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Soyer SM, Ozbek P, Kasavi C. Lung Adenocarcinoma Systems Biomarker and Drug Candidates Identified by Machine Learning, Gene Expression Data, and Integrative Bioinformatics Pipeline. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:408-420. [PMID: 38979602 DOI: 10.1089/omi.2024.0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Lung adenocarcinoma (LUAD) is a significant planetary health challenge with its high morbidity and mortality rate, not to mention the marked interindividual variability in treatment outcomes and side effects. There is an urgent need for robust systems biomarkers that can help with early cancer diagnosis, prediction of treatment outcomes, and design of precision/personalized medicines for LUAD. The present study aimed at systems biomarkers of LUAD and deployed integrative bioinformatics and machine learning tools to harness gene expression data. Predictive models were developed to stratify patients based on prognostic outcomes. Importantly, we report here several potential key genes, for example, PMEL and BRIP1, and pathways implicated in the progression and prognosis of LUAD that could potentially be targeted for precision/personalized medicine in the future. Our drug repurposing analysis and molecular docking simulations suggested eight drug candidates for LUAD such as heat shock protein 90 inhibitors, cardiac glycosides, an antipsychotic agent (trifluoperazine), and a calcium ionophore (ionomycin). In summary, this study identifies several promising leads on systems biomarkers and drug candidates for LUAD. The findings also attest to the importance of integrative bioinformatics, structural biology and machine learning techniques in biomarker discovery, and precision oncology research and development.
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Affiliation(s)
- Semra Melis Soyer
- Department of Bioengineering, Faculty of Engineering, Marmara University, İstanbul, Türkiye
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, İstanbul, Türkiye
| | - Ceyda Kasavi
- Department of Bioengineering, Faculty of Engineering, Marmara University, İstanbul, Türkiye
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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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Kimbrough EO, Marin-Acevedo JA, Drusbosky LM, Mooradian A, Zhao Y, Manochakian R, Lou Y. Sex- and Age-Associated Differences in Genomic Alterations among Patients with Advanced Non-Small Cell Lung Cancer (NSCLC). Cancers (Basel) 2024; 16:2366. [PMID: 39001428 PMCID: PMC11240325 DOI: 10.3390/cancers16132366] [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: 04/11/2024] [Revised: 06/15/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
Genomic mutations impact non-small cell lung cancer (NSCLC) biology. The influence of sex and age on the distribution of these alterations is unclear. We analyzed circulating-tumor DNA from individuals with advanced NSCLC from March 2018 to October 2020. EGFR, KRAS, ALK, ROS1, BRAF, NTRK, ERBB2, RET, MET, PIK3CA, STK11, and TP53 alterations were assessed. We evaluated the differences by sex and age (<70 and ≥70) using Fisher's exact test. Of the 34,277 samples, 30,790 (89.83%) had a detectable mutation and 19,923 (58.12%) had an alteration of interest. The median age of the ctDNA positive population was 69 (18-102), 16,756 (54.42%) were female, and 28,835 (93.65%) had adenocarcinoma. Females had more alterations in all the assessed EGFR mutations, KRAS G12C, and ERBB2 ex20 ins. Males had higher numbers of MET amp and alterations in STK11 and TP53. Patients <70 years were more likely to have alterations in EGFR exon 19 del/exon 20 ins/T790M, KRAS G12C/D, ALK, ROS1, BRAF V600E, ERBB2 Ex20ins, MET amp, STK11, and TP53. Individuals ≥70 years were more likely to have alterations in EGFR L861Q, MET exon 14 skipping, and PIK3CA. We provided evidence of sex- and age-associated differences in the distribution of genomic alterations in individuals with advanced NSCLC.
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Affiliation(s)
- ErinMarie O Kimbrough
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Hematology and Oncology, Division of Internal Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
| | - Julian A Marin-Acevedo
- Department of Hematology and Oncology, Division of Internal Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
| | | | - Ariana Mooradian
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL 32224, USA
- Division of Hematology and Medical Oncology, University of Florida, Jacksonville, FL 32209, USA
| | - Yujie Zhao
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Rami Manochakian
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Yanyan Lou
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL 32224, USA
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4
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Imyanitov EN, Preobrazhenskaya EV, Orlov SV. Current status of molecular diagnostics for lung cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:742-765. [PMID: 38966170 PMCID: PMC11220319 DOI: 10.37349/etat.2024.00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/08/2024] [Indexed: 07/06/2024] Open
Abstract
The management of lung cancer (LC) requires the analysis of a diverse spectrum of molecular targets, including kinase activating mutations in EGFR, ERBB2 (HER2), BRAF and MET oncogenes, KRAS G12C substitutions, and ALK, ROS1, RET and NTRK1-3 gene fusions. Administration of immune checkpoint inhibitors (ICIs) is based on the immunohistochemical (IHC) analysis of PD-L1 expression and determination of tumor mutation burden (TMB). Clinical characteristics of the patients, particularly age, gender and smoking history, significantly influence the probability of finding the above targets: for example, LC in young patients is characterized by high frequency of kinase gene rearrangements, while heavy smokers often have KRAS G12C mutations and/or high TMB. Proper selection of first-line therapy influences overall treatment outcomes, therefore, the majority of these tests need to be completed within no more than 10 working days. Activating events in MAPK signaling pathway are mutually exclusive, hence, fast single-gene testing remains an option for some laboratories. RNA next-generation sequencing (NGS) is capable of detecting the entire repertoire of druggable gene alterations, therefore it is gradually becoming a dominating technology in LC molecular diagnosis.
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Affiliation(s)
- Evgeny N. Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
- Department of Clinical Genetics, St.-Petersburg State Pediatric Medical University, 194100 St.-Petersburg, Russia
- I.V. Kurchatov Complex for Medical Primatology, National Research Centre “Kurchatov Institute”, 354376 Sochi, Russia
| | - Elena V. Preobrazhenskaya
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
- Department of Clinical Genetics, St.-Petersburg State Pediatric Medical University, 194100 St.-Petersburg, Russia
| | - Sergey V. Orlov
- I.V. Kurchatov Complex for Medical Primatology, National Research Centre “Kurchatov Institute”, 354376 Sochi, Russia
- Department of Oncology, I.P. Pavlov St.-Petersburg State Medical University, 197022 St.-Petersburg, Russia
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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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Gou Q, Gou Q, Gan X, Xie Y. Novel therapeutic strategies for rare mutations in non-small cell lung cancer. Sci Rep 2024; 14:10317. [PMID: 38705930 PMCID: PMC11070427 DOI: 10.1038/s41598-024-61087-2] [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: 12/27/2023] [Accepted: 04/30/2024] [Indexed: 05/07/2024] Open
Abstract
Lung cancer is still the leading cause of cancer-related mortality. Over the past two decades, the management of non-small cell lung cancer (NSCLC) has undergone a significant revolution. Since the first identification of activating mutations in the epidermal growth factor receptor (EGFR) gene in 2004, several genetic aberrations, such as anaplastic lymphoma kinase rearrangements (ALK), neurotrophic tropomyosin receptor kinase (NTRK) and hepatocyte growth factor receptor (MET), have been found. With the development of gene sequencing technology, the development of targeted drugs for rare mutations, such as multikinase inhibitors, has provided new strategies for treating lung cancer patients with rare mutations. Patients who harbor this type of oncologic driver might acquire a greater survival benefit from the use of targeted therapy than from the use of chemotherapy and immunotherapy. To date, more new agents and regimens can achieve satisfactory results in patients with NSCLC. In this review, we focus on recent advances and highlight the new approval of molecular targeted therapy for NSCLC patients with rare oncologic drivers.
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Affiliation(s)
- Qitao Gou
- Department of Radiation Oncology and Department of Head & Neck Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qiheng Gou
- Department of Radiation Oncology and Department of Head & Neck Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Xiaochuan Gan
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuxin Xie
- Department of Medical Oncology of Cancer Center, West China Hospital, Sichuan University, Chengdu, China
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7
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Li D, Zhu Y, Song J, Yang D, Cui S, Liu X, Wang L, Zhang J, Pan E, Dai Z. Rapid response to fifth-line brigatinib plus entrectinib in an ALK-rearranged lung adenocarcinoma with an acquired ETV6- NTRK3 fusion: a case report. Front Oncol 2024; 14:1339511. [PMID: 38699646 PMCID: PMC11063249 DOI: 10.3389/fonc.2024.1339511] [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: 11/17/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
The management of non-small cell lung cancer (NSCLC), specifically targeting the anaplastic lymphoma kinase (ALK) with tyrosine kinase inhibitors (TKIs), is challenged by the emergence of therapeutic resistance. Resistance mechanisms to ALK TKIs can be broadly classified into ALK-dependent and ALK-independent pathways. Here, we present a case with lung adenocarcinoma (LUAD) harboring an ALK rearrangement. The patient had developed resistance to sequential ALK TKI therapies, with an acquired ETV6-NTRK3 (E4:N14) fusion as a potential mechanism of ALK-independent resistance to lorlatinib. Subsequently, the patient was treated with the combination of brigatinib plus entrectinib and demonstrated a positive response, achieving an 8-month progression-free survival. Our case provides a potential treatment option for LUAD patients with ALK rearrangements and highlights the utility of next-generation sequencing (NGS) in uncovering genetic alterations that can guide the selection of effective treatment strategies.
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Affiliation(s)
- Dan Li
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Yue Zhu
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Jincheng Song
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Dafu Yang
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Saiqiong Cui
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Xin Liu
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Le Wang
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Jiangyan Zhang
- Department of Medical Services, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Evenki Pan
- Department of Medical Services, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Zhaoxia Dai
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, China
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8
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Theik NWY, Muminovic M, Alvarez-Pinzon AM, Shoreibah A, Hussein AM, Raez LE. NTRK Therapy among Different Types of Cancers, Review and Future Perspectives. Int J Mol Sci 2024; 25:2366. [PMID: 38397049 PMCID: PMC10889397 DOI: 10.3390/ijms25042366] [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: 01/03/2024] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Neurotrophic tyrosine receptor kinase (NTRK) has been a remarkable therapeutic target for treating different malignancies, playing an essential role in oncogenic signaling pathways. Groundbreaking trials like NAVIGATE led to the approval of NTRK inhibitors by the Food and Drug Administration (FDA) to treat different malignancies, significantly impacting current oncology treatment. Accurate detection of NTRK gene fusion becomes very important for possible targeted therapy. Various methods to detect NTRK gene fusion have been applied widely based on sensitivity, specificity, and accessibility. The utility of different tests in clinical practice is discussed in this study by providing insights into their effectiveness in targeting patients who may benefit from therapy. Widespread use of NTRK inhibitors in different malignancies could remain limited due to resistance mechanisms that cause challenges to medication efficacy in addition to common side effects of the medications. This review provides a succinct overview of the application of NTRK inhibitors in various types of cancer by emphasizing the critical clinical significance of NTRK fusion gene detection. The discussion also provides a solid foundation for understanding the current challenges and potential changes for improving the efficacy of NTRK inhibitor therapy to treat different malignancies.
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Affiliation(s)
- Nyein Wint Yee Theik
- Division of Internal Medicine, Memorial Healthcare System, Pembroke Pines, FL 33028, USA; (N.W.Y.T.); (A.S.)
| | - Meri Muminovic
- Memorial Cancer Institute, Memorial Healthcare System, Pembroke Pines, FL 33028, USA;
| | - Andres M. Alvarez-Pinzon
- Memorial Cancer Institute, Office of Human Research, Florida Atlantic University (FAU), Pembroke Pines, FL 33028, USA
| | - Ahmed Shoreibah
- Division of Internal Medicine, Memorial Healthcare System, Pembroke Pines, FL 33028, USA; (N.W.Y.T.); (A.S.)
| | - Atif M. Hussein
- Memorial Cancer Institute, Memorial Healthcare System, Florida Atlantic University (FAU), Pembroke Pines, FL 33028, USA;
| | - Luis E. Raez
- Memorial Cancer Institute, Memorial Healthcare System, Florida Atlantic University (FAU), Pembroke Pines, FL 33028, USA;
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Sheikhshabani SH, Modarres P, Ghafouri‐Fard S, Amini‐Farsani Z, Khodaee L, Shaygan N, Amini‐Farsani Z, Omrani MD. Meta-analysis of microarray data to determine gene indicators involved in cisplatin resistance in non-small cell lung cancer. Cancer Rep (Hoboken) 2024; 7:e1970. [PMID: 38351531 PMCID: PMC10864718 DOI: 10.1002/cnr2.1970] [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: 07/14/2023] [Revised: 12/02/2023] [Accepted: 12/28/2023] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Lung cancer is a major cause of cancer-related mortality worldwide, with a 5-year survival rate of approximately 22%. Cisplatin is one of the standard first-line chemotherapeutic agents for non-small cell lung cancer (NSCLC), but its efficacy is often limited by the development of resistance. Despite extensive research on the molecular mechanisms of chemoresistance, the underlying causes remain elusive and complex. AIMS We analyzed three microarray datasets to find the gene signature and key pathways related to cisplatin resistance in NSCLC. METHODS AND RESULTS We compared the gene expression of sensitive and resistant NSCLC cell lines treated with cisplatin. We found 274 DEGs, including 111 upregulated and 163 downregulated genes, in the resistant group. Gene set enrichment analysis showed the potential roles of several DEGs, such as TUBB2B, MAPK7, TUBAL3, MAP2K5, SMUG1, NTHL1, PARP3, NTRK1, G6PD, PDK1, HEY1, YTHDF2, CD274, and MAGEA1, in cisplatin resistance. Functional analysis revealed the involvement of pathways, such as gap junction, base excision repair, central carbon metabolism, and Notch signaling in the resistant cell lines. CONCLUSION We identified several molecular factors that contribute to cisplatin resistance in NSCLC cell lines, involving genes and pathways that regulate gap junction communication, DNA damage repair, ROS balance, EMT induction, and stemness maintenance. These genes and pathways could be targets for future studies to overcome cisplatin resistance in NSCLC.
