK4/6 inhibitors: a pharmacovigilance study using the World Health Organization's database. Front Pharmacol 2023; 14:1278682. [PMID: 37927591 PMCID: PMC10622981 DOI: 10.3389/fphar.2023.1278682] [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: 08/16/2023] [Accepted: 10/04/2023] [Indexed: 11/07/2023] Open
Abstract
Importance: Endocrine therapies (ETs) and inhibitors of cyclin-dependent kinases-4/6 (iCDK4/6s) are a standard treatment in breast cancer. However, data on potential neurocognitive impacts remain inconsistent for ET and are scarce for iCDK4/6s. Objective: To evaluate whether ET and iCDK4/6s are associated with neurocognitive impairment (NCI). Methods: We used observational, real-world cases of NCI from the World Health Organization's database VigiBase® to perform disproportionality analysis. Cases were defined as any symptom of NCI in females treated with ETs or iCDK4/6s. The study period was from the date of the first adverse event reported in VigiBase® with iCDK4/6s (1 January 2014) until the date of data extraction (16 March 2022). In our primary analysis, we calculated the reporting odds ratio (ROR) adjusted for age to identify a potential association between NCI and individual ETs in isolation or in combination with iCDK4/6s. We also performed subgroup analyses by the NCI class. Results: We identified 2.582 and 1.943 reports of NCI associated with ETs and iCDK4/6s, respectively. NCI was significantly associated with each ET [anastrozole: n = 405, aROR = 1.52 (95% CI: 1.37-1.67); letrozole: n = 741, aROR = 1.37 (95% CI: 1.27-1.47); exemestane: n = 316, aROR = 1.37 (95% CI: 1.22-1.53); tamoxifen: n = 311, aROR = 1.25 (95% CI: 1.12-1.40); and fulvestrant: n = 319, aROR = 1.19 (95% CI: 1.06-1.33)] and only with palbociclib for iCDK4/6s [n = 1,542, aROR = 1.41 (95% CI: 1.34-1.48)]. Conclusion: These findings suggest that in females treated for breast cancer, all ETs may be associated with NCI. However, amongst iCDK4/6s, NCI may be specific to palbociclib. NCI most frequently involved learning and memory as well as language. Neurocognitive impact of treatments requires better consideration and management.
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Affiliation(s)
- Rachel Prevost
- Department of Pharmacology, University Teaching Hospital of Caen-Normandie, Caen, France
| | - Basile Chretien
- Department of Pharmacology, University Teaching Hospital of Caen-Normandie, Caen, France
| | - Elise-Marie Minoc
- Department of Pharmacology, University Teaching Hospital of Caen-Normandie, Caen, France
- Normandie University, UNICAEN, INSERM COMETE, U1075, Caen, France
| | - Charles Dolladille
- Department of Pharmacology, University Teaching Hospital of Caen-Normandie, Caen, France
- Normandie University, UNICAEN, INSERM U1086 “Interdisciplinary Research Unit for Cancers Prevention and Treatment” (ANTICIPE), Caen, France
| | - Angélique Da-Silva
- Department of Pharmacology, University Teaching Hospital of Caen-Normandie, Caen, France
| | - Ahmad Nehme
- Department of Neurology, University Teaching Hospital of Caen-Normandie, Caen, France
| | - Florence Joly
- Normandie University, UNICAEN, INSERM U1086 “Interdisciplinary Research Unit for Cancers Prevention and Treatment” (ANTICIPE), Caen, France
- Comprehensive Cancer Center Baclesse, Unicancer, Caen, France
| | - Véronique Lelong-Boulouard
- Department of Pharmacology, University Teaching Hospital of Caen-Normandie, Caen, France
- Normandie University, UNICAEN, INSERM COMETE, U1075, Caen, France
| | - Etienne Bastien
- Department of Pharmacology, University Teaching Hospital of Caen-Normandie, Caen, France
- Comprehensive Cancer Center Baclesse, Unicancer, Caen, France
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13
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Meira DD, de Castro e Caetano MC, Casotti MC, Zetum ASS, Gonçalves AFM, Moreira AR, de Oliveira AH, Pesente F, Santana GM, de Almeida Duque D, Pereira GSC, de Castro GDSC, Pavan IP, Chagas JPS, Bourguignon JHB, de Oliveira JR, Barbosa KRM, Altoé LSC, Louro LS, Merigueti LP, Alves LNR, Machado MRR, Roque MLRO, Prates PS, de Paula Segáua SH, dos Santos Uchiya T, Louro TES, Daleprane VE, Guaitolini YM, Vicente CR, dos Reis Trabach RS, de Araújo BC, dos Santos EDVW, de Paula F, Lopes TJS, de Carvalho EF, Louro ID. Prognostic Factors and Markers in Non-Small Cell Lung Cancer: Recent Progress and Future Challenges. Genes (Basel) 2023; 14:1906. [PMID: 37895255 PMCID: PMC10606762 DOI: 10.3390/genes14101906] [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: 09/01/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/29/2023] Open
Abstract
Lung cancer is a highly aggressive neoplasm and, despite the development of recent therapies, tumor progression and recurrence following the initial response remains unsolved. Several questions remain unanswered about non-small cell lung cancer (NSCLC): (1) Which patients will actually benefit from therapy? (2) What are the predictive factors of response to MAbs and TKIs? (3) What are the best combination strategies with conventional treatments or new antineoplastic drugs? To answer these questions, an integrative literature review was carried out, searching articles in PUBMED, NCBI-PMC, Google Academic, and others. Here, we will examine the molecular genetics of lung cancer, emphasizing NSCLC, and delineate the primary categories of inhibitors based on their molecular targets, alongside the main treatment alternatives depending on the type of acquired resistance. We highlighted new therapies based on epigenetic information and a single-cell approach as a potential source of new biomarkers. The current and future of NSCLC management hinges upon genotyping correct prognostic markers, as well as on the evolution of precision medicine, which guarantees a tailored drug combination with precise targeting.
