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Murata MM, Igari F, Urbanowicz R, Mouakkad L, Kim S, Chen Z, DiVizio D, Posadas EM, Giuliano AE, Tanaka H. A Practical Approach for Targeting Structural Variants Genome-wide in Plasma Cell-free DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.25.564058. [PMID: 37961589 PMCID: PMC10634834 DOI: 10.1101/2023.10.25.564058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Plasma cell-free DNA (cfDNA) is a promising source of gene mutations for cancer detection by liquid biopsy. However, no current tests interrogate chromosomal structural variants (SVs) genome-wide. Here, we report a simple molecular and sequencing workflow called Genome-wide Analysis of Palindrome Formation (GAPF-seq) to probe DNA palindromes, a type of SV that often demarcates gene amplification. With low-throughput next-generation sequencing and automated machine learning, tumor DNA showed skewed chromosomal distributions of high-coverage 1-kb bins (HCBs), which differentiated 39 breast tumors from matched normal DNA with an average Area Under the Curve (AUC) of 0.9819. A proof-of-concept liquid biopsy study using cfDNA from prostate cancer patients and healthy individuals yielded an average AUC of 0.965. HCBs on the X chromosome emerged as a determinant feature and were associated with androgen receptor gene amplification. As a novel agnostic liquid biopsy approach, GAPF-seq could fill the technological gap offering unique cancer-specific SV profiles.
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Bertoli E, De Carlo E, Basile D, Zara D, Stanzione B, Schiappacassi M, Del Conte A, Spina M, Bearz A. Liquid Biopsy in NSCLC: An Investigation with Multiple Clinical Implications. Int J Mol Sci 2023; 24:10803. [PMID: 37445976 DOI: 10.3390/ijms241310803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Tissue biopsy is essential for NSCLC diagnosis and treatment management. Over the past decades, liquid biopsy has proven to be a powerful tool in clinical oncology, isolating tumor-derived entities from the blood. Liquid biopsy permits several advantages over tissue biopsy: it is non-invasive, and it should provide a better view of tumor heterogeneity, gene alterations, and clonal evolution. Consequentially, liquid biopsy has gained attention as a cancer biomarker tool, with growing clinical applications in NSCLC. In the era of precision medicine based on molecular typing, non-invasive genotyping methods became increasingly important due to the great number of oncogene drivers and the small tissue specimen often available. In our work, we comprehensively reviewed established and emerging applications of liquid biopsy in NSCLC. We made an excursus on laboratory analysis methods and the applications of liquid biopsy either in early or metastatic NSCLC disease settings. We deeply reviewed current data and future perspectives regarding screening, minimal residual disease, micrometastasis detection, and their implication in adjuvant and neoadjuvant therapy management. Moreover, we reviewed liquid biopsy diagnostic utility in the absence of tissue biopsy and its role in monitoring treatment response and emerging resistance in metastatic NSCLC treated with target therapy and immuno-therapy.
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Affiliation(s)
- Elisa Bertoli
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
| | - Elisa De Carlo
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Debora Basile
- Department of Medical Oncology, San Giovanni Di Dio Hospital, 88900 Crotone, Italy
| | - Diego Zara
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
| | - Brigida Stanzione
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Monica Schiappacassi
- Molecular Oncology Unit, (OMMPPT) Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Alessandro Del Conte
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Michele Spina
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Alessandra Bearz
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
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Kemper M, Krekeler C, Menck K, Lenz G, Evers G, Schulze AB, Bleckmann A. Liquid Biopsies in Lung Cancer. Cancers (Basel) 2023; 15:1430. [PMID: 36900221 PMCID: PMC10000706 DOI: 10.3390/cancers15051430] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023] Open
Abstract
As lung cancer has the highest cancer-specific mortality rates worldwide, there is an urgent need for new therapeutic and diagnostic approaches to detect early-stage tumors and to monitor their response to the therapy. In addition to the well-established tissue biopsy analysis, liquid-biopsy-based assays may evolve as an important diagnostic tool. The analysis of circulating tumor DNA (ctDNA) is the most established method, followed by other methods such as the analysis of circulating tumor cells (CTCs), microRNAs (miRNAs), and extracellular vesicles (EVs). Both PCR- and NGS-based assays are used for the mutational assessment of lung cancer, including the most frequent driver mutations. However, ctDNA analysis might also play a role in monitoring the efficacy of immunotherapy and its recent accomplishments in the landscape of state-of-the-art lung cancer therapy. Despite the promising aspects of liquid-biopsy-based assays, there are some limitations regarding their sensitivity (risk of false-negative results) and specificity (interpretation of false-positive results). Hence, further studies are needed to evaluate the usefulness of liquid biopsies for lung cancer. Liquid-biopsy-based assays might be integrated into the diagnostic guidelines for lung cancer as a tool to complement conventional tissue sampling.
