51
|
Christopoulos P, Bozorgmehr F, Brückner L, Chung I, Krisam J, Schneider MA, Stenzinger A, Eickhoff R, Mueller DW, Thomas M. Brigatinib versus other second-generation ALK inhibitors as initial treatment of anaplastic lymphoma kinase positive non-small cell lung cancer with deep phenotyping: study protocol of the ABP trial. BMC Cancer 2021; 21:743. [PMID: 34182952 PMCID: PMC8240323 DOI: 10.1186/s12885-021-08460-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/08/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Availability of potent anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors (TKI) has pushed the median survival of ALK+ non-smallcell lung cancer (NSCLC) patients to over five years. In particular, second-generation ALK TKI have demonstrated superiority compared to the first-generation compound crizotinib and are meanwhile standard first-line treatment. However, clinical courses of individual patients vary widely, with secondary development of drug resistance and intracranial progression remaining important problems. While these limitations highlight the need for better disease monitoring and additional therapeutic tools, molecular tumor features are increasingly recognized as crucial determinants of clinical outcome. This trial aims to optimize management of ALK+ NSCLC by analyzing the efficacy of second-generation ALK inhibitors in conjunction with deep longitudinal phenotyping across two treatment lines. METHODS/DESIGN In this exploratory prospective phase II clinical trial, newly diagnosed ALK+ NSCLC patients will be randomized into two treatment arms, stratified by presence of brain metastases and ECOG performance status: brigatinib (experimental arm) vs. any other approved second-generation ALK TKI. Tumor tissue and blood samples will be collected for biomarker analysis at the beginning and throughout the study period to investigate baseline molecular tumor properties and analyze the development of acquired drug resistance. In addition, participating investigators and patients will have the possibility of fast-track molecular tumor and ctDNA profiling at the time of disease progression using state-of-the-art next-generation sequencing (NGS), in order to support decisions regarding next-line therapy. DISCUSSION Besides supporting therapeutic decisions for enrolled patients, the ABP trial primarily aims to deepen the understanding of the underlying biology and facilitate development of a framework for individualized management of ALK+ NSCLC according to molecular features. Patients with low molecular risk and the perspective of a "chronic disease" will be distinguished from "high-risk" cases, molecular properties of which will be utilized to elaborate improved methods of non-invasive monitoring and novel preclinical models in order to advance therapeutic strategies. TRIAL REGISTRATION Clinicaltrials.gov , NCT04318938. Registered March 182,020, https://www.clinicaltrials.gov/ct2/show/NCT04318938 Eudra-CT, 2019-001828-36. Registered September 302,019, https://www.clinicaltrialsregister.eu/ctr-search/search?query=2019-001828-36.
Collapse
Affiliation(s)
- Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik at University Hospital of Heidelberg, Röntgenstraße 1, 69126, Heidelberg, Germany.,Translational Lung Research Center Heidelberg TLRCH, Member of the German Center for Lung Research DZL, Im Neuenheimer Feld 156, 69120, Heidelberg, Germany
| | - Farastuk Bozorgmehr
- Department of Thoracic Oncology, Thoraxklinik at University Hospital of Heidelberg, Röntgenstraße 1, 69126, Heidelberg, Germany.,Translational Lung Research Center Heidelberg TLRCH, Member of the German Center for Lung Research DZL, Im Neuenheimer Feld 156, 69120, Heidelberg, Germany
| | - Lena Brückner
- Department of Thoracic Oncology, Thoraxklinik at University Hospital of Heidelberg, Röntgenstraße 1, 69126, Heidelberg, Germany.,Translational Lung Research Center Heidelberg TLRCH, Member of the German Center for Lung Research DZL, Im Neuenheimer Feld 156, 69120, Heidelberg, Germany
| | - Inn Chung
- Department of Thoracic Oncology, Thoraxklinik at University Hospital of Heidelberg, Röntgenstraße 1, 69126, Heidelberg, Germany.,Translational Lung Research Center Heidelberg TLRCH, Member of the German Center for Lung Research DZL, Im Neuenheimer Feld 156, 69120, Heidelberg, Germany
| | - Johannes Krisam
- University Hospital of Heidelberg, Institute of Medical Biometry and Informatics, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
| | - Marc A Schneider
- Translational Lung Research Center Heidelberg TLRCH, Member of the German Center for Lung Research DZL, Im Neuenheimer Feld 156, 69120, Heidelberg, Germany.,Translational Research Unit (STF), Thoraxklinik at University Hospital of Heidelberg, Röntgenstraße 1, 69126, Heidelberg, Germany
| | - Albrecht Stenzinger
- Translational Lung Research Center Heidelberg TLRCH, Member of the German Center for Lung Research DZL, Im Neuenheimer Feld 156, 69120, Heidelberg, Germany.,University of Heidelberg, Institute of Pathology, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Regina Eickhoff
- Institut für Klinische Krebsforschung IKF GmbH am Krankenhaus Nordwest, Steinbacher Hohl 2-26, 60488, Frankfurt am Main, Germany
| | - Daniel W Mueller
- Institut für Klinische Krebsforschung IKF GmbH am Krankenhaus Nordwest, Steinbacher Hohl 2-26, 60488, Frankfurt am Main, Germany
| | - Michael Thomas
- Department of Thoracic Oncology, Thoraxklinik at University Hospital of Heidelberg, Röntgenstraße 1, 69126, Heidelberg, Germany. .,Translational Lung Research Center Heidelberg TLRCH, Member of the German Center for Lung Research DZL, Im Neuenheimer Feld 156, 69120, Heidelberg, Germany.
| |
Collapse
|
52
|
Artibani M, Masuda K, Hu Z, Rauher PC, Mallett G, Wietek N, Morotti M, Chong K, KaramiNejadRanjbar M, Zois CE, Dhar S, El-Sahhar S, Campo L, Blagden SP, Damato S, Pathiraja PN, Nicum S, Gleeson F, Laios A, Alsaadi A, Santana Gonzalez L, Motohara T, Albukhari A, Lu Z, Bast RC, Harris AL, Ejsing CS, Klemm RW, Yau C, Sauka-Spengler T, Ahmed AA. Adipocyte-like signature in ovarian cancer minimal residual disease identifies metabolic vulnerabilities of tumor-initiating cells. JCI Insight 2021; 6:147929. [PMID: 33945502 PMCID: PMC8262282 DOI: 10.1172/jci.insight.147929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022] Open
Abstract
Similar to tumor-initiating cells (TICs), minimal residual disease (MRD) is capable of reinitiating tumors and causing recurrence. However, the molecular characteristics of solid tumor MRD cells and drivers of their survival have remained elusive. Here we performed dense multiregion transcriptomics analysis of paired biopsies from 17 ovarian cancer patients before and after chemotherapy. We reveal that while MRD cells share important molecular signatures with TICs, they are also characterized by an adipocyte-like gene expression signature and a portion of them had undergone epithelial-mesenchymal transition (EMT). In a cell culture MRD model, MRD-mimic cells showed the same phenotype and were dependent on fatty acid oxidation (FAO) for survival and resistance to cytotoxic agents. These findings identify EMT and FAO as attractive targets to eradicate MRD in ovarian cancer and make a compelling case for the further testing of FAO inhibitors in treating MRD.
Collapse
Affiliation(s)
- Mara Artibani
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
- Gene Regulatory Networks in Development and Disease Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Kenta Masuda
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Zhiyuan Hu
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Pascal C. Rauher
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Garry Mallett
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
- Gene Regulatory Networks in Development and Disease Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Nina Wietek
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
- Department of Gynaecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
| | - Matteo Morotti
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
- Department of Gynaecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
| | - Kay Chong
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Mohammad KaramiNejadRanjbar
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Christos E. Zois
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Sunanda Dhar
- Department of Histopathology, Oxford University Hospitals, Oxford, United Kingdom
| | - Salma El-Sahhar
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Leticia Campo
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Sarah P. Blagden
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Stephen Damato
- Department of Histopathology, Oxford University Hospitals, Oxford, United Kingdom
| | - Pubudu N. Pathiraja
- Department of Gynaecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
| | - Shibani Nicum
- Department of Gynaecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
| | - Fergus Gleeson
- Department of Radiology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
| | - Alexandros Laios
- Department of Gynaecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
| | - Abdulkhaliq Alsaadi
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Laura Santana Gonzalez
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Takeshi Motohara
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Chuo-ku, Kumamoto, Japan
| | - Ashwag Albukhari
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zhen Lu
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Robert C. Bast
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Adrian L. Harris
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Christer S. Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Robin W. Klemm
- Department of Physiology, Anatomy and Genetics, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Christopher Yau
- Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology Medicine and Health, the University of Manchester, Manchester, United Kingdom
| | - Tatjana Sauka-Spengler
- Gene Regulatory Networks in Development and Disease Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Ahmed Ashour Ahmed
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
- Department of Gynaecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
- Oxford National Institute for Health Research (NIHR) Biomedical Research Centre, Oxford, United Kingdom
| |
Collapse
|
53
|
Schubert L, Le AT, Estrada-Bernal A, Doak AE, Yoo M, Ferrara SE, Goodspeed A, Kinose F, Rix U, Tan AC, Doebele RC. Novel Human-Derived RET Fusion NSCLC Cell Lines Have Heterogeneous Responses to RET Inhibitors and Differential Regulation of Downstream Signaling. Mol Pharmacol 2021; 99:435-447. [PMID: 33795352 PMCID: PMC11033948 DOI: 10.1124/molpharm.120.000207] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
Rearranged during transfection (RET) rearrangements occur in 1% to 2% of lung adenocarcinomas as well as other malignancies and are now established targets for tyrosine kinase inhibitors. We developed three novel RET fusion-positive (RET+) patient-derived cancer cell lines, CUTO22 [kinesin 5B (KIF5B)-RET fusion], CUTO32 (KIF5B-RET fusion), and CUTO42 (echinoderm microtubule-associated protein-like 4-RET fusion), to study RET signaling and response to therapy. We confirmed each of our cell lines expresses the RET fusion protein and assessed their sensitivity to RET inhibitors. We found that the CUTO22 and CUTO42 cell lines were sensitive to multiple RET inhibitors, whereas the CUTO32 cell line was >10-fold more resistant to three RET inhibitors. We discovered that our RET+ cell lines had differential regulation of the mitogen-activated protein kinase and phosphoinositide 3-kinase/protein kinase B (AKT) pathways. After inhibition of RET, the CUTO42 cells had robust inhibition of phosphorylated AKT (pAKT), whereas CUTO22 and CUTO32 cells had sustained AKT activation. Next, we performed a drug screen, which revealed that the CUTO32 cells were sensitive (<1 nM IC50) to inhibition of two cell cycle-regulating proteins, polo-like kinase 1 and Aurora kinase A. Finally, we show that two of these cell lines, CUTO32 and CUTO42, successfully establish xenografted tumors in nude mice. We demonstrated that the RET inhibitor BLU-667 was effective at inhibiting tumor growth in CUTO42 tumors but had a much less profound effect in CUTO32 tumors, consistent with our in vitro experiments. These data highlight the utility of new RET+ models to elucidate differences in response to tyrosine kinase inhibitors and downstream signaling regulation. Our RET+ cell lines effectively recapitulate the interpatient heterogeneity observed in response to RET inhibitors and reveal opportunities for alternative or combination therapies. SIGNIFICANCE STATEMENT: We have derived and characterized three novel rearranged during transfection (RET) fusion non-small cell lung cancer cell lines and demonstrated that they have differential responses to RET inhibition as well as regulation of downstream signaling, an area that has previously been limited by a lack of diverse cell line modes with endogenous RET fusions. These data offer important insight into regulation of response to RET tyrosine kinase inhibitors and other potential therapeutic targets.
Collapse
Affiliation(s)
- Laura Schubert
- Department of Medicine, Division of Medical Oncology, University of Colorado School of Medicine, Aurora, Colorado (L.S., A.T.L., A.E.-B., A.E.D., M.Y., A.-C.T., R.C.D.); University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado (S.E.F., A.G.); Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado (A.G.); and Department of Thoracic Oncology (F.K.), Department of Drug Discovery (U.R.), and Department of Biostatistics and Bioinformatics (A.-C.T.), Moffitt Cancer Center, Tampa, Florida
| | - Anh T Le
- Department of Medicine, Division of Medical Oncology, University of Colorado School of Medicine, Aurora, Colorado (L.S., A.T.L., A.E.-B., A.E.D., M.Y., A.-C.T., R.C.D.); University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado (S.E.F., A.G.); Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado (A.G.); and Department of Thoracic Oncology (F.K.), Department of Drug Discovery (U.R.), and Department of Biostatistics and Bioinformatics (A.-C.T.), Moffitt Cancer Center, Tampa, Florida
| | - Adriana Estrada-Bernal
- Department of Medicine, Division of Medical Oncology, University of Colorado School of Medicine, Aurora, Colorado (L.S., A.T.L., A.E.-B., A.E.D., M.Y., A.-C.T., R.C.D.); University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado (S.E.F., A.G.); Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado (A.G.); and Department of Thoracic Oncology (F.K.), Department of Drug Discovery (U.R.), and Department of Biostatistics and Bioinformatics (A.-C.T.), Moffitt Cancer Center, Tampa, Florida
| | - Andrea E Doak
- Department of Medicine, Division of Medical Oncology, University of Colorado School of Medicine, Aurora, Colorado (L.S., A.T.L., A.E.-B., A.E.D., M.Y., A.-C.T., R.C.D.); University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado (S.E.F., A.G.); Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado (A.G.); and Department of Thoracic Oncology (F.K.), Department of Drug Discovery (U.R.), and Department of Biostatistics and Bioinformatics (A.-C.T.), Moffitt Cancer Center, Tampa, Florida
| | - Minjae Yoo
- Department of Medicine, Division of Medical Oncology, University of Colorado School of Medicine, Aurora, Colorado (L.S., A.T.L., A.E.-B., A.E.D., M.Y., A.-C.T., R.C.D.); University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado (S.E.F., A.G.); Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado (A.G.); and Department of Thoracic Oncology (F.K.), Department of Drug Discovery (U.R.), and Department of Biostatistics and Bioinformatics (A.-C.T.), Moffitt Cancer Center, Tampa, Florida
| | - Sarah E Ferrara
- Department of Medicine, Division of Medical Oncology, University of Colorado School of Medicine, Aurora, Colorado (L.S., A.T.L., A.E.-B., A.E.D., M.Y., A.-C.T., R.C.D.); University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado (S.E.F., A.G.); Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado (A.G.); and Department of Thoracic Oncology (F.K.), Department of Drug Discovery (U.R.), and Department of Biostatistics and Bioinformatics (A.-C.T.), Moffitt Cancer Center, Tampa, Florida
| | - Andrew Goodspeed
- Department of Medicine, Division of Medical Oncology, University of Colorado School of Medicine, Aurora, Colorado (L.S., A.T.L., A.E.-B., A.E.D., M.Y., A.-C.T., R.C.D.); University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado (S.E.F., A.G.); Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado (A.G.); and Department of Thoracic Oncology (F.K.), Department of Drug Discovery (U.R.), and Department of Biostatistics and Bioinformatics (A.-C.T.), Moffitt Cancer Center, Tampa, Florida
| | - Fumi Kinose
- Department of Medicine, Division of Medical Oncology, University of Colorado School of Medicine, Aurora, Colorado (L.S., A.T.L., A.E.-B., A.E.D., M.Y., A.-C.T., R.C.D.); University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado (S.E.F., A.G.); Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado (A.G.); and Department of Thoracic Oncology (F.K.), Department of Drug Discovery (U.R.), and Department of Biostatistics and Bioinformatics (A.-C.T.), Moffitt Cancer Center, Tampa, Florida
| | - Uwe Rix
- Department of Medicine, Division of Medical Oncology, University of Colorado School of Medicine, Aurora, Colorado (L.S., A.T.L., A.E.-B., A.E.D., M.Y., A.-C.T., R.C.D.); University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado (S.E.F., A.G.); Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado (A.G.); and Department of Thoracic Oncology (F.K.), Department of Drug Discovery (U.R.), and Department of Biostatistics and Bioinformatics (A.-C.T.), Moffitt Cancer Center, Tampa, Florida
| | - Aik-Choon Tan
- Department of Medicine, Division of Medical Oncology, University of Colorado School of Medicine, Aurora, Colorado (L.S., A.T.L., A.E.-B., A.E.D., M.Y., A.-C.T., R.C.D.); University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado (S.E.F., A.G.); Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado (A.G.); and Department of Thoracic Oncology (F.K.), Department of Drug Discovery (U.R.), and Department of Biostatistics and Bioinformatics (A.-C.T.), Moffitt Cancer Center, Tampa, Florida
| | - Robert C Doebele
- Department of Medicine, Division of Medical Oncology, University of Colorado School of Medicine, Aurora, Colorado (L.S., A.T.L., A.E.-B., A.E.D., M.Y., A.-C.T., R.C.D.); University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado (S.E.F., A.G.); Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado (A.G.); and Department of Thoracic Oncology (F.K.), Department of Drug Discovery (U.R.), and Department of Biostatistics and Bioinformatics (A.-C.T.), Moffitt Cancer Center, Tampa, Florida
| |
Collapse
|
54
|
Christopoulos P, Dietz S, Angeles AK, Rheinheimer S, Kazdal D, Volckmar AL, Janke F, Endris V, Meister M, Kriegsmann M, Zemojtel T, Reck M, Stenzinger A, Thomas M, Sültmann H. Earlier extracranial progression and shorter survival in ALK-rearranged lung cancer with positive liquid rebiopsies. Transl Lung Cancer Res 2021; 10:2118-2131. [PMID: 34164264 PMCID: PMC8182700 DOI: 10.21037/tlcr-21-32] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Liquid rebiopsies can detect resistance mutations to guide therapy of anaplastic lymphoma kinase-rearranged (ALK+) non-small-cell lung cancer (NSCLC) failing tyrosine kinase inhibitors (TKI). Here, we analyze how their results relate to the anatomical pattern of disease progression and patient outcome. Methods Clinical, molecular, and radiologic characteristics of consecutive TKI-treated ALK+ NSCLC patients were analyzed using prospectively collected plasma samples and the 17-gene targeted AVENIO kit, which covers oncogenic drivers and all TP53 exons. Results In 56 patients, 139 instances of radiologic changes were analyzed, of which 133 corresponded to disease progression. Circulating tumor DNA (ctDNA) alterations were identified in most instances of extracranial progression (58/94 or 62%), especially if concomitant intracranial progression was also present (89%, P<0.001), but rarely in case of isolated central nervous system (CNS) progression (8/39 or 21%, P<0.001). ctDNA detectability correlated with presence of “short” echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusion variants (mainly V3, E6:A20) and/or TP53 mutations (P<0.05), and presented therapeutic opportunities in <50% of cases. Patients with extracranial progression and positive liquid biopsies had shorter survival from the start of palliative treatment (mean 52 vs. 69 months, P=0.002), regardless of previous and subsequent therapy and initial ECOG performance status. Furthermore, for patients with extracranial progression, ctDNA detectability was associated with shorter next-line progression-free survival (PFS) (3 vs. 13 months, P=0.003) if they were switched to another systemic therapy (49/86 samples), and with shorter time-to-next-treatment (TNT) (3 vs. 8 months, P=0.004) if they were continued on the same treatment due to oligoprogression (37/86). In contrast, ctDNA detectability was not associated with the outcome of patients showing CNS-only progression. In 6/6 cases with suspicion of non-neoplastic radiologic lung changes (mainly infection or pneumonitis), ctDNA results remained negative. Conclusions Positive blood-based liquid rebiopsies in ALK+ NSCLC characterize biologically more aggressive disease and are common with extracranial, but rare with CNS-only progression or benign radiologic changes. These results reconcile the increased detection of ALK resistance mutations with other features of the high-risk EML4-ALK V3-associated phenotype. Conversely, most oligoprogressive patients with negative liquid biopsies have a more indolent course without need for early change of systemic treatment.