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Affiliation(s)
- Débora Dummer Meira
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Maria Clara de Castro e Caetano
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Matheus Correia Casotti
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Aléxia Stefani Siqueira Zetum
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - André Felipe Monteiro Gonçalves
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - André Rodrigues Moreira
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Augusto Henrique de Oliveira
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Fellipe Pesente
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Gabriel Mendonça Santana
- Centro de Ciências da Saúde, Curso de Medicina, Universidade Federal do Espírito Santo (UFES), Vitória 29090-040, Brazil
| | - Daniel de Almeida Duque
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Gierleson Santos Cangussu Pereira
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Giulia de Souza Cupertino de Castro
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Isabele Pagani Pavan
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - João Pedro Sarcinelli Chagas
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - José Henrique Borges Bourguignon
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Juliana Ribeiro de Oliveira
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Karen Ruth Michio Barbosa
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Lorena Souza Castro Altoé
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Luana Santos Louro
- Centro de Ciências da Saúde, Curso de Medicina, Universidade Federal do Espírito Santo (UFES), Vitória 29090-040, Brazil
| | - Luiza Poppe Merigueti
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Lyvia Neves Rebello Alves
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Marlon Ramos Rosado Machado
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Maria Luísa Rodrigues Oliveira Roque
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Pedro Santana Prates
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Sayuri Honorio de Paula Segáua
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Taissa dos Santos Uchiya
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Thomas Erik Santos Louro
- Escola Superior de Ciências da Santa Casa de Misericórdia de Vitória (EMESCAM), Curso de Medicina, Vitória 29027-502, Brazil
| | - Vinicius Eduardo Daleprane
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Yasmin Moreto Guaitolini
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Creuza Rachel Vicente
- Departamento de Medicina Social, Universidade Federal do Espírito Santo, Vitória 29090-040, Brazil
| | - Raquel Silva dos Reis Trabach
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Bruno Cancian de Araújo
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Eldamária de Vargas Wolfgramm dos Santos
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Flávia de Paula
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Tiago José S. Lopes
- Department of Reproductive Biology, National Center for Child Health and Development Research Institute, Tokyo 157-8535, Japan
| | - Elizeu Fagundes de Carvalho
- Instituto de Biologia Roberto Alcântara Gomes (IBRAG), Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20551-030, Brazil
| | - Iúri Drumond Louro
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
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14
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Adam J, Stang NL, Uguen A, Badoual C, Chenard MP, Lantuéjoul S, Maran-Gonzalez A, Robin YM, Rochaix P, Sabourin JC, Soubeyran I, Sturm N, Svrcek M, Vincent-Salomon A, Radosevic-Robin N, Penault-Llorca F. Multicenter Harmonization Study of Pan-Trk Immunohistochemistry for the Detection of NTRK3 Fusions. Mod Pathol 2023; 36:100192. [PMID: 37084942 DOI: 10.1016/j.modpat.2023.100192] [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: 10/25/2022] [Revised: 03/14/2023] [Accepted: 04/12/2023] [Indexed: 04/23/2023]
Abstract
Pan-Trk immunohistochemistry has been described as a screening test for the detection of NTRK fusions in a broad spectrum of tumor types. However, pan-Trk testing in the clinical setting may be limited by many factors, including analytical parameters such as clones, platforms, and protocols used. This study aimed to harmonize pan-Trk testing using various clones and immunohistochemical (IHC) platforms and to evaluate the level of analytical variability across pathology laboratories. We developed several IHC pan-Trk assays using clones EPR17341 (Abcam) and A7H6R (Cell Signaling Technology) on Ventana/Roche, Agilent, and Leica platforms. To compare them, we sent unstained sections of a tissue microarray containing 9 cases with NTRK3 fusions to participating laboratories, to perform staining on Ventana/Roche (10 centers), Agilent (4 centers), and Leica (3 centers) platforms. A ready-to-use pan-Trk IVD assay (Ventana/Roche) was also performed in 3 centers. All slides were centrally and blindly reviewed for the percentage of stained tumor cells. Laboratory-developed tests with clone EPR17341 were able to detect pan-Trk protein expression in all cases, whereas lower rates of positivity were observed with clone A7H6R. Moderate to strong variability of the positive cases rate was observed with both antibodies in each IHC platforms type and each of the positivity cut points evaluated (≥1%, ≥10%, and ≥50% of stained tumor cells). The rate of false-negative cases was lower when pan-Trk staining was assessed with the lowest positivity threshold (≥1%). In conclusion, most evaluated pan-Trk IHC laboratory-developed tests were able to detect NTRK3-fusion proteins; however, a significant analytical variability was observed between antibodies, platforms, and centers.