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Affiliation(s)
- Marcel Kemper
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Carolin Krekeler
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Kerstin Menck
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Georg Lenz
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Georg Evers
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Arik Bernard Schulze
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Annalen Bleckmann
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
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The Landscape of ALK-Rearranged Non-Small Cell Lung Cancer: A Comprehensive Review of Clinicopathologic, Genomic Characteristics, and Therapeutic Perspectives. Cancers (Basel) 2022; 14:cancers14194765. [PMID: 36230686 PMCID: PMC9563286 DOI: 10.3390/cancers14194765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary In recent years, prognosis of non-small cell lung cancer (NSCLC) patients significantly improved thanks to the introduction of tyrosine kinase inhibitors (TKIs) in clinical practice. ALK-rearranged NSCLC patients benefit from treatment with ALK inhibitors (ALK-i), which have shown a greater efficacy and a better intracranial activity than chemotherapy. Comparative studies between next-generation ALK-i are still lacking and clinicians are looking for reliable tools to determine which drug suits best for each patient. The aim of this review is to deepen the role of clinical and pathological characteristics influencing patients’ prognosis during treatment with ALK-i and to provide an overview of molecular mechanisms of ALK-i resistance. In this setting, liquid biopsy may play an important role in predicting tumor response and monitoring resistance mutations. We will summarize ongoing trials developing new ALK-i or combinations between ALK-i and other agents, which may represent future scenarios in the field of NSCLC research. Abstract During the last decade, the identification of oncogenic driver mutations and the introduction of tyrosine kinase inhibitors (TKIs) in daily clinical practice have substantially revamped the therapeutic approach of oncogene-addicted, non-small cell lung cancer (NSCLC). Rearrangements in the anaplastic lymphoma kinase (ALK) gene are detected in around 3–5% of all NSCLC patients. Following the promising results of Crizotinib, a first-generation ALK inhibitor (ALK-i), other second-generation and more recently third-generation TKIs have been developed and are currently a landmark in NSCLC treatment, leading to a significant improvement in patients prognosis. As clinical trials have already demonstrated high efficacy of each ALK-i, both in terms of systemic and intracranial disease control, comparative studies between second and third generation ALK-i are still lacking, and primary or secondary ALK-i resistance inevitably limit their efficacy. Resistance to ALK-i can be due to ALK-dependent or ALK-independent mechanisms, including the activation of bypass signaling pathways and histological transformation: these findings may play an important role in the future to select patients’ subsequent therapy. This review aims to provide an overview of underlying molecular alterations of ALK-i resistance and point out promising role of liquid biopsy in predicting tumor response and monitoring resistance mutations. The purpose of this review is also to summarize current approval for ALK-rearranged NSCLC patients, to help clinicians in making decisions on therapeutic sequence, and to deepen the role of clinicopathological and genomic characteristics influencing patients’ prognosis during treatment with ALK-i.
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García-Pardo M, Makarem M, Li JJN, Kelly D, Leighl NB. Integrating circulating-free DNA (cfDNA) analysis into clinical practice: opportunities and challenges. Br J Cancer 2022; 127:592-602. [PMID: 35347327 PMCID: PMC9381753 DOI: 10.1038/s41416-022-01776-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 12/12/2022] Open
Abstract
In the current era of precision medicine, the identification of genomic alterations has revolutionised the management of patients with solid tumours. Recent advances in the detection and characterisation of circulating tumour DNA (ctDNA) have enabled the integration of liquid biopsy into clinical practice for molecular profiling. ctDNA has also emerged as a promising biomarker for prognostication, monitoring disease response, detection of minimal residual disease and early diagnosis. In this Review, we discuss current and future clinical applications of ctDNA primarily in non-small cell lung cancer in addition to other solid tumours.
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Affiliation(s)
- Miguel García-Pardo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Maisam Makarem
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Janice J N Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Deirdre Kelly
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Natasha B Leighl
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
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Itchins M, Pavlakis N. The quantum leap in therapeutics for advanced ALK+ non-small cell lung cancer and pursuit to cure with precision medicine. Front Oncol 2022; 12:959637. [PMID: 36003760 PMCID: PMC9393505 DOI: 10.3389/fonc.2022.959637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Since the discovery 15 years ago, we have seen a quantum leap in the treatment and survival for individuals diagnosed with ALK+ lung cancers. Unfortunately however, for most, the diagnosis is made in an incurable circumstance given the late presentation of symptoms. Through a revolutionary wave of therapeutics, individuals may remarkably live over a decade, however many fall short of this milestone, as the molecular profile of this disease is very heterogeneous, reflected in variable survival outcomes. Despite a significant improval in survival and quality of life with ALK-inhibitor monotherapies, now available across multiple-generations, drug resistance and disease relapse remains inevitable, and treatment is offered in an empiric, stepwise, non personalised biomarker informed fashion. A proposed future focus to treating ALK to improve the chronicity of this disease and even promote cure, is to deliver a personalised dynamic approach to care, with rational combinations of drugs in conjunction with local ablative therapies to prevent and constantly proactively alter clonal selection. Such an approach would be informed by precision imaging with MRI-brain and FDG-PETs sequentially, and by regular plasma sampling including for circulating tumour DNA sequencing with personalised therapeutic switches occurring prior to the emergence of radiological and clinical relapse. Such an approach to care will require a complete paradigm shift in the way we approach the treatment of advanced cancer, however evidence to date in ALK+ lung cancers, support this new frontier of investigation.
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Affiliation(s)
- Malinda Itchins
- Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, St Leonards, NSW, Australia
- Northern Clinical School, University of Sydney, Kolling Institute, St Leonards, NSW, Australia
- North Shore Health Hub, GenesisCare, St Leonards, NSW, Australia
- *Correspondence: Malinda Itchins,
| | - Nick Pavlakis
- Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, St Leonards, NSW, Australia
- Northern Clinical School, University of Sydney, Kolling Institute, St Leonards, NSW, Australia
- North Shore Health Hub, GenesisCare, St Leonards, NSW, Australia
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Liquid biopsy and non-small cell lung cancer: are we looking at the tip of the iceberg? Br J Cancer 2022; 127:383-393. [PMID: 35264788 PMCID: PMC9345955 DOI: 10.1038/s41416-022-01777-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
The possibility to analyse the tumour genetic material shed in the blood is undoubtedly one of the main achievements of translational research in the latest years. In the modern clinical management of advanced non-small cell lung cancer, molecular characterisation plays an essential role. In parallel, immunotherapy is widely employed, but reliable predictive markers are not available yet. Liquid biopsy has the potential to face the two issues and to increase its role in advanced NSCLC in the next future. The aim of this review is to summarise the main clinical applications of liquid biopsy in advanced non-small cell lung cancer, underlining both its potential and limitations from a clinically driven perspective.