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Affiliation(s)
| | - Paratoo Modarres
- Department of Cell and Molecular Biology and Microbiology, Faculty of Science and TechnologyUniversity of IsfahanIsfahanIran
| | - Soudeh Ghafouri‐Fard
- Department of Medical GeneticsShahid Beheshti University of Medical SciencesTehranIran
| | - Zeinab Amini‐Farsani
- Department of Medical GeneticsShahid Beheshti University of Medical SciencesTehranIran
| | - Lavin Khodaee
- Department of Biotechnology and Plant BreedingIslamic Azad University Science and Research BranchTehranIran
| | - Nasibeh Shaygan
- Department of Medical GeneticsShahid Beheshti University of Medical SciencesTehranIran
| | - Zahra Amini‐Farsani
- Bayesian Imaging and Spatial Statistics Group, Institute of StatisticsLudwig‐Maximilian‐Universität MünchenMunichGermany
- Department of StatisticsLorestan UniversityKhorramabadIran
| | - Mir Davood Omrani
- Urogenital Stem Cell Research CenterShahid Beheshti University of Medical SciencesTehranIran
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10
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LoPiccolo J, Gusev A, Christiani DC, Jänne PA. Lung cancer in patients who have never smoked - an emerging disease. Nat Rev Clin Oncol 2024; 21:121-146. [PMID: 38195910 PMCID: PMC11014425 DOI: 10.1038/s41571-023-00844-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2023] [Indexed: 01/11/2024]
Abstract
Lung cancer is the most common cause of cancer-related deaths globally. Although smoking-related lung cancers continue to account for the majority of diagnoses, smoking rates have been decreasing for several decades. Lung cancer in individuals who have never smoked (LCINS) is estimated to be the fifth most common cause of cancer-related deaths worldwide in 2023, preferentially occurring in women and Asian populations. As smoking rates continue to decline, understanding the aetiology and features of this disease, which necessitate unique diagnostic and treatment paradigms, will be imperative. New data have provided important insights into the molecular and genomic characteristics of LCINS, which are distinct from those of smoking-associated lung cancers and directly affect treatment decisions and outcomes. Herein, we review the emerging data regarding the aetiology and features of LCINS, particularly the genetic and environmental underpinnings of this disease as well as their implications for treatment. In addition, we outline the unique diagnostic and therapeutic paradigms of LCINS and discuss future directions in identifying individuals at high risk of this disease for potential screening efforts.
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Affiliation(s)
- Jaclyn LoPiccolo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- The Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - David C Christiani
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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11
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Xu Y, Zhao W, Zhang X, Yu X, Chen Y, Wang Z, Chu Y, Zhu X, Zhang P. Design, synthesis and evaluate of indazolylaminoquinazoline derivatives as potent Tropomyosin receptor kinase (TRK) inhibitors. Bioorg Med Chem 2024; 99:117608. [PMID: 38271867 DOI: 10.1016/j.bmc.2024.117608] [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: 11/13/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
Tropomyosin receptor kinases (TRKs), the superfamily of transmembrane receptor tyrosine kinases, have recently become an attractive method for precision anticancer therapies since the approval of Larotrectinib and Entrectinib by FDA. Herein, we reported the discovery of a series of novel indazolylaminoquinazoline and indazolylaminoindazole as TRK inhibitors. The representative compound 30f exhibited good inhibitory activity against TRKWT, TRKG595R and TRKG667C with IC50 values of 0.55 nM, 25.1 nM and 5.4 nM, respectively. The compound also demonstrated potent superior to Larotrectinib antiproliferative activity against a panel of Ba/F3 cell lines transformed with both NTRK wild type and mutant fusions (IC50 = 10-200 nM). In addition, compound 30f exhibited good in vitro metabolic stability (T1/2 = 73.0 min), indicating that the quinazoline derivatives may have better metabolic stability. Finally, the binding mode of compound 30f predicted by molecular docking well explained the good enzyme inhibitory activity of indazolylaminoquinazoline compounds as TRK inhibitor. Thus, compound 30f can be used as a promising lead molecule for further structural optimization.
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Affiliation(s)
- Yunsheng Xu
- National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co., Ltd, China State Institute of Pharmaceutical Industry Co., Ltd., 285 Gebaini Road, Shanghai 201203, China
| | - Wei Zhao
- National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co., Ltd, China State Institute of Pharmaceutical Industry Co., Ltd., 285 Gebaini Road, Shanghai 201203, China
| | - Xinyi Zhang
- National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co., Ltd, China State Institute of Pharmaceutical Industry Co., Ltd., 285 Gebaini Road, Shanghai 201203, China
| | - Xihua Yu
- National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co., Ltd, China State Institute of Pharmaceutical Industry Co., Ltd., 285 Gebaini Road, Shanghai 201203, China
| | - Yinbo Chen
- National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co., Ltd, China State Institute of Pharmaceutical Industry Co., Ltd., 285 Gebaini Road, Shanghai 201203, China
| | - Zhenghai Wang
- National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co., Ltd, China State Institute of Pharmaceutical Industry Co., Ltd., 285 Gebaini Road, Shanghai 201203, China
| | - Yong Chu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Xueyan Zhu
- National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co., Ltd, China State Institute of Pharmaceutical Industry Co., Ltd., 285 Gebaini Road, Shanghai 201203, China.
| | - Peng Zhang
- National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co., Ltd, China State Institute of Pharmaceutical Industry Co., Ltd., 285 Gebaini Road, Shanghai 201203, China.
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12
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Dyrbekk APH, Warsame AA, Suhrke P, Ludahl MO, Zecic N, Moe JO, Lund-Iversen M, Brustugun OT. Evaluation of NTRK expression and fusions in a large cohort of early-stage lung cancer. Clin Exp Med 2024; 24:10. [PMID: 38240952 PMCID: PMC10798916 DOI: 10.1007/s10238-023-01273-0] [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: 10/26/2023] [Accepted: 11/29/2023] [Indexed: 01/22/2024]
Abstract
Tropomyosin receptor kinases (TRK) are attractive targets for cancer therapy. As TRK-inhibitors are approved for all solid cancers with detectable fusions involving the Neurotrophic tyrosine receptor kinase (NTRK)-genes, there has been an increased interest in optimizing testing regimes. In this project, we wanted to find the prevalence of NTRK fusions in a cohort of various histopathological types of early-stage lung cancer in Norway and to investigate the association between TRK protein expression and specific histopathological types, including their molecular and epidemiological characteristics. We used immunohistochemistry (IHC) as a screening tool for TRK expression, and next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) as confirmatory tests for underlying NTRK-fusion. Among 940 cases, 43 (4.6%) had positive TRK IHC, but in none of these could a NTRK fusion be confirmed by NGS or FISH. IHC-positive cases showed various staining intensities and patterns including cytoplasmatic or nuclear staining. IHC-positivity was more common in squamous cell carcinoma (LUSC) (10.3%) and adenoid cystic carcinoma (40.0%), where the majority showed heterogeneous staining intensity. In comparison, only 1.1% of the adenocarcinomas were positive. IHC-positivity was also more common in men, but this association could be explained by the dominance of LUSC in TRK IHC-positive cases. Protein expression was not associated with differences in time to relapse or overall survival. Our study indicates that NTRK fusion is rare in early-stage lung cancer. Due to the high level of false positive cases with IHC, Pan-TRK IHC is less suited as a screening tool for NTRK-fusions in LUSC and adenoid cystic carcinoma.
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Affiliation(s)
- Anne Pernille Harlem Dyrbekk
- University of Oslo, NO-0316, Oslo, Norway.
- Department of Pathology, Vestfold Hospital Trust, NO-3103, Tønsberg, Norway.
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, NO-0310, Oslo, Norway.
| | - Abdirashid Ali Warsame
- Department of Pathology, Oslo University Hospital, The Norwegian Radium Hospital, NO-0310, Oslo, Norway
| | - Pål Suhrke
- Department of Pathology, Vestfold Hospital Trust, NO-3103, Tønsberg, Norway
| | - Marianne Odnakk Ludahl
- Department of Microbiology/Division for Gene-Technology, Vestfold Hospital Trust, NO-3103, Tønsberg, Norway
| | - Nermin Zecic
- Department of Microbiology/Division for Gene-Technology, Vestfold Hospital Trust, NO-3103, Tønsberg, Norway
| | - Joakim Oliu Moe
- Department of Internal Medicine, Vestfold Hospital Trust, NO-3103, Tønsberg, Norway
| | - Marius Lund-Iversen
- Department of Pathology, Oslo University Hospital, The Norwegian Radium Hospital, NO-0310, Oslo, Norway
| | - Odd Terje Brustugun
- University of Oslo, NO-0316, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, NO-0310, Oslo, Norway
- Department of Oncology, Vestre Viken Hospital Trust, NO-3004, Drammen, Norway
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13
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Karakas C, Giampoli EJ, Love T, Hicks DG, Velez MJ. Validation and interpretation of Pan-TRK immunohistochemistry: a practical approach and challenges with interpretation. Diagn Pathol 2024; 19:10. [PMID: 38200576 PMCID: PMC10777531 DOI: 10.1186/s13000-023-01426-5] [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: 03/17/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024] Open
Abstract
OBJECTIVES Actionable, solid tumor activating neurotrophic receptor tyrosine kinase (NTRK) fusions are best detected via nucleic acid-based assays, while Pan-TRK immunohistochemistry (IHC) serves as a reasonable screening modality. We describe a practical and cost-effective approach to validate pan-TRK and discuss challenges that may be encountered. METHODS Pan-TRK Clone EPR17341 was validated in accordance with the 2014 consensus statements set forth by the College of American Pathologists. Confirmation of IHC results were guided by the European Society of Medical Oncology recommendations for standard methods to detect NTRK fusions. RESULTS Within 36 samples, ETV6-NTRK3 (n = 8) and TPM4-NTRK3 (n = 1) fusions were confirmed. ETV6-NTRK3 fusion positive cases revealed cytoplasmic and nuclear staining. A TPM4-NTRK3 fusion positive high grade malignant peripheral nerve sheath tumor revealed diffuse cytoplasmic staining. A high grade ovarian serous carcinoma revealed focal punctate staining and revealed a non-actionable NTRK1 truncation at intron 2. Diffuse cytoplasmic staining was observed in a case of fusion-negative polymorphous adenocarcinoma. Wild-type expression of TRK in pulmonary meningothelial-like nodules was discovered following a false-positive IHC interpretation. CONCLUSION Pan-TRK IHC shows some utility as a diagnostic and surrogate marker for NTRK screening however, physiologic or non-specific expression may lead to false-positive results.
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Affiliation(s)
- Cansu Karakas
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Ellen J Giampoli
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Tanzy Love
- Department of Biostatistics and Computation Biology, University of Rochester, Rochester, NY, USA
| | - David G Hicks
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Moises J Velez
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA.
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14
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Berezowska S, Maillard M, Keyter M, Bisig B. Pulmonary squamous cell carcinoma and lymphoepithelial carcinoma - morphology, molecular characteristics and differential diagnosis. Histopathology 2024; 84:32-49. [PMID: 37936498 DOI: 10.1111/his.15076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023]
Abstract
Squamous cell carcinoma (SCC) comprises one of the major groups of non-small-cell carcinoma of the lung, and is subtyped into keratinising, non-keratinising and basaloid SCC. SCC can readily be diagnosed using histomorphology alone in keratinising SCC. Confirmatory immunohistochemical analyses should always be applied in non-keratinising and basaloid tumours to exclude differential diagnoses, most prominently adenocarcinoma and high-grade neuroendocrine carcinoma, which may have important therapeutic consequences. According to the World Health Organisation (WHO) classification 2015, the diagnosis of SCC can be rendered in resections of morphologically ambiguous tumours with squamous immunophenotype. In biopsies and cytology preparations in the same setting the current guidelines propose a diagnosis of 'non-small-cell carcinoma, favour SCC' in TTF1-negative and p40-positive tumours to acknowledge a possible sampling bias and restrict extended immunohistochemical evaluation in order to preserve tissue for molecular testing. Most SCC feature a molecular 'tobacco-smoke signature' with enrichment in GG > TT mutations, in line with the strong epidemiological association of SCC with smoking. Targetable mutations are extremely rare but they do occur, in particular in younger and non- or light-smoking patients, warranting molecular investigations. Lymphoepithelial carcinoma (LEC) is a poorly differentiated SCC with a syncytial growth pattern and a usually prominent lymphoplasmacytic infiltrate and frequent Epstein-Barr virus (EBV) association. In this review, we describe the morphological and molecular characteristics of SCC and LEC and discuss the most pertinent differential diagnoses.