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Affiliation(s)
- Julien Adam
- Pathology Department, Groupe Hospitalier Paris Saint-Joseph, Paris, and Inserm U1186, Gustave Roussy, Villejuif, France.
| | - Nolwenn Le Stang
- National Reference Center Mesopath, Centre Leon Berard, Lyon, France; Now with General Cancer Registry of Poitou-Charentes, Biology, Pharmacy and Public Health Unit, University Hospital, Poitiers, France
| | - Arnaud Uguen
- LBAI-UMR1227 - Inserm & Department of Pathology, CHU de Brest, Université de Brest, Brest, France
| | | | | | - Sylvie Lantuéjoul
- Université de Grenoble Alpes, Grenoble and Pathology Department, Centre Leon Berard, Lyon, France
| | | | | | | | | | | | | | - Magali Svrcek
- Pathology Department, Hôpital Saint-Antoine, AP-HP, Paris, France
| | | | - Nina Radosevic-Robin
- Pathology Department, Centre Jean Perrin, Clermont-Ferrand, France; University Clermont Auvergne, INSERM U1240, Clermont-Ferrand, France
| | - Frédérique Penault-Llorca
- Pathology Department, Centre Jean Perrin, Clermont-Ferrand, France; University Clermont Auvergne, INSERM U1240, Clermont-Ferrand, France
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15
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Zhang Y, Zhang J, Zhang W, Wang M, Wang S, Xu Y, Zhao L, Li X, Li G. Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:573-588. [PMID: 36702236 PMCID: PMC10787015 DOI: 10.1016/j.gpb.2023.01.004] [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: 08/25/2021] [Revised: 11/30/2022] [Accepted: 01/17/2023] [Indexed: 01/25/2023]
Abstract
Studies on the lung cancer genome are indispensable for developing a cure for lung cancer. Whole-genome resequencing, genome-wide association studies, and transcriptome sequencing have greatly improved our understanding of the cancer genome. However, dysregulation of long-range chromatin interactions in lung cancer remains poorly described. To better understand the three-dimensional (3D) genomic interaction features of the lung cancer genome, we used the A549 cell line as a model system and generated high-resolution chromatin interactions associated with RNA polymerase II (RNAPII), CCCTC-binding factor (CTCF), enhancer of zeste homolog 2 (EZH2), and histone 3 lysine 27 trimethylation (H3K27me3) using long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). Analysis showed that EZH2/H3K27me3-mediated interactions further repressed target genes, either through loops or domains, and their distributions along the genome were distinct from and complementary to those associated with RNAPII. Cancer-related genes were highly enriched with chromatin interactions, and chromatin interactions specific to the A549 cell line were associated with oncogenes and tumor suppressor genes, such as additional repressive interactions on FOXO4 and promoter-promoter interactions between NF1 and RNF135. Knockout of an anchor associated with chromatin interactions reversed the dysregulation of cancer-related genes, suggesting that chromatin interactions are essential for proper expression of lung cancer-related genes. These findings demonstrate the 3D landscape and gene regulatory relationships of the lung cancer genome.
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Affiliation(s)
- Yan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingwen Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Mohan Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangqi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Yao Xu
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China.
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16
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Stockley TL, Lo B, Box A, Corredor AG, DeCoteau J, Desmeules P, Feilotter H, Grafodatskaya D, Greer W, Hawkins C, Huang WY, Izevbaye I, Lépine G, Martins Filho SN, Papadakis AI, Park PC, Riviere JB, Sheffield BS, Spatz A, Spriggs E, Tran-Thanh D, Yip S, Zhang T, Torlakovic E, Tsao MS. CANTRK: A Canadian Ring Study to Optimize Detection of NTRK Gene Fusions by Next-Generation RNA Sequencing. J Mol Diagn 2023; 25:168-174. [PMID: 36586421 DOI: 10.1016/j.jmoldx.2022.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/01/2022] [Accepted: 12/06/2022] [Indexed: 12/29/2022] Open
Abstract
The Canadian NTRK (CANTRK) study is an interlaboratory comparison ring study to optimize testing for neurotrophic receptor tyrosine kinase (NTRK) fusions in Canadian laboratories. Sixteen diagnostic laboratories used next-generation sequencing (NGS) for NTRK1, NTRK2, or NTRK3 fusions. Each laboratory received 12 formalin-fixed, paraffin-embedded tumor samples with unique NTRK fusions and two control non-NTRK fusion samples (one ALK and one ROS1). Laboratories used validated protocols for NGS fusion detection. Panels included Oncomine Comprehensive Assay v3, Oncomine Focus Assay, Oncomine Precision Assay, AmpliSeq for Illumina Focus, TruSight RNA Pan-Cancer Panel, FusionPlex Lung, and QIAseq Multimodal Lung. One sample was withdrawn from analysis because of sample quality issues. Of the remaining 13 samples, 6 of 11 NTRK fusions and both control fusions were detected by all laboratories. Two fusions, WNK2::NTRK2 and STRN3::NTRK2, were not detected by 10 laboratories using the Oncomine Comprehensive or Focus panels, due to absence of WNK2 and STRN3 in panel designs. Two fusions, TPM3::NTRK1 and LMNA::NTRK1, were challenging to detect on the AmpliSeq for Illumina Focus panel because of bioinformatics issues. One ETV6::NTRK3 fusion at low levels was not detected by two laboratories using the TruSight Pan-Cancer Panel. Panels detecting all fusions included FusionPlex Lung, Oncomine Precision, and QIAseq Multimodal Lung. The CANTRK study showed competency in detection of NTRK fusions by NGS across different panels in 16 Canadian laboratories and identified key test issues as targets for improvements.