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8
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Salas C, Martín-López J, Martínez-Pozo A, Hernández-Iglesias T, Carcedo D, Ruiz de Alda L, García JF, Rojo F. Real-world biomarker testing rate and positivity rate in NSCLC in Spain: Prospective Central Lung Cancer Biomarker Testing Registry (LungPath) from the Spanish Society of Pathology (SEAP). J Clin Pathol 2022; 75:193-200. [PMID: 33722840 PMCID: PMC8862081 DOI: 10.1136/jclinpath-2020-207280] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 01/09/2023]
Abstract
AIM The aim of this study was to describe the testing rate and frequency of molecular alterations observed in the Lung Cancer Biomarker Testing Registry (LungPath). METHODS A descriptive study of NSCLC biomarker determinations collected from March 2018 to January 2019, from 38 Spanish hospitals, was carried out. Only adenocarcinoma and not otherwise specified histologies were included for epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), c-ros oncogene 1 (ROS1) and programmed death ligand-1 (PD-L1) expression. The testing rate and the positivity rate were calculated. Multivariate logistic regression was used to explore the joint relationship between independent explanatory factors and both testing and positivity rates. Two models were adjusted: one with sample type and histology as independent factors, and the other adding the testing rate or the positivity rate of the other biomarkers. RESULTS 3226 patient samples were analysed, where EGFR, ALK, ROS1 and PD-L1 information was collected (a total of 12 904 determinations). Overall, 9118 (71.4%) determinations were finally assessed. EGFR (91.4%) and ALK (80.1%) were the mainly tested biomarkers. Positivity rates for EGFR, ALK, ROS1 and PD-L1 were 13.6%, 3.4%, 2.0% and 49.2%, respectively. Multivariate models showed a lower testing rate for ALK in surgical pieces, fine-needle aspiration or other types of samples versus biopsies. CONCLUSIONS Despite the high testing rate in EGFR and ALK in NSCLC, the real-world evidence obtained from the LungPath demonstrates that ROS1 and PD-L1 were not determined in a significant portion of patients. LungPath provides crucial information to improve the coverage in molecular testing in lung cancer, to monitor the positivity rate and the introduction of new biomarker testing in clinical practice.
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Affiliation(s)
- Clara Salas
- Hospital Universitario Puerta de Hierro, Majadahonda, Madrid, Spain,External Quality Asessment (GCP) of the Spanish Society of Pathology (SEAP), Madrid, Spain
| | | | - Antonio Martínez-Pozo
- External Quality Asessment (GCP) of the Spanish Society of Pathology (SEAP), Madrid, Spain,Pathology Department, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | | | | | | | | | - Federico Rojo
- External Quality Asessment (GCP) of the Spanish Society of Pathology (SEAP), Madrid, Spain,IIS-Fundacion Jimenez Diaz University Hospital CIBERONC, Madrid, Spain
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Recommendations for a practical implementation of circulating tumor DNA mutation testing in metastatic non-small-cell lung cancer. ESMO Open 2022; 7:100399. [PMID: 35202954 PMCID: PMC8867049 DOI: 10.1016/j.esmoop.2022.100399] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/10/2021] [Accepted: 01/19/2022] [Indexed: 12/17/2022] Open
Abstract
Background Liquid biopsy (LB) is a rapidly evolving diagnostic tool for precision oncology that has recently found its way into routine practice as an adjunct to tissue biopsy (TB). The concept of LB refers to any tumor-derived material, such as circulating tumor DNA (ctDNA) or circulating tumor cells that are detectable in blood. An LB is not limited to the blood and may include other fluids such as cerebrospinal fluid, pleural effusion, and urine, among others. Patients and methods The objective of this paper, devised by international experts from various disciplines, is to review current challenges as well as state-of-the-art applications of ctDNA mutation testing in metastatic non-small-cell lung cancer (NSCLC). We consider pragmatic scenarios for the use of ctDNA from blood plasma to identify actionable targets for therapy selection in NSCLCs. Results Clinical scenarios where ctDNA mutation testing may be implemented in clinical practice include complementary tissue and LB testing to provide the full picture of patients’ actual predictive profiles to identify resistance mechanism (i.e. secondary mutations), and ctDNA mutation testing to assist when a patient has a discordant clinical history and is suspected of showing intertumor or intratumor heterogeneity. ctDNA mutation testing may provide interesting insights into possible targets that may have been missed on the TB. Complementary ctDNA LB testing also provides an option if the tumor location is hard to biopsy or if an insufficient sample was taken. These clinical use cases highlight practical scenarios where ctDNA LB may be considered as a complementary tool to TB analysis. Conclusions Proper implementation of ctDNA LB testing in routine clinical practice is envisioned in the near future. As the clinical evidence of utility expands, the use of LB alongside tissue sample analysis may occur in the patient cases detailed here. LB is a rapidly evolving diagnostic tool that may be an adjunct or an alternative to TB in clinic. Pragmatic scenarios for ctDNA mutation testing to identify actionable targets in NSCLC are explored. ctDNA mutation testing may identify resistance mechanisms, discordant clinical history, and intertumor/intratumor heterogeneity. ctDNA mutation testing may be useful if the tumor location is hard to biopsy or if an insufficient tumor sample was taken. Proper implementation of ctDNA mutation testing in routine clinical practice is envisioned in the near future.