Collapse
Affiliation(s)
- Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany.,Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany
| | - Steffen Dietz
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Arlou K Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stephan Rheinheimer
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany.,Department of Diagnostic and Interventional Radiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Kazdal
- Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Volker Endris
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Meister
- Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany.,Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Mark Kriegsmann
- Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomasz Zemojtel
- Charité - Universitätsmedizin Berlin, BIH - Genomics Core Unit, Berlin, Germany
| | - Martin Reck
- Lungenclinic Großhansdorf, Großhansdorf, Germany
| | - Albrecht Stenzinger
- Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Thomas
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| |
Collapse
|
55
|
Cucchiara F, Petrini I, Romei C, Crucitta S, Lucchesi M, Valleggi S, Scavone C, Capuano A, De Liperi A, Chella A, Danesi R, Del Re M. Combining liquid biopsy and radiomics for personalized treatment of lung cancer patients. State of the art and new perspectives. Pharmacol Res 2021; 169:105643. [PMID: 33940185 DOI: 10.1016/j.phrs.2021.105643] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/22/2021] [Accepted: 04/22/2021] [Indexed: 12/11/2022]
Abstract
Lung cancer has become a paradigm for precision medicine in oncology, and liquid biopsy (LB) together with radiomics may have a great potential in this scenario. They are both minimally invasive, easy to perform, and can be repeated during patient's follow-up. Also, increasing evidence suggest that LB and radiomics may provide an efficient way to screen and diagnose tumors at an early stage, including the monitoring of any change in the tumor molecular profile. This could allow treatment optimization, improvement of patients' quality of life, and healthcare-related costs reduction. Latest reports on lung cancer patients suggest a combination of these two strategies, along with cutting-edge data analysis, to decode valuable information regarding tumor type, aggressiveness, progression, and response to treatment. The approach seems more compatible with clinical practice than the current standard, and provides new diagnostic companions being able to suggest the best treatment strategy compared to conventional methods. To implement radiomics and liquid biopsy directly into clinical practice, an artificial intelligence (AI)-based system could help to link patients' clinical data together with tumor molecular profiles and imaging characteristics. AI could also solve problems and limitations related to LB and radiomics methodologies. Further work is needed, including new health policies and the access to large amounts of high-quality and well-organized data, allowing a complementary and synergistic combination of LB and imaging, to provide an attractive choice e in the personalized treatment of lung cancer.
Collapse
Affiliation(s)
- Federico Cucchiara
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Iacopo Petrini
- Unit of Pneumology, Department of Translational Research and New Technologies in Medicine, University Hospital of Pisa, Pisa, Italy
| | - Chiara Romei
- Unit II of Radio-diagnostics, Department of Diagnostic and Imaging, University Hospital of Pisa, Pisa, Italy
| | - Stefania Crucitta
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Maurizio Lucchesi
- Unit of Pneumology, Department of Translational Research and New Technologies in Medicine, University Hospital of Pisa, Pisa, Italy
| | - Simona Valleggi
- Unit of Pneumology, Department of Translational Research and New Technologies in Medicine, University Hospital of Pisa, Pisa, Italy
| | - Cristina Scavone
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Annalisa Capuano
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Annalisa De Liperi
- Unit II of Radio-diagnostics, Department of Diagnostic and Imaging, University Hospital of Pisa, Pisa, Italy
| | - Antonio Chella
- Unit of Pneumology, Department of Translational Research and New Technologies in Medicine, University Hospital of Pisa, Pisa, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy.
| | - Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| |
Collapse
|
56
|
Hofman P. Next-Generation Sequencing with Liquid Biopsies from Treatment-Naïve Non-Small Cell Lung Carcinoma Patients. Cancers (Basel) 2021; 13:2049. [PMID: 33922637 PMCID: PMC8122958 DOI: 10.3390/cancers13092049] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/11/2021] [Accepted: 04/20/2021] [Indexed: 12/16/2022] Open
Abstract
Recently, the liquid biopsy (LB), a non-invasive and easy to repeat approach, has started to compete with the tissue biopsy (TB) for detection of targets for administration of therapeutic strategies for patients with advanced stages of lung cancer at tumor progression. A LB at diagnosis of late stage non-small cell lung carcinoma (NSCLC) is also being performed. It may be asked if a LB can be complementary (according to the clinical presentation or systematics) or even an alternative to a TB for treatment-naïve advanced NSCLC patients. Nucleic acid analysis with a TB by next-generation sequencing (NGS) is gradually replacing targeted sequencing methods for assessment of genomic alterations in lung cancer patients with tumor progression, but also at baseline. However, LB is still not often used in daily practice for NGS. This review addresses different aspects relating to the use of LB for NGS at diagnosis in advanced NSCLC, including its advantages and limitations.
Collapse
Affiliation(s)
- Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Université Côte d’Azur, CHU Nice, FHU OncoAge, Pasteur Hospital, 30 avenue de la voie romaine, BP69, CEDEX 01, 06001 Nice, France; ; Tel.: +33-4-92-03-88-55 or +33-4-92-03-87-49; Fax: +33-4-92-88-50
- Hospital-Integrated Biobank BB-0033-00025, Université Côte d’Azur, CHU Nice, FHU OncoAge, 06001 Nice, France
| |
Collapse
|
57
|
Elsayed M, Bozorgmehr F, Kazdal D, Volckmar AL, Sültmann H, Fischer JR, Kriegsmann M, Stenzinger A, Thomas M, Christopoulos P. Feasibility and Challenges for Sequential Treatments in ALK-Rearranged Non-Small-Cell Lung Cancer. Front Oncol 2021; 11:670483. [PMID: 33959513 PMCID: PMC8096170 DOI: 10.3389/fonc.2021.670483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 03/25/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Anaplastic lymphoma kinase-rearranged non-small-cell lung cancer (ALK+ NSCLC) is a model disease for use of targeted therapies (TKI), which are administered sequentially to maximize patient survival. METHODS We retrospectively analyzed the flow of 145 consecutive TKI-treated ALK+ NSCLC patients across therapy lines. Suitable patients that could not receive an available next-line therapy ("attrition") were determined separately for various treatments, based on the approval status of the respective targeted drugs when each treatment failure occurred in each patient. RESULTS At the time of analysis, 70/144 (49%) evaluable patients were still alive. Attrition rates related to targeted treatments were approximately 25-30% and similar for administration of a second-generation (2G) ALK inhibitor (22%, 17/79) or any subsequent systemic therapy (27%, 27/96) after crizotinib, and for the administration of lorlatinib (27%, 6/22) or any subsequent systemic therapy (25%, 15/61) after any 2G TKI. The rate of chemotherapy implementation was 67% (62/93). Both administration of additional TKI (median overall survival [mOS] 59 vs. 41 months for multiple vs. one TKI lines, logrank p=0.002), and chemotherapy (mOS 41 vs. 16 months, logrank p<0.001) were significantly associated with longer survival. Main reason for patients foregoing any subsequent systemic treatment was rapid clinical deterioration (n=40/43 or 93%) caused by tumor progression. In 2/3 of cases (29/43), death occurred under the first failing therapy, while in 11/43 the treatment was switched, but the patient did not respond, deteriorated further, and died within 8 weeks. CONCLUSIONS Despite absence of regulatory obstacles and no requirement for specific acquired mutations, 25-30% of ALK+ NSCLC patients forego subsequent systemic therapy due to rapid clinical deterioration, in several cases (approximately 1/3) associated with an ineffective first next-line choice. These results underline the need for closer patient monitoring and broader profiling in order to support earlier and better directed use of available therapies.
Collapse
Affiliation(s)
- Mei Elsayed
- Department of Thoracic Oncology, Thoraxklinik and National Center for Tumor diseases (NCT) at Heidelberg University Hospital, Heidelberg, Germany
| | - Farastuk Bozorgmehr
- Department of Thoracic Oncology, Thoraxklinik and National Center for Tumor diseases (NCT) at Heidelberg University Hospital, Heidelberg, Germany
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
| | - Daniel Kazdal
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Holger Sültmann
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jürgen R. Fischer
- Department of Thoracic Oncology, Lungenklinik Löwenstein, Löwenstein, Germany
| | - Mark Kriegsmann
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Albrecht Stenzinger
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Thomas
- Department of Thoracic Oncology, Thoraxklinik and National Center for Tumor diseases (NCT) at Heidelberg University Hospital, Heidelberg, Germany
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
| | - Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik and National Center for Tumor diseases (NCT) at Heidelberg University Hospital, Heidelberg, Germany
- Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
| |
Collapse
|
58
|
Ferreira D, Miranda J, Martins-Lopes P, Adega F, Chaves R. Future Perspectives in Detecting EGFR and ALK Gene Alterations in Liquid Biopsies of Patients with NSCLC. Int J Mol Sci 2021; 22:ijms22083815. [PMID: 33916986 PMCID: PMC8067613 DOI: 10.3390/ijms22083815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/28/2021] [Accepted: 04/03/2021] [Indexed: 02/07/2023] Open
Abstract
Non-small-cell lung cancer (NSCLC) is a major cause of death worldwide. Alterations in such genes as EGFR and ALK are considered important biomarkers in NSCLC due to the existence of targeted therapies with specific tyrosine kinase inhibitors (TKIs). However, specific resistance-related mutations can occur during TKI treatment, which often result in therapy inefficacy. Liquid biopsies arise as a reliable tool for the early detection of these types of alterations, allowing a non-invasive follow-up of the patients. Furthermore, they can be essential for cancer screening, initial diagnosis and to check surgery success. Despite the great advantages of liquid biopsies in NSCLC and the high input that next-generation sequencing (NGS) approaches can provide in this field, its use in oncology is still limited. With improvement of assay sensitivity and the establishment of clinical guidelines for liquid biopsy analysis, it is expected that they will be used in routine procedures. This review focuses on the usefulness of liquid biopsies of NSCLC patients as a means to detect alterations in EGFR and ALK genes and in disease management, highlighting the impact of NGS methods.
Collapse
Affiliation(s)
- Daniela Ferreira
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
| | - Juliana Miranda
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
| | - Paula Martins-Lopes
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
- Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Filomena Adega
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
| | - Raquel Chaves
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
- Correspondence: ; Tel.: +351-259-350936
| |
Collapse
|
59
|
Nakamura IT, Ikegami M, Hasegawa N, Hayashi T, Ueno T, Kawazu M, Yagishita S, Goto Y, Shinno Y, Kojima Y, Takamochi K, Takahashi F, Takahashi K, Mano H, Kohsaka S. Development of an optimal protocol for molecular profiling of tumor cells in pleural effusions at single-cell level. Cancer Sci 2021; 112:2006-2019. [PMID: 33484069 PMCID: PMC8088920 DOI: 10.1111/cas.14821] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsy analyzes the current status of primary tumors and their metastatic regions. We aimed to develop an optimized protocol for single-cell sequencing of floating tumor cells (FTCs) in pleural effusion as a laboratory test. FTCs were enriched using a negative selection of white blood cells by a magnetic-activated cell sorting system, and CD45-negative and cytokeratin-positive selection using a microfluidic cell separation system with a dielectrophoretic array. The enriched tumor cells were subjected to whole-genome amplification (WGA) followed by genome sequencing. The FTC analysis detected an EGFR exon 19 deletion in Case 1 (12/19 cells, 63.2%), and EML4-ALK fusion (17/20 cells, 85%) with an alectinib-resistant mutation of ALK (p.G1202R) in Case 2. To eliminate WGA-associated errors and increase the uniformity of the WGA product, the protocol was revised to sequence multiple single FTCs individually. An analytical pipeline, accurate single-cell mutation detector (ASMD), was developed to identify somatic mutations of FTCs. The large numbers of WGA-associated errors were cleaned up, and the somatic mutations detected in FTCs by ASMD were concordant with those found in tissue specimens. This protocol is applicable to circulating tumor cells analysis of peripheral blood and expands the possibility of utilizing molecular profiling of cancers.