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Affiliation(s)
- Tracy L Stockley
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
| | - Bryan Lo
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Adrian Box
- Alberta Precision Labs, Calgary, Alberta, Canada
| | | | - John DeCoteau
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Patrice Desmeules
- IUCPQ-UL, Quebec Heart and Lung Institute, Quebec City, Quebec, Canada
| | - Harriet Feilotter
- Kingston Health Sciences Centre, Kingston, Ontario, Canada; Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Daria Grafodatskaya
- Hamilton Health Sciences Centre, Hamilton, Ontario, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Wenda Greer
- Nova Scotia Health Authority, Halifax, Nova Scotia, Canada
| | - Cynthia Hawkins
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Weei Yuarn Huang
- Nova Scotia Health Authority, Halifax, Nova Scotia, Canada; Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Iyare Izevbaye
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Sebastiao N Martins Filho
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Paul C Park
- Shared Health Manitoba, Winnipeg, Manitoba, Canada
| | | | | | - Alan Spatz
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | | | - Danh Tran-Thanh
- CHUM-Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Stephen Yip
- BC Cancer, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Tong Zhang
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Emina Torlakovic
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ming Sound Tsao
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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17
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Zhang H, He F, Gao G, Lu S, Wei Q, Hu H, Wu Z, Fang M, Wang X. Approved Small-Molecule ATP-Competitive Kinases Drugs Containing Indole/Azaindole/Oxindole Scaffolds: R&D and Binding Patterns Profiling. Molecules 2023; 28:molecules28030943. [PMID: 36770611 PMCID: PMC9920796 DOI: 10.3390/molecules28030943] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
Kinases are among the most important families of biomolecules and play an essential role in the regulation of cell proliferation, apoptosis, metabolism, and other critical physiological processes. The dysregulation and gene mutation of kinases are linked to the occurrence and development of various human diseases, especially cancer. As a result, a growing number of small-molecule drugs based on kinase targets are being successfully developed and approved for the treatment of many diseases. The indole/azaindole/oxindole moieties are important key pharmacophores of many bioactive compounds and are generally used as excellent scaffolds for drug discovery in medicinal chemistry. To date, 30 ATP-competitive kinase inhibitors bearing the indole/azaindole/oxindole scaffold have been approved for the treatment of diseases. Herein, we summarize their research and development (R&D) process and describe their binding models to the ATP-binding sites of the target kinases. Moreover, we discuss the significant role of the indole/azaindole/oxindole skeletons in the interaction of their parent drug and target kinases, providing new medicinal chemistry inspiration and ideas for the subsequent development and optimization of kinase inhibitors.
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Affiliation(s)
- Haofan Zhang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Fengming He
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Guiping Gao
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
- School of Medicine, Huaqiao University, Quanzhou 362021, China
| | - Sheng Lu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Qiaochu Wei
- School of Public Health, Xiamen University, Xiamen 361102, China
| | - Hongyu Hu
- Xingzhi College, Zhejiang Normal University, Lanxi 321004, China
| | - Zhen Wu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Meijuan Fang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
- Correspondence: (M.F.); (X.W.)
| | - Xiumin Wang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
- Correspondence: (M.F.); (X.W.)
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18
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Fernández Aceñero MJ, Díaz Del Arco C, Dinarés C, Labiano T, Tejerina E, Bernabé MJ, Forcen E, Saiz-Pardo M, Pérez P, Lozano MD. Overview and update on molecular testing in non-small cell lung carcinoma utilizing endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) samples. Diagn Cytopathol 2023; 51:26-35. [PMID: 35899869 DOI: 10.1002/dc.25019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 12/13/2022]
Abstract
Lung carcinoma remains one of the most frequent and aggressive human neoplasms. Fortunately, in the last decades, the increasing knowledge of the molecular mechanisms leading to cancer development has allowed the use of targeted therapies with improvement of prognosis in many patients. Clinical management has also changed after the introduction of endobronchialultrasonographic bronchoscopy that allows a conservative staging of lung tumors, avoiding the need of mediastinoscopy for lymph node staging. Lung pathologists and cytopathologists are facing the challenge of giving the more comprehensive prognostic and predictive information with ever smaller tissue or cytological samples. The aim of this review is to summarize the molecular testing for non-small cell lung carcinoma and how pathologists can contribute to the patient's outcome with a conscious management of biological samples.