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Fernandes MGO, Cruz-Martins N, Machado JC, Costa JL, Hespanhol V. The value of cell-free circulating tumour DNA profiling in advanced non-small cell lung cancer (NSCLC) management. Cancer Cell Int 2021; 21:675. [PMID: 34915883 PMCID: PMC8680243 DOI: 10.1186/s12935-021-02382-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/30/2021] [Indexed: 01/04/2023] Open
Abstract
AbstractLiquid biopsy (LB) has boosted a remarkable change in the management of cancer patients by contributing to tumour genomic profiling. Plasma circulating cell-free tumour DNA (ctDNA) is the most widely searched tumour-related element for clinical application. Specifically, for patients with lung cancer, LB has revealed valuable to detect the diversity of targetable genomic alterations and to detect and monitor the emergence of resistance mechanisms. Furthermore, its non-invasive nature helps to overcome the difficulty in obtaining tissue samples, offering a comprehensive view about tumour diversity. However, the use of the LB to support diagnostic and therapeutic decisions still needs further clarification. In this sense, this review aims to provide a critical view of the clinical importance of plasma ctDNA analysis, the most widely applied LB, and its limitations while anticipating concepts that will intersect the present and future of LB in non-small cell lung cancer patients.
Graphical Abstract
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11
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Clinical Outcomes for Plasma-Based Comprehensive Genomic Profiling Versus Standard-of-Care Tissue Testing in Advanced Non-Small Cell Lung Cancer. Clin Lung Cancer 2021; 23:72-81. [PMID: 34782240 DOI: 10.1016/j.cllc.2021.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 02/02/2023]
Abstract
BACKGROUND Somatic genomic testing is recommended by numerous expert guidelines to inform targeted therapy treatment for patients with advanced nonsquamous non-small cell lung cancer (aNSCLC). The NILE study was a prospective observational study that demonstrated noninferiority of cell-free circulating tumor DNA (cfDNA)-based tumor genotyping compared to tissue-based genotyping to find targetable genomic alterations in patients with newly diagnosed nonsquamous aNSCLC. As the cohort has matured, clinical outcomes data can now be analyzed. METHODS This prospective, multicenter North American study enrolled patients with previously untreated nonsquamous aNSCLC who had standard of care (SOC) tissue genotyping performed and concurrent comprehensive cfDNA analysis (Guardant360). Patients with targetable genomic alterations, as defined by NCCN guidelines, who were treated with physician's choice of therapy had objective response rates, disease control rate, and time to treatment collected and compared to published outcomes. RESULTS Among 282 patients, 89 (31.6%) had an actionable biomarker, as defined by NCCN, detected by tissue (21.3%) and/or cfDNA (27.3%) analysis. Sixty-one (68.5%) of these were treated with an FDA-approved targeted therapy guided by somatic genotyping results (EGFR, ALK, ROS1). Thirty-three patients were eligible for clinical response evaluation and demonstrated an objective response rate of 58% and disease control rate of 94%. Twenty-five (76%) and 17 (52%) achieved a durable response > 6 months and 12 months, respectively. The time to treatment (TtT) was significantly faster for cfDNA-informed biomarker detection as compared to tissue genotyping (18 vs. 31 days, respectively; P = .0008). CONCLUSIONS cfDNA detects guideline-recommended biomarkers at a rate similar to tissue genotyping, and therapeutic outcomes based on plasma-based comprehensive genomic profiling are comparable to published targeted therapy outcomes with tissue profiling, even in community-based centers.
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12
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Malapelle U, Buono M, Pisapia P, Russo G, Tufano R, Pepe F, Rolfo C, Troncone G. Circulating tumor DNA in cancer: Predictive molecular pathology meets mathematics. Crit Rev Oncol Hematol 2021; 163:103394. [PMID: 34119656 DOI: 10.1016/j.critrevonc.2021.103394] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 12/11/2022] Open
Abstract
The cancer secretome is a valuable reservoir of cancer biomarkers. Besides containing circulating tumor cells, extracellular vesicles, and proteins, it is also rich in circulating tumor DNA (ctDNA)-a subpopulation of cell free DNA. The most efficient technology to capture ctDNA is next generation sequencing (NGS). Indeed, this analysis enables the identification of both quantitative (e.g., mutant allelic fraction - MAF) and qualitative (e.g., the variant type) information. Strikingly, by calculating these data in relation to time, cytopathologists can decodify and graphically report the ctDNA "message", which may help to diagnose cancer, define treatment, and monitor disease evolution. In this paper, we report the most compelling evidence steadily accumulating on the successful application of NGS-based ctDNA analysis in cancer diagnosis, treatment decision, and monitoring of cancer progression. We also propose a mathematical model that calculates MAF evolution in relation to time.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mauro Buono
- School of Specialization in Medical Physics, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy.