Collapse
Affiliation(s)
- Ikuko Takeda Nakamura
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.,Department of Respiratory Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Masachika Ikegami
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.,Department of Orthopedic Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobuhiko Hasegawa
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.,Department of Orthopedic Surgery, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Shigehiro Yagishita
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasushi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuki Shinno
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuki Kojima
- Department of Breast and Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Kazuya Takamochi
- Department of General Thoracic Surgery, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Fumiyuki Takahashi
- Department of Respiratory Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kazuhisa Takahashi
- Department of Respiratory Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| |
Collapse
|
60
|
Therapeutic strategies in RET gene rearranged non-small cell lung cancer. J Hematol Oncol 2021; 14:50. [PMID: 33771190 PMCID: PMC7995721 DOI: 10.1186/s13045-021-01063-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/12/2021] [Indexed: 12/13/2022] Open
Abstract
The recent approvals by the Food and Drug Administration several tumor-agnostic drugs have resulted in a paradigm shift in cancer treatment from an organ/histology-specific strategy to biomarker-guided approaches. RET gene fusions are oncogenic drivers in multiple tumor types and are known to occur in 1-2% of non-squamous NSCLC patients. RET gene fusions give rise to chimeric, cytosolic proteins with constitutively active RET kinase domain. Standard therapeutic regimens provide limited benefit for NSCLC patients with RET fusion-positive tumors, and the outcomes with immunotherapy in the these patients are generally poor. Selpercatinib (LOXO-292) and pralsetinib (BLU-667) are potent and selective inhibitors that target RET alterations, including fusions and mutations, irrespective of the tissue of origin. Recently, the results from the LIBRETTO-001 and ARROW clinical trials demonstrated significant clinical benefits with selpercatinib and pralsetinib respectively, in NSCLC patients with RET gene fusions, with tolerable toxicity profiles. These studies also demonstrated that these RET-TKIs crossed the blood brain barrier with significant activity. As has been observed with other TKIs, the emergence of acquired resistance may limit long-term efficacy of these agents. Therefore, understanding the mechanisms of resistance is necessary for the development of strategies to overcome them.
Collapse
|
61
|
Yang SR, Aypar U, Rosen EY, Mata DA, Benayed R, Mullaney K, Jayakumaran G, Zhang Y, Frosina D, Drilon A, Ladanyi M, Jungbluth AA, Rekhtman N, Hechtman JF. A Performance Comparison of Commonly Used Assays to Detect RET Fusions. Clin Cancer Res 2021; 27:1316-1328. [PMID: 33272981 PMCID: PMC8285056 DOI: 10.1158/1078-0432.ccr-20-3208] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/23/2020] [Accepted: 11/30/2020] [Indexed: 01/02/2023]
Abstract
PURPOSE Selpercatinib and pralsetinib induce deep and durable responses in patients with advanced RET fusion-positive lung and thyroid cancer. RET fusion testing strategies with rapid and reliable results are critical given recent FDA approval. Here, we assess various clinical assays in a large pan-cancer cohort. EXPERIMENTAL DESIGN Tumors underwent DNA-based next-generation sequencing (NGS) with reflex to RNA-based NGS if no mitogenic driver or if a RET structural variant of unknown significance (SVUS) were present. Canonical DNA-level RET fusions and RNA-confirmed RET fusions were considered true fusions. Break-apart FISH and IHC performance were assessed in subgroups. RESULTS A total of 171 of 41,869 patients with DNA NGS harbored RET structural variants, including 139 canonical fusions and 32 SVUS. Twelve of 32 (37.5%) SVUS were transcribed into RNA-level fusions, resulting in 151 oncogenic RET fusions. The most common RET fusion-positive tumor types were lung (65.6%) and thyroid (23.2%). The most common partners were KIF5B (45%), CCDC6 (29.1%), and NCOA4 (13.3%). DNA NGS showed 100% (46/46) sensitivity and 99.6% (4,459/4,479) specificity. FISH showed 91.7% (44/48) sensitivity, with lower sensitivity for NCOA4-RET (66.7%, 8/12). A total of 87.5% (7/8) of RET SVUS negative for RNA-level fusions demonstrated rearrangement by FISH. The sensitivity of IHC varied by fusion partner: KIF5B sensitivity was highest (100%, 31/31), followed by CCDC6 (88.9%, 16/18) and NCOA4 (50%, 6/12). Specificity of RET IHC was 82% (73/89). CONCLUSIONS Although DNA sequencing has high sensitivity and specificity, RNA sequencing of RET SVUS is necessary. Both FISH and IHC demonstrated lower sensitivity for NCOA4-RET fusions.
Collapse
Affiliation(s)
- Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Umut Aypar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ezra Y Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Douglas A Mata
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kerry Mullaney
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Denise Frosina
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
62
|
Decoding the Evolutionary Response to Ensartinib in Patients With ALK-Positive NSCLC by Dynamic Circulating Tumor DNA Sequencing. J Thorac Oncol 2021; 16:827-839. [PMID: 33588113 DOI: 10.1016/j.jtho.2021.01.1615] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/10/2020] [Accepted: 01/09/2021] [Indexed: 02/05/2023]
Abstract
INTRODUCTION By implementing dynamic circulating tumor DNA (ctDNA) analysis, we explored the impact of TP53 mutations on tumor evolution and resistance mechanisms to ensartinib in patients with ALK-positive NSCLC. METHODS In a multicenter phase 2 trial, patients with ALK-positive NSCLC who progressed on crizotinib were treated with ensartinib. Blood samples for ctDNA analysis were collected at baseline, cycle 3 day 1, and progression disease (PD) and analyzed with a 212-gene panel. RESULTS A total of 440 samples were collected from 168 patients. Baseline TP53 mutations (20.2%) significantly correlated with inferior progression-free survival (4.2 mo versus 11.7 mo, p < 0.0001). Patients with TP53 mutations had higher mutation load than those without TP53 mutations at baseline (13.79 ± 3.72 versus 4.67 ± 0.39, p < 0.001). Although there was no significant difference in mutation load between these groups at cycle 3 day 1 (5.89 ± 2.25 versus 3.72 ± 0.62, p = 0.425), patients with mutated TP53 developed more mutations at PD (7.07 ± 1.25 versus 3.20 ± 0.33, p = 0.003). Frequency and abundance of secondary ALK mutations G1269A, G1202R, and E1210K increased markedly at PD than baseline. In patients without secondary ALK mutations, we identified ALK-independent resistance mechanisms including bypass signaling activation, downstream effector protein reactivation, epithelial-mesenchymal transformation, and epigenetic dysregulation. CONCLUSIONS Our study highlighted the advantage of ctDNA analysis for monitoring tumor evolution. TP53 mutations promoted genetic evolution and accelerated occurrence of resistance. We also unveiled ALK-dependent resistance mechanisms, mainly by G1269A, G1202R, and E1210K mutations, and ALK-independent resistance mechanisms to ensartinib.
Collapse
|
63
|
Pinzani P, D'Argenio V, Del Re M, Pellegrini C, Cucchiara F, Salvianti F, Galbiati S. Updates on liquid biopsy: current trends and future perspectives for clinical application in solid tumors. Clin Chem Lab Med 2021; 59:1181-1200. [PMID: 33544478 DOI: 10.1515/cclm-2020-1685] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/20/2021] [Indexed: 01/19/2023]
Abstract
Despite advances in screening and therapeutics cancer continues to be one of the major causes of morbidity and mortality worldwide. The molecular profile of tumor is routinely assessed by surgical or bioptic samples, however, genotyping of tissue has inherent limitations: it represents a single snapshot in time and it is subjected to spatial selection bias owing to tumor heterogeneity. Liquid biopsy has emerged as a novel, non-invasive opportunity of detecting and monitoring cancer in several body fluids instead of tumor tissue. Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), RNA (mRNA and microRNA), microvesicles, including exosomes and tumor "educated platelets" were recently identified as a source of genomic information in cancer patients which could reflect all subclones present in primary and metastatic lesions allowing sequential monitoring of disease evolution. In this review, we summarize the currently available information concerning liquid biopsy in breast cancer, colon cancer, lung cancer and melanoma. These promising issues still need to be standardized and harmonized across laboratories, before fully adopting liquid biopsy approaches into clinical practice.
Collapse
Affiliation(s)
- Pamela Pinzani
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Valeria D'Argenio
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Rome, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Marzia Del Re
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Cristina Pellegrini
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Federico Cucchiara
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesca Salvianti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Silvia Galbiati
- Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| |
Collapse
|
64
|
Ilié M, Mazières J, Chamorey E, Heeke S, Benzaquen J, Thamphya B, Boutros J, Tiotiu A, Fayada J, Cadranel J, Poudenx M, Moro-Sibilot D, Barlesi F, Thariat J, Clément-Duchêne C, Tomasini P, Hofman V, Marquette CH, Hofman P. Prospective Multicenter Validation of the Detection of ALK Rearrangements of Circulating Tumor Cells for Noninvasive Longitudinal Management of Patients With Advanced NSCLC. J Thorac Oncol 2021; 16:807-816. [PMID: 33545389 DOI: 10.1016/j.jtho.2021.01.1617] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Patients with advanced-stage NSCLC whose tumors harbor an ALK gene rearrangement benefit from treatment with multiple ALK inhibitors (ALKi). Approximately 30% of tumor biopsy samples contain insufficient tissue for successful ALK molecular characterization. This study evaluated the added value of analyzing circulating tumor cells (CTCs) as a surrogate to ALK tissue analysis and as a function of the response to ALKi. METHODS We conducted a multicenter, prospective observational study (NCT02372448) of 203 patients with stage IIIB/IV NSCLC across nine French centers, of whom 81 were ALK positive (immunohistochemistry or fluorescence in situ hybridization [FISH]) and 122 ALK negative on paraffin-embedded tissue specimens. Blood samples were collected at baseline and at 6 and 12 weeks after ALKi initiation or at disease progression. ALK gene rearrangement was evaluated with CTCs using immunocytochemistry and FISH analysis after enrichment using a filtration method. RESULTS At baseline, there was a high concordance between the detection of an ALK rearrangement in the tumor tissue and in CTCs as determined by immunocytochemistry (sensitivity, 94.4%; specificity 89.4%). The performance was lower for the FISH analysis (sensitivity, 35.6%; specificity, 56.9%). No significant association between the baseline levels or the dynamic change of CTCs and overall survival (hazard ratio = 0.59, 95% confidence interval: 0.24-1.5, p = 0.244) or progression-free survival (hazard ratio = 0.84, 95% confidence interval: 0.44-1.6, p = 0.591) was observed in the patients with ALK-positive NSCLC. CONCLUSIONS CTCs can be used as a complementary tool to a tissue biopsy for the detection of ALK rearrangements. Longitudinal analyses of CTCs revealed promise for real-time patient monitoring and improved delivery of molecularly guided therapy in this population.
Collapse
Affiliation(s)
- Marius Ilié
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France; Hospital-Related Biobank (BB-0033-00025), FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France; Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS, INSERM, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Julien Mazières
- Department of Pulmonology, Centre Hospitalier Universitaire Toulouse, Institut Universitaire du Cancer, Université Paul Sabatier, Toulouse, France
| | - Emmanuel Chamorey
- Biostatistics Unit, Antoine Lacassagne Comprehensive Cancer Center, Nice, France
| | - Simon Heeke
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France; Hospital-Related Biobank (BB-0033-00025), FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France; Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS, INSERM, FHU OncoAge, Université Côte d'Azur, Nice, France; Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jonathan Benzaquen
- Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS, INSERM, FHU OncoAge, Université Côte d'Azur, Nice, France; Department of Pulmonary Medicine and Oncology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Brice Thamphya
- Biostatistics Unit, Antoine Lacassagne Comprehensive Cancer Center, Nice, France
| | - Jacques Boutros
- Department of Pulmonary Medicine and Oncology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Angélica Tiotiu
- Department of Pulmonology, Centre Hospitalier Régional Universitaire de Nancy, Nancy, France; Development, Adaptation and Disadvantage, Cardio-Respiratory Regulations and Motor Control, Université de Lorraine, Nancy, France
| | - Julien Fayada
- Hospital-Related Biobank (BB-0033-00025), FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Jacques Cadranel
- Department of Pulmonology, APHP, Hôpital Tenon and GRC04 Theranoscan, Sorbonne Université, Paris, France
| | - Michel Poudenx
- Department of Pulmonary Medicine and Oncology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France; Department of Oncology, Centre Antoine Lacassagne, Nice, France
| | - Denis Moro-Sibilot
- Thoracic Oncology Unit, Centre hospitalier universitaire Grenoble-Alpes, Grenoble, France
| | - Fabrice Barlesi
- Centre d'Essais Précoces en Cancérologie de Marseille CLIP(2), Aix Marseille University, CNRS, INSERM, CRCM, APHM, Marseille, France; Department of Cancer Medicine, Institut Gustave Roussy, Villejuif, France
| | - Juliette Thariat
- Department of Radiation Therapy, Centre François Baclesse-ARCHADE, Université de Caen Normandie, Caen, France
| | | | - Pascale Tomasini
- Centre d'Essais Précoces en Cancérologie de Marseille CLIP(2), Aix Marseille University, CNRS, INSERM, CRCM, APHM, Marseille, France
| | - Véronique Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France; Hospital-Related Biobank (BB-0033-00025), FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France; Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS, INSERM, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Charles-Hugo Marquette
- Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS, INSERM, FHU OncoAge, Université Côte d'Azur, Nice, France; Department of Pulmonary Medicine and Oncology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France; Hospital-Related Biobank (BB-0033-00025), FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France; Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS, INSERM, FHU OncoAge, Université Côte d'Azur, Nice, France.
| |
Collapse
|
65
|
Hofman P. Detecting Resistance to Therapeutic ALK Inhibitors in Tumor Tissue and Liquid Biopsy Markers: An Update to a Clinical Routine Practice. Cells 2021; 10:168. [PMID: 33467720 PMCID: PMC7830674 DOI: 10.3390/cells10010168] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 12/16/2022] Open
Abstract
The survival of most patients with advanced stage non-small cell lung cancer is prolonged by several months when they are treated with first- and next-generation inhibitors targeting ALK rearrangements, but resistance inevitably emerges. Some of the mechanisms of resistance are sensitive to novel ALK inhibitors but after an initial tumor response, more or less long-term resistance sets in. Therefore, to adapt treatment it is necessary to repeat biological sampling over time to look for different mechanisms of resistance. To this aim it is essential to obtain liquid and/or tissue biopsies to detect therapeutic targets, in particular for the analysis of different genomic alterations. This review discusses the mechanisms of resistance to therapeutics targeting genomic alterations in ALK as well as the advantages and the limitations of liquid biopsies for their identification.
Collapse
Affiliation(s)
- Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Université Côte d’Azur, CHU Nice, FHU OncoAge, Pasteur Hospital, 30 Avenue de la Voie Romaine, BP69, CEDEX 01, 06001 Nice, France; ; Tel.: +33-4-92-03-88-55; Fax: +33-4-92-88-50
- Hospital-Integrated Biobank BB-0033-00025, Université Côte d’Azur, CHU Nice, FHU OncoAge, 06001 Nice, France
| |
Collapse
|
66
|
Dagogo-Jack I, Ritterhouse LL. The role of plasma genotyping in ALK- and ROS1-rearranged lung cancer. Transl Lung Cancer Res 2020; 9:2557-2570. [PMID: 33489818 PMCID: PMC7815348 DOI: 10.21037/tlcr-2019-cnsclc-09] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Several subsets of non-small cell lung cancer (NSCLC) are defined by the presence of oncogenic rearrangements that result in constitutive activation of a chimeric fusion protein. In NSCLCs that harbor ALK or ROS1 rearrangements, aberrant signaling from these fusion proteins can be overcome by potent and selective tyrosine kinase inhibitors (TKIs). These targeted therapies can induce durable responses and significantly improve prognostic outcomes. Historically, analysis of tissue biopsies was the primary approach to identifying key activating rearrangements. In recent years, non-invasive genotyping of tumor-derived nucleic acids in the circulation has gained ground as a strategy for determining the genetic composition of NSCLCs at diagnosis and throughout the disease course based on prospective and retrospective studies validating the utility of plasma analysis in heterogeneous populations of patients with metastatic NSCLC. Notably, these practice-changing studies predominantly included patients with NSCLCs with oncogenic mutations. Compared to other types of molecular alterations such as mutations and insertions/deletions, oncogenic rearrangements are more complex as they incorporate a variety of fusion partners and diverse breakpoints. Because of this structural complexity, detecting oncogenic rearrangements with plasma assays is more challenging than identifying disease-defining point mutations. In this review, we discuss technical aspects of plasma genotyping strategies and summarize findings from studies exploring plasma genotyping (including ctDNA analysis and profiling of nucleic acids contained in other plasma components) in two rearrangement-driven NSCLC subsets (ALK-rearranged and ROS1-rearranged).