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Affiliation(s)
| | | | - Carme Dinarés
- Department of Surgical Pathology, Valld'Hebron, Barcelona, Spain
| | - Tania Labiano
- Department of Surgical Pathology, Clínica Universitaria of Navarra, Pamplona, Spain
| | - Eva Tejerina
- Department of Surgical Pathology, Clínica Puerta de Hierro, Madrid, Spain
| | - Mª José Bernabé
- Department of Pneumology, Hospital Clínico San Carlos, Madrid, Spain
| | - Elena Forcen
- Department of Pneumology, Hospital Clínico San Carlos, Madrid, Spain
| | - Melchor Saiz-Pardo
- Departments of Surgical Pathology, Hospital Clínico San Carlos, Madrid, Spain
| | - Pablo Pérez
- Departments of Surgical Pathology, Hospital Clínico San Carlos, Madrid, Spain
| | - Maria D Lozano
- Department of Surgical Pathology, Clínica Universitaria of Navarra, Pamplona, Spain
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19
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Wang Z, Xing Y, Li B, Li X, Liu B, Wang Y. Molecular pathways, resistance mechanisms and targeted interventions in non-small-cell lung cancer. MOLECULAR BIOMEDICINE 2022; 3:42. [PMID: 36508072 PMCID: PMC9743956 DOI: 10.1186/s43556-022-00107-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. The discovery of tyrosine kinase inhibitors effectively targeting EGFR mutations in lung cancer patients in 2004 represented the beginning of the precision medicine era for this refractory disease. This great progress benefits from the identification of driver gene mutations, and after that, conventional and new technologies such as NGS further illustrated part of the complex molecular pathways of NSCLC. More targetable driver gene mutation identification in NSCLC patients greatly promoted the development of targeted therapy and provided great help for patient outcomes including significantly improved survival time and quality of life. Herein, we review the literature and ongoing clinical trials of NSCLC targeted therapy to address the molecular pathways and targeted intervention progress in NSCLC. In addition, the mutations in EGFR gene, ALK rearrangements, and KRAS mutations in the main sections, and the less common molecular alterations in MET, HER2, BRAF, ROS1, RET, and NTRK are discussed. The main resistance mechanisms of each targeted oncogene are highlighted to demonstrate the current dilemma of targeted therapy in NSCLC. Moreover, we discuss potential therapies to overcome the challenges of drug resistance. In this review, we manage to display the current landscape of targetable therapeutic patterns in NSCLC in this era of precision medicine.
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Affiliation(s)
- Zixi Wang
- grid.412901.f0000 0004 1770 1022Thoracic Oncology Ward, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yurou Xing
- grid.412901.f0000 0004 1770 1022Thoracic Oncology Ward, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Bingjie Li
- grid.412901.f0000 0004 1770 1022Thoracic Oncology Ward, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Xiaoyu Li
- grid.412901.f0000 0004 1770 1022Clinical Trial Center, National Medical Products Administration Key Laboratory for Clinical Research and Evaluation of Innovative Drugs, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Bin Liu
- grid.54549.390000 0004 0369 4060Department of Medical Oncology, School of Medicine, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, University of Electronic Science and Technology of China, Chengdu, Sichuan China
| | - Yongsheng Wang
- grid.412901.f0000 0004 1770 1022Thoracic Oncology Ward, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
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20
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Pang K, Wang W, Qin J, Shi Z, Hao L, Ma Y, Xu H, Wu Z, Pan D, Chen Z, Han C. Role of protein phosphorylation in cell signaling, disease, and the intervention therapy. MedComm (Beijing) 2022; 3:e175. [DOI: 10.1002/mco2.175] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Kun Pang
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College The Affiliated Xuzhou Hospital of Medical College of Southeast University The Affiliated Xuzhou Center Hospital of Nanjing University of Chinese Medicine Xuzhou Jiangsu China
| | - Wei Wang
- Department of Medical College Southeast University Nanjing Jiangsu China
| | - Jia‐Xin Qin
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College The Affiliated Xuzhou Hospital of Medical College of Southeast University The Affiliated Xuzhou Center Hospital of Nanjing University of Chinese Medicine Xuzhou Jiangsu China
| | - Zhen‐Duo Shi
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College The Affiliated Xuzhou Hospital of Medical College of Southeast University The Affiliated Xuzhou Center Hospital of Nanjing University of Chinese Medicine Xuzhou Jiangsu China
| | - Lin Hao
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College The Affiliated Xuzhou Hospital of Medical College of Southeast University The Affiliated Xuzhou Center Hospital of Nanjing University of Chinese Medicine Xuzhou Jiangsu China
| | - Yu‐Yang Ma