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Affiliation(s)
- Sabina Berezowska
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Marie Maillard
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Mark Keyter
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Bettina Bisig
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
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15
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Fan Y, Zhang B, Du X, Wang B, Yan Q, Guo L, Yao W. Regulating Tumorigenicity and Cancer Metastasis through TRKA Signaling. Curr Cancer Drug Targets 2024; 24:271-287. [PMID: 37670705 DOI: 10.2174/1568009623666230904150957] [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: 02/14/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 09/07/2023]
Abstract
Tropomyosin receptor kinase (TRK) A, TRKA, is a specific binding receptor of nerve growth factor (NGF), which plays an essential role in the occurrence and progression of human cancers. TRKA overexpression has been proven to be a powerful carcinogenic driver and has been verified in many tumors. The TRKA receptor kinase domain is over-activated in an NGF-dependent manner, accompanied by activation of downstream signal pathways, such as RAS-MAPK, PI3K-AKT, JAK2-STAT3 pathway, PLC γ pathway, and Hippo pathway, which participate in tumor cell proliferation, invasion, epithelial-mesenchymal transition (EMT), perineural invasion (PNI), drug resistance, and cancer pain. In addition, chimeric oncogenes produced by the fusion of NTRK1 and other genes are also the direct cause of tumorigenesis and cancer development. The newly developed TRK inhibitors can improve symptoms and tumor regression in cancer patients with overexpression of TRKA or NTRK1 fusion gene. With the emergence of drug resistance, next generation of TRK inhibitors can still maintain strong clinical efficacy in the case of TRK kinase domain mutations, and these inhibitors are in clinical trials. This review summarizes the characteristics and research progress of TRKA, focusing on the regulatory role of the TRKA signal pathway in different tumors. In addition, we have summarized the clinical significance of TRKA and the TRK inhibitors. This review may provide a new reference for the study of the mechanism of TRKA in different tumors, and also provide a new perspective for the in-depth understanding of the role of TRKA as a biomarker and therapeutic target in human cancer.
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Affiliation(s)
- Yichao Fan
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Boya Zhang
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Xinhui Du
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Bangmin Wang
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Qiang Yan
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Liangyu Guo
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Weitao Yao
- Henan Cancer Hospital, Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
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16
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Hyrcza MD, Martins-Filho SN, Spatz A, Wang HJ, Purgina BM, Desmeules P, Park PC, Bigras G, Jung S, Cutz JC, Xu Z, Berman DM, Sheffield BS, Cheung CC, Leduc C, Hwang DM, Ionescu D, Klonowski P, Chevarie-Davis M, Chami R, Lo B, Stockley TL, Tsao MS, Torlakovic E. Canadian Multicentric Pan-TRK (CANTRK) Immunohistochemistry Harmonization Study. Mod Pathol 2024; 37:100384. [PMID: 37972928 DOI: 10.1016/j.modpat.2023.100384] [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: 05/16/2023] [Revised: 10/19/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
Tumor-agnostic testing for NTRK1-3 gene rearrangements is required to identify patients who may benefit from TRK inhibitor therapies. The overarching objective of this study was to establish a high-quality pan-TRK immunohistochemistry (IHC) screening assay among 18 large regional pathology laboratories across Canada using pan-TRK monoclonal antibody clone EPR17341 in a ring study design. TRK-fusion positive and negative tumor samples were collected from participating sites, with fusion status confirmed by panel next-generation sequencing assays. Each laboratory received: (1) unstained sections from 30 cases of TRK-fusion-positive or -negative tumors, (2) 2 types of reference standards: TRK calibrator slides and IHC critical assay performance controls (iCAPCs), (3) EPR17341 antibody, and (4) suggestions for developing IHC protocols. Participants were asked to optimize the IHC protocol for their instruments and detection systems by using iCAPCs, to stain the 30 study cases, and to report the percentage scores for membranous, cytoplasmic, and nuclear staining. TRK calibrators were used to assess the analytical sensitivity of IHC protocols developed by using the 2 reference standards. Fifteen of 18 laboratories achieved diagnostic sensitivity of 100% against next-generation sequencing. The diagnostic specificity ranged from 40% to 90%. The results did not differ significantly between positive scores based on the presence of any type of staining vs the presence of overall staining in ≥1% of cells. The median limit of detection measured by TRK calibrators was 76,000 molecules/cell (range 38,000 to >200,000 molecules/cell). Three different patterns of staining were observed in 19 TRK-positive cases, cytoplasmic-only in 7 samples, nuclear and cytoplasmic in 9 samples, and cytoplasmic and membranous in 3 samples. The Canadian multicentric pan-TRK study illustrates a successful strategy to accelerate the multicenter harmonization and implementation of pan-TRK immunohistochemical screening that achieves high diagnostic sensitivity by using laboratory-developed tests where laboratories used centrally developed reference materials. The measurement of analytical sensitivity by using TRK calibrators provided additional insights into IHC protocol performance.
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Affiliation(s)
- Martin D Hyrcza
- Department of Pathology and Laboratory Medicine, University of Calgary, Arnie Charbonneau Cancer Institute, Calgary, Alberta, Canada
| | - Sebastiao N Martins-Filho
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada; University Health Network, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Alan Spatz
- McGill University Health Center, Lady Davis Institute, McGill University, Montreal, Quebec, Canada
| | - Han-Jun Wang
- McGill University Health Center, Lady Davis Institute, McGill University, Montreal, Quebec, Canada
| | - Bibianna M Purgina
- Department of Pathology and Laboratory Medicine, Ottawa Hospital, University of Ottawa, Ottawa, Ontario, Canada
| | - Patrice Desmeules
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada
| | - Paul C Park
- Shared Health, Department of Pathology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gilbert Bigras
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sungmi Jung
- Department of Pathology, McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Jean-Claude Cutz
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Zhaolin Xu
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David M Berman
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Brandon S Sheffield
- Department of Pathology, William Osler Health System, Brampton, Ontario, Canada
| | - Carol C Cheung
- University Health Network, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Charles Leduc
- Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - David M Hwang
- Department of Laboratory Medicine and Pathobiology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Diana Ionescu
- Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, University of British Columbia, Vancouver, British Columbia, Canada
| | - Paul Klonowski
- Department of Pathology and Laboratory Medicine, University of Calgary Cumming School of Medicine Diagnostic and Scientific Centre, Calgary, Alberta, Canada
| | - Myriam Chevarie-Davis
- Département de Pathologie et Biologie Cellulaire, Hôpital Maisonneuve-Rosemont, Université de Montréal, Montreal, Quebec, Canada
| | - Rose Chami
- Department of Laboratory Medicine and Pathobiology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Bryan Lo
- Department of Pathology and Laboratory Medicine, Ottawa Hospital, University of Ottawa, Ottawa, Ontario, Canada
| | - Tracy L Stockley
- University Health Network, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- University Health Network, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Emina Torlakovic
- Department of Pathology and Laboratory Medicine, Royal University Hospital, Saskatchewan Health Authority, and College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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17
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Sharma R, Kamireddy AP, Hussaini SM, Chatterjee S, Hasan Q, Jain J. The landscape of actionable genomic alterations in lung adenocarcinomas in India. Front Genet 2023; 14:1256756. [PMID: 38155717 PMCID: PMC10754624 DOI: 10.3389/fgene.2023.1256756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/05/2023] [Indexed: 12/30/2023] Open
Abstract
Lung adenocarcinoma (LUAD), the most prevalent form of non-small cell lung cancer (NSCLC), remains a leading cause of cancer-related death globally, including in India, with a 5-year survival rate below 10%. Despite these grim statistics, recent advances in the use of next-generation sequencing (NGS) for identifying genetic alterations and the emergence of targeted therapies have opened new possibilities for personalized treatment based on distinct molecular signatures. To understand the molecular pattern of NSCLC, a retrospective study was conducted with 53 Indian LUAD patient samples, using a targeted NGS panel of 46 cancer-relevant oncogenes to identify clinically relevant variants. Pathogenic or likely pathogenic variants were detected in 94% of the 53 cases. Non-synonymous mutations, rearrangements, copy number alterations, insertions, and deletions of functional relevance were observed in 31 out of 46 genes. The most frequently mutated genes included TP53 (52.8%) and EGFR (50.9%), followed by RET, PIK3CA and ERBB2; some patients had multiple alterations in the same gene. Gender-based enrichment analysis indicated that ALK and IDH2 alterations were more prevalent in females, while TP53 and PTEN were more common in males. No significant correlation was found between mutations and other clinicopathological attributes, such as age, stage, and subtype. A higher prevalence of EGFR, RET, PIK3CA, ERBB2 and ALK mutations were observed compared to previous LUAD genetic studies coupled with a lower frequency of KRAS mutations. Clinically actionable variants were annotated using OncoKB and categorized into the four therapeutic levels based on their clinical evidence. Seventy-nine percent of cases had at least one clinically actionable alteration. Most patients (39.6%) had the highest level of actionability (Level 1) wherein an FDA-approved drug is available specifically for the observed mutation in lung cancer patients. EGFR Exon19 in-frame deletions and EGFR L858R were the most frequent among targetable variants (20.7%). These findings emphasize the importance of a selective NGS panel in enabling personalized medicine approaches by identifying actionable molecular alterations and informing the choice of targeted therapy for more effective treatment options in Indian NSCLC patients.
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Affiliation(s)
- Rakesh Sharma
- Sapien Biosciences Private Limited, Hyderabad, Telangana, India
| | - Aruna Priya Kamireddy
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, Telangana, India
| | | | - Soma Chatterjee
- Sapien Biosciences Private Limited, Hyderabad, Telangana, India
| | - Qurratulain Hasan
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, Telangana, India
| | - Jugnu Jain
- Sapien Biosciences Private Limited, Hyderabad, Telangana, India
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18
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de Oliveira Cavagna R, de Andrade ES, Tadin Reis M, de Paula FE, Noriz Berardinelli G, Bonatelli M, Ramos Teixeira G, Garbe Zaniolo B, Mourão Dias J, da Silva FAF, Baston Silva CE, Xavier Reis M, Lopes Maia E, de Alencar TS, Jacinto AA, da Nóbrega Oliveira REN, Molina-Vila MA, Ferro Leal L, Reis RM. Detection of NTRK fusions by RNA-based nCounter is a feasible diagnostic methodology in a real-world scenario for non-small cell lung cancer assessment. Sci Rep 2023; 13:21168. [PMID: 38036758 PMCID: PMC10689426 DOI: 10.1038/s41598-023-48613-4] [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: 09/03/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023] Open
Abstract
NTRK1, 2, and 3 fusions are important therapeutic targets for NSCLC patients, but their prevalence in South American admixed populations needs to be better explored. NTRK fusion detection in small biopsies is a challenge, and distinct methodologies are used, such as RNA-based next-generation sequencing (NGS), immunohistochemistry, and RNA-based nCounter. This study aimed to evaluate the frequency and concordance of positive samples for NTRK fusions using a custom nCounter assay in a real-world scenario of a single institution in Brazil. Out of 147 NSCLC patients, 12 (8.2%) cases depicted pan-NTRK positivity by IHC. Due to the absence of biological material, RNA-based NGS and/or nCounter could be performed in six of the 12 IHC-positive cases (50%). We found one case exhibiting an NTRK1 fusion and another an NTRK3 gene fusion by both RNA-based NGS and nCounter techniques. Both NTRK fusions were detected in patients diagnosed with lung adenocarcinoma, with no history of tobacco consumption. Moreover, no concomitant EGFR, KRAS, and ALK gene alterations were detected in NTRK-positive patients. The concordance rate between IHC and RNA-based NGS was 33.4%, and between immunohistochemistry and nCounter was 40%. Our findings indicate that NTRK fusions in Brazilian NSCLC patients are relatively rare (1.3%), and RNA-based nCounter methodology is a suitable approach for NRTK fusion identification in small biopsies.
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Affiliation(s)
- Rodrigo de Oliveira Cavagna
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela, Barretos, São Paulo, 14784-400, Brazil
| | - Edilene Santos de Andrade
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela, Barretos, São Paulo, 14784-400, Brazil
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | - Murilo Bonatelli
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
| | - Gustavo Ramos Teixeira
- Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
- Barretos School of Health Sciences Dr. Paulo Prata-FACISB, Barretos, Brazil
| | - Beatriz Garbe Zaniolo
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela, Barretos, São Paulo, 14784-400, Brazil
- Barretos School of Health Sciences Dr. Paulo Prata-FACISB, Barretos, Brazil
| | | | | | | | - Marina Xavier Reis
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil
| | - Erika Lopes Maia
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | - Miguel A Molina-Vila
- Laboratory of Oncology/Pangaea Oncology, Dexeus University Hospital, Barcelona, Spain
| | - Letícia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela, Barretos, São Paulo, 14784-400, Brazil
- Barretos School of Health Sciences Dr. Paulo Prata-FACISB, Barretos, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela, Barretos, São Paulo, 14784-400, Brazil.