Collapse
Affiliation(s)
- Ibiayi Dagogo-Jack
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Lauren L Ritterhouse
- Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| |
Collapse
|
67
|
The Role of the Liquid Biopsy in Decision-Making for Patients with Non-Small Cell Lung Cancer. J Clin Med 2020; 9:jcm9113674. [PMID: 33207619 PMCID: PMC7696948 DOI: 10.3390/jcm9113674] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022] Open
Abstract
Liquid biopsy is a rapidly emerging tool of precision oncology enabling minimally invasive molecular diagnostics and longitudinal monitoring of treatment response. For the clinical management of advanced stage lung cancer patients, detection and quantification of circulating tumor DNA (ctDNA) is now widely adopted into clinical practice. Still, interpretation of results and validation of ctDNA-based treatment decisions remain challenging. We report here our experience implementing liquid biopsies into the clinical management of lung cancer. We discuss advantages and limitations of distinct ctDNA assay techniques and highlight our approach to the analysis of recurrent molecular alterations found in lung cancer. Moreover, we report three exemplary clinical cases illustrating the complexity of interpreting liquid biopsy results in clinical practice. These cases underscore the potential and current limitations of liquid biopsy, focusing on the difficulty of interpreting discordant findings. In our view, despite all current limitations, the analysis of ctDNA in lung cancer patients is an essential and highly versatile complementary diagnostic tool for the clinical management of lung cancer patients in the era of precision oncology.
Collapse
|
68
|
Longitudinal therapy monitoring of ALK-positive lung cancer by combined copy number and targeted mutation profiling of cell-free DNA. EBioMedicine 2020; 62:103103. [PMID: 33161228 PMCID: PMC7670098 DOI: 10.1016/j.ebiom.2020.103103] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/15/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
Background Targeted therapies (TKI) have improved the prognosis of ALK-rearranged lung cancer (ALK+ NSCLC), but clinical courses vary widely. Early identification and molecular characterisation of treatment failure have key importance for subsequent therapies. We performed copy number variation (CNV) profiling and targeted panel sequencing from cell-free DNA (cfDNA) to monitor ALK+ NSCLC. Methods 271 longitudinal plasma DNA samples from 73 patients with TKI-treated metastatic ALK+ NSCLC were analysed by capture-based targeted (average coverage 4,100x), and shallow whole genome sequencing (sWGS, 0.5x). Mutations were called using standard algorithms. CNVs were quantified using the trimmed median absolute deviation from copy number neutrality (t-MAD). Findings cfDNA mutations were identified in 58% of patients. They included several potentially actionable alterations, e.g. in the genes BRAF, ERBB2, and KIT. sWGS detected CNVs in 18% of samples, compared to 6% using targeted sequencing. Several of the CNVs included potentially druggable targets, such as regions harboring EGFR, ERBB2, and MET. Circulating tumour DNA (ctDNA) mutations and t-MAD scores increased during treatment, correlated with markers of higher molecular risk, such as the EML4-ALK variant 3 and/or TP53 mutations, and were associated with shorter patient survival. Importantly, t-MAD scores reflected the tumour remission status in serial samples similar to mutant ctDNA allele frequencies, and increased with disease progression in 79% (34/43) of cases, including those without detectable single nucleotide variant (SNV). Interpretation Combined copy number and targeted mutation profiling could improve monitoring of ALK+ NSCLC. Potential advantages include the identification of treatment failure, in particular for patients without detectable mutations, and broader detection of genomic changes acquired during therapy, especially in later treatment lines and in high-risk patients. Funding This work was supported by the German Center for Lung Research (DZL), by the German Cancer Consortium (DKTK), by the Heidelberg Center for Personalized Oncology at the German Cancer Research Center (DKFZ-HIPO), and by Roche Sequencing Solutions (Pleasanton, CA, USA).
Collapse
|
69
|
Gobbini E, Swalduz A, Giaj Levra M, Ortiz-Cuaran S, Toffart AC, Pérol M, Moro-Sibilot D, Saintigny P. Implementing ctDNA Analysis in the Clinic: Challenges and Opportunities in Non-Small Cell Lung Cancer. Cancers (Basel) 2020; 12:E3112. [PMID: 33114393 PMCID: PMC7693855 DOI: 10.3390/cancers12113112] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
Tumor genomic profiling has a dramatic impact on the selection of targeted treatment and for the identification of resistance mechanisms at the time of progression. Solid tissue biopsies are sometimes challenging, and liquid biopsies are used as a non-invasive alternative when tissue is limiting. The clinical relevance of tumor genotyping through analysis of ctDNA is now widely recognized at all steps of the clinical evaluation process in metastatic non-small cell lung cancer (NSCLC) patients. ctDNA analysis through liquid biopsy has recently gained increasing attention as well in the management of early and locally advanced, not oncogene-addicted, NSCLC. Its potential applications in early disease detection and the response evaluation to radical treatments are promising. The aim of this review is to summarize the landscape of liquid biopsies in clinical practice and also to provide an overview of the potential perspectives of development focusing on early detection and screening, the assessment of minimal residual disease, and its potential role in predicting response to immunotherapy. In addition to available studies demonstrating the clinical relevance of liquid biopsies, there is a need for standardization and well-designed clinical trials to demonstrate its clinical utility.
Collapse
Affiliation(s)
- Elisa Gobbini
- Thoracic Oncology Unit, CHU Grenoble-Alpes, 38700 Grenoble, France or (E.G.); (M.G.L.); (A.-C.T.); (D.M.-S.)
- Univ Lyon, Université Claude Bernard Lyon, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69373 Lyon, France; (S.O.-C.)
| | - Aurélie Swalduz
- Department of Medical Oncology, Centre Léon Bérard, 69373 Lyon, France; (A.S.); (M.P.)
| | - Matteo Giaj Levra
- Thoracic Oncology Unit, CHU Grenoble-Alpes, 38700 Grenoble, France or (E.G.); (M.G.L.); (A.-C.T.); (D.M.-S.)
| | - Sandra Ortiz-Cuaran
- Univ Lyon, Université Claude Bernard Lyon, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69373 Lyon, France; (S.O.-C.)
| | - Anne-Claire Toffart
- Thoracic Oncology Unit, CHU Grenoble-Alpes, 38700 Grenoble, France or (E.G.); (M.G.L.); (A.-C.T.); (D.M.-S.)
| | - Maurice Pérol
- Department of Medical Oncology, Centre Léon Bérard, 69373 Lyon, France; (A.S.); (M.P.)
| | - Denis Moro-Sibilot
- Thoracic Oncology Unit, CHU Grenoble-Alpes, 38700 Grenoble, France or (E.G.); (M.G.L.); (A.-C.T.); (D.M.-S.)
| | - Pierre Saintigny
- Univ Lyon, Université Claude Bernard Lyon, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69373 Lyon, France; (S.O.-C.)
- Department of Medical Oncology, Centre Léon Bérard, 69373 Lyon, France; (A.S.); (M.P.)
| |
Collapse
|
70
|
Li M, Hou X, Zhou C, Feng W, Jiang G, Long H, Yang S, Chen J, Wang N, Wang K, Chen L. Prevalence and Clinical Impact of Concomitant Mutations in Anaplastic Lymphoma Kinase Rearrangement Advanced Non-small-Cell Lung Cancer (Guangdong Association of Thoracic Oncology Study 1055). Front Oncol 2020; 10:1216. [PMID: 32974126 PMCID: PMC7471725 DOI: 10.3389/fonc.2020.01216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 06/15/2020] [Indexed: 12/02/2022] Open
Abstract
Background: In patients with anaplastic lymphoma kinase (ALK) rearrangement-positive advanced non–small-cell lung cancer (NSCLC), ALK inhibitors are now the standard treatment, but their clinical efficacy varies widely for each patient. In this multicenter retrospective study, we evaluated the clinical efficacy of crizotinib according to the ALK rearrangement variants and concomitant mutations present. Patients and Methods: A total 132 patients with ALK rearrangement advanced NSCLC from 4 centers in Guangdong province, China were evaluated. All patients received crizotinib treatment and their ALK rearrangement status was identified by next-generation sequencing (NGS). Results: The median progression-free survival (PFS) in patients with EML4-ALK rearrangement (n = 121), non-EML4-ALK rearrangement (n = 5), and EML4-ALK arrangement accompanied by non-EML4-ALK rearrangement (n = 6) was 12.8, 7.5, and 7.4 months, respectively, with no significant difference between them (p = 0.1554). Similarly, among patients with various EML4-ALK variants (variant 1, variant 3a/b, and other variants), the median PFS values were again comparable. According to baseline NGS data, the median PFS in patients who had ALK rearrangement only, ALK rearrangement and concomitant tumor-suppressor gene mutations, and ALK rearrangement and concomitant oncogene mutations was 14.2, 10.9, and 4.9 months, respectively; (p = 0.0002). A multivariable analysis indicated that concomitant oncogene mutations and tumor-suppressor gene mutations were both negative factors influencing the efficacy of crizotinib in ALK rearrangement NSCLC. Conclusion: Concomitant oncogene mutations and tumor-suppressor gene mutations had negative effects on the efficacy of crizotinib, while various ALK variants had a similar influence.
Collapse
Affiliation(s)
- Meichen Li
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xue Hou
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Chengzhi Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Weineng Feng
- Department of Head and Neck/Thoracic Medical Oncology, The First People's Hospital of Foshan, Foshan, China
| | | | - Hao Long
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shuang Yang
- Department of Head and Neck/Thoracic Medical Oncology, The First People's Hospital of Foshan, Foshan, China
| | - Jing Chen
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Na Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Kaicheng Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Likun Chen
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| |
Collapse
|
71
|
Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing. Cell 2020; 182:1232-1251.e22. [PMID: 32822576 PMCID: PMC7484178 DOI: 10.1016/j.cell.2020.07.017] [Citation(s) in RCA: 323] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 05/04/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
Abstract
Lung cancer, the leading cause of cancer mortality, exhibits heterogeneity that enables adaptability, limits therapeutic success, and remains incompletely understood. Single-cell RNA sequencing (scRNA-seq) of metastatic lung cancer was performed using 49 clinical biopsies obtained from 30 patients before and during targeted therapy. Over 20,000 cancer and tumor microenvironment (TME) single-cell profiles exposed a rich and dynamic tumor ecosystem. scRNA-seq of cancer cells illuminated targetable oncogenes beyond those detected clinically. Cancer cells surviving therapy as residual disease (RD) expressed an alveolar-regenerative cell signature suggesting a therapy-induced primitive cell-state transition, whereas those present at on-therapy progressive disease (PD) upregulated kynurenine, plasminogen, and gap-junction pathways. Active T-lymphocytes and decreased macrophages were present at RD and immunosuppressive cell states characterized PD. Biological features revealed by scRNA-seq were biomarkers of clinical outcomes in independent cohorts. This study highlights how therapy-induced adaptation of the multi-cellular ecosystem of metastatic cancer shapes clinical outcomes. scRNA-seq is feasible in metastatic human NSCLCs and reveals a rich tumor ecosystem Individual tumors and cancer cells exhibit substantial molecular diversity Cancer and tumor microenvironment cells exhibit marked therapy-induced plasticity scRNA-seq of metastatic NSCLCs unveils new opportunities to improve clinical outcomes
Collapse
|
72
|
Song Z, Liu T, Shi L, Yu Z, Shen Q, Xu M, Huang Z, Cai Z, Wang W, Xu C, Sun J, Chen M. The deep learning model combining CT image and clinicopathological information for predicting ALK fusion status and response to ALK-TKI therapy in non-small cell lung cancer patients. Eur J Nucl Med Mol Imaging 2020; 48:361-371. [PMID: 32794105 DOI: 10.1007/s00259-020-04986-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/31/2020] [Indexed: 11/26/2022]
Abstract
PURPOSE This study aimed to investigate the deep learning model (DLM) combining computed tomography (CT) images and clinicopathological information for predicting anaplastic lymphoma kinase (ALK) fusion status in non-small cell lung cancer (NSCLC) patients. MATERIALS AND METHODS Preoperative CT images, clinicopathological information as well as the ALK fusion status from 937 patients in three hospitals were retrospectively collected to train and validate the DLM for the prediction of ALK fusion status in tumors. Another cohort of patients (n = 91) received ALK tyrosine kinase inhibitor (TKI) treatment was also included to evaluate the value of the DLM in predicting the clinical outcomes of the patients. RESULTS The performances of the DLM trained only by CT images in the primary and validation cohorts were AUC = 0.8046 (95% CI 0.7715-0.8378) and AUC = 0.7754 (95% CI 0.7199-0.8310), respectively, while the DLM trained by both CT images and clinicopathological information exhibited better performance for the prediction of ALK fusion status (AUC = 0.8540, 95% CI 0.8257-0.8823 in the primary cohort, p < 0.001; AUC = 0.8481, 95% CI 0.8036-0.8926 in the validation cohort, p < 0.001). In addition, the deep learning scores of the DLMs showed significant differences between the wild-type and ALK infusion tumors. In the ALK-target therapy cohort (n = 91), the patients predicted as ALK-positive by the DLM showed better performance of progression-free survival than the patients predicted as ALK-negative (16.8 vs. 7.5 months, p = 0.010). CONCLUSION Our findings showed that the DLM trained by both CT images and clinicopathological information could effectively predict the ALK fusion status and treatment responses of patients. For the small size of the ALK-target therapy cohort, larger data sets would be collected to further validate the performance of the model for predicting the response to ALK-TKI treatment.
Collapse
Affiliation(s)
- Zhengbo Song
- Department of Clinical Trial, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310022, Zhejiang, China
| | - Tianchi Liu
- Shanghai Key Laboratory of Artificial Intelligence for Medical Image and Knowledge Graph, Shanghai, 200336, China
- YITU AI Research Institute for Healthcare, Hangzhou, 310000, Zhejiang, China
| | - Lei Shi
- Shanghai Key Laboratory of Artificial Intelligence for Medical Image and Knowledge Graph, Shanghai, 200336, China
- YITU AI Research Institute for Healthcare, Hangzhou, 310000, Zhejiang, China
| | - Zongyang Yu
- Department of Medical Oncology, 900th Hospital, Fuzhou, 350000, Fujian, China
| | - Qing Shen
- Shanghai Key Laboratory of Artificial Intelligence for Medical Image and Knowledge Graph, Shanghai, 200336, China
- YITU AI Research Institute for Healthcare, Hangzhou, 310000, Zhejiang, China
| | - Mengdi Xu
- Shanghai Key Laboratory of Artificial Intelligence for Medical Image and Knowledge Graph, Shanghai, 200336, China
- YITU AI Research Institute for Healthcare, Hangzhou, 310000, Zhejiang, China
| | - Zhangzhou Huang
- Department of Medical Oncology, Fujian Cancer Hospital, Fuzhou, 350001, China
| | - Zhijian Cai
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Wenxian Wang
- Department of Clinical Trial, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310022, Zhejiang, China
| | - Chunwei Xu
- Department of Pathology, Fujian Cancer Hospital, Fuzhou, 350001, China
| | - Jingjing Sun
- Department of Radiology, Cancer Hospital of the University of Chinese Academy of Sciences(Zhejiang Cancer Hospital), Hangzhou, 310022, Zhejiang, China
| | - Ming Chen
- Department of Radiotherapy, Cancer Hospital of the University of Chinese Academy of Sciences(Zhejiang Cancer Hospital), Hangzhou, 310022, Zhejiang, China.
| |
Collapse
|
73
|
Zhang EW, Dagogo-Jack I, Kuo A, Rooney MM, Shaw AT, Digumarthy SR. Association between circulating tumor DNA burden and disease burden in patients with ALK-positive lung cancer. Cancer 2020; 126:4473-4484. [PMID: 32757294 DOI: 10.1002/cncr.33118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/24/2020] [Accepted: 07/02/2020] [Indexed: 01/12/2023]
Abstract
BACKGROUND Plasma genotyping is an emerging approach for the identification of genetic alterations mediating resistance to anaplastic lymphoma kinase (ALK)-targeted therapy. The authors reviewed plasma genotyping and imaging findings to assess the correlation between circulating tumor DNA (ctDNA) burden and disease burden in patients with ALK-positive lung cancer. METHODS The authors analyzed 97 plasma specimens from 75 patients with ALK-positive lung cancer to identify ALK and non-ALK alterations. Disease burden was estimated by tabulating lesions per organ and calculating lesion diameters, areas, and volumes. Disease burden was correlated with the allelic frequency (AF) of plasma alterations. RESULTS The mean interval between plasma collection and imaging was 8 days. ctDNA was detected in approximately 85% of plasma specimens. An ALK fusion and ALK mutation were detected in 79% and 76%, respectively, of plasma specimens. Using the maximum plasma alteration AF and maximum ALK alteration AF as independent surrogates of ctDNA burden, a higher disease burden measurement on imaging was found to be associated with higher ctDNA burden. Total body and extrathoracic tumor volume but not intrathoracic tumor volume correlated with ctDNA burden. Of all the disease sites assessed, the ctDNA burden correlated most with involvement of the liver, bones, and adrenal glands. Despite being the defining alteration in ALK-positive lung cancer, isolated plasma ALK fusion AF did not perform as well as the maximum plasma alteration AF or maximum ALK alteration AF for correlating tumor burden. CONCLUSIONS In patients with ALK-positive lung cancer, the maximum plasma alteration AF and maximum ALK alteration AF correlate with the extrathoracic burden of disease and are more predictive of tumor burden compared with the ALK fusion AF alone. LAY SUMMARY Analysis of genetic material shed from cancer cells into the circulation offers insights into the molecular composition of tumors. The circulating tumor DNA (ctDNA) varies over time and across individuals and is impacted by the distribution of disease. Herein, the authors estimated tumor burden on imaging and correlated it with ctDNA by calculating the maximum allelic frequency. The current study findings demonstrated that the greatest correlation exists between extrathoracic, extracranial tumor burden (particularly involvement of the liver, adrenal glands, or bones) and ctDNA burden, suggesting a biological basis for the interpatient and temporal intrapatient differences in ctDNA yield that have been described in previous studies.