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13
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Russo A, Incorvaia L, Del Re M, Malapelle U, Capoluongo E, Gristina V, Castiglia M, Danesi R, Fassan M, Giuffrè G, Gori S, Marchetti A, Normanno N, Pinto C, Rossi G, Santini D, Sartore-Bianchi A, Silvestris N, Tagliaferri P, Troncone G, Cinieri S, Beretta GD. The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM-SIAPEC-IAP-SIBioC-SIC-SIF Italian Scientific Societies. ESMO Open 2021; 6:100164. [PMID: 34091263 PMCID: PMC8182269 DOI: 10.1016/j.esmoop.2021.100164] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 02/08/2023] Open
Abstract
The term liquid biopsy (LB) refers to the use of various biological fluids as a surrogate for neoplastic tissue to achieve information for diagnostic, prognostic and predictive purposes. In the current clinical practice, LB is used for the identification of driver mutations in circulating tumor DNA derived from both tumor tissue and circulating neoplastic cells. As suggested by a growing body of evidence, however, there are several clinical settings where biological samples other than tissue could be used in the routine practice to identify potentially predictive biomarkers of either response or resistance to targeted treatments. New applications are emerging as useful clinical tools, and other blood derivatives, such as circulating tumor cells, circulating tumor RNA, microRNAs, platelets, extracellular vesicles, as well as other biofluids such as urine and cerebrospinal fluid, may be adopted in the near future. Despite the evident advantages compared with tissue biopsy, LB still presents some limitations due to both biological and technological issues. In this context, the absence of harmonized procedures corresponds to an unmet clinical need, ultimately affecting the rapid implementation of LB in clinical practice. In this position paper, based on experts’ opinions, the AIOM–SIAPEC-IAP–SIBIOC–SIF Italian Scientific Societies critically discuss the most relevant technical issues of LB, the current and emerging evidences, with the aim to optimizing the applications of LB in the clinical setting. In the current clinical practice LB is used for the identification of driver mutations in circulating tumor DNA (ctDNA). New applications in tumors other than non-small-cell lung cancer (NSCLC) are emerging as useful clinical tools. Other blood derivatives, together with other biofluids, are an active field of research and may be adopted in the near future. Despite the evident advantages, liquid biopsy still presents limitations due to both biological and technological issues. Standardization of the procedures needs to be addressed to ensure widespread implementation in clinical practice.
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Affiliation(s)
- A Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy.
| | - L Incorvaia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - M Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - U Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - E Capoluongo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; CEINGE, Biotecnologie Avanzate, Naples, Italy
| | - V Gristina
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - M Castiglia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - R Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - M Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, Italy; Veneto Institute of Oncology (IOV-IRCCS), Padua, Italy
| | - G Giuffrè
- Department of Human Pathology in Adult and Developmental Age 'Gaetano Barresi', Section of Pathology, University of Messina, Messina, Italy
| | - S Gori
- Department of Oncology, IRCCS Ospedale Sacro Cuore Don Calabria, Negrar di Valpolicella, Italy
| | - A Marchetti
- Center of Predictive Molecular Medicine, University-Foundation, CeSI Biotech Chieti, Chieti, Italy
| | - N Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy
| | - C Pinto
- Medical Oncology Unit, Clinical Cancer Centre, IRCCS-AUSL di Reggio Emilia, Reggio Emilia, Italy
| | - G Rossi
- Pathology Unit, Ospedale Santa Maria Delle Croci, Ravenna, Italy
| | - D Santini
- Department of Medical Oncology, University Campus Biomedico, Rome, Italy
| | - A Sartore-Bianchi
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - N Silvestris
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori 'Giovanni Paolo II' of Bari, Bari, Italy; Department of Biomedical Sciences and Human Oncology, Aldo Moro University of Bari, Bari, Italy
| | - P Tagliaferri
- Medical and Translational Oncology Unit, Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro, Italy
| | - G Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - S Cinieri
- Medical Oncology Division and Breast Unit, Senatore Antonio Perrino Hospital, ASL Brindisi, Brindisi, Italy
| | - G D Beretta
- Department of Oncology, Humanitas Gavazzeni, Bergamo, Italy
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14
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Park S, Lee JC, Choi CM. Clinical Applications of Liquid Biopsy in Non-Small Cell Lung Cancer Patients: Current Status and Recent Advances in Clinical Practice. J Clin Med 2021; 10:2236. [PMID: 34064038 PMCID: PMC8196764 DOI: 10.3390/jcm10112236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/15/2021] [Accepted: 05/18/2021] [Indexed: 01/10/2023] Open
Abstract
Recent advances in targeted and immune therapies have enabled tailored treatment strategies for advanced lung cancer. Identifying and understanding the genomic alterations that arise in the course of tumor evolution has become hugely valuable, but tissue biopsies are often insufficient for representing the whole cancer genome due to tumor heterogeneity. A liquid biopsy refers to the isolation and analysis of any tumor-derived material in the blood, and recent studies of this material have mostly focused on cell-free tumor DNA (ctDNA) in plasma. Indeed, liquid biopsy analysis is now expected to expand in utility and scope in clinical practice. In this review, we assess the biology and technical aspects of ctDNA analysis and discuss how it is currently applied in the clinic. Key points: Liquid biopsy is a potentially powerful tool in the era of personalized medicine for guiding targeted therapies in non-small cell lung cancer.
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Affiliation(s)
- Shinhee Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea;
| | - Jae-Cheol Lee
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
| | - Chang-Min Choi
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
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15
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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: 5] [Impact Index Per Article: 1.7] [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.
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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
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16
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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.