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil.
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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19
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Leatham B, McNall K, Subramanian HKK, Jacky L, Alvarado J, Yurk D, Wang M, Green DC, Tsongalis GJ, Rajagopal A, Schwartz JJ. A rapid, multiplex digital PCR assay to detect gene variants and fusions in non-small cell lung cancer. Mol Oncol 2023; 17:2221-2234. [PMID: 37714814 PMCID: PMC10620117 DOI: 10.1002/1878-0261.13523] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/22/2023] [Accepted: 09/15/2023] [Indexed: 09/17/2023] Open
Abstract
Digital PCR (dPCR) is emerging as an ideal platform for the detection and tracking of genomic variants in cancer due to its high sensitivity and simple workflow. The growing number of clinically actionable cancer biomarkers creates a need for fast, accessible methods that allow for dense information content and high accuracy. Here, we describe a proof-of-concept amplitude modulation-based multiplex dPCR assay capable of detecting 12 single-nucleotide and insertion/deletion (indel) variants in EGFR, KRAS, BRAF, and ERBB2, 14 gene fusions in ALK, RET, ROS1, and NTRK1, and MET exon 14 skipping present in non-small cell lung cancer (NSCLC). We also demonstrate the use of multi-spectral target-signal encoding to improve the specificity of variant detection by reducing background noise by up to an order of magnitude. The assay reported an overall 100% positive percent agreement (PPA) and 98.5% negative percent agreement (NPA) compared with a sequencing-based assay in a cohort of 62 human formalin-fixed paraffin-embedded (FFPE) samples. In addition, the dPCR assay rescued actionable information in 10 samples that failed to sequence, highlighting the utility of a multiplexed dPCR assay as a potential reflex solution for challenging NSCLC samples.
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Affiliation(s)
| | | | | | | | | | - Dominic Yurk
- ChromaCode IncCarlsbadCAUSA
- Department of Electrical EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Mimi Wang
- ChromaCode IncCarlsbadCAUSA
- Slack TechnologiesSan FranciscoCAUSA
| | - Donald C. Green
- Department of Pathology and Laboratory MedicineDartmouth Hitchcock Medical CenterLebanonNHUSA
| | - Gregory J. Tsongalis
- Department of Pathology and Laboratory MedicineDartmouth Hitchcock Medical CenterLebanonNHUSA
| | - Aditya Rajagopal
- ChromaCode IncCarlsbadCAUSA
- Department of Electrical EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
- Department of Biomedical EngineeringUniversity of Southern CaliforniaLos AngelesCAUSA
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20
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Sposito M, Belluomini L, Pontolillo L, Tregnago D, Trestini I, Insolda J, Avancini A, Milella M, Bria E, Carbognin L, Pilotto S. Adjuvant Targeted Therapy in Solid Cancers: Pioneers and New Glories. J Pers Med 2023; 13:1427. [PMID: 37888038 PMCID: PMC10608226 DOI: 10.3390/jpm13101427] [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: 08/24/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
Targeted therapy (TT) has revolutionized cancer treatment, successfully applied in various settings. Adjuvant TT in resected early-stage gastrointestinal stromal tumors (GIST), melanoma, non-small cell lung cancer (NSCLC), and breast cancer has led to practice-changing achievements. In particular, standard treatments include BRAF inhibitors for melanoma, osimertinib for NSCLC, hormone therapy or HER2 TT for breast cancer, and imatinib for GIST. Despite the undeniable benefit derived from adjuvant TT, the optimal duration of TT and the appropriate managing of the relapse remain open questions. Furthermore, neoadjuvant TT is emerging as valuable, particularly in breast cancer, and ongoing studies evaluate TT in the perioperative setting for early-stage NSCLC. In this review, we aim to collect and describe the large amount of data available in the literature about adjuvant TT across different histologies, focusing on epidemiology, major advances, and future directions.
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Affiliation(s)
- Marco Sposito
- Section of Innovation Biomedicine—Oncology Area, Department of Engineering for Innovation Medicine (DIMI), University of Verona and University and Hospital Trust (AOUI) of Verona, 37134 Verona, Italy; (M.S.); (L.B.); (D.T.); (I.T.); (J.I.); (A.A.); (M.M.)
| | - Lorenzo Belluomini
- Section of Innovation Biomedicine—Oncology Area, Department of Engineering for Innovation Medicine (DIMI), University of Verona and University and Hospital Trust (AOUI) of Verona, 37134 Verona, Italy; (M.S.); (L.B.); (D.T.); (I.T.); (J.I.); (A.A.); (M.M.)
| | - Letizia Pontolillo
- Comprehensive Cancer Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Roma, Italy; (L.P.); (E.B.)
- Medical Oncology, Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Daniela Tregnago
- Section of Innovation Biomedicine—Oncology Area, Department of Engineering for Innovation Medicine (DIMI), University of Verona and University and Hospital Trust (AOUI) of Verona, 37134 Verona, Italy; (M.S.); (L.B.); (D.T.); (I.T.); (J.I.); (A.A.); (M.M.)
| | - Ilaria Trestini
- Section of Innovation Biomedicine—Oncology Area, Department of Engineering for Innovation Medicine (DIMI), University of Verona and University and Hospital Trust (AOUI) of Verona, 37134 Verona, Italy; (M.S.); (L.B.); (D.T.); (I.T.); (J.I.); (A.A.); (M.M.)
| | - Jessica Insolda
- Section of Innovation Biomedicine—Oncology Area, Department of Engineering for Innovation Medicine (DIMI), University of Verona and University and Hospital Trust (AOUI) of Verona, 37134 Verona, Italy; (M.S.); (L.B.); (D.T.); (I.T.); (J.I.); (A.A.); (M.M.)
| | - Alice Avancini
- Section of Innovation Biomedicine—Oncology Area, Department of Engineering for Innovation Medicine (DIMI), University of Verona and University and Hospital Trust (AOUI) of Verona, 37134 Verona, Italy; (M.S.); (L.B.); (D.T.); (I.T.); (J.I.); (A.A.); (M.M.)
| | - Michele Milella
- Section of Innovation Biomedicine—Oncology Area, Department of Engineering for Innovation Medicine (DIMI), University of Verona and University and Hospital Trust (AOUI) of Verona, 37134 Verona, Italy; (M.S.); (L.B.); (D.T.); (I.T.); (J.I.); (A.A.); (M.M.)
| | - Emilio Bria
- Comprehensive Cancer Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Roma, Italy; (L.P.); (E.B.)
- Medical Oncology, Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Luisa Carbognin
- Gynecology Oncology, Fondazione Policlinico Universitario Agostino Gemelli IRCSS, 00168 Roma, Italy;
| | - Sara Pilotto
- Section of Innovation Biomedicine—Oncology Area, Department of Engineering for Innovation Medicine (DIMI), University of Verona and University and Hospital Trust (AOUI) of Verona, 37134 Verona, Italy; (M.S.); (L.B.); (D.T.); (I.T.); (J.I.); (A.A.); (M.M.)
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21
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McLaughlin J, Berkman J, Nana-Sinkam P. Targeted therapies in non-small cell lung cancer: present and future. Fac Rev 2023; 12:22. [PMID: 37675274 PMCID: PMC10477963 DOI: 10.12703/r/12-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
Lung cancer is the leading cause of malignancy-related death in the United States and the second most common cancer diagnosis worldwide. In the last two decades, lung cancer treatment has evolved to include advances in the development of mutation-based targeting, immunotherapy, radiation therapy, and minimally invasive surgical techniques. The discovery of lung cancer as a molecularly heterogeneous disease has driven investigation into the development of targeted therapies resulting in improved patient outcomes. Despite these advances, there remain opportunities, through further investigation of mechanisms of resistance, to develop novel therapeutics that better direct the personalization of lung cancer therapy. In this review, we highlight developments in the evolution of targeted therapies in non-small cell lung cancer, as well as future directions shaped by emerging patterns of resistance.
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Affiliation(s)
- Jessica McLaughlin
- Department of Internal Medicine, Division of Pulmonary Disease and Critical Care Medicine, Virginia Commonwealth University Health System, Richmond, VA 23298
| | - Jonathan Berkman
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University Health System, Richmond, VA 23298
| | - Patrick Nana-Sinkam
- Department of Internal Medicine, Division of Pulmonary Disease and Critical Care Medicine, Virginia Commonwealth University Health System, Richmond, VA 23298
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22
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Araghi M, Mannani R, Heidarnejad maleki A, Hamidi A, Rostami S, Safa SH, Faramarzi F, Khorasani S, Alimohammadi M, Tahmasebi S, Akhavan-Sigari R. Recent advances in non-small cell lung cancer targeted therapy; an update review. Cancer Cell Int 2023; 23:162. [PMID: 37568193 PMCID: PMC10416536 DOI: 10.1186/s12935-023-02990-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/12/2023] [Indexed: 08/13/2023] Open
Abstract
Lung cancer continues to be the leading cause of cancer-related death worldwide. In the last decade, significant advancements in the diagnosis and treatment of lung cancer, particularly NSCLC, have been achieved with the help of molecular translational research. Among the hopeful breakthroughs in therapeutic approaches, advances in targeted therapy have brought the most successful outcomes in NSCLC treatment. In targeted therapy, antagonists target the specific genes, proteins, or the microenvironment of tumors supporting cancer growth and survival. Indeed, cancer can be managed by blocking the target genes related to tumor cell progression without causing noticeable damage to normal cells. Currently, efforts have been focused on improving the targeted therapy aspects regarding the encouraging outcomes in cancer treatment and the quality of life of patients. Treatment with targeted therapy for NSCLC is changing rapidly due to the pace of scientific research. Accordingly, this updated study aimed to discuss the tumor target antigens comprehensively and targeted therapy-related agents in NSCLC. The current study also summarized the available clinical trial studies for NSCLC patients.
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Affiliation(s)
- Mahmood Araghi
- Department of Pathology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Reza Mannani
- Vascular Surgeon, Department of Surgery, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Adel Hamidi
- Razi Vaccine and Serum Research Institute, Arak Branch, karaj, Iran
| | - Samaneh Rostami
- School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Fatemeh Faramarzi
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sahar Khorasani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mina Alimohammadi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Safa Tahmasebi
- Student Research Committee, Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Akhavan-Sigari
- Department of Neurosurgery, University Medical Center, Tuebingen, Germany
- Department of Health Care Management and Clinical Research, Collegium Humanum Warsaw Management University Warsaw, Warsaw, Poland
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23
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Naito Y, Mishima S, Akagi K, Hayashi N, Hirasawa A, Hishiki T, Igarashi A, Ikeda M, Kadowaki S, Kajiyama H, Kato M, Kenmotsu H, Kodera Y, Komine K, Koyama T, Maeda O, Miyachi M, Nishihara H, Nishiyama H, Ohga S, Okamoto W, Oki E, Ono S, Sanada M, Sekine I, Takano T, Tao K, Terashima K, Tsuchihara K, Yatabe Y, Yoshino T, Baba E. Japanese Society of Medical Oncology/Japan Society of Clinical Oncology/Japanese Society of Pediatric Hematology/Oncology-led clinical recommendations on the diagnosis and use of tropomyosin receptor kinase inhibitors in adult and pediatric patients with neurotrophic receptor tyrosine kinase fusion-positive advanced solid tumors. Int J Clin Oncol 2023:10.1007/s10147-023-02345-7. [PMID: 37212982 DOI: 10.1007/s10147-023-02345-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/13/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Clinical trials have reported the efficacy of tropomyosin receptor kinase (TRK) inhibitors against neurotrophic receptor tyrosine kinase (NTRK) fusion gene-positive advanced solid tumors. The accumulated evidence of tumor-agnostic agent has made since TRK inhibitors were approved and used in clinical practice. Therefore, we have revised the 'Japan Society of Clinical Oncology (JSCO)/Japanese Society of Medical Oncology (JSMO)-led clinical recommendations on the diagnosis and use of tropomyosin receptor kinase inhibitors in adult and pediatric patients with neurotrophic receptor tyrosine kinase fusion-positive advanced solid tumors, cooperated by the Japanese Society of Pediatric Hematology/Oncology (JSPHO)'. METHODS Clinical questions regarding medical care were formulated for patients with NTRK fusion-positive advanced solid tumors. Relevant publications were searched by PubMed and Cochrane Database. Critical publications and conference reports were added manually. Systematic reviews were performed for each clinical question for the purpose of developing clinical recommendations. The committee members identified by JSCO, JSMO, and JSPHO voted to determine the level of each recommendation considering the strength of evidence, expected risks and benefits to patients, and other related factors. Thereafter, a peer review by experts nominated from JSCO, JSMO, and JSPHO, and the public comments among all societies' members was done. RESULTS The current guideline describes 3 clinical questions and 14 recommendations for whom, when, and how NTRK fusion should be tested, and what is recommended for patients with NTRK fusion-positive advanced solid tumors. CONCLUSION The committee proposed 14 recommendations for performing NTRK testing properly to select patients who are likely to benefit from TRK inhibitors.