Collapse
Affiliation(s)
- Eric W Zhang
- Division of Thoracic Imaging and Intervention, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | - Ibiayi Dagogo-Jack
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Anderson Kuo
- Division of Cardiovascular Imaging, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | - Marguerite M Rooney
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Subba R Digumarthy
- Division of Thoracic Imaging and Intervention, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| |
Collapse
|
74
|
Wessels S, Muley T, Christopoulos P, Meister M, Heinzmann-Groth I, Warth A, Herpel E, Hummler S, Klingmüller U, Kuon J, Heussel CP, Eberhardt R, Herth FJF, Winter H, Bischoff H, Stenzinger A, Reck M, Huber RM, Thomas M, Schneider MA. Comprehensive serial biobanking in advanced NSCLC: feasibility, challenges and perspectives. Transl Lung Cancer Res 2020; 9:1000-1014. [PMID: 32953480 PMCID: PMC7481602 DOI: 10.21037/tlcr-20-137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background Availability of tumor material at baseline and disease progression is increasingly important for patient management in non-small-cell lung cancer (NSCLC), especially for the application of targeted therapies like tyrosine kinase inhibitors and for immune checkpoint inhibitor treatment. Here we report the experience of prospective biomaterial acquisition in advanced NSCLC from a pilot project. Methods Main objective was the longitudinal collection of high-quality, cryoconserved biopsies in addition to formalin-fixed paraffin-embedded (FFPE) biopsies required for routine diagnostics, along with blood samples and detailed clinical annotation using standardized questionnaires. Results Over five years, 205 patients were enrolled for the project, yielding 387 cryoconserved biopsies and 1,098 serum, plasma and buffy-coat samples. The feasibility of obtaining the cryoconserved biopsies in addition to the FFPE biopsies was 89% for newly diagnosed cases, but dropped down to 56% and 47% at first and second disease progression, respectively. While forceps biopsy was the preferred procedure for tissue acquisition, the highest tissue amounts were received using the cryobiopsy method. Biopsies had a median tumor cellularity of 34% and yielded in median 13.6 µg DNA and 12 µg RNA (median RIN =8). During the five-year project, a maximum of 38 follow-up blood samples per patient were assembled in up to four therapy lines. Conclusions Despite the poor condition and limited prognosis of most NSCLC patients, this serial biomaterial acquisition including routine collection of cryoconserved biopsies is feasible to support individualized management. The standardized collection of high-quality material has enabled and enriched several translational research studies that can advance therapeutic options.
Collapse
Affiliation(s)
- Sabine Wessels
- Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Thomas Muley
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany
| | - Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Michael Meister
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany
| | - Ingrid Heinzmann-Groth
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany
| | - Arne Warth
- Institute of Pathology, University Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Esther Herpel
- Institute of Pathology, University Hospital Heidelberg, D-69120 Heidelberg, Germany.,NCT Tissue Bank, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Simone Hummler
- Department of Pneumology and Critical Care Medicine, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany
| | - Ursula Klingmüller
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Division Systems Biology of Signal Transduction, German Cancer Research Centre (DKFZ), INF 280, Heidelberg, Germany
| | - Jonas Kuon
- Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany
| | - Claus-Peter Heussel
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Department of Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany.,Department of Diagnostic and Interventional Radiology, University Hospital, D-69120 Heidelberg, Germany
| | - Ralf Eberhardt
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Department of Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany
| | - Felix J F Herth
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Department of Pneumology and Critical Care Medicine, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany
| | - Hauke Winter
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Department of Surgery, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany
| | - Helge Bischoff
- Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany
| | - Albrecht Stenzinger
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, D-69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg Site, Germany
| | - Martin Reck
- Department of Thoracic Oncology, Lung Clinic Grosshansdorf, D-22927 Grosshansdorf, Germany.,Airway Research Centre North (ARCN), German Centre for Lung Research (DZL), Grosshansdorf, Germany
| | - Rudolf Maria Huber
- University Hospital Munich and Thoracic Oncology Centre Munich, D-80337 Munich, Germany.,Comprehensive Pneumology Centre Munich (CPC-M), German Centre for Lung Research (DZL), Munich, Germany
| | - Michael Thomas
- Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Marc A Schneider
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, D-69126 Heidelberg, Germany
| |
Collapse
|
75
|
Esagian SM, Grigoriadou GΙ, Nikas IP, Boikou V, Sadow PM, Won JK, Economopoulos KP. Comparison of liquid-based to tissue-based biopsy analysis by targeted next generation sequencing in advanced non-small cell lung cancer: a comprehensive systematic review. J Cancer Res Clin Oncol 2020; 146:2051-2066. [PMID: 32462295 PMCID: PMC7456570 DOI: 10.1007/s00432-020-03267-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE To explore whether targeted next generation sequencing (NGS) of liquid biopsy in advanced non-small cell lung cancer (NSCLC) could potentially overcome the innate problems that arise with standard tissue biopsy, like intratumoral heterogeneity and the inability to obtain adequate samples for analysis. METHODS The Scopus, Cochrane Library, and MEDLINE (via PubMed) databases were searched for studies with matched tissue and liquid biopsies from advanced NSCLC patients, analyzed with targeted NGS. The number of mutations detected in tissue biopsy only, liquid biopsy only, or both was assessed and the positive percent agreement (PPA) of the two methods was calculated for every clinically relevant gene. RESULTS A total of 644 unique relevant articles were retrieved and data were extracted from 38 studies fulfilling the inclusion criteria. The sample size was composed of 2000 mutations tested in matched tissue and liquid biopsies derived from 1141 patients. No studies analyzed circulating tumor cells. The calculated PPA rates were 53.6% (45/84) for ALK, 53.9% (14/26) for BRAF, 56.5% (13/23) for ERBB2, 67.8% (428/631) for EGFR, 64.2% (122/190) for KRAS, 58.6% (17/29) for MET, 54.6% (12/22) for RET, and 53.3% (8/15) for ROS1. We additionally recorded data for 65 genes that are not recommended by current guidelines for mutational testing. An extra category containing results of unspecified genes was added, with a PPA rate of 55.7% (122/219). CONCLUSION Despite many advantages, liquid biopsy might be unable to fully substitute its tissue counterpart in detecting clinically relevant mutations in advanced NSCLC patients. However, it may serve as a helpful tool when making therapeutic decisions. More studies are needed to evaluate its role in everyday clinical practice.
Collapse
Affiliation(s)
- Stepan M Esagian
- Oncology Working Group, Society of Junior Doctors, Athens, Greece
| | - Georgia Ι Grigoriadou
- Oncology Working Group, Society of Junior Doctors, Athens, Greece
- 1st Department of Medical Oncology, Theageneio Anticancer Hospital, Thessaloníki, Greece
| | - Ilias P Nikas
- School of Medicine, European University of Cyprus, Nicosia, Cyprus
| | - Vasileios Boikou
- Oncology Working Group, Society of Junior Doctors, Athens, Greece
- Athens University of Economics and Business, Athens, Greece
| | - Peter M Sadow
- Department of Pathology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Jae-Kyung Won
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Konstantinos P Economopoulos
- Oncology Working Group, Society of Junior Doctors, Athens, Greece.
- Department of Surgery, Duke University Medical Center, 2301 Erwin Rd, Durham, NC, 27710, USA.
| |
Collapse
|
76
|
Zhu Y, Jia R, Shao YW, Zhu L, Ou Q, Yu M, Wu X, Zhang Y. Durable Complete Response to Alectinib in a Lung Adenocarcinoma Patient With Brain Metastases and Low-Abundance EML4-ALK Variant in Liquid Biopsy: A Case Report. Front Oncol 2020; 10:1259. [PMID: 32850382 PMCID: PMC7411253 DOI: 10.3389/fonc.2020.01259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 06/18/2020] [Indexed: 11/25/2022] Open
Abstract
EML4-ALK fusions are targetable oncogenic drivers in a subset of advanced non-small cell lung cancer (NSCLC) patients that can benefit from selected ALK inhibitors. Precise detection of ALK fusions may yield critical information for selection of appropriate therapy and hence improve patient survival. Analysis of circulating tumor DNA (ctDNA) in liquid biopsies using next generation sequencing (NGS) prior to or during treatment hold great promise for disease monitoring and treatment guidance of various cancers including NSCLC. Herein, we report a case of a 21-year-old advanced lung adenocarcinoma patient with a low abundance (0.03%) of EML4-ALK rearrangement identified in plasma ctDNA upon progression on two lines of chemotherapy that demonstrated long-term complete response to alectinib (>13 months) including metastatic brain tumors. Patient's clinical and pathologic characteristics, computerized tomography (CT) scans and brain magnetic resonance imaging (MRI) were reviewed retrospectively. Taken together, our report not only reinforces the translational utility of NGS-based genomic sequencing of liquid biopsy in guiding clinical practice, but also highlights the superior efficacy of alectinib than chemotherapy in ALK+ NSCLC with brain metastases, albeit at a low variant allele abundance.
Collapse
Affiliation(s)
- Yingying Zhu
- Department of Geriatric Respiratory and Critical Care, Institute of Respiratory Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ran Jia
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yang W Shao
- Medical Department, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Liuqing Zhu
- Medical Department, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Qiuxiang Ou
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, ON, Canada
| | - Man Yu
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, ON, Canada
| | - Xue Wu
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, ON, Canada
| | - Yanbei Zhang
- Department of Geriatric Respiratory and Critical Care, Institute of Respiratory Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| |
Collapse
|
77
|
Bruno R, Fontanini G. Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review. Diagnostics (Basel) 2020; 10:E521. [PMID: 32726941 PMCID: PMC7460167 DOI: 10.3390/diagnostics10080521] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 02/07/2023] Open
Abstract
Gene fusions have a pivotal role in non-small cell lung cancer (NSCLC) precision medicine. Several techniques can be used, from fluorescence in situ hybridization and immunohistochemistry to next generation sequencing (NGS). Although several NGS panels are available, gene fusion testing presents more technical challenges than other variants. This is a PubMed-based narrative review aiming to summarize NGS approaches for gene fusion analysis and their performance on NSCLC clinical samples. The analysis can be performed at DNA or RNA levels, using different target enrichment (hybrid-capture or amplicon-based) and sequencing chemistries, with both custom and commercially available panels. DNA sequencing evaluates different alteration types simultaneously, but large introns and repetitive sequences can impact on the performance and it does not discriminate between expressed and unexpressed gene fusions. RNA-based targeted approach analyses and quantifies directly fusion transcripts and is more accurate than DNA panels on tumor tissue, but it can be limited by RNA quality and quantity. On liquid biopsy, satisfying data have been published on circulating tumor DNA hybrid-capture panels. There is not a perfect method for gene fusion analysis, but NGS approaches, though still needing a complete standardization and optimization, present several advantages for the clinical practice.
Collapse
Affiliation(s)
- Rossella Bruno
- Unit of Pathological Anatomy, University Hospital of Pisa, Via Roma 67, 56126 Pisa, Italy;
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy
| |
Collapse
|
78
|
Mack PC, Banks KC, Espenschied CR, Burich RA, Zill OA, Lee CE, Riess JW, Mortimer SA, Talasaz A, Lanman RB, Gandara DR. Spectrum of driver mutations and clinical impact of circulating tumor DNA analysis in non-small cell lung cancer: Analysis of over 8000 cases. Cancer 2020; 126:3219-3228. [PMID: 32365229 PMCID: PMC7383626 DOI: 10.1002/cncr.32876] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/16/2019] [Accepted: 11/12/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND Circulating cell-free tumor DNA (ctDNA)-based mutation profiling, if sufficiently sensitive and comprehensive, can efficiently identify genomic targets in advanced lung adenocarcinoma. Therefore, the authors investigated the accuracy and clinical utility of a commercially available digital next-generation sequencing platform in a large series of patients with non-small cell lung cancer (NSCLC). METHODS Plasma-based comprehensive genomic profiling results from 8388 consecutively tested patients with advanced NSCLC were analyzed. Driver and resistance mutations were examined with regard to their distribution, frequency, co-occurrence, and mutual exclusivity. RESULTS Somatic alterations were detected in 86% of samples. The median variant allele fraction was 0.43% (range, 0.03%-97.62%). Activating alterations in actionable oncogenes were identified in 48% of patients, including EGFR (26.4%), MET (6.1%), and BRAF (2.8%) alterations and fusions (ALK, RET, and ROS1) in 2.3%. Treatment-induced resistance mutations were common in this cohort, including driver-dependent and driver-independent alterations. In the subset of patients who had progressive disease during EGFR therapy, 64% had known or putative resistance alterations detected in plasma. Subset analysis revealed that ctDNA increased the identification of driver mutations by 65% over standard-of-care, tissue-based testing at diagnosis. A pooled data analysis on this plasma-based assay demonstrated that targeted therapy response rates were equivalent to those reported from tissue analysis. CONCLUSIONS Comprehensive ctDNA analysis detected the presence of therapeutically targetable driver and resistance mutations at the frequencies and distributions predicted for the study population. These findings add support for comprehensive ctDNA testing in patients who are incompletely tested at the time of diagnosis and as a primary option at the time of progression on targeted therapies.
Collapse
Affiliation(s)
- Philip C. Mack
- Division of Hematology‐OncologyDepartment of Internal MedicineUniversity of California Davis Comprehensive Cancer CenterSacramentoCalifornia
- College of MedicineCalifornia Northstate UniversityElk GroveCalifornia
| | | | | | - Rebekah A. Burich
- Division of Hematology‐OncologyDepartment of Internal MedicineUniversity of California Davis Comprehensive Cancer CenterSacramentoCalifornia
| | - Oliver A. Zill
- Guardant Health, IncRedwood CityCalifornia
- Present address:
GenentechSouth San FranciscoCalifornia
| | | | - Jonathan W. Riess
- Division of Hematology‐OncologyDepartment of Internal MedicineUniversity of California Davis Comprehensive Cancer CenterSacramentoCalifornia
| | | | | | | | - David R. Gandara
- Division of Hematology‐OncologyDepartment of Internal MedicineUniversity of California Davis Comprehensive Cancer CenterSacramentoCalifornia
| |
Collapse
|
79
|
Emerging Precision Oncology Applications of Liquid Biopsy using Circulating Tumour DNA and Methylome Profiling. Clin Oncol (R Coll Radiol) 2020; 32:626-631. [PMID: 32586654 DOI: 10.1016/j.clon.2020.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/13/2020] [Accepted: 05/29/2020] [Indexed: 01/13/2023]
|
80
|
König D, Meier UR, Klaeser B, Savic S, Pless M. Successful Treatment of a Resistant Subclone in ALK-Rearranged NSCLC. Case Rep Oncol 2020; 13:729-732. [PMID: 32774266 PMCID: PMC7383154 DOI: 10.1159/000507850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 11/19/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors (TKIs) are established effective therapies in patients with ALK-rearranged advanced non-small-cell lung cancer (NSCLC). Upon progressive disease, patients normally receive a subsequent ALK TKI. However, when disease progression occurs in a limited number of sites, an oligoprogressive approach is a treatment option. In our case, FDG-PET/CT scan detected a progressive site in a patient with ceritinib therapy. Biopsy of the lesion was not possible because of its location. Progression was therefore confirmed by liquid biopsy with identification of the resistant subclone ALK G1202R. Definitive radiotherapy of the progressive site led to the disappearance of the ALK-resistant mutation. Meanwhile, ceritinib therapy was continued. The absence of disease both on repeated imaging and liquid biopsy indicates that eradication of a resistant subclone with an oligoprogressive treatment approach might be possible.