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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
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17
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Applications of liquid biopsy in the Pharmacological Audit Trail for anticancer drug development. Nat Rev Clin Oncol 2021; 18:454-467. [PMID: 33762744 DOI: 10.1038/s41571-021-00489-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 02/06/2023]
Abstract
Anticancer drug development is a costly and protracted activity, and failure at late phases of clinical testing is common. We have previously proposed the Pharmacological Audit Trail (PhAT) intended to improve the efficiency of drug development, with a focus on the use of tumour tissue-based biomarkers. Blood-based 'liquid biopsy' approaches, such as targeted or whole-genome sequencing studies of plasma circulating cell-free tumour DNA (ctDNA) and circulating tumour cells (CTCs), are of increasing relevance to this drug development paradigm. Liquid biopsy assays can provide quantitative and qualitative data on prognostic, predictive, pharmacodynamic and clinical response biomarkers, and can also enable the characterization of disease evolution and resistance mechanisms. In this Perspective, we examine the promise of integrating liquid biopsy analyses into the PhAT, focusing on the current evidence, advances, limitations and challenges. We emphasize the continued importance of analytical validation and clinical qualification of circulating tumour biomarkers through prospective clinical trials.
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Current treatment and future challenges in ROS1- and ALK-rearranged advanced non-small cell lung cancer. Cancer Treat Rev 2021; 95:102178. [PMID: 33743408 DOI: 10.1016/j.ctrv.2021.102178] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
Non─small cell lung cancer (NSCLC) presents different druggable genetic abnormalities, including ROS1 and ALK rearrangements, which share relevant clinical features and therapeutic strategies. The homology between the tyrosine kinase domains of ROS1 and ALK defines unique subsets of patients highly sensitive to targeted tyrosine kinase inhibitors (TKIs). Genomic profiling in advanced NSCLC is standard, immunohistochemistry and fluorescence in situ hybridization being the main techniques used to detect genomic rearrangements. Personalized treatment with TKIs in ROS1- and ALK-positive NSCLC patients has dramatically improved patients' outcomes. Crizotinib has been the first-line standard of care treatment in ALK-rearranged NSCLC patients for a long time, while crizotinib still represents the best upfront therapeutic option in ROS1-positive NSCLC patients, followed by next-generation TKIs at the time of disease progression. However, the improved intracranial efficacy of next-generation TKIs has led to these drugs becoming first-line options, widening treatment opportunities for these patients. Since all patients will develop disease progression under TKI therapy, understanding the mechanisms of acquired resistance is crucial to define the optimal sequential therapeutic strategy. Despite the positive correlation between personalized treatment and patients' outcome, access to next-generation TKIs and genomic profiling at the time of disease progression are major challenges to achieving this goal. In this review, we present updated evidence on ROS1- and ALK-rearranged NSCLC regarding epidemiology and diagnostics, current therapies and the most suitable sequential treatment approaches, as well as mechanisms of acquired resistance and strategies to overcome them.
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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: 23] [Impact Index Per Article: 7.7] [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.
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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
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20
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Alexander M, Kim SY, Cheng H. Update 2020: Management of Non-Small Cell Lung Cancer. Lung 2020; 198:897-907. [PMID: 33175991 PMCID: PMC7656891 DOI: 10.1007/s00408-020-00407-5] [Citation(s) in RCA: 238] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/02/2020] [Indexed: 12/19/2022]
Abstract
The past decade has seen a revolution of new advances in the management of non-small cell lung cancer (NSCLC) with remarkable progresses in screening, diagnosis, and treatment. The advances in systemic treatment have been driven primarily by the development of molecularly targeted therapeutics, immune checkpoint inhibitors, and anti-angiogenic agents, all of which have transformed this field with significantly improved patient outcomes. This review will address updates in lung cancer screening, liquid biopsy, and immunotherapy in the front-line setting. We discuss recent advances and highlight the plethora of new approvals of molecular-targeted therapy for subgroups of NSCLC patients with sensitizing EGFR, ALK, ROS1, RET, BRAF V600E, MET, and NTRK alterations.
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Affiliation(s)
- Mariam Alexander
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - So Yeon Kim
- Department of Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Haiying Cheng
- Department of Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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21
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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.
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22
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Clinical and analytical validation of FoundationOne Liquid CDx, a novel 324-Gene cfDNA-based comprehensive genomic profiling assay for cancers of solid tumor origin. PLoS One 2020; 15:e0237802. [PMID: 32976510 PMCID: PMC7518588 DOI: 10.1371/journal.pone.0237802] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/30/2020] [Indexed: 12/25/2022] Open
Abstract
As availability of precision therapies expands, a well-validated circulating cell-free DNA (cfDNA)-based comprehensive genomic profiling assay has the potential to provide considerable value as a complement to tissue-based testing to ensure potentially life-extending therapies are administered to patients most likely to benefit. Additional data supporting the clinical validity of cfDNA-based testing is necessary to inform optimal use of these assays in the clinic. The FoundationOne®Liquid CDx assay is a pan-cancer cfDNA-based comprehensive genomic profiling assay that was recently approved by FDA. Validation studies included >7,500 tests and >30,000 unique variants across >300 genes and >30 cancer types. Clinical validity results across multiple tumor types are presented. Additionally, results demonstrated a 95% limit of detection of 0.40% variant allele fraction for select substitutions and insertions/deletions, 0.37% variant allele fraction for select rearrangements, 21.7% tumor fraction for copy number amplifications, and 30.4% TF for copy number losses. The limit of detection for microsatellite instability and blood tumor mutational burden were also determined. The false positive variant rate was 0.013% (approximately 1 in 8,000). Reproducibility of variant calling was 99.59%. In comparison with an orthogonal method, an overall positive percent agreement of 96.3% and negative percent agreement of >99.9% was observed. These study results demonstrate that FoundationOne Liquid CDx accurately and reproducibly detects the major types of genomic alterations in addition to complex biomarkers such as microsatellite instability, blood tumor mutational burden, and tumor fraction. Critically, clinical validity data is presented across multiple cancer types.