- Graduate School Bengbu Medical College Bengbu Anhui China
| | - Hao Xu
- Graduate School Bengbu Medical College Bengbu Anhui China
| | - Zhuo‐Xun Wu
- Department of Pharmaceutical Sciences College of Pharmacy and Health Sciences St. John's University, Queens New York New York USA
| | - Deng Pan
- Graduate School Bengbu Medical College Bengbu Anhui China
| | - Zhe‐Sheng Chen
- Department of Pharmaceutical Sciences College of Pharmacy and Health Sciences St. John's University, Queens New York New York USA
| | - Cong‐Hui Han
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College The Affiliated Xuzhou Hospital of Medical College of Southeast University The Affiliated Xuzhou Center Hospital of Nanjing University of Chinese Medicine Xuzhou Jiangsu China
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21
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Wang J, Zhou Y, Tang X, Yu X, Wang Y, Chan S, Song X, Tu Z, Zhang Z, Lu X, Zhang Z, Ding K. JND4135, a New Type II TRK Inhibitor, Overcomes TRK xDFG and Other Mutation Resistance In Vitro and In Vivo. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196500. [PMID: 36235036 PMCID: PMC9570838 DOI: 10.3390/molecules27196500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/17/2022] [Accepted: 09/27/2022] [Indexed: 11/09/2022]
Abstract
The tropomyosin receptor kinases (TRKs) have been validated as effective targets in anticancer drug discovery. Two first-generation TRK inhibitors have been approved into market and displayed an encouraging therapeutic response in cancer patients harboring TRK fusion proteins. However, acquired resistance mediated by secondary TRK mutations especially in the xDFG motif remains an unsolved challenge in the clinic. Herein, we report the preclinical pharmacological results of JND4135, a new type II pan-TRK inhibitor, in overcoming TRK mutant resistance, including the xDFG mutations in vitro and in vivo. At a low nanomolar level, JND4135 displays a strong activity against wild-type TRKA/B/C and secondary mutations involving xDFG motif substitutions in kinase assays and cellular models; occupies the TRK proteins for an extended time; and has a slower dissociation rate than other TRK inhibitors. Moreover, by intraperitoneal injection, JND4135 exhibits tumor growth inhibition (TGI) of 81.0% at a dose of 40 mg/kg in BaF3-CD74-TRKA-G667C mice xenograft model. Therefore, JND4135 can be considered as a lead compound for drug discovery overcoming the resistance of TRK inhibitor drugs mediated by xDFG mutations.
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Affiliation(s)
- Jie Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yang Zhou
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xia Tang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xiuwen Yu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yongjin Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Shingpan Chan
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xiaojuan Song
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China
| | - Zhengchao Tu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China
| | - Zhimin Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Correspondence: (X.L.); (Z.Z.); (K.D.); Tel.: +86-020-8522-3764 (Z.Z.)
| | - Zhang Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Correspondence: (X.L.); (Z.Z.); (K.D.); Tel.: +86-020-8522-3764 (Z.Z.)
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Lingling Road, Shanghai 200032, China
- Correspondence: (X.L.); (Z.Z.); (K.D.); Tel.: +86-020-8522-3764 (Z.Z.)
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Montella L, Del Gaudio N, Bove G, Cuomo M, Buonaiuto M, Costabile D, Visconti R, Facchini G, Altucci L, Chiariotti L, Della Monica R. Looking Beyond the Glioblastoma Mask: Is Genomics the Right Path? Front Oncol 2022; 12:926967. [PMID: 35875139 PMCID: PMC9306486 DOI: 10.3389/fonc.2022.926967] [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: 04/23/2022] [Accepted: 06/09/2022] [Indexed: 11/15/2022] Open
Abstract
Glioblastomas are the most frequent and malignant brain tumor hallmarked by an invariably poor prognosis. They have been classically differentiated into primary isocitrate dehydrogenase 1 or 2 (IDH1 -2) wild-type (wt) glioblastoma (GBM) and secondary IDH mutant GBM, with IDH wt GBMs being commonly associated with older age and poor prognosis. Recently, genetic analyses have been integrated with epigenetic investigations, strongly implementing typing and subtyping of brain tumors, including GBMs, and leading to the new WHO 2021 classification. GBM genomic and epigenomic profile influences evolution, resistance, and therapeutic responses. However, differently from other tumors, there is a wide gap between the refined GBM profiling and the limited therapeutic opportunities. In addition, the different oncogenes and tumor suppressor genes involved in glial cell transformation, the heterogeneous nature of cancer, and the restricted access of drugs due to the blood–brain barrier have limited clinical advancements. This review will summarize the more relevant genetic alterations found in GBMs and highlight their potential role as potential therapeutic targets.