Collapse
Affiliation(s)
- David König
- Department of Medical Oncology, University Hospital Basel, Basel, Switzerland
| | - Urs R Meier
- Department of Radio-Oncology, Cantonal Hospital Winterthur, Winterthur, Switzerland
| | - Bernd Klaeser
- Department of Nuclear Medicine, Cantonal Hospital Winterthur, Winterthur, Switzerland
| | - Spasenija Savic
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Miklos Pless
- Department of Medical Oncology, Cantonal Hospital Winterthur, Winterthur, Switzerland
| |
Collapse
|
81
|
Reckamp KL, Patil T, Kirtane K, Rich TA, Espenschied CR, Weipert CM, Raymond VM, Santana-Davila R, Doebele RC, Baik CS. Duration of Targeted Therapy in Patients With Advanced Non-small-cell Lung Cancer Identified by Circulating Tumor DNA Analysis. Clin Lung Cancer 2020; 21:545-552.e1. [PMID: 32665165 DOI: 10.1016/j.cllc.2020.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Outcomes of therapy targeting molecular driver alterations detected in advanced non-small-cell lung (NSCLC) using circulating tumor DNA (ctDNA) have not been widely reported in patients who are targeted therapy-naive. PATIENTS AND METHODS We performed a multicenter retrospective review of patients with unresectable stage IIIB to IV NSCLC who received matched therapy after a targetable driver alteration was identified using a commercial ctDNA assay through usual clinical care. Eligible patients must not have received targeted therapy prior to ctDNA testing (prior chemotherapy or immunotherapy was permitted). Kaplan-Meier analysis was used to estimate the median duration of targeted therapy. Patients still on targeted therapy were censored at last follow-up. RESULTS Seventy-six patients met inclusion criteria. The median age of diagnosis of NSCLC was 64.5 years (range, 31-87 years), 67% were female, 74% were never-smokers, and 97% had adenocarcinoma histology. Twenty-one (28%) patients received systemic treatment prior to targeted therapy, including chemotherapy (n = 17), immunotherapy (n = 5), and/or a biologic (n = 4). Thirty-three (43%) patients remain on targeted therapy at the time of data analysis. The median time on targeted therapy was similar to what has been reported for tissue-detected oncogenic driver mutations in the targeted therapy-naive setting. CONCLUSIONS Patients with ctDNA-detected drivers had durable time on targeted therapy. These treatment outcomes data compliment previous studies that have shown enhanced targetable biomarker discovery rates and high tissue concordance of ctDNA testing when incorporated at initial diagnosis of NSCLC. Identification of NSCLC driver mutations using well-validated ctDNA assays can be used for clinical decision-making and targeted therapy assignment.
Collapse
Affiliation(s)
| | - Tejas Patil
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Kedar Kirtane
- Division of Medical Oncology, University of Washington, Seattle Cancer Care Alliance, Seattle, WA
| | | | | | | | | | - Rafael Santana-Davila
- Division of Medical Oncology, University of Washington, Seattle Cancer Care Alliance, Seattle, WA
| | - Robert C Doebele
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Christina S Baik
- Division of Medical Oncology, University of Washington, Seattle Cancer Care Alliance, Seattle, WA.
| |
Collapse
|
82
|
Negrao MV, Raymond VM, Lanman RB, Robichaux JP, He J, Nilsson MB, Ng PKS, Amador BE, Roarty EB, Nagy RJ, Banks KC, Zhu VW, Ng C, Chae YK, Clarke JM, Crawford JA, Meric-Bernstam F, Ignatius Ou SH, Gandara DR, Heymach JV, Bivona TG, McCoach CE. Molecular Landscape of BRAF-Mutant NSCLC Reveals an Association Between Clonality and Driver Mutations and Identifies Targetable Non-V600 Driver Mutations. J Thorac Oncol 2020; 15:1611-1623. [PMID: 32540409 DOI: 10.1016/j.jtho.2020.05.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/22/2020] [Accepted: 05/05/2020] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Approximately 4% of NSCLC harbor BRAF mutations, and approximately 50% of these are non-V600 mutations. Treatment of tumors harboring non-V600 mutations is challenging because of functional heterogeneity and lack of knowledge regarding their clinical significance and response to targeted agents. METHODS We conducted an integrative analysis of BRAF non-V600 mutations using genomic profiles of BRAF-mutant NSCLC from the Guardant360 database. BRAF mutations were categorized by clonality and class (1 and 2: RAS-independent; 3: RAS-dependent). Cell viability assays were performed in Ba/F3 models. Drug screens were performed in NSCLC cell lines. RESULTS A total of 305 unique BRAF mutations were identified. Missense mutations were most common (276, 90%), and 45% were variants of unknown significance. F468S and N581Y were identified as novel activating mutations. Class 1 to 3 mutations had higher clonality than mutations of unknown class (p < 0.01). Three patients were treated with MEK with or without BRAF inhibitors. Patients harboring G469V and D594G mutations did not respond, whereas a patient with the L597R mutation had a durable response. Trametinib with or without dabrafenib, LXH254, and lifirafenib had more potent inhibition of BRAF non-V600-mutant NSCLC cell lines than other MEK, BRAF, and ERK inhibitors, comparable with the inhibition of BRAF V600E cell line. CONCLUSIONS In BRAF-mutant NSCLC, clonality is higher in known functional mutations and may allow identification of variants of unknown significance that are more likely to be oncogenic drivers. Our data indicate that certain non-V600 mutations are responsive to MEK and BRAF inhibitors. This integration of genomic profiling and drug sensitivity may guide the treatment for BRAF-mutant NSCLC.
Collapse
Affiliation(s)
- Marcelo V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Jacqulyne P Robichaux
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junqin He
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Monique B Nilsson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick K S Ng
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bianca E Amador
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Emily B Roarty
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Viola W Zhu
- Chao Family Comprehensive Cancer Center, Department of Medicine, Division of Hematology-Oncology, University of California Irvine, Orange, California
| | - Chun Ng
- Kaiser Permanente, Stockton, California
| | - Young Kwang Chae
- Robert H. Lurie Comprehensive Cancer Center, Division of Hematology-Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | | | | | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sai-Hong Ignatius Ou
- Chao Family Comprehensive Cancer Center, Department of Medicine, Division of Hematology-Oncology, University of California Irvine, Orange, California
| | - David R Gandara
- Division of Hematology-Oncology, Department of Internal Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, California
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Trever G Bivona
- Division of Hematology and Oncology, University of California San Francisco, San Francisco, California
| | - Caroline E McCoach
- Division of Hematology and Oncology, University of California San Francisco, San Francisco, California.
| |
Collapse
|
83
|
Wang W, Chen D, Chen W, Xin Z, Huang Z, Zhang X, Xi K, Wang G, Zhang R, Zhao D, Liu L, Zhang L. Early Detection of Non-Small Cell Lung Cancer by Using a 12-microRNA Panel and a Nomogram for Assistant Diagnosis. Front Oncol 2020; 10:855. [PMID: 32596148 PMCID: PMC7301755 DOI: 10.3389/fonc.2020.00855] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/30/2020] [Indexed: 12/19/2022] Open
Abstract
Background: We previously identified a 12-microRNA (miRNA) panel (miRNA-17, miRNA-146a, miRNA-200b, miRNA-182, miRNA-155, miRNA-221, miRNA-205, miRNA-126, miRNA-7, miRNA-21, miRNA-145, and miRNA-210) that aided in the early diagnosis of non-small cell lung cancer (NSCLC). We validated the diagnostic value of this miRNA panel and compared it with that of traditional tumor markers and radiological diagnosis. We constructed a nomogram based on the miRNA panel's results to predict the risk of NSCLC. Methods: Eighty-two participants with pulmonary nodules on a CT scan and who underwent a pathological examination and surgical treatment were enrolled in our study. Patients were randomly divided into a training group or a validation group. The miRNA concentrations were quantified by RT-PCR and log-transformed for analysis. The cutoff value was determined in the training group and then applied in the validation group. A comparison between the miRNAs and traditional tumor markers [CEA, NSE, and cytokeratin 19 fragment 21-1 (Cyfra21-1)] and radiological diagnosis was performed. A nomogram based on the miRNA panel's results to predict the risk of NSCLC was constructed. Results: The expression level of these 12 miRNAs was significantly higher in NSCLC patients than in benign patients. In the validation group, the specificity and positive predictive value were 96.4 and 95.8%, respectively, which were significantly higher than those using traditional tumor markers or radiological diagnosis. The sensitivity was 42.6%, which was also higher than that using tumor markers. Moreover, the sensitivity increased to 63.6% when the nodule diameters were larger than 2 cm. The miRNAs and seven clinical factors were integrated into the nomogram, and the calibration curves showed optimal agreement between the predicted and actual probabilities. Conclusions: Our miRNA panel has clinical value for the early detection of NSCLC. A nomogram was constructed and internally validated, and the results indicate that it can assist clinicians in making treatment recommendations in the clinic.
Collapse
Affiliation(s)
- Weidong Wang
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Dongni Chen
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Weiwei Chen
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ziya Xin
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zirui Huang
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xuewen Zhang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kexing Xi
- Department of Colorectal Surgery, Peking Union Medical College, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Gongming Wang
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Rusi Zhang
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Dechang Zhao
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Li Liu
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Lanjun Zhang
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| |
Collapse
|
84
|
Liam CK, Mallawathantri S, Fong KM. Is tissue still the issue in detecting molecular alterations in lung cancer? Respirology 2020; 25:933-943. [PMID: 32335992 DOI: 10.1111/resp.13823] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/23/2020] [Accepted: 03/29/2020] [Indexed: 02/07/2023]
Abstract
Molecular biomarker testing of advanced-stage NSCLC is now considered standard of care and part of the diagnostic algorithm to identify subsets of patients for molecular-targeted treatment. Tumour tissue biopsy is essential for an accurate initial diagnosis, determination of the histological subtype and for molecular testing. With the increasing use of small biopsies and cytological specimens for diagnosis and the need to identify an increasing number of predictive biomarkers, proper management of the limited amount of sampling materials available is important. Many patients with advanced NSCLC do not have enough tissue for molecular testing and/or do not have a biopsy-amenable lesion and/or do not want to go through a repeat biopsy given the potential risks. Molecular testing can be difficult or impossible if the sparse material from very small biopsy specimens has already been exhausted for routine diagnostic purposes. A limited diagnostic workup is recommended to preserve sufficient tissue for biomarker testing. In addition, tumour biopsies are limited by tumour heterogeneity, particularly in the setting of disease resistance, and thus may yield false-negative results. Hence, there have been considerable efforts to determine if liquid biopsy in which molecular alterations can be non-invasively identified in plasma cell-free ctDNA, a potential surrogate for the entire tumour genome, can overcome the issues with tissue biopsies and replace the need for the latter.
Collapse
Affiliation(s)
- Chong-Kin Liam
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Kwun M Fong
- Thoracic Medicine, The Prince Charles Hospital, The University of Queensland Thoracic Research Centre at TPCH, Brisbane, QLD, Australia
| |
Collapse
|
85
|
Chang S, Hur JY, Choi YL, Lee CH, Kim WS. Current status and future perspectives of liquid biopsy in non-small cell lung cancer. J Pathol Transl Med 2020; 54:204-212. [PMID: 32460474 PMCID: PMC7253954 DOI: 10.4132/jptm.2020.02.27] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/27/2020] [Indexed: 12/17/2022] Open
Abstract
With advances in target therapy, molecular analysis of tumors is routinely required for treatment decisions in patients with advanced non-small cell lung cancer (NSCLC). Liquid biopsy refers to the sampling and analysis of circulating cell-free tumor DNA (ctDNA) in various body fluids, primarily blood. Because the technique is minimally invasive, liquid biopsies are the future in cancer management. Epidermal growth factor receptor (EGFR) ctDNA tests have been performed in routine clinical practice in advanced NSCLC patients to guide tyrosine kinase inhibitor treatment. In the near future, liquid biopsy will be a crucial prognostic, predictive, and diagnostic method in NSCLC. Here we present the current status and future perspectives of liquid biopsy in NSCLC.
Collapse
Affiliation(s)
- Sunhee Chang
- Department of Pathology, Inje University Ilsan Paik Hospital, Goyang, Korea
| | - Jae Young Hur
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Yoon-La Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chang Hun Lee
- Department of Pathology, Pusan National University Hospital, Pusan National University School of Medicine, Busan, Korea
| | - Wan Seop Kim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| |
Collapse
|
86
|
Madsen AT, Winther-Larsen A, McCulloch T, Meldgaard P, Sorensen BS. Genomic Profiling of Circulating Tumor DNA Predicts Outcome and Demonstrates Tumor Evolution in ALK-Positive Non-Small Cell Lung Cancer Patients. Cancers (Basel) 2020; 12:E947. [PMID: 32290439 PMCID: PMC7226192 DOI: 10.3390/cancers12040947] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/29/2022] Open
Abstract
With the rapid development of targeted therapies for the treatment of cancer, methods for predicting response and outcome are in high demand. Non-small cell lung cancer driven by genomic rearrangements of the anaplastic lymphoma kinase (ALK) gene can be successfully treated with ALK-targeted therapy. Unfortunately, a subset of patients does not respond, and all patients ultimately acquire resistance, highlighting the need for better clinical tools to manage these patients. Here, we performed targeted next-generation sequencing on plasma circulating tumor DNA (ctDNA) from 24 patients to assess the clinical utility of ctDNA genomic profiling. Patients with detectable ctDNA prior to treatment had worse progression-free survival (PFS) than those without (median 8.7 vs. 15.2 months, p = 0.028). In addition, the presence of ctDNA within two months after treatment initiation predicted inferior PFS (median 4.6 vs. 14.5 months, p = 0.028). Longitudinal monitoring of ctDNA with droplet digital PCR during treatment reflected the radiological response and revealed potential acquired resistance mutations. Interestingly, an increase in the ctDNA concentration was evident prior to the determination of progressive disease by conventional radiological imaging, with a median lead time of 69 days (range 30-113). Genomic profiling of ctDNA is a promising tool for predicting outcome and monitoring response to targeted therapy.