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Madison R, Schrock AB, Castellanos E, Gregg JP, Snider J, Ali SM, Miller VA, Singal G, Alexander BM, Venstrom JM, Chung JH. Retrospective analysis of real-world data to determine clinical outcomes of patients with advanced non-small cell lung cancer following cell-free circulating tumor DNA genomic profiling. Lung Cancer 2020; 148:69-78. [PMID: 32823229 DOI: 10.1016/j.lungcan.2020.07.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/12/2020] [Accepted: 07/27/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Liquid biopsy and comprehensive genomic profiling (CGP) of circulating tumor DNA (ctDNA) are increasingly used for detection of targetable genomic alterations (GA) in non-small cell lung cancer (NSCLC). To examine the clinical outcomes for patients following CGP using liquid biopsy versus tissue biopsy, receipt of matched targeted therapy post-CGP and associated outcomes were evaluated in the real-world setting. METHODS 6491 patients with NSCLC and liquid biopsy (N = 937 tests) and/or tissue (N = 5582 tests) CGP were included in a de-identified commercial clinico-genomic database. Targetable GAs included National Comprehensive Cancer Network NSCLC guideline biomarkers. Clinical characteristics, real-world progression, and real-world response (rwR) were obtained via technology-enabled abstraction of clinician notes and radiology/pathology reports. RESULTS At the time of liquid biopsy CGP, 53% (496/937) of patients were documented to have received ≥1 line of prior therapy (tissue CGP: 13%, 735/5582). 90% (832/928) of liquid biopsy cases had evidence of ctDNA. A targetable GA was detected in 20% (188/937) of liquid biopsy and 22% (1215/5582) of tissue CGP cases. Use of matched targeted therapy overall was similar post-liquid biopsy or post-tissue CGP but varied considerably across emerging (25%, 79/317) versus standard of care (SOC) (74%, 475/640) GA. Real-world-progression free survival for patients receiving SOC first line matched targeted therapy administered following liquid biopsy (n = 33) and tissue (n = 229) CGP were similar (13.8 vs 10.6 months; aHR = 0.68 [0.36-1.26]). Among patients evaluated for rwR, overall response rate (partial/complete response) to matched targeted therapy post-liquid biopsy CGP was 75% (39/52) versus 66% post-tissue CGP (254/385, P = 0.51). CONCLUSION Retrospective analysis of real-world clinico-genomic data demonstrated that clinical outcomes on matched targeted therapy were similar following liquid biopsy and tissue CGP in NSCLC, which suggests routine clinical use of liquid biopsy CGP can reliably guide therapy selection.
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Rolfo C, Cardona AF, Cristofanilli M, Paz-Ares L, Diaz Mochon JJ, Duran I, Raez LE, Russo A, Lorente JA, Malapelle U, Gil-Bazo I, Jantus-Lewintre E, Pauwels P, Mok T, Serrano MJ. Challenges and opportunities of cfDNA analysis implementation in clinical practice: Perspective of the International Society of Liquid Biopsy (ISLB). Crit Rev Oncol Hematol 2020; 151:102978. [PMID: 32428812 DOI: 10.1016/j.critrevonc.2020.102978] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023] Open
Abstract
Precision medicine was born with the development of new diagnostic techniques and targeted drugs, yielding better outcomes in cancer care. With the evolution and increasing sensitivity for detecting oncogenic drivers, liquid biopsies (LBs), specifically cell-free DNA (cfDNA) analysis, have been proposed as a minimally-invasive technique for genomic profiling. Ranging from sequencing techniques to PCR-based methods and other more complex strategies, this approach, currently applicable in some solid tumors with robust evidence, is showing promising opportunities in other cancers. However, difficulties in validating their clinical utility exist within limitation at different levels among several techniques, reporting of the results, lack of appropriate clinical trial designs, and unknown economic impact. One of the aims of the ISLB is to create recommendations to develop reliable and sustainable diagnostic, prognostic and predictive tools using LBs. This paper is addressing these objectives, helping the healthcare providers and scientific community to understand the potential of LB.
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Affiliation(s)
- Christian Rolfo
- Thoracic Oncology Department and Early Phase Clinical Trials Section, School of Medicine, Maryland University, Maryland, USA.