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Affiliation(s)
- Liliana Montella
- Oncology Operative Unit, "Santa Maria delle Grazie" Hospital, ASL Napoli 2 NORD-, Pozzuoli, Italy
| | - Nunzio Del Gaudio
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Guglielmo Bove
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Mariella Cuomo
- CEINGE Biotecnologie Avanzate scarl, Napoli, Italy.,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Napoli, Italy
| | - Michela Buonaiuto
- CEINGE Biotecnologie Avanzate scarl, Napoli, Italy.,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Napoli, Italy
| | - Davide Costabile
- CEINGE Biotecnologie Avanzate scarl, Napoli, Italy.,SEMM-European School of Molecular Medicine, Milano, Italy
| | - Roberta Visconti
- CEINGE Biotecnologie Avanzate scarl, Napoli, Italy.,Institute of Experimental Endocrinology and Oncology, Consiglio Nazionale delle Ricerche, Napoli, Italy
| | - Gaetano Facchini
- Oncology Operative Unit, "Santa Maria delle Grazie" Hospital, ASL Napoli 2 NORD-, Pozzuoli, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Napoli, Italy.,BIOGEM, Ariano Irpino, Italy
| | - Lorenzo Chiariotti
- CEINGE Biotecnologie Avanzate scarl, Napoli, Italy.,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Napoli, Italy
| | - Rosa Della Monica
- CEINGE Biotecnologie Avanzate scarl, Napoli, Italy.,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Napoli, Italy
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23
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Wang Z, Ren J, Jia K, Zhao Y, Liang L, Cheng Z, Huang F, Zhao X, Cheng J, Song S, Sheng T, Wan W, Shu Q, Wu D, Zhang J, Lu T, Chen Y, Ran T, Lu S. Identification and structural analysis of a selective tropomyosin receptor kinase C (TRKC) inhibitor. Eur J Med Chem 2022; 241:114601. [PMID: 35872544 DOI: 10.1016/j.ejmech.2022.114601] [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: 02/02/2022] [Revised: 04/11/2022] [Accepted: 07/07/2022] [Indexed: 11/04/2022]
Abstract
Tropomyosin receptor kinases (TRKs) are a family of TRKA, TRKB and TRKC isoforms. It has been widely reported that TRKs are implicated in a variety of tumors with several Pan-TRK inhibitors currently being used or evaluated in clinical treatment. However, off-target adverse events frequently occur in the clinical use of Pan-TRK inhibitors, which result in poor patient compliance, even drug discontinuation. Although a subtype-selectivity TRK inhibitor may avert the potential off-target adverse events and can act as a more powerful tool compound in the biochemical studies on TRKs, the high sequence similarities of TRKs hinder the development of subtype-selectivity TRK inhibitors. For example, no selective TRKC inhibitor has been reported. Herein, a selective TRKC inhibitor (L13) was disclosed, with potent TRKC inhibitory activity and 107.5-/34.9-fold selectivity over TRKA/B (IC50 TRKA/B/C = 1400 nM, 454 nM, 13 nM, respectively). Extensive molecular dynamics simulations illustrated that key interactions of L13 with the residues and diversely conserved water molecules in the ribose regions of different TRKs may be the structural basis of selectivity. This will provide inspiring insights into the development of subtype-selectivity TRK inhibitors. Moreover, L13 could serve as a tool compound to investigate the distinct biological functions of TRKC and a starting point for further research on drugs specifically targeting TRKC.
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Affiliation(s)
- Zhijie Wang
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Jiwei Ren
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Kun Jia
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Yuming Zhao
- Edmond H. Fischer Translational Medical Research Laboratory, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, PR China
| | - Li Liang
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Zitian Cheng
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Fei Huang
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Xiaofei Zhao
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Jie Cheng
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Shiyu Song
- School of Life Sciences and Technology, China Pharmaceutical University, Nanjing, 210038, PR China
| | - Tiancheng Sheng
- School of Engineering, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Weiqi Wan
- School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Qingqing Shu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Donglin Wu
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Junhao Zhang
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Tao Lu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing, 211198, PR China.
| | - Ting Ran
- Drug and Vaccine Research Center, Guangzhou Laboratory, Guangzhou, 510005, PR China.
| | - Shuai Lu
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China.
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24
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Hamdan A, Ewing A. Unravelling the tumour genome: the evolutionary and clinical impacts of structural variants in tumourigenesis. J Pathol 2022; 257:479-493. [PMID: 35355264 PMCID: PMC9321913 DOI: 10.1002/path.5901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/16/2022] [Accepted: 03/28/2022] [Indexed: 11/15/2022]
Abstract
Structural variants (SVs) represent a major source of aberration in tumour genomes. Given the diversity in the size and type of SVs present in tumours, the accurate detection and interpretation of SVs in tumours is challenging. New classes of complex structural events in tumours are discovered frequently, and the definitions of the genomic consequences of complex events are constantly being refined. Detailed analyses of short‐read whole‐genome sequencing (WGS) data from large tumour cohorts facilitate the interrogation of SVs at orders of magnitude greater scale and depth. However, the inherent technical limitations of short‐read WGS prevent us from accurately detecting and investigating the impact of all the SVs present in tumours. The expanded use of long‐read WGS will be critical for improving the accuracy of SV detection, and in fully resolving complex SV events, both of which are crucial for determining the impact of SVs on tumour progression and clinical outcome. Despite the present limitations, we demonstrate that SVs play an important role in tumourigenesis. In particular, SVs contribute significantly to late‐stage tumour development and to intratumoural heterogeneity. The evolutionary trajectories of SVs represent a window into the clonal dynamics in tumours, a comprehensive understanding of which will be vital for influencing patient outcomes in the future. Recent findings have highlighted many clinical applications of SVs in cancer, from early detection to biomarkers for treatment response and prognosis. As the methods to detect and interpret SVs improve, elucidating the full breadth of the complex SV landscape and determining how these events modulate tumour evolution will improve our understanding of cancer biology and our ability to capitalise on the utility of SVs in the clinical management of cancer patients. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Alhafidz Hamdan
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.,Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ailith Ewing
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.,Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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25
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Yang C, Guo X, Li J, Han J, Jia L, Wen HL, Sun C, Wang X, Zhang B, Li J, Chi Y, An T, Wang Y, Wang Z, Li H, Li L. Significant Upregulation of HERV-K (HML-2) Transcription Levels in Human Lung Cancer and Cancer Cells. Front Microbiol 2022; 13:850444. [PMID: 35359739 PMCID: PMC8960717 DOI: 10.3389/fmicb.2022.850444] [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: 01/07/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is the second most common cancer worldwide and the leading cause of cancer death in the world. Therefore, there is an urgent need to develop new and effective biomarkers for diagnosis and treatment. Under this circumstance, human endogenous retroviruses (HERVs) were recently introduced as novel biomarkers for cancer diagnosis. This study focused on the correlation between lung cancer and HERV-K (HML-2) transcription levels. At the cellular level, different types of lung cancer cells and human normal lung epithelial cells were used to analyze the transcription levels of the HERV-K (HML-2) gag, pol, and env genes by RT–qPCR. At the level of lung cancer patients, blood samples with background information from 734 lung cancer patients and 96 healthy persons were collected to analyze the transcription levels of HERV-K (HML-2) gag, pol, and env genes. The results showed that the transcriptional levels of the HERV-K (HML-2) gag, pol, and env genes in lung cancer cells and lung cancer patient blood samples were significantly higher than those in the healthy controls, which was also verified by RNAScope ISH technology. In addition, we also found that there was a correlation between the abnormal transcription levels of HERV-K (HML-2) genes in lung cancer patients and the clinicopathological parameters of lung cancer. We also identified the distribution locations of the gag, pol, and env primer sequences on each chromosome and analyzed the function of these loci. In conclusion, HERV-K (HML-2) genes may be a potential biomarker for the diagnosis of lung cancer.