Collapse
Affiliation(s)
- Anne Tranberg Madsen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus N, Denmark; (A.W.-L.); (B.S.S.)
| | - Anne Winther-Larsen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus N, Denmark; (A.W.-L.); (B.S.S.)
| | - Tine McCulloch
- Department of Oncology, Aalborg University Hospital, 9000 Aalborg, Denmark;
| | - Peter Meldgaard
- Department of Oncology, Aarhus University Hospital, 8200 Aarhus N, Denmark;
| | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus N, Denmark; (A.W.-L.); (B.S.S.)
| |
Collapse
|
87
|
Mezquita L, Swalduz A, Jovelet C, Ortiz-Cuaran S, Howarth K, Planchard D, Avrillon V, Recondo G, Marteau S, Benitez JC, De Kievit F, Plagnol V, Lacroix L, Odier L, Rouleau E, Fournel P, Caramella C, Tissot C, Adam J, Woodhouse S, Nicotra C, Auclin E, Remon J, Morris C, Green E, Massard C, Pérol M, Friboulet L, Besse B, Saintigny P. Clinical Relevance of an Amplicon-Based Liquid Biopsy for Detecting ALK and ROS1 Fusion and Resistance Mutations in Patients With Non-Small-Cell Lung Cancer. JCO Precis Oncol 2020; 4:PO.19.00281. [PMID: 32923908 PMCID: PMC7448797 DOI: 10.1200/po.19.00281] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Liquid biopsy specimen genomic profiling is integrated in non-small-cell lung cancer (NSCLC) guidelines; however, data on the clinical relevance for ALK /ROS1 alterations are scarce. We evaluated the clinical utility of a targeted amplicon-based assay in a large prospective cohort of patients with ALK/ROS1-positive NSCLC and its impact on outcomes. PATIENTS AND METHODS Patients with advanced ALK/ROS1-positive NSCLC were prospectively enrolled in the study by researchers at eight French institutions. Plasma samples were analyzed using InVisionFirst-Lung and correlated with clinical outcomes. RESULTS Of the 128 patients included in the study, 101 were positive for ALK and 27 for ROS1 alterations. Blood samples (N = 405) were collected from 29 patients naïve for treatment with tyrosine kinase inhibitors (TKI) or from 375 patients under treatment, including 105 samples collected at disease progression (PD). Sensitivity was 67% (n = 18 of 27) for ALK/ROS1 fusion detection. Higher detection was observed for ALK fusions at TKI failure (n = 33 of 74; 46%) versus in patients with therapeutic response (n = 12 of 109; 11%). ALK-resistance mutations were detected in 22% patients (n = 16 of 74) overall; 43% of the total ALK-resistance mutations identified occurred after next-generation TKI therapy. ALK G1202R was the most common mutation detected (n = 7 of 16). Heterogeneity of resistance was observed. ROS1 G2032R resistance was detected in 30% (n = 3 of 10). The absence of circulating tumor DNA mutations at TKI failure was associated with prolonged median overall survival (105.7 months). Complex ALK-resistance mutations correlated with poor overall survival (median, 26.9 months v NR for single mutation; P = .003) and progression-free survival to subsequent therapy (median 1.7 v 6.3 months; P = .003). CONCLUSION Next-generation, targeted, amplicon-based sequencing for liquid biopsy specimen profiling provides clinically relevant detection of ALK/ROS1 fusions in TKI-naïve patients and allows for the identification of resistance mutations in patients treated with TKIs. Liquid biopsy specimens from patients treated with TKIs may affect clinical outcomes and capture heterogeneity of TKI resistance, supporting their role in selecting sequential therapy.
Collapse
Affiliation(s)
- Laura Mezquita
- Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | - Aurélie Swalduz
- Department of Medical Oncology, Centre Léon Bérard Lyon, France
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS UMR5286, Centre Léon Bérard, Cancer Research Center of Lyon, 69008 Lyon, France
| | - Cécile Jovelet
- Plateforme de Génomique, Module de Biopathologie Moléculaire et Centre de Ressources Biologiques, AMMICa, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - Sandra Ortiz-Cuaran
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS UMR5286, Centre Léon Bérard, Cancer Research Center of Lyon, 69008 Lyon, France
| | | | - David Planchard
- Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | | | - Gonzalo Recondo
- INSERM U981, Gustave Roussy, Université Paris Saclay, Villejuif, France
| | - Solène Marteau
- Department of Medical Oncology, Centre Léon Bérard Lyon, France
| | | | | | | | - Ludovic Lacroix
- Plateforme de Génomique, Module de Biopathologie Moléculaire et Centre de Ressources Biologiques, AMMICa, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - Luc Odier
- Department of Pneumology, Hôpital Nord-Ouest Villefranche, Villefranche Sur Saône, France
| | - Etienne Rouleau
- Plateforme de Génomique, Module de Biopathologie Moléculaire et Centre de Ressources Biologiques, AMMICa, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - Pierre Fournel
- Department of Medical Oncology, Institut de Cancérologie de la Loire, Saint-Priest-en-Jarez, France
| | | | - Claire Tissot
- Department of Pneumology, CHU Nord Saint-Etienne, Saint-Priest-en-Jarez, France
| | - Julien Adam
- Pathology Department, Gustave Roussy, Villejuif, France
| | | | - Claudio Nicotra
- Early Drug Development Department, Gustave Roussy, Villejuif, France
| | - Edouard Auclin
- Medical Oncology Department, George Pompidou Hospital, Paris, France
| | | | | | | | - Christophe Massard
- INSERM U981, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Early Drug Development Department, Gustave Roussy, Villejuif, France
| | - Maurice Pérol
- Department of Medical Oncology, Centre Léon Bérard Lyon, France
| | - Luc Friboulet
- INSERM U981, Gustave Roussy, Université Paris Saclay, Villejuif, France
| | - Benjamin Besse
- Cancer Medicine Department, Gustave Roussy, Villejuif, France
- INSERM U981, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Paris-Sud University, Orsay, France
| | - Pierre Saintigny
- Department of Medical Oncology, Centre Léon Bérard Lyon, France
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS UMR5286, Centre Léon Bérard, Cancer Research Center of Lyon, 69008 Lyon, France
| |
Collapse
|
88
|
Solomon B. Identifying Mechanisms of Resistance to ALK Tyrosine Kinase Inhibitors Using Analysis of Circulating Tumor DNA. J Thorac Oncol 2020; 15:482-484. [DOI: 10.1016/j.jtho.2019.12.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 10/24/2022]
|
89
|
Remon J, Tabbò F, Jimenez B, Collazo A, de Castro J, Novello S. Sequential blinded treatment decisions in ALK-positive non-small cell lung cancers in the era of precision medicine. Clin Transl Oncol 2020; 22:1425-1429. [PMID: 31955355 DOI: 10.1007/s12094-020-02290-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/03/2020] [Indexed: 11/25/2022]
Abstract
Next-generation ALK TKIs have become the new standard of care in first-line setting in advanced ALK-positive NSCLC patients. However, sequential strategies at progression are relevant, as may have an impact on patients' outcome. In this commentary we discuss whether genomic-tailored strategies at progression would be more suitable for improving outcome of ALK-positive NSCLC patients.
Collapse
Affiliation(s)
- J Remon
- Department of Medical Oncology, Centro Integral Oncológico Clara Campal (HM-CIOCC), Hospital HM Delfos, HM Hospitales, Avinguda de Vallcarca, 151, 08023, Barcelona, Spain.
| | - F Tabbò
- Thoracic Oncology Unit, Department of Oncology, University of Torino, Regione Gonzole, 10, 10043, Orbassano (TO), Turin, Italy
| | - B Jimenez
- Medical Oncology Department, Centro Integral Oncológico Clara Campal Madrid, HM Sanchinarro, Calle Oña, 10, 28050, Madrid, Spain
| | - A Collazo
- Medical Oncology Department, Centro Integral Oncológico Clara Campal Madrid, HM Sanchinarro, Calle Oña, 10, 28050, Madrid, Spain
| | - J de Castro
- Medical Oncology Department, Centro Integral Oncológico Clara Campal Madrid, HM Sanchinarro, Calle Oña, 10, 28050, Madrid, Spain
| | - S Novello
- Thoracic Oncology Unit, Department of Oncology, University of Torino, Regione Gonzole, 10, 10043, Orbassano (TO), Turin, Italy
| |
Collapse
|
90
|
Liquid Biopsy in Non-Small Cell Lung Cancer: Highlights and Challenges. Cancers (Basel) 2019; 12:cancers12010017. [PMID: 31861557 PMCID: PMC7017364 DOI: 10.3390/cancers12010017] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022] Open
Abstract
Non-small cell lung cancer is one leading cause of death worldwide, and patients would greatly benefit from an early diagnosis. Since targeted and immunotherapies have emerged as novel approaches for more tailored treatments, repeated assessments of the tumor biology have become pivotal to drive clinical decisions. Currently, tumor tissue biopsy is the gold standard to investigate potentially actionable biomarkers, but this procedure is invasive and may prove inadequate to represent the whole malignancy. In this regard, liquid biopsy represents a minimally invasive and more comprehensive option for early detection and investigation of this tumor. Today, cell-free DNA is the only approved circulating marker to select patients for a targeted therapy. Conversely, the other tumor-derived markers (i.e., circulating tumor cells, miRNAs, exosomes, and tumor educated platelets) are still at a pre-clinical phase, although they show promising results for their application in screening programs or as prognostic/predictive biomarkers. The main challenges for their clinical translation are the lack of reliable cutoffs and, especially for miRNAs, the great variability among the studies. Moreover, no established tool has been approved for circulating tumor cells and exosome isolation. Finally, large prospective clinical trials are mandatory to provide evidence of their clinical utility.
Collapse
|
91
|
Dietz S, Christopoulos P, Gu L, Volckmar AL, Endris V, Yuan Z, Ogrodnik SJ, Zemojtel T, Heussel CP, Schneider MA, Meister M, Muley T, Reck M, Schlesner M, Thomas M, Stenzinger A, Sültmann H. Serial liquid biopsies for detection of treatment failure and profiling of resistance mechanisms in KLC1-ALK-rearranged lung cancer. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004630. [PMID: 31753813 PMCID: PMC6913150 DOI: 10.1101/mcs.a004630] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/04/2019] [Indexed: 12/19/2022] Open
Abstract
Genetic rearrangements involving the anaplastic lymphoma kinase (ALK) gene confer sensitivity to ALK tyrosine kinase inhibitors (TKIs) and superior outcome in non-small-cell lung cancer (NSCLC). However, clinical courses vary widely, and recent studies suggest that molecular profiling of ALK+ NSCLC can provide additional predictors of therapy response that could assist further individualization of patient management. As repeated tissue biopsies often pose technical difficulties and significant procedural risk, analysis of tumor constituents circulating in the blood, including ctDNA and various proteins, is increasingly recognized as an alternative method of tumor sampling (“liquid biopsy”). Here, we report the case of a KLC1–ALK-rearranged NSCLC patient responding to crizotinib treatment and demonstrate how analysis of plasma and serum biomarkers can be used to identify the ALK fusion partner and monitor therapy over time. Results of ctDNA sequencing and copy-number alteration profiling as well as serum protein concentrations at various time points during therapy reflected the current remission status and could predict the subsequent clinical course. At the time of disease progression, we identified four distinct secondary mutations in the ALK gene in ctDNA potentially causing treatment failure, accompanied by rising levels of CEA and CYFRA 21–1. Moreover, several copy-number variations were detected at the end of the treatment, including an amplification of a region on Chromosome 12 encompassing the TP53 regulator MDM2. In summary, our findings illustrate the utility of noninvasive longitudinal molecular profiling for assessing remission status, exploring mechanisms of treatment failure, predicting subsequent clinical course, and dissecting dynamics of drug-resistant clones in ALK+ lung cancer.
Collapse
Affiliation(s)
- Steffen Dietz
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany.,German Center for Lung Research (DZL), TLRC Heidelberg, 69120 Heidelberg, Germany
| | - Petros Christopoulos
- German Center for Lung Research (DZL), TLRC Heidelberg, 69120 Heidelberg, Germany.,Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, 69120 Heidelberg, Germany.,Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Lisa Gu
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany.,German Center for Lung Research (DZL), TLRC Heidelberg, 69120 Heidelberg, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany
| | - Volker Endris
- Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany
| | - Zhao Yuan
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Simon J Ogrodnik
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany.,German Center for Lung Research (DZL), TLRC Heidelberg, 69120 Heidelberg, Germany
| | - Tomasz Zemojtel
- Berlin Institute of Health (BIH) Genomics Core Facility, Charité, University Medical Center, 10017 Berlin, Germany
| | - Claus-Peter Heussel
- German Center for Lung Research (DZL), TLRC Heidelberg, 69120 Heidelberg, Germany.,Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik at University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Marc A Schneider
- German Center for Lung Research (DZL), TLRC Heidelberg, 69120 Heidelberg, Germany.,Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Michael Meister
- German Center for Lung Research (DZL), TLRC Heidelberg, 69120 Heidelberg, Germany.,Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Thomas Muley
- German Center for Lung Research (DZL), TLRC Heidelberg, 69120 Heidelberg, Germany.,Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Martin Reck
- Lung Clinic Grosshansdorf, Airway Research Center North, German Center for Lung Research (DZL), 22927 Großhansdorf, Germany
| | - Matthias Schlesner
- German Center for Lung Research (DZL), TLRC Heidelberg, 69120 Heidelberg, Germany.,Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Michael Thomas
- German Center for Lung Research (DZL), TLRC Heidelberg, 69120 Heidelberg, Germany.,Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Albrecht Stenzinger
- German Center for Lung Research (DZL), TLRC Heidelberg, 69120 Heidelberg, Germany.,Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany.,German Center for Lung Research (DZL), TLRC Heidelberg, 69120 Heidelberg, Germany
| |
Collapse
|
92
|
A review of predictive, prognostic and diagnostic biomarkers for non-small-cell lung cancer: towards personalised and targeted cancer therapy. JOURNAL OF RADIOTHERAPY IN PRACTICE 2019. [DOI: 10.1017/s1460396919000876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractIntroduction:Lung cancer has a high mortality rate mainly due to the lack of early detection or outward signs and symptoms, thereby often progressing to advanced stages (e.g., stage IV) before it is diagnosed. However, if lung cancers can be diagnosed at an early stage and also if clinicians can prospectively identify patients likely to respond to specific treatments, then there is a very high potential to increase patients’ survival. In recent years, several investigations have been conducted to identify cancer biomarkers for lung cancer risk assessment, early detection and diagnosis, the likelihood of identifying the group of patients who will benefit from a particular treatment and monitoring patient response to treatment.Materials and Methods:This paper reports on the review of 19 current clinical and emerging biomarkers used in risk assessment, screening for early detection and diagnosis and monitoring the response of treatment of non-small-cell lung cancers.Conclusion:The future holds promise for personalised and targeted medicine from prevention, diagnosis to treatment, which take into account individual patient’s variability, though it depends on the development of effective biomarkers interrogating the key aberrant pathways and potentially targetable with molecular targeted or immunologic therapies. Lung cancer biomarkers have the potential to guide clinical decision-making since they can potentially detect the disease early, measure the risk of developing the disease and the risk of progression, provide accurate information of patient response to a specific treatment and are capable of informing clinicians about the likely outcome of a cancer diagnosis independent of the treatment received. Moreover, lung cancer biomarkers are increasingly linked to specific molecular pathway deregulations and/or cancer pathogenesis and can be used to justify the application of certain therapeutic or interventional strategies.
Collapse
|
93
|
Xu C, Cao H, Shi C, Feng J. The Role Of Circulating Tumor DNA In Therapeutic Resistance. Onco Targets Ther 2019; 12:9459-9471. [PMID: 31807023 PMCID: PMC6850686 DOI: 10.2147/ott.s226202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/09/2019] [Indexed: 12/22/2022] Open
Abstract
The application of precision medicine in cancer treatment has partly succeeded in reducing the side effects of unnecessary chemotherapeutics and in improving the survival rate of patients. However, with the long-term use of therapy, the dynamically changing intratumoral and intertumoral heterogeneity eventually gives rise to therapeutic resistance. In recent years, a novel testing technology (termed liquid biopsy) using circulating tumor DNAs (ctDNAs) extracted from peripheral blood samples from patients with cancer has brought about new expectations to the medical community. Using ctDNAs, clinicians can trace the heterogeneity pattern to duly adjust individual therapy and prolong overall survival for patients with cancer. Technological advances in detecting and characterizing ctDNAs (eg, development of next-generation sequencing) have provided clinicians with a valuable tool for genotyping tumors individually and identifying genetic and epigenetic alterations of the entire tumor to capture mutations associated with therapeutic resistance.