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Affiliation(s)
- Yoichi Naito
- National Cancer Center Hospital East, Kashiwa, Japan
| | - Saori Mishima
- National Cancer Center Hospital East, Kashiwa, Japan
| | | | - Naomi Hayashi
- The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | | | | | - Ataru Igarashi
- Yokohama City University School of Medicine, Yokohama, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Eiji Oki
- Kyushu University, Fukuoka, Japan
| | | | - Masashi Sanada
- National Hospital Organization Nagoya Medical Center, Aichi, Japan
| | | | | | - Kayoko Tao
- National Cancer Center Hospital, Tokyo, Japan
| | - Keita Terashima
- National Center for Child Health and Development, Tokyo, Japan
| | | | | | | | - Eishi Baba
- Department of Oncology and Social Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
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24
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Harada G, Yang SR, Cocco E, Drilon A. Rare molecular subtypes of lung cancer. Nat Rev Clin Oncol 2023; 20:229-249. [PMID: 36806787 PMCID: PMC10413877 DOI: 10.1038/s41571-023-00733-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2023] [Indexed: 02/22/2023]
Abstract
Oncogenes that occur in ≤5% of non-small-cell lung cancers have been defined as 'rare'; nonetheless, this frequency can correspond to a substantial number of patients diagnosed annually. Within rare oncogenes, less commonly identified alterations (such as HRAS, NRAS, RIT1, ARAF, RAF1 and MAP2K1 mutations, or ERBB family, LTK and RASGRF1 fusions) can share certain structural or oncogenic features with more commonly recognized alterations (such as KRAS, BRAF, MET and ERBB family mutations, or ALK, RET and ROS1 fusions). Over the past 5 years, a surge in the identification of rare-oncogene-driven lung cancers has challenged the boundaries of traditional clinical grade diagnostic assays and profiling algorithms. In tandem, the number of approved targeted therapies for patients with rare molecular subtypes of lung cancer has risen dramatically. Rational drug design has iteratively improved the quality of small-molecule therapeutic agents and introduced a wave of antibody-based therapeutics, expanding the list of actionable de novo and resistance alterations in lung cancer. Getting additional molecularly tailored therapeutics approved for rare-oncogene-driven lung cancers in a larger range of countries will require ongoing stakeholder cooperation. Patient advocates, health-care agencies, investigators and companies with an interest in diagnostics, therapeutics and real-world evidence have already taken steps to surmount the challenges associated with research into low-frequency drivers.
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Affiliation(s)
- Guilherme Harada
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emiliano Cocco
- Department of Biochemistry and Molecular Biology/Sylvester Comprehensive Cancer Center, University of Miami/Miller School of Medicine, Miami, FL, 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.
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25
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Zhou KI, Vashistha V, Guo A, Ahmed S, Kelley MJ. Real-world Experience With Neurotrophic Tyrosine Receptor Kinase Fusion-positive Tumors and Tropomyosin Receptor Kinase Inhibitors in Veterans. JCO Precis Oncol 2023; 7:e2200692. [PMID: 36926986 DOI: 10.1200/po.22.00692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 03/18/2023] Open
Abstract
PURPOSE Neurotrophic tyrosine receptor kinase 1-3 (NTRK1-3) gene fusions are found in a broad range of tumor types. Clinical trials demonstrated high response rates to tropomyosin receptor kinase (TRK) inhibitors in NTRK fusion-positive cancers, but few reports have described real-world experience with these targeted agents. We evaluated the prevalence of NTRK fusions and the outcomes with TRK inhibitor therapy in a real-world population of patients in the Veterans Health Administration. METHODS Patients with NTRK fusions or rearrangements were identified from the Veterans Affairs (VA) National Precision Oncology Program (NPOP), and patients who were prescribed TRK inhibitors were identified from the Corporate Data Warehouse. Baseline data and clinical outcomes were obtained by retrospective review of medical records. RESULTS A total of 33 patients with NTRK fusions or rearrangements were identified, including 25 patients comprising 0.12% of all patients with solid tumors sequenced through VA NPOP. Twelve patients with NTRK fusions or rearrangements were treated with TRK inhibitors, none of whom had objective responses. Eight patients experienced toxicities leading to drug interruption, dose reduction, or discontinuation. CONCLUSION In this retrospective study of VA patients, NTRK fusions and rearrangements were less common than in previous studies, and objective responses to TRK inhibitors were not observed. Real-world experience with TRK inhibitors differs markedly from clinical trial findings, possibly due to differences in patient demographics, tumor types, and sequencing methods. Our findings highlight the need to study TRK inhibitors in the real-world setting and in populations underrepresented in clinical trials.
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Affiliation(s)
- Katherine I Zhou
- Division of Hematology-Oncology, Durham VA Medical Center, Durham, NC
- Division of Medical Oncology, Department of Medicine, Duke University, Durham, NC
| | - Vishal Vashistha
- Section of Hematology-Oncology, New Mexico VA Medical Center, Albuquerque, NM
| | - Aixia Guo
- National Oncology Program, Department of Veterans Affairs, Durham, NC
| | - Sara Ahmed
- National Oncology Program, Department of Veterans Affairs, Durham, NC
| | - Michael J Kelley
- Division of Hematology-Oncology, Durham VA Medical Center, Durham, NC
- Division of Medical Oncology, Department of Medicine, Duke University, Durham, NC
- National Oncology Program, Department of Veterans Affairs, Durham, NC
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26
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Frehner L, Haefliger S, Cerciello F, Grob T, Schmid S. Complete Response on Larotrectinib in NTRK2 Fusion-Positive Non-Small Cell Lung Cancer. Case Rep Oncol 2023; 16:871-877. [PMID: 37900816 PMCID: PMC10601816 DOI: 10.1159/000533572] [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: 05/25/2023] [Accepted: 08/07/2023] [Indexed: 10/31/2023] Open
Abstract
In patients with non-small cell lung cancer (NSCLC) harboring a fusion of the neurotrophic receptor kinase (NTRK) gene 1 or 3, treatment with tropomyosin kinase (TRK) inhibitors have shown promising results, however so far no data on efficacy of these agents in patients with NSCLC and NTRK2 fusion are available. We present a case of a female patient with NTRK2-positive NSCLC with a complete ongoing response on therapy with larotrectinib, suggesting efficacy of first-generation TRK inhibitors also in NTRK2-positive NSCLC.
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Affiliation(s)
- Lorenz Frehner
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ferdinando Cerciello
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Tobias Grob
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Sabine Schmid
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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27
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Cappellesso R, Nicolè L, Del Fiore P, Barzon L, Sinigaglia A, Riccetti S, Franco R, Zito Marino F, Munari G, Zamuner C, Cavallin F, Sbaraglia M, Galuppini F, Bassetto F, Alaibac M, Chiarion-Sileni V, Piccin L, Benna C, Fassan M, Mocellin S, Dei Tos AP. TRK Protein Expression in Merkel Cell Carcinoma Is Not Caused by NTRK Fusions. Int J Mol Sci 2022; 23:ijms232315366. [PMID: 36499693 PMCID: PMC9737899 DOI: 10.3390/ijms232315366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Merkel cell carcinoma (MCC) is a rare and aggressive cutaneous malignant tumor with neuroendocrine differentiation, with a rapidly growing incidence rate, high risk of recurrence, and aggressive behavior. The available therapeutic options for advanced disease are limited and there is a pressing need for new treatments. Tumors harboring fusions involving one of the neurotrophin receptor tyrosine kinase (NTRK) genes are now actionable with targeted inhibitors. NTRK-fused genes have been identified in neuroendocrine tumors of other sites; thus, a series of 76 MCCs were firstly analyzed with pan-TRK immunohistochemistry and the positive ones with real-time RT-PCR, RNA-based NGS, and FISH to detect the eventual underlying gene fusion. Despite 34 MCCs showing pan-TRK expression, NTRK fusions were not found in any cases. As in other tumors with neural differentiation, TRK expression seems to be physiological and not caused by gene fusions.
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Affiliation(s)
- Rocco Cappellesso
- Pathological Anatomy Unit, Padua University Hospital, 35121 Padua, Italy
- Correspondence: ; Tel.: +39-049-8217962
| | - Lorenzo Nicolè
- Department of Pathology, Angelo Hospital, 30174 Venice, Italy
- Department of Medicine (DIMED), University of Padua, 35121 Padua, Italy
| | - Paolo Del Fiore
- Soft-Tissue, Peritoneum and Melanoma Surgical Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy
| | - Luisa Barzon
- Department of Molecular Medicine (DMM), University of Padua, 35121 Padua, Italy
| | | | - Silvia Riccetti
- Department of Molecular Medicine (DMM), University of Padua, 35121 Padua, Italy
| | - Renato Franco
- Pathology Unit, University of Campania “L. Vanvitelli”, 80129 Naples, Italy
| | | | - Giada Munari
- Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy
| | | | | | - Marta Sbaraglia
- Department of Medicine (DIMED), University of Padua, 35121 Padua, Italy
| | | | - Franco Bassetto
- Department of Neurosciences (DNS), University of Padua, 35128 Padua, Italy
| | - Mauro Alaibac
- Department of Medicine (DIMED), University of Padua, 35121 Padua, Italy
| | - Vanna Chiarion-Sileni
- Melanoma Unit, Oncology 2 Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy
| | - Luisa Piccin
- Melanoma Unit, Oncology 2 Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy
| | - Clara Benna
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University of Padua, 35128 Padua, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), University of Padua, 35121 Padua, Italy
- Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy
| | - Simone Mocellin
- Soft-Tissue, Peritoneum and Melanoma Surgical Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University of Padua, 35128 Padua, Italy
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Wang T, Wei L, Lu Q, Shao Y, You S, Yin JC, Wang S, Shao Y, Chen Z, Wang Z. Landscape of potentially targetable receptor tyrosine kinase fusions in diverse cancers by DNA-based profiling. NPJ Precis Oncol 2022; 6:84. [DOI: 10.1038/s41698-022-00325-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
AbstractRecurrent fusions of receptor tyrosine kinases (RTKs) are often driving events in tumorigenesis that carry important diagnostic value and are potentially targetable by the increasing number of tyrosine kinase inhibitors (TKIs). Here, we characterized the spectrum of 1324 RTK fusions with intact kinase domains in solid tumors by DNA-based high-throughput sequencing. Overall, the prevalence of RTK fusions were 4.7%, with variable frequencies and diverse genomic structures and fusion partners across cancer types. Cancer types, such as thyroid cancers, urological cancers and neuroendocrine tumors are selective in the RTK fusions they carry, while others exhibit highly complex spectra of fusion events. Notably, most RTKs were promiscuous in terms of the partner genes they recombine with. A large proportion of RTK fusions had one of the breakpoints localized to intergenic regions. Comprehensive genomic profiling revealed differences in co-mutational patterns pre- and post-TKI treatments across various RTK fusions. At baseline, multiple cases were detected with co-occurring RTK fusions or concomitant oncogenic mutations in driver genes, such as KRAS and EGFR. Following TKI resistance, we observed differences in potential on- and off-target resistance mutations among fusion variants. For example, the EML4-ALK v3 variant displayed more complex on-target resistance mechanisms, which might explain the reduced survival outcome compared with the v1 variant. Finally, we identified two lung cancer patients with MET+ and NTRK1+ tumors, respectively, who responded well to crizotinib treatment. Taken together, our findings demonstrate the diagnostic and prognostic values of screening for RTK fusions using DNA-based sequencing in solid tumors.
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Bridgewater J, Jiao X, Parimi M, Flach C, Stratford J, Kamburov A, Schmitz AA, Zong J, Reeves JA, Keating K, Bruno A, Fellous M, Pereira MB, Bazhenova L. Prognosis and oncogenomic profiling of patients with tropomyosin receptor kinase fusion cancer in the 100,000 genomes project. Cancer Treat Res Commun 2022; 33:100623. [PMID: 36041373 DOI: 10.1016/j.ctarc.2022.100623] [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: 02/28/2022] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Neurotrophic tyrosine receptor kinase (NTRK) gene fusions are oncogenic drivers in various tumor types. Limited data exist on the overall survival (OS) of patients with tumors with NTRK gene fusions and on the co-occurrence of NTRK fusions with other oncogenic drivers. MATERIALS AND METHODS This retrospective study included patients enrolled in the Genomics England 100,000 Genomes Project who had linked clinical data from UK databases. Patients who had undergone tumor whole genome sequencing between March 2016 and July 2019 were included. Patients with and without NTRK fusions were matched. OS was analyzed along with oncogenic alterations in ALK, BRAF, EGFR, ERBB2, KRAS, and ROS1, and tumor mutation burden (TMB) and microsatellite instability (MSI). RESULTS Of 15,223 patients analyzed, 38 (0.25%) had NTRK gene fusions in 11 tumor types, the most common were breast cancer, colorectal cancer (CRC), and sarcoma. Median OS was not reached in both the NTRK gene fusion-positive and -negative groups (hazard ratio 1.47, 95% CI 0.39-5.57, P = 0.572). A KRAS mutation was identified in two (5%) patients with NTRK gene fusions, and both had hepatobiliary cancer. High TMB and MSI were both more common in patients with NTRK gene fusions, due to the CRC subset. While there was a higher risk of death in patients with NTRK gene fusions compared to those without, the difference was not statistically significant. CONCLUSION This study supports the hypothesis that NTRK gene fusions are primary oncogenic drivers and the co-occurrence of NTRK gene fusions with other oncogenic alterations is rare.