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Affiliation(s)
- Caiqin Yang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Xin Guo
- Department of Nutrition and Food Hygiene, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jianjie Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Medical Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jingwan Han
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Lei Jia
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Hong-Ling Wen
- Key Laboratory for the Prevention and Control of Infectious Diseases, Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chengxi Sun
- Department of Clinical Laboratory, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaolin Wang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Bohan Zhang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Jingyun Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Yujia Chi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Medical Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Tongtong An
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Medical Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yuyan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Medical Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ziping Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Medical Oncology, Peking University Cancer Hospital & Institute, Beijing, China
- *Correspondence: Ziping Wang,
| | - Hanping Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
- Hanping Li,
| | - Lin Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
- Lin Li,
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26
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Ambrosini-Spaltro A, Farnedi A, Calistri D, Rengucci C, Prisinzano G, Chiadini E, Capelli L, Angeli D, Bennati C, Valli M, De Luca G, Caruso D, Ulivi P, Rossi G. The role of next-generation sequencing in detecting gene FUSIONS with KNOWN and UNKNOWN partners: A single-center experience with methodologies' integration. Hum Pathol 2022; 123:20-30. [PMID: 35181377 DOI: 10.1016/j.humpath.2022.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 12/22/2022]
Abstract
AIMS Next-generation sequencing (NGS) is becoming a new gold standard for determining molecular predictive biomarkers. This study aimed to evaluate the reliability of NGS in detecting gene fusions, focusing on comparing gene fusions with known and unknown partners. METHODS We collected all gene fusions from a consecutive case series using an amplicon-based DNA/RNA NGS platform and subdivided them into two groups: gene fusions with known partners and gene fusions with unknown partners. Gene fusions involving ALK, ROS1 and RET were also examined by immunohistochemistry (IHC) and/or fluorescent in situ hybridization (FISH). RESULTS Overall, 1174 malignancies underwent NGS analysis. NGS detected gene fusions in 67 cases (5.7%), further subdivided into 43 (64.2%) with known partners and 24 (35.8%) with unknown partners. Gene fusions were predominantly found in non-small cell lung carcinomas (52/67, 77.6%). Gene fusions with known partners frequently involved ALK (20/43, 46.5%) and MET (9/43, 20.9%), while gene fusions with unknown partners mostly involved RET (18/24, 75.0%). FISH/IHC confirmed rearrangement status in most (89.3%) of the gene fusions with known partners, but in only one (4.8%) of the gene fusions with unknown partners, with a significant difference (p<0.001). In 17 patients undergoing targeted therapy, the log-rank test revealed that the overall survival was higher in the known partner group than in the unknown partner group (p=0.002). CONCLUSIONS NGS is a reliable method for detecting gene fusions with known partners, but it is less accurate in identifying gene fusions with unknown partners, for which further analyses (such as FISH) are required.
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Affiliation(s)
| | - Anna Farnedi
- Pathology Unit, Morgagni-Pierantoni Hospital, Forlì, AUSL Romagna, Italy
| | - Daniele Calistri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Claudia Rengucci
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giovanna Prisinzano
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Elisa Chiadini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Laura Capelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Davide Angeli
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Chiara Bennati
- Oncology Unit, Santa Maria Delle Croci Hospital, Ravenna, AUSL Romagna, Italy
| | - Mirca Valli
- Pathology Unit, Infermi Hospital, Rimini, AUSL Romagna, Italy
| | | | - Dora Caruso
- Pathology Unit, Santa Maria Delle Croci Hospital, Ravenna, AUSL Romagna, Italy
| | - Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giulio Rossi
- Pathology Unit, Department of Oncology, Fondazione Poliambulanza, Brescia, Italy
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