| | - Andrés F Cardona
- Clinical and Translational Oncology Group, Clínica del Country, Bogotá, Colombia; Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia; Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia
| | - Massimo Cristofanilli
- Department of Medicine, Division of Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, 710 N Fairbanks Court, Suite 8-250A, Chicago, IL, 60611, USA
| | - Luis Paz-Ares
- Hospital Universitario 12 de Octubre, CNIO-H12o Lung Cancer Unit, Universidad Complutense and CIBERONC, Madrid, Spain
| | - Juan Jose Diaz Mochon
- DestiNA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, 18016, Armilla, Granada, Spain; GENYO Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. PTS Granada - Avenida de la Ilustración, 114- 18016, Granada, Spain; Department Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain
| | - Ignacio Duran
- Servicio de Oncologia Medica, Medical Oncology Department, Hospital Universitario Marques de Valdecilla, Edificio Sur, 2 Planta, Despacho 277, 39008, Santander, Spain
| | - Luis E Raez
- Memorial Cancer Institute, Memorial Health Care System, Florida International University, Florida, USA
| | - Alessandro Russo
- Thoracic Oncology Department and Early Phase Clinical Trials Section, School of Medicine, Maryland University, Maryland, USA; Medical Oncology Unit A.O. Papardo & Department of Human Pathology, University of Messina, Italy
| | - Jose A Lorente
- Laboratory of Genetic Identification, Department of Legal Medicine, University of Granada, Av. de la Investigación, 11, 18071, Granada, Spain; Centre for Genomics and Oncological Research - GENYO, Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Umberto Malapelle
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - Ignacio Gil-Bazo
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Navarra, Spain; University of Navarra, Center for Applied Medical Research, Program of Solid Tumors, Pamplona, Navarra, Spain; Idisna, Navarra Institute for Health Research, Pamplona, Navarra, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Eloisa Jantus-Lewintre
- Molecular Oncology Laboratory, Fundación Investigación, Valencia General University Hospital, Valencia, Spain
| | - Patrick Pauwels
- Center for Oncological Research (CORE), University of Antwerp, & Department of Pathology, Antwerp University Hospital, Edegem, Belgium
| | - Tony Mok
- State Key Laboratory in Oncology in South China, Hong Kong, China
| | - María José Serrano
- Centre for Genomics and Oncological Research - GENYO, Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain; Bio-Health Research Institute (Instituto de Investigación Biosanitaria ibs. GRANADA), Spain; Complejo Hospitalario Universitario Granada (CHUG), Department of Medical Oncology, University of Granada, Granada, Spain.
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25
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Makarem M, Leighl NB. Molecular testing for lung adenocarcinoma: Is it time to adopt a "plasma-first" approach? Cancer 2020; 126:3176-3180. [PMID: 32365225 DOI: 10.1002/cncr.32875] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/11/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Maisam Makarem
- Division of Medical Oncology, Princess Margaret Cancer Center, University of Toronto, Toronto, Ontario, Canada
| | - Natasha B Leighl
- Division of Medical Oncology, Princess Margaret Cancer Center, University of Toronto, Toronto, Ontario, Canada
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Heeke S, Hofman V, Ilié M, Allegra M, Lespinet V, Bordone O, Benzaquen J, Boutros J, Poudenx M, Lalvée S, Tanga V, Salacroup C, Bonnetaud C, Marquette CH, Hofman P. Prospective evaluation of NGS-based liquid biopsy in untreated late stage non-squamous lung carcinoma in a single institution. J Transl Med 2020; 18:87. [PMID: 32066459 PMCID: PMC7027049 DOI: 10.1186/s12967-020-02259-2] [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: 11/30/2019] [Accepted: 02/05/2020] [Indexed: 01/05/2023] Open
Abstract
Background NGS from plasma samples in non-squamous cell lung carcinoma (NSCC) can aid in the detection of actionable genomic alterations. However, the absolute clinical value of NGS in liquid biopsy (LB) made at baseline is currently uncertain. We assessed the impact of plasma-based NGS using an in-house test and an outsourced test in comparison to a routine molecular pathology workflow. Methods Twenty-four advanced/metastatic treatment-naïve NSCC patients were prospectively included. NGS analyses were conducted both in-house using the Oncomine cfTNA Panel and in an external testing center using the Foundation Liquid assay. NGS analysis and/or specific molecular based assays were conducted in parallel on tissue or cytological samples. Results Both LB tests were well correlated. Tissue NGS results were obtained in 67% of patients and demonstrated good correlation with LB assays. Activating EGFR mutations were detected using LB tests in three patients. PD-L1 expression assessed in tissue sections enabled the initiation of pembrolizumab treatment in five patients. Conclusion NGS from LB is feasible in routine clinical practice using an in-house or an outsourced test at baseline. However, the impact on therapy selection was limited in this small series of patients and LB was not able to replace tissue-based testing in our hands.
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Affiliation(s)
- Simon Heeke
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France.,Hospital-related Biobank (BB-00033-0025), Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France.,FHU OncoAge, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France
| | - Véronique Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France.,Hospital-related Biobank (BB-00033-0025), Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France.,FHU OncoAge, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France.,Hospital-related Biobank (BB-00033-0025), Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France.,FHU OncoAge, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France
| | - Maryline Allegra
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France
| | - Virginie Lespinet
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France
| | - Olivier Bordone
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France
| | - Jonathan Benzaquen
- FHU OncoAge, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France.,Pulmonary Department, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France
| | - Jacques Boutros
- Pulmonary Department, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France
| | - Michel Poudenx
- FHU OncoAge, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France.,Pulmonary Department, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France
| | - Salomé Lalvée
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France
| | - Virginie Tanga
- Hospital-related Biobank (BB-00033-0025), Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France
| | - Carole Salacroup
- Hospital-related Biobank (BB-00033-0025), Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France
| | - Christelle Bonnetaud
- Hospital-related Biobank (BB-00033-0025), Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France
| | - Charles-Hugo Marquette
- FHU OncoAge, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France. .,Pulmonary Department, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France.
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France. .,Hospital-related Biobank (BB-00033-0025), Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France. .,FHU OncoAge, Pasteur Hospital, Université Côte d'Azur, 30 Avenue de la Voie Romaine, 06000, Nice, France.
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