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Affiliation(s)
- John Bridgewater
- University College London Hospitals NHS Trust, London, United Kingdom; University College London Cancer Institute, London, United Kingdom.
| | - Xiaolong Jiao
- Bayer HealthCare Pharmaceuticals, Inc., Whippany, NJ, United States of America
| | | | - Clare Flach
- Real World Solutions, IQVIA, London, United Kingdom
| | | | | | | | - Jihong Zong
- Bayer HealthCare Pharmaceuticals, Inc., Whippany, NJ, United States of America
| | - John A Reeves
- Bayer HealthCare Pharmaceuticals, Inc., Whippany, NJ, United States of America
| | - Karen Keating
- Bayer HealthCare Pharmaceuticals, Inc., Whippany, NJ, United States of America
| | - Amanda Bruno
- Bayer HealthCare Pharmaceuticals, Inc., Whippany, NJ, United States of America
| | - Marc Fellous
- Bayer HealthCare Pharmaceuticals, Inc., Basel, Switzerland
| | | | - Lyudmila Bazhenova
- University of California San Diego Moores Cancer Center, San Diego, CA, United States of America
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30
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Guo Q, Liu L, Chen Z, Fan Y, Zhou Y, Yuan Z, Zhang W. Current treatments for non-small cell lung cancer. Front Oncol 2022; 12:945102. [PMID: 36033435 PMCID: PMC9403713 DOI: 10.3389/fonc.2022.945102] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/06/2022] [Indexed: 12/12/2022] Open
Abstract
Despite improved methods of diagnosis and the development of different treatments, mortality from lung cancer remains surprisingly high. Non-small cell lung cancer (NSCLC) accounts for the large majority of lung cancer cases. Therefore, it is important to review current methods of diagnosis and treatments of NSCLC in the clinic and preclinic. In this review, we describe, as a guide for clinicians, current diagnostic methods and therapies (such as chemotherapy, chemoradiotherapy, targeted therapy, antiangiogenic therapy, immunotherapy, and combination therapy) for NSCLC.
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Affiliation(s)
- Qianqian Guo
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, China
| | - Liwei Liu
- Department of Pharmacy, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zelong Chen
- Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Artificial Intelligence and IoT Smart Medical Engineering Research Center of Henan Province, Zhengzhou, China
| | - Yannan Fan
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, China
| | - Yang Zhou
- Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Ziqiao Yuan
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, China
- *Correspondence: Wenzhou Zhang, ; Ziqiao Yuan,
| | - Wenzhou Zhang
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, China
- *Correspondence: Wenzhou Zhang, ; Ziqiao Yuan,
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Yao Y, Wang J, Yang F, Gao W. Exploration of Novel Immunological Terms in Lung Cancer With Large Populations: Implications for Immunotherapy. Front Immunol 2022; 13:924498. [PMID: 35844536 PMCID: PMC9280191 DOI: 10.3389/fimmu.2022.924498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/08/2022] [Indexed: 12/03/2022] Open
Abstract
Background Ideal biomarkers to predict the response to immunotherapy in lung cancer are still lacking. Therefore, there is a need to explore effective biomarkers in large populations. Objective The objective of this study is to explore novel immunological classifications that are associated with immunotherapy response through the ssGSEA algorithm. Methods Six independent lung cancer cohorts were collected for analysis including The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and the EMBL-EBI database. The ssGSEA algorithm was performed to extract immune terms. Then, TCGA samples were involved as a training group and other cohorts were used as a validation group. After LASSO and Cox regression, prognostic associated immune terms were extracted and an immune-related risk score (IRS) signature was constructed. Furthermore, the association between IRS signature and clinical data, genome features, stemness indices analysis, tumor immune microenvironment, immunotherapy efficiency, and targeted therapy response was also investigated. Results A total of 1,997 samples were enrolled in this study including six large lung cancer cohorts. Fifty-four immune terms were calculated through the ssGSEA algorithm in combined cohorts. Then, a nine-immune-term risk score model named IRS signature was established to predict the prognosis in combined cohorts. We classified patients into high-risk and low-risk subgroups according to the cutoff point. Subsequently, analysis of clinical data and genome features indicated that the patients in the high-IRS group tend to have advanced clinical features (clinical stage and T classification), as well as a higher level of copy number variation burden, higher tumor burden mutation, and higher tumor stemness indices. Immune landscape analysis demonstrated that high-IRS groups exhibited lower immune cell infiltration and immune-suppressive state. More importantly, the predicted result of the Tumor Immune Dysfunction and Exclusion analysis showed that high-IRS groups might be more insensitive to immunotherapy. Meanwhile, we have also identified that high-IRS groups were associated with better efficiency of several targeted drugs. Conclusion To summarize, we identified a novel IRS model based on nine immune terms, which was quantified by the ssGSEA algorithm. This model had good efficacy in predicting overall survival and immunotherapy response in non-small cell lung cancer patients, which might be an underlying biomarker.
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NSCLC as the Paradigm of Precision Medicine at Its Finest: The Rise of New Druggable Molecular Targets for Advanced Disease. Int J Mol Sci 2022; 23:ijms23126748. [PMID: 35743191 PMCID: PMC9223783 DOI: 10.3390/ijms23126748] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023] Open
Abstract
Standard treatment for advanced non-small cell lung cancer (NSCLC) historically consisted of systemic cytotoxic chemotherapy until the early 2000s, when precision medicine led to a revolutionary change in the therapeutic scenario. The identification of oncogenic driver mutations in EGFR, ALK and ROS1 rearrangements identified a subset of patients who largely benefit from targeted agents. However, since the proportion of patients with druggable alterations represents a minority, the discovery of new potential driver mutations is still an urgent clinical need. We provide a comprehensive review of the emerging molecular targets in NSCLC and their applications in the advanced setting.
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Dai Y, Liu P, He W, Yang L, Ni Y, Ma X, Du F, Song C, Liu Y, Sun Y. Genomic Features of Solid Tumor Patients Harboring ALK/ROS1/NTRK Gene Fusions. Front Oncol 2022; 12:813158. [PMID: 35785159 PMCID: PMC9243239 DOI: 10.3389/fonc.2022.813158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
The fusions of receptor tyrosine kinase (RTK) involving anaplastic lymphoma kinase (ALK), c-ros oncogene 1 (ROS1), and neurotrophic receptor tyrosine kinase (NTRK) represent the potential targets of therapeutic intervention for various types of solid tumors. Here, the genomic features of 180 Chinese solid tumor patients with ALK, ROS1, and NTRK fusions by next generation sequencing (NGS) were comprehensively characterized, and the data from 121 patients in Memorial Sloan Kettering Cancer Center (MSKCC) database were used to compare. We found that ALK, ROS1, and NTRK fusions were more common in younger female patients (p<0.001) and showed a higher expression of programmed death ligand 1 (PD-L1). The gene-intergenic fusion and the fusion with rare formation directions accounted for a certain proportion in all samples and 62 novel fusions were discovered. Alterations in TP53 and MUC16 were common in patients with RTK fusions. The mutational signatures of patients were mainly distributed in COSMIC signature 1, 2, 3, 15 and 30, while had a higher frequency in copy number variations (CNVs) of individual genes, such as IL-7R. In the MSKCC cohort, patients with fusions and CNVs showed shorter overall survival than those with only fusions. Furthermore, the differentially mutated genes between fusion-positive and -negative patients mainly concentrated on MAPK signaling and FOXO signaling pathways. These results may provide genomic information for the personalized clinical management of solid tumor patients with ALK, ROS1, and NTRK fusions in the era of precision medicine.
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Affiliation(s)
- Yinghuan Dai
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ping Liu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wenlong He
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Lizhen Yang
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yang Ni
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
- Department of Medicine, Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Xuejiao Ma
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
- Department of Medicine, Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Furong Du
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
- Department of Medicine, Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Chao Song
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
- Department of Medicine, Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
- *Correspondence: Yi Sun, ; Yang Liu, ; Chao Song,
| | - Yang Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
- *Correspondence: Yi Sun, ; Yang Liu, ; Chao Song,
| | - Yi Sun
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yi Sun, ; Yang Liu, ; Chao Song,
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Bang H, Lee MS, Sung M, Choi J, An S, Kim SH, Lee SE, Choi YL. NTRK Fusions in 1113 Solid Tumors in a Single Institution. Diagnostics (Basel) 2022; 12:diagnostics12061450. [PMID: 35741260 PMCID: PMC9222038 DOI: 10.3390/diagnostics12061450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
Most NTRK fusions occur at very low frequencies in various common cancers. Recent recommendations on NTRK testing recommend immunohistochemistry (IHC) as the initial test for tumor types with a low frequency of NTRK fusions. This study investigated the accuracy of an IHC assay to detect NTRK fusions and characterize the clinicopathological and molecular features of NTRK-rearranged tumors. This retrospective study was conducted on 1113 solid tumor samples known to harbor no oncogenic driver alterations, including 510 non-small cell lung cancers (NSCLC), 503 colorectal cancers (CRC), and 79 inflammatory myofibroblastic tumors (IMT). Additionally, 21 ALK expression-positive cases were included. TRK expression was evaluated using a pan-Trk IHC assay, and positive cases were validated using NGS. TRK expression was observed in three NSCLCs (0.6%), six CRCs (1.2%), and six IMTs (6%). NTRK fusions were finally detected in two NSCLCs (0.4%), six CRCs (1.2%), and one IMT (1%). In NSCLC and CRC, the majority of NTRK fusions were readily discernible due to diffuse moderate-to-strong cytoplasmic staining on pan-Trk IHC. In IMT, focal weak nuclear staining indicated the presence of NTRK fusion. Therefore, the utility of pan-Trk IHC should be assessed considering that the difference in performance depends on tumor type.
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Affiliation(s)
- Heejin Bang
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul 05030, Korea;
| | - Mi-Sook Lee
- Laboratory of Theranotics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (M.-S.L.); (M.S.); (J.C.); (S.A.)
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
| | - Minjung Sung
- Laboratory of Theranotics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (M.-S.L.); (M.S.); (J.C.); (S.A.)
| | - Juyoung Choi
- Laboratory of Theranotics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (M.-S.L.); (M.S.); (J.C.); (S.A.)
| | - Sungbin An
- Laboratory of Theranotics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (M.-S.L.); (M.S.); (J.C.); (S.A.)
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
| | - Seok-Hyung Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Seung Eun Lee
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul 05030, Korea;
- Correspondence: (S.E.L.); (Y.-L.C.); Tel.: +82-2-2030-5644 (S.E.L.); +82-2-3410-2800 (Y.-L.C.); Fax: +82-2-2030-5629 (S.E.L.); +82-2-3410-6396 (Y.-L.C.)
| | - Yoon-La Choi
- Laboratory of Theranotics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (M.-S.L.); (M.S.); (J.C.); (S.A.)
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
- Correspondence: (S.E.L.); (Y.-L.C.); Tel.: +82-2-2030-5644 (S.E.L.); +82-2-3410-2800 (Y.-L.C.); Fax: +82-2-2030-5629 (S.E.L.); +82-2-3410-6396 (Y.-L.C.)
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Marchetti A, Ferro B, Pasciuto MP, Zampacorta C, Buttitta F, D'Angelo E. NTRK gene fusions in solid tumors: agnostic relevance, prevalence and diagnostic strategies. Pathologica 2022; 114:199-216. [PMID: 35775706 PMCID: PMC9248239 DOI: 10.32074/1591-951x-787] [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: 06/19/2022] [Accepted: 01/23/2022] [Indexed: 11/30/2022] Open
Abstract
A number of innovative drugs, developed for precision medicine, have shown impressive activity in neoplastic patients with rare molecular targets, independently from the site and type of tumor. This gave rise to the concept of agnostic treatments in oncology. The detection of such rare targets is a prerequisite for these treatments and is nowadays one of the main challenges in diagnostic molecular pathology. Various algorithms, new diagnostic strategies and pathological workflows have been suggested to help pathologists in the detection of these rare molecular alterations. An emblematic example of biological targets for agnostic treatments is represented by genetic rearrangements affecting members of the Neurotrophic Tyrosine Receptor Kinase (NTRK) gene family. These gene rearrangements have an unusual dual mode of distribution: the first, at high frequency in some very rare neoplasms, and the second with extremely lower frequencies in more common tumors. Even in the context of an agnostic approach, knowledge of site, histotype and prevalence of the tumors carrying these genetic lesions may be helpful to guide the pathologist in the daily effort in search of these molecular alterations. This review examines the prevalence of NTRK gene fusions in different forms of solid tumors, based on the largest studies to date, reports a comprehensive diagnostic algorithm and an innovative pathological workflow for rapid screening.