Collapse
Affiliation(s)
- Chenxin Xu
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, Jiangsu Province, People's Republic of China
| | - Haixia Cao
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Chen Shi
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, Jiangsu Province, People's Republic of China
| | - Jifeng Feng
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, Jiangsu Province, People's Republic of China
| |
Collapse
|
94
|
McCoach CE. A Cautionary Analysis of Immunotherapy Prior to Targeted Therapy. J Thorac Oncol 2019; 14:8-10. [PMID: 30579546 DOI: 10.1016/j.jtho.2018.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 10/12/2018] [Indexed: 10/27/2022]
Affiliation(s)
- Caroline E McCoach
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California.
| |
Collapse
|
95
|
Tabbò F, Novello S. Expanding anaplastic lymphoma kinase therapeutic indication to early stage non-small cell lung cancer. Transl Lung Cancer Res 2019; 8:S290-S297. [PMID: 31857952 PMCID: PMC6894993 DOI: 10.21037/tlcr.2019.07.07] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/15/2019] [Indexed: 01/06/2023]
Abstract
Oncogene-addicted non-small cell lung cancer (NSCLC) patients have been witnessing overwhelming therapeutic improvements, especially in advanced disease management, due to the advent of more potent tyrosine kinase inhibitors (TKIs). However, the concrete chance to cure anaplastic lymphoma kinase (ALK)-rearranged patients remains prerogative of surgical and peri-operative medical approaches to early disease stage. Clinical investigations in the adjuvant setting of genotype-restricted lung cancers (i.e., EGFR+, ALK+, etc.) are under-represented owing to the need of large patients' enrollment and solid overall survival (OS) data, which solely can show real long-term impact of these therapeutic interventions. Current available radiological and molecular technologies will widely increase the number of surgical early stage patients, including ALK+, spurring the development of rational approaches aimed to prevent disease recurrence and prolong patients' survival. Ongoing clinical trials, evaluating crizotinib and alectinib as adjuvant treatments, will gauge the real impact of TKIs in terms of patients' disease free survival (DFS) and OS; other peri-operative investigations (e.g., neo-adjuvant strategies) will add information about ALK inhibitors' tumor growth restraint capacities and early adaptation mechanisms to ALK targeting. Nevertheless, multiple questions are and will remain unanswered: if should be treated indifferently all ALK+ patients or, alternatively, should be stratified in different risk groups based on the detectable residual disease [i.e., minimal residual disease (MRD) after surgery]; whether ALK inhibitors administration could facilitate the accumulations of persister cells driving resistance mechanisms to targeted therapies; if alternative strategies, as combined treatments targeting different molecular hubs, could enhance disease control and cancer eradication.
Collapse
Affiliation(s)
- Fabrizio Tabbò
- Department of Oncology, University of Torino, Torino, Italy
| | - Silvia Novello
- Department of Oncology, University of Torino, Torino, Italy
| |
Collapse
|
96
|
Sharma GG, Cortinovis D, Agustoni F, Arosio G, Villa M, Cordani N, Bidoli P, Bisson WH, Pagni F, Piazza R, Gambacorti-Passerini C, Mologni L. A Compound L1196M/G1202R ALK Mutation in a Patient with ALK-Positive Lung Cancer with Acquired Resistance to Brigatinib Also Confers Primary Resistance to Lorlatinib. J Thorac Oncol 2019; 14:e257-e259. [DOI: 10.1016/j.jtho.2019.06.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 11/26/2022]
|
97
|
Horn L, Whisenant JG, Wakelee H, Reckamp KL, Qiao H, Leal TA, Du L, Hernandez J, Huang V, Blumenschein GR, Waqar SN, Patel SP, Nieva J, Oxnard GR, Sanborn RE, Shaffer T, Garg K, Holzhausen A, Harrow K, Liang C, Lim LP, Li M, Lovly CM. Monitoring Therapeutic Response and Resistance: Analysis of Circulating Tumor DNA in Patients With ALK+ Lung Cancer. J Thorac Oncol 2019; 14:1901-1911. [PMID: 31446141 PMCID: PMC6823161 DOI: 10.1016/j.jtho.2019.08.003] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 08/01/2019] [Accepted: 08/01/2019] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Despite initial effectiveness of ALK receptor tyrosine kinase inhibitors (TKIs) in patients with ALK+ NSCLC, therapeutic resistance will ultimately develop. Serial tracking of genetic alterations detected in circulating tumor DNA (ctDNA) can be an informative strategy to identify response and resistance. This study evaluated the utility of analyzing ctDNA as a function of response to ensartinib, a potent second-generation ALK TKI. METHODS Pre-treatment plasma was collected from 76 patients with ALK+ NSCLC who were ALK TKI-naive or had received prior ALK TKI, and analyzed for specific genetic alterations. Longitudinal plasma samples were analyzed from a subset (n = 11) of patients. Analysis of pre-treatment tumor biopsy specimens from 22 patients was compared with plasma. RESULTS Disease-associated genetic alterations were detected in 74% (56 of 76) of patients, the most common being EML4-ALK. Concordance of ALK fusion between plasma and tissue was 91% (20 of 22 blood and tissue samples). Twenty-four ALK kinase domain mutations were detected in 15 patients, all had previously received an ALK TKI; G1269A was the most prevalent (4 of 24). Patients with a detectable EML4-ALK variant 1 (V1) fusion had improved response (9 of 17 patients; 53%) to ensartinib compared to patients with EML4-ALK V3 fusion (one of seven patients; 14%). Serial changes in ALK alterations were observed during therapy. CONCLUSIONS Clinical utility of ctDNA was shown, both at pre-treatment by identifying a potential subgroup of ALK+ NSCLC patients who may derive more benefit from ensartinib and longitudinally by tracking resistance. Prospective application of this technology may translate to improved outcomes for NSCLC patients treated with ALK TKIs.
Collapse
Affiliation(s)
- Leora Horn
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee.
| | - Jennifer G. Whisenant
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN 37232,Vanderbilt-Ingram Cancer Center, 2220 Pierce Avenue, Nashville, TN 37232
| | - Heather Wakelee
- Stanford Advanced Medicine Center, 875 Blake Wilbur Dr, Palo Alto, CA 94304
| | - Karen L. Reckamp
- City of Hope Comprehensive Cancer Center, 1500 E Duarte Rd, Duarte, CA 91010
| | - Huan Qiao
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN 37232
| | - Ticiana A. Leal
- University of Wisconsin School of Medicine and Public Health, 750 Highland Ave, Madison, WI 53726
| | - Liping Du
- Department of Biostatistics, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN 37232
| | | | - Vincent Huang
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN 37232
| | - George R. Blumenschein
- Department of Thoracic/Head and Neck Medical Oncology, The University of TX MD Anderson Cancer Center, 1840 Old Spanish Trial, Houston, TX 77054
| | - Saiama N. Waqar
- Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110
| | - Sandip P. Patel
- University of California at San Diego Moores Cancer Center, 3855 Health Sciences Drive La Jolla, CA 92037
| | - Jorge Nieva
- University of Southern California Keck School of Medicine, 1975 Zonal Ave, Los Angeles, CA 90033
| | | | - Rachel E. Sanborn
- Earle A. Chiles Research Institute, Providence Cancer Center, 4805 NE Glisan St. Suite 2N35, Portland, OR 97213
| | | | - Kavita Garg
- Resolution Biosciences, 550 Kirkland Way Suite, Redmond, WA
| | - Allison Holzhausen
- Xcovery Holdings, Inc., 11780 U.S. Hwy One, Suite 202, Palm Beach Gardens, FL 33408
| | - Kimberly Harrow
- Xcovery Holdings, Inc., 11780 U.S. Hwy One, Suite 202, Palm Beach Gardens, FL 33408
| | - Chris Liang
- Xcovery Holdings, Inc., 11780 U.S. Hwy One, Suite 202, Palm Beach Gardens, FL 33408
| | - Lee P. Lim
- Resolution Biosciences, 550 Kirkland Way Suite, Redmond, WA
| | - Mark Li
- Resolution Biosciences, 550 Kirkland Way Suite, Redmond, WA
| | - Christine M. Lovly
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN 37232,Vanderbilt-Ingram Cancer Center, 2220 Pierce Avenue, Nashville, TN 37232
| |
Collapse
|
98
|
Clifton K, Rich TA, Parseghian C, Raymond VM, Dasari A, Pereira AAL, Willis J, Loree JM, Bauer TM, Chae YK, Sherrill G, Fanta P, Grothey A, Hendifar A, Henry D, Mahadevan D, Nezami MA, Tan B, Wainberg ZA, Lanman R, Kopetz S, Morris V. Identification of Actionable Fusions as an Anti-EGFR Resistance Mechanism Using a Circulating Tumor DNA Assay. JCO Precis Oncol 2019; 3:1900141. [PMID: 33015522 PMCID: PMC7526699 DOI: 10.1200/po.19.00141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2019] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Gene fusions are established oncogenic drivers and emerging therapeutic targets in advanced colorectal cancer. This study aimed to detail the frequencies and clinicopathological features of gene fusions in colorectal cancer using a circulating tumor DNA assay. METHODS Circulating tumor DNA samples in patients with advanced colorectal cancer were analyzed at 4,581 unique time points using a validated plasma-based multigene assay that includes assessment of fusions in FGFR2, FGFR3, RET, ALK, NTRK1, and ROS1. Associations between fusions and clinicopathological features were measured using Fisher's exact test. Relative frequencies of genomic alterations were compared between fusion-present and fusion-absent cases using an unpaired t test. RESULTS Forty-four unique fusions were identified in 40 (1.1%) of the 3,808 patients with circulating tumor DNA detected: RET (n = 6; 36% of all fusions detected), FGFR3 (n = 2; 27%), ALK (n = 10, 23%), NTRK1 (n = 3; 7%), ROS1 (n = 2; 5%), and FGFR2 (n = 1; 2%). Relative to nonfusion variants detected, fusions were more likely to be subclonal (odds ratio, 8.2; 95% CI, 2.94 to 23.00; P < .001). Mutations associated with a previously reported anti-epidermal growth factor receptor (anti-EGFR) therapy resistance signature (subclonal RAS and EGFR mutations) were found with fusions in FGFR3 (10 of 12 patients), RET (nine of 16 patients), and ALK (seven of 10 patients). For the 27 patients with available clinical histories, 21 (78%) had EGFR monoclonal antibody treatment before fusion detection. CONCLUSION Diverse and potentially actionable fusions can be detected using a circulating tumor DNA assay in patients with advanced colorectal cancer. Distribution of coexisting subclonal mutations in EGFR, KRAS, and NRAS in a subset of the patients with fusion-present colorectal cancer suggests that these fusions may arise as a novel mechanism of resistance to anti-EGFR therapies in patients with metastatic colorectal cancer.
Collapse
Affiliation(s)
| | | | | | | | - Arvind Dasari
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jason Willis
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Todd M Bauer
- Tennessee Oncology Sarah Cannon Research Institute, Nashville, TN
| | - Young Kwang Chae
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | | | - Paul Fanta
- University of San Diego Moores Cancer Center, La Jolla, CA
| | - Axel Grothey
- The University of Tennessee West Cancer Center, Memphis, TN
| | | | - David Henry
- University of Pennsylvania, Philadelphia, PA
| | | | | | - Benjamin Tan
- Washington University School of Medicine, St Louis, MO
| | | | | | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Van Morris
- The University of Texas MD Anderson Cancer Center, Houston, TX
| |
Collapse
|
99
|
Rotow JK, Gui P, Wu W, Raymond VM, Lanman RB, Kaye FJ, Peled N, Fece de la Cruz F, Nadres B, Corcoran RB, Yeh I, Bastian BC, Starostik P, Newsom K, Olivas VR, Wolff AM, Fraser JS, Collisson EA, McCoach CE, Camidge DR, Pacheco J, Bazhenova L, Li T, Bivona TG, Blakely CM. Co-occurring Alterations in the RAS-MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer. Clin Cancer Res 2019; 26:439-449. [PMID: 31548343 DOI: 10.1158/1078-0432.ccr-19-1667] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/19/2019] [Accepted: 09/10/2019] [Indexed: 01/07/2023]
Abstract
PURPOSE Although patients with advanced-stage non-small cell lung cancers (NSCLC) harboring MET exon 14 skipping mutations (METex14) often benefit from MET tyrosine kinase inhibitor (TKI) treatment, clinical benefit is limited by primary and acquired drug resistance. The molecular basis for this resistance remains incompletely understood. EXPERIMENTAL DESIGN Targeted sequencing analysis was performed on cell-free circulating tumor DNA obtained from 289 patients with advanced-stage METex14-mutated NSCLC. RESULTS Prominent co-occurring RAS-MAPK pathway gene alterations (e.g., in KRAS, NF1) were detected in NSCLCs with METex14 skipping alterations as compared with EGFR-mutated NSCLCs. There was an association between decreased MET TKI treatment response and RAS-MAPK pathway co-occurring alterations. In a preclinical model expressing a canonical METex14 mutation, KRAS overexpression or NF1 downregulation hyperactivated MAPK signaling to promote MET TKI resistance. This resistance was overcome by cotreatment with crizotinib and the MEK inhibitor trametinib. CONCLUSIONS Our study provides a genomic landscape of co-occurring alterations in advanced-stage METex14-mutated NSCLC and suggests a potential combination therapy strategy targeting MAPK pathway signaling to enhance clinical outcomes.
Collapse
Affiliation(s)
- Julia K Rotow
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Philippe Gui
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | | | | | - Frederic J Kaye
- Department of Medicine, University of Florida, Gainesville, Florida
| | - Nir Peled
- Soroka Medical Center, Ben-Gurion University, Beer-Sheva, Israel
| | - Ferran Fece de la Cruz
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Brandon Nadres
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Iwei Yeh
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Departments of Dermatology and Pathology, and Clinical Cancer Genomics Laboratory, University of California, San Francisco, California
| | - Boris C Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Departments of Dermatology and Pathology, and Clinical Cancer Genomics Laboratory, University of California, San Francisco, California
| | - Petr Starostik
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida
| | - Kimberly Newsom
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida
| | - Victor R Olivas
- Department of Medicine, University of California, San Francisco, California
| | - Alexander M Wolff
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| | - Eric A Collisson
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Caroline E McCoach
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | | | | | | | - Tianhong Li
- Department of Internal Medicine, University of California, Davis, California
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, California. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, California. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| |
Collapse
|
100
|
Zhou X, Shou J, Sheng J, Xu C, Ren S, Cai X, Chu Q, Wang W, Zhen Q, Zhou Y, Li W, Pan H, Li H, Sun T, Cheng H, Wang H, Lou F, Rao C, Cao S, Pan H, Fang Y. Molecular and clinical analysis of Chinese patients with anaplastic lymphoma kinase (ALK)-rearranged non-small cell lung cancer. Cancer Sci 2019; 110:3382-3390. [PMID: 31444835 PMCID: PMC6778633 DOI: 10.1111/cas.14177] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/08/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) fusions have been recognized as a therapeutic target in non‐small cell lung cancer (NSCLC). However, molecular signatures and clinical characteristics of the Chinese population with ALK‐rearranged NSCLC are not well elucidated. In the present study, we carried out targeted next‐generation sequencing on tissue and plasma ctDNA samples in 1688 patients with NSCLC. Overall, ALK fusions were detected in 70 patients (4.1%), and the frequencies of ALK fusions detected in tissue and plasma samples were 5.1% and 3.3%, respectively. Additionally, the prevalence of breakpoint locations for EML4‐ALK fusions in ctDNA was significantly correlated with that in tumor tissues (R2 = .91, P = .045). According to age, the incidence rates of ALK fusions among young (age <45 years), middle‐aged (between 45 and 70 years) and elderly (>70 years) patients were significantly different (P < .001). In 70 ALK‐rearranged cases, coexistence of epidermal growth factor receptor (EGFR) alterations and ALK fusions was detected in 12 cases (17.1%) and EGFR mutations tended to coexist with non‐EML4‐ALK rearrangements. Notably, novel ALK fusion partners, including TRIM66,SWAP70,WNK3,ERC1,TCF12 and FBN1 were identified in the present study. Among EML4‐ALK fusion variants, patients with variant V1 were younger than patients with variant V3 (P = .023), and TP53 mutations were more frequently concurrent with variant V3 compared with variant V1 (P = .009). In conclusion, these findings provide new insights into the molecular‐clinical profiles of patients with ALK‐rearranged NSCLC that may improve the treatment strategy of this population.
Collapse
Affiliation(s)
- Xiaoyun Zhou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jiawei Shou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jin Sheng
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Chunwei Xu
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University, Fuzhou, China
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiuyu Cai
- Sun Yet-Sen University Cancer Center, Guangzhou, China
| | - Qian Chu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenxian Wang
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou, China
| | - Qinhong Zhen
- Department of Medical Oncology, Quzhou People's Hospital, Quzhou, China
| | - Yuefen Zhou
- Department of Medical Oncology, Lishui Municipal Central Hospital, Lishui, China
| | - Wenfeng Li
- Department of Medical Oncology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hong Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Hongsen Li
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Tao Sun
- Department of Surgery, University of Chicago, Chicago, USA
| | | | - Huina Wang
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Feng Lou
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Chuangzhou Rao
- Department of Radiation and Chemotherapy, Hwamei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Yong Fang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| |
Collapse
|