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Affiliation(s)
- Antonio Marchetti
- Diagnostic Molecular Oncology Section, Center for Advanced Studies and Technology (CAST), University of Chieti-Pescara, Italy
| | - Benedetta Ferro
- Diagnostic Molecular Oncology Section, Center for Advanced Studies and Technology (CAST), University of Chieti-Pescara, Italy
| | - Maria Paola Pasciuto
- Diagnostic Molecular Oncology Section, Center for Advanced Studies and Technology (CAST), University of Chieti-Pescara, Italy
| | - Claudia Zampacorta
- Diagnostic Molecular Oncology Section, Center for Advanced Studies and Technology (CAST), University of Chieti-Pescara, Italy
| | - Fiamma Buttitta
- Diagnostic Molecular Oncology Section, Center for Advanced Studies and Technology (CAST), University of Chieti-Pescara, Italy
| | - Emanuela D'Angelo
- Diagnostic Molecular Oncology Section, Center for Advanced Studies and Technology (CAST), University of Chieti-Pescara, Italy
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Liu F, Wei Y, Zhang H, Jiang J, Zhang P, Chu Q. NTRK Fusion in Non-Small Cell Lung Cancer: Diagnosis, Therapy, and TRK Inhibitor Resistance. Front Oncol 2022; 12:864666. [PMID: 35372074 PMCID: PMC8968138 DOI: 10.3389/fonc.2022.864666] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/10/2022] [Indexed: 12/25/2022] Open
Abstract
Neurotrophic tropomyosin receptor kinase (NTRK) gene fusion has been identified as an oncogenic driver of various solid tumors, and it is rare in non-smalll cell lung cancer (NSCLC) with a frequency of approximately less than 1%. Next-generation sequencing (NGS) is of priority for detecting NTRK fusions, especially RNA-based NGS. Currently, the tropomyosin receptor kinase (TRK) inhibitors have shown promising efficacy and well tolerance in patients with NTRK fusion-positive solid tumors, regardless of tumor histology. The first-generation TRK inhibitors (larotrectinib and entrectinib) are recommended as the first-line treatment for locally advanced or metastatic NSCLC patients with positive NTRK fusion. However, TRK inhibitor resistance can eventually occur due to on-target or off-target mechanisms. Further studies are under investigation to overcome resistance and improve survival. Interestingly, NTRK fusion might be the mechanism of resistance to epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKI) in NSCLC patients with EGFR mutation. Regarding immunotherapy, the efficacy of immune checkpoint inhibitors in NSCLC patients harboring NTRK fusion has yet to be well described. In this review, we elucidate the function of NTRK genes, summarize the diagnostic techniques for NTRK fusions, and present clinical data for TRK inhibitors; we also discuss potential mechanisms of resistance to TRK inhibitors.
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Affiliation(s)
- Fangfang Liu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuxuan Wei
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huan Zhang
- The Second Clinical College of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jizong Jiang
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Jizong Jiang,
| | - Peng Zhang
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Chu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Rocco D, Della Gravara L, Maione P, Palazzolo G, Gridelli C. Identification of drug combinations for lung cancer patients whose tumors are unresponsive to targeted therapy: clinical bases and future directions. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2022. [DOI: 10.1080/23808993.2022.2050369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Danilo Rocco
- Department of Pulmonary Oncology, AORN dei Colli Monaldi, Naples, Italy
| | - Luigi Della Gravara
- Department of Experimental Medicine, Università degli studi della Campania “Luigi Vanvitelli”, Naples, Italy
| | - Paolo Maione
- Division of Medical Oncology, “S.g. Moscati” Hospital, Avellino, Italy
| | | | - Cesare Gridelli
- Division of Medical Oncology, “S.g. Moscati” Hospital, Avellino, Italy
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Koopman B, Kuijpers CCHJ, Groen HJM, Timens W, Schuuring E, Willems SM, van Kempen LC. Detection of NTRK Fusions and TRK Expression and Performance of pan-TRK Immunohistochemistry in Routine Diagnostics: Results from a Nationwide Community-Based Cohort. Diagnostics (Basel) 2022; 12:diagnostics12030668. [PMID: 35328221 PMCID: PMC8946871 DOI: 10.3390/diagnostics12030668] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 02/01/2023] Open
Abstract
Gene fusions involving NTRK1, NTRK2, and NTRK3 are rare drivers of cancer that can be targeted with histology-agnostic inhibitors. This study aimed to determine the nationwide landscape of NTRK/TRK testing in the Netherlands and the usage of pan-TRK immunohistochemistry (IHC) as a preselection tool to detect NTRK fusions. All pathology reports in 2017–2020 containing the search term ‘TRK’ were retrieved from the Dutch Pathology Registry (PALGA). Patient characteristics, tumor histology, NTRK/TRK testing methods, and reported results were extracted. NTRK/TRK testing was reported for 7457 tumors. Absolute testing rates increased from 815 (2017) to 3380 (2020). Tumors were tested with DNA/RNA-based molecular assay(s) (48%), IHC (47%), or in combination (5%). A total of 69 fusions involving NTRK1 (n = 22), NTRK2 (n = 6) and NTRK3 (n = 41) were identified in tumors from adult (n = 51) and pediatric (n = 18) patients. In patients tested with both IHC and a molecular assay (n = 327, of which 29 NTRK fusion-positive), pan-TRK IHC had a sensitivity of 77% (95% confidence interval (CI), 56–91) and a specificity of 84% (95% CI, 78–88%). These results showed that pan-TRK IHC has a low sensitivity in current routine practice and warrants the introduction of quality guidelines regarding the implementation and interpretation of pan-TRK IHC.
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Affiliation(s)
- Bart Koopman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (W.T.); (E.S.); (S.M.W.)
| | | | - Harry J. M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands;
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (W.T.); (E.S.); (S.M.W.)
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (W.T.); (E.S.); (S.M.W.)
| | - Stefan M. Willems
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (W.T.); (E.S.); (S.M.W.)
| | - Léon C. van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (W.T.); (E.S.); (S.M.W.)
- Correspondence: ; Tel.: +31-50-361-5129
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Qin H, Patel MR. The Challenge and Opportunity of NTRK Inhibitors in Non-Small Cell Lung Cancer. Int J Mol Sci 2022; 23:2916. [PMID: 35328336 PMCID: PMC8954929 DOI: 10.3390/ijms23062916] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 02/05/2023] Open
Abstract
With the development of targeted therapy, non-small cell lung cancer (NSCLC) patients could have more treatment choices if target mutation presents. The neurotrophic tropomyosin receptor kinase (NTRK) has a low prevalence in NSCLC, roughly around 0.5%. FDA had approved two first generation NTRK inhibitors, larotrectinib and entrectinib. Both medications have excellent CNS penetration. This manuscript will review available data on targeting NTRK fusions in NSCLC and mechanisms of drug resistance.
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Affiliation(s)
| | - Manish R. Patel
- Department of Hematology, Oncology and Bone Marrow Transplant, University of Minnesota, Minneapolis, MN 55455, USA;
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Shi DD, Guo JA, Hoffman HI, Su J, Mino-Kenudson M, Barth JL, Schenkel JM, Loeffler JS, Shih HA, Hong TS, Wo JY, Aguirre AJ, Jacks T, Zheng L, Wen PY, Wang TC, Hwang WL. Therapeutic avenues for cancer neuroscience: translational frontiers and clinical opportunities. Lancet Oncol 2022; 23:e62-e74. [PMID: 35114133 PMCID: PMC9516432 DOI: 10.1016/s1470-2045(21)00596-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/28/2021] [Accepted: 10/08/2021] [Indexed: 02/03/2023]
Abstract
With increasing attention on the essential roles of the tumour microenvironment in recent years, the nervous system has emerged as a novel and crucial facilitator of cancer growth. In this Review, we describe the foundational, translational, and clinical advances illustrating how nerves contribute to tumour proliferation, stress adaptation, immunomodulation, metastasis, electrical hyperactivity and seizures, and neuropathic pain. Collectively, this expanding knowledge base reveals multiple therapeutic avenues for cancer neuroscience that warrant further exploration in clinical studies. We discuss the available clinical data, including ongoing trials investigating novel agents targeting the tumour-nerve axis, and the therapeutic potential for repurposing existing neuroactive drugs as an anti-cancer approach, particularly in combination with established treatment regimens. Lastly, we discuss the clinical challenges of these treatment strategies and highlight unanswered questions and future directions in the burgeoning field of cancer neuroscience.
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Affiliation(s)
- Diana D Shi
- Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - Jimmy A Guo
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA; School of Medicine, University of California, San Francisco, San Francisco, CA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hannah I Hoffman
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Health Sciences and Technology Program, Harvard Medical School, Boston, MA, USA
| | - Jennifer Su
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jaimie L Barth
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason M Schenkel
- Department of Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jay S Loeffler
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Helen A Shih
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Jennifer Y Wo
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tyler Jacks
- Department of Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lei Zheng
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Timothy C Wang
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, NY, USA
| | - William L Hwang
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Kazdal D, Hofman V, Christopoulos P, Ilié M, Stenzinger A, Hofman P. Fusion-positive non-small cell lung carcinoma: Biological principles, clinical practice, and diagnostic implications. Genes Chromosomes Cancer 2022; 61:244-260. [PMID: 34997651 DOI: 10.1002/gcc.23022] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/26/2021] [Accepted: 12/27/2021] [Indexed: 12/11/2022] Open
Abstract
Based on superior efficacy and tolerability, targeted therapy is currently preferred over chemotherapy and/or immunotherapy for actionable gene fusions that occur in late-stage non-small cell lung carcinoma (NSCLC). Consequently, current clinical practice guidelines mandate testing for ALK, ROS1, NTRK, and RET gene fusions in all patients with newly diagnosed advanced non-squamous NSCLC (NS-NSCLC). Gene fusions can be detected using different approaches, but today RNA next-generation sequencing (NGS) or combined DNA/RNA NGS is the method of choice. The discovery of other gene fusions (involving, eg, NRG1, NUT, FGFR1, FGFR2, MET, BRAF, EGFR, SMARC fusions) and their partners has increased progressively in recent years, leading to the development of new and promising therapies and mandating the development and implementation of comprehensive detection methods. The purpose of this review is to focus on recent data concerning the main gene fusions identified in NSCLC, followed by the discussion of major challenges in this domain.
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Affiliation(s)
- Daniel Kazdal
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center (TLRC) Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany
| | - Véronique Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, FHU OncoAge, Nice, France.,Centre Antoine Lacassagne Cancer Center, Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU OncoAge, Nice, France.,Hospital-Integrated Biobank BB-0033-00025, Université Côte d'Azur, CHU Nice, FHU OncoAge, Nice, France
| | - Petros Christopoulos
- Translational Lung Research Center (TLRC) Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany.,Thoraxklinik and National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, FHU OncoAge, Nice, France.,Centre Antoine Lacassagne Cancer Center, Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU OncoAge, Nice, France.,Hospital-Integrated Biobank BB-0033-00025, Université Côte d'Azur, CHU Nice, FHU OncoAge, Nice, France
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, FHU OncoAge, Nice, France.,Centre Antoine Lacassagne Cancer Center, Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU OncoAge, Nice, France.,Hospital-Integrated Biobank BB-0033-00025, Université Côte d'Azur, CHU Nice, FHU OncoAge, Nice, France
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42
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Koga T, Suda K, Mitsudomi T. Utility of the Ba/F3 cell system for exploring on-target mechanisms of resistance to targeted therapies for lung cancer. Cancer Sci 2022; 113:815-827. [PMID: 34997674 PMCID: PMC8898722 DOI: 10.1111/cas.15263] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/03/2021] [Accepted: 12/12/2021] [Indexed: 11/30/2022] Open
Abstract
Molecular targeted therapies are the standard of care for front‐line treatment of metastatic non‐small‐cell lung cancers (NSCLCs) harboring driver gene mutations. However, despite the initial dramatic responses, the emergence of acquired resistance is inevitable. Acquisition of secondary mutations in the target gene (on‐target resistance) is one of the major mechanisms of resistance. The mouse pro‐B cell line Ba/F3 is dependent on interleukin‐3 for survival and proliferation. Upon transduction of a driver gene, Ba/F3 cells become independent of interleukin‐3 but dependent on the transduced driver gene. Therefore, the Ba/F3 cell line has been a popular system to generate models with oncogene dependence and vulnerability to specific targeted therapies. These models have been used to estimate oncogenicity of driver mutations or efficacies of molecularly targeted drugs. In addition, Ba/F3 models, together with N‐ethyl‐N‐nitrosourea mutagenesis, have been used to derive acquired resistant cells to investigate on‐target resistance mechanisms. Here, we reviewed studies that used Ba/F3 models with EGFR mutations, ALK/ROS1/NTRK/RET fusions, MET exon 14 skipping mutations, or KRAS G12C mutations to investigate secondary/tertiary drug resistant mutations. We determined that 68% of resistance mutations reproducibly detected in clinical cases were also found in Ba/F3 models. In addition, sensitivity data generated with Ba/F3 models correlated well with clinical responses to each drug. Ba/F3 models are useful to comprehensively identify potential mutations that induce resistance to molecularly targeted drugs and to explore drugs to overcome the resistance.
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Affiliation(s)
- Takamasa Koga
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
| | - Kenichi Suda
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
| | - Tetsuya Mitsudomi
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
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Corral de la Fuente E, Benito Berlinches A, Gomez Rueda A, Olmedo García ME, Lage Alfranca Y, Lario M, Santón Roldán A, Garrido P. ALK rearranged non–small cell lung carcinoma with EML4-NTRK3 fusion as a possible mechanism of resistance to third-generation ALK inhibitors. CURRENT PROBLEMS IN CANCER: CASE REPORTS 2021. [DOI: 10.1016/j.cpccr.2021.100124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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44
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Harada G, Santini FC, Wilhelm C, Drilon A. NTRK fusions in lung cancer: From biology to therapy. Lung Cancer 2021; 161:108-113. [PMID: 34563714 PMCID: PMC8530887 DOI: 10.1016/j.lungcan.2021.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
Fusions involving TRK protein tyrosine kinases are oncogenic drivers in a variety of tumors in children and adults, with a prevalence of ∼0.2% in non-small cell lung cancer. Diagnosis can be challenging due to structural features such as NTRK intron length, but next-generation sequencing (NGS), including RNA-based NGS, increases detection. The first-generation TRK inhibitors, larotrectinib and entrectinib, have demonstrated clinically meaningful antitumor activity in TRK fusion-positive cancers in a tumor-agnostic fashion and should be considered first-line therapeutic options for TRK fusion-positive lung cancers. Furthermore, the first-generation TRK inhibitors are well tolerated. Care should be taken, however, to monitor on-target adverse events, such as dizziness, weight gain, paresthesias, and withdrawal pain. On-target and off-target mechanisms mediating TRK inhibitor resistance may occur. Next-generation TRK inhibitors, such as selitrectinib, repotrectinib, and taletrectinib, are available on ongoing clinical trials and address on-target resistance. This review will focus on NTRK fusions and TRK-directed targeted therapy specifically in the context of lung cancer.
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Affiliation(s)
- Guilherme Harada
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Fernando C Santini
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Clare Wilhelm
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA.
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Zhao R, Yao F, Xiang C, Zhao J, Shang Z, Guo L, Ding W, Ma S, Yu A, Shao J, Zhu L, Han Y. Identification of NTRK gene fusions in lung adenocarcinomas in the Chinese population. J Pathol Clin Res 2021; 7:375-384. [PMID: 33768710 PMCID: PMC8185368 DOI: 10.1002/cjp2.208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 02/09/2021] [Accepted: 02/14/2021] [Indexed: 12/30/2022]
Abstract
The molecular profile of neurotrophic tyrosine kinase receptor (NTRK) gene fusions in lung adenocarcinoma (LUAD) is not fully understood. Next-generation sequencing (NGS) and pan-tyrosine kinase receptor (TRK) immunohistochemistry (IHC) are powerful tools for NTRK fusion detection. In this study, a total of 4,619 LUAD formalin-fixed, paraffin-embedded tissues were collected from patients who underwent biopsy or resection at the Shanghai Chest Hospital during 2017-2019. All specimens were screened for NTRK1 rearrangements using DNA-based NGS. Thereafter, the cases with NTRK1 rearrangements and cases negative for common driver mutations were analyzed for NTRK1/2/3 fusions using total nucleic acid (TNA)-based NGS and pan-TRK IHC. Overall, four NTRK1/2 fusion events were identified, representing 0.087% of the original sample set. At the DNA level, seven NTRK1 rearrangements were identified, while only two TPM3-NTRK1 fusions were confirmed on TNA-based NGS as functional. In addition, two NTRK2 fusions (SQSTM1-NTRK2 and KIF5B-NTRK2) were identified by TNA-based NGS in 350 'pan-negative' cases. Two patients harboring NTRK1/2 fusions were diagnosed with invasive adenocarcinoma, while the other two were diagnosed with adenocarcinoma in situ and minimally invasive adenocarcinoma. All four samples with NTRK fusions were positive for the expression of pan-TRK. The two samples with NTRK2 fusions showed cytoplasmic staining alone, while the other two samples with NTRK1 fusions exhibited both cytoplasmic and membranous staining. In summary, functional NTRK fusions are found in early-stage LUAD; however, they are extremely rare. According to this study's results, they are independent oncogenic drivers, mutually exclusive with other driver mutations. We demonstrated that NTRK rearrangement analysis using a DNA-based approach should be verified with an RNA-based assay.
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Affiliation(s)
- Ruiying Zhao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Feng Yao
- Department of Thoracic Surgery, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Chan Xiang
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Jikai Zhao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Zhanxian Shang
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Lianying Guo
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Wenjie Ding
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Shengji Ma
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Anbo Yu
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Jinchen Shao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Yuchen Han
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
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Selecting the optimal immunotherapy regimen in driver-negative metastatic NSCLC. Nat Rev Clin Oncol 2021; 18:625-644. [PMID: 34168333 DOI: 10.1038/s41571-021-00520-1] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 12/12/2022]
Abstract
The treatment landscape of driver-negative non-small-cell lung cancer (NSCLC) is rapidly evolving. Immune-checkpoint inhibitors, specifically those targeting PD-1 or PD-L1, have demonstrated durable efficacy in a subset of patients with NSCLC, and these agents have become the cornerstone of first-line therapy. Approved immunotherapeutic strategies for treatment-naive patients now include monotherapy, immunotherapy-exclusive regimens or chemotherapy-immunotherapy combinations. Decision making in this space is complex given the absence of head-to-head prospective comparisons, although a thorough analysis of long-term efficacy and safety data from pivotal clinical trials can provide insight into the optimal management of each subset of patients. Indeed, histological subtype and the extent of tumour cell PD-L1 expression are paramount to regimen selection, although other clinicopathological factors and patient preferences might also be relevant in certain scenarios. Finally, several emerging biomarkers and novel therapeutic strategies are currently under investigation, and these might further refine the current treatment paradigm. In this Review, we discuss the current treatment landscape and detail our approach to first-line immunotherapy regimen selection for patients with advanced-stage, driver-negative NSCLC.
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What Is New in Biomarker Testing at Diagnosis of Advanced Non-Squamous Non-Small Cell Lung Carcinoma? Implications for Cytology and Liquid Biopsy. JOURNAL OF MOLECULAR PATHOLOGY 2021. [DOI: 10.3390/jmp2020015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The discovery and clinical validation of biomarkers predictive of the response of non-squamous non-small-cell lung carcinomas (NS-NSCLC) to therapeutic strategies continue to provide new data. The evaluation of novel treatments is based on molecular analyses aimed at determining their efficacy. These tests are increasing in number, but the tissue specimens are smaller and smaller and/or can have few tumor cells. Indeed, in addition to tissue samples, complementary cytological and/or blood samples can also give access to these biomarkers. To date, it is recommended and necessary to look for the status of five genomic molecular biomarkers (EGFR, ALK, ROS1, BRAFV600, NTRK) and of a protein biomarker (PD-L1). However, the short- and more or less long-term emergence of new targeted treatments of genomic alterations on RET and MET, but also on others’ genomic alteration, notably on KRAS, HER2, NRG1, SMARCA4, and NUT, have made cellular and blood samples essential for molecular testing. The aim of this review is to present the interest in using cytological and/or liquid biopsies as complementary biological material, or as an alternative to tissue specimens, for detection at diagnosis of new predictive biomarkers of NS-NSCLC.
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Chang S, Shim HS, Kim TJ, Choi YL, Kim WS, Shin DH, Kim L, Park HS, Lee GK, Lee CH. Molecular biomarker testing for non-small cell lung cancer: consensus statement of the Korean Cardiopulmonary Pathology Study Group. J Pathol Transl Med 2021; 55:181-191. [PMID: 33966368 PMCID: PMC8141968 DOI: 10.4132/jptm.2021.03.23] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
Molecular biomarker testing is the standard of care for non–small cell lung cancer (NSCLC) patients. In 2017, the Korean Cardiopulmonary Pathology Study Group and the Korean Molecular Pathology Study Group co-published a molecular testing guideline which contained almost all known genetic changes that aid in treatment decisions or predict prognosis in patients with NSCLC. Since then there have been significant changes in targeted therapies as well as molecular testing including newly approved targeted drugs and liquid biopsy. In order to reflect these changes, the Korean Cardiopulmonary Pathology Study Group developed a consensus statement on molecular biomarker testing. This consensus statement was crafted to provide guidance on what genes should be tested, as well as methodology, samples, patient selection, reporting and quality control.
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Affiliation(s)
- Sunhee Chang
- Department of Pathology, Inje University Ilsan Paik Hospital, Goyang, Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Tae Jung Kim
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yoon-La Choi
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Wan Seop Kim
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
| | - Dong Hoon Shin
- Department of Pathology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Lucia Kim
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
| | - Heae Surng Park
- Department of Pathology, Ewha Womans University Seoul Hospital, Seoul, Korea
| | - Geon Kook Lee
- Department of Pathology, National Cancer Center, Goyang, Korea
| | - Chang Hun Lee
- Department of Pathology, Pusan National University Hospital, Pusan National University School of Medicine, Busan, Korea
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Treatment of Rare Mutations in Patients with Lung Cancer. Biomedicines 2021; 9:biomedicines9050534. [PMID: 34064757 PMCID: PMC8151457 DOI: 10.3390/biomedicines9050534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is a worldwide prevalent malignancy. This disease has a low survival rate due to diagnosis at a late stage challenged by the involvement of metastatic sites. Non-small-cell lung cancer (NSCLC) is presented in 85% of cases. The last decade has experienced substantial advancements in scientific research, leading to a novel targeted therapeutic approach. The newly developed pharmaceutical agents are aimed towards specific mutations, detected in individual patients inflicted by lung cancer. These drugs have longer and improved response rates compared to traditional chemotherapy. Recent studies were able to identify rare mutations found in pulmonary tumors. Among the gene alterations detected were mesenchymal epithelial transition factor (MET), human epidermal growth factor 2 (HER2), B-type Raf kinase (BRAF), c-ROS proto-oncogene (ROS1), rearranged during transfection (RET) and neurotrophic tyrosine kinase (NTRK). Ongoing clinical trials are gaining insight onto possible first and second lines of medical treatment options intended to enable progression-free survival to lung cancer patients.
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50
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Strohmeier S, Brcic I, Popper H, Liegl-Atzwanger B, Lindenmann J, Brcic L. Applicability of pan-TRK immunohistochemistry for identification of NTRK fusions in lung carcinoma. Sci Rep 2021; 11:9785. [PMID: 33963267 PMCID: PMC8105314 DOI: 10.1038/s41598-021-89373-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
In the last two decades, various therapies have been introduced for lung carcinoma patients, including tyrosine-kinase inhibitors for different mutations. While some of them are specific to specific tumor types, others, like NTRK1-3 fusions, are found in various solid tumors. The occurrence of an NTRK1,2 or 3 fusion acts as a biomarker for efficient treatment with NTRK inhibitors, irrespectively of the tumor type. However, the occurrence of the NTRK1-3 fusions in lung carcinomas is extremely rare. We performed a retrospective analysis to evaluate the applicability of immunohistochemistry with the pan-TRK antibody in the detection of NTRK fusions in lung carcinomas. The study cohort included 176 adenocarcinomas (AC), 161 squamous cell carcinomas (SCC), 31 large-cell neuroendocrine carcinomas (LCNEC), and 19 small cell lung carcinomas (SCLC). Immunohistochemistry (IHC) was performed using the pan-TRK antibody (clone EPR17341, Ventana) on tissue microarrays, while confirmation for all positive cases was done using RNA-based Archer FusionPlex MUG Lung Panel. On IHC staining, 12/387 samples (3.1%) demonstrated a positive reaction. Ten SCC cases (10/161, 6.2%), and two LCNEC cases (2/31, 6.5%) were positive. Positive cases demonstrated heterogeneous staining of tumor cells, mostly membranous with some cytoplasmic and in one case nuclear pattern. RNA-based sequencing did not demonstrate any NTRK1-3 fusion in our patients' collective. Our study demonstrates that pan-TRK expression in lung carcinoma is very low across different histologic types. NTRK1-3 fusions using an RNA-based sequencing approached could not be detected. This stresses the importance of confirmation of immunohistochemistry results by molecular methods.
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Affiliation(s)
- Simon Strohmeier
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - Iva Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - Helmut Popper
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - Bernadette Liegl-Atzwanger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - Jörg Lindenmann
- Division of Thoracic Surgery and Hyperbaric Surgery, Department of Surgery, Medical University of Graz, Auenbruggerplatz 29/3, 8036, Graz, Austria
| | - Luka Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria.
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