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La Salvia A, Meyer ML, Hirsch FR, Kerr KM, Landi L, Tsao MS, Cappuzzo F. Rediscovering immunohistochemistry in lung cancer. Crit Rev Oncol Hematol 2024; 200:104401. [PMID: 38815876 DOI: 10.1016/j.critrevonc.2024.104401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024] Open
Abstract
Several observations indicate that protein expression analysis by immunohistochemistry (IHC) remains relevant in individuals with non-small-cell lung cancer (NSCLC) when considering targeted therapy, as an early step in diagnosis and for therapy selection. Since the advent of next-generation sequencing (NGS), the role of IHC in testing for NSCLC biomarkers has been forgotten or ignored. We discuss how protein-level investigations maintain a critical role in defining sensitivity to lung cancer therapies in oncogene- and non-oncogene-addicted cases and in patients eligible for immunotherapy, suggesting that IHC testing should be reconsidered in clinical practice. We also argue how a panel of IHC tests should be considered complementary to NGS and other genomic assays. This is relevant to current clinical diagnostic practice but with potential future roles to optimize the selection of patients for innovative therapies. At the same time, strict validation of antibodies, assays, scoring systems, and intra- and interobserver reproducibility is needed.
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Affiliation(s)
- Anna La Salvia
- National Center for Drug Research and Evaluation, National Institute of Health (ISS), Rome 00161, Italy
| | - May-Lucie Meyer
- Center for Thoracic Oncology/Tisch Cancer Institute and Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fred R Hirsch
- Center for Thoracic Oncology/Tisch Cancer Institute and Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Keith M Kerr
- Aberdeen University School of Medicine & Aberdeen Royal Infirmary, Aberdeen, UK
| | - Lorenza Landi
- Medical Oncology, Istituto Nazionale Tumori IRCCS "Regina Elena", Rome, Italy
| | - Ming-Sound Tsao
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Federico Cappuzzo
- Medical Oncology, Istituto Nazionale Tumori IRCCS "Regina Elena", Rome, Italy.
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2
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Trifonova OP, Maslov DL, Balashova EE, Lokhov PG. Current State and Future Perspectives on Personalized Metabolomics. Metabolites 2023; 13:metabo13010067. [PMID: 36676992 PMCID: PMC9863827 DOI: 10.3390/metabo13010067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Metabolomics is one of the most promising 'omics' sciences for the implementation in medicine by developing new diagnostic tests and optimizing drug therapy. Since in metabolomics, the end products of the biochemical processes in an organism are studied, which are under the influence of both genetic and environmental factors, the metabolomics analysis can detect any changes associated with both lifestyle and pathological processes. Almost every case-controlled metabolomics study shows a high diagnostic accuracy. Taking into account that metabolomics processes are already described for most nosologies, there are prerequisites that a high-speed and comprehensive metabolite analysis will replace, in near future, the narrow range of chemical analyses used today, by the medical community. However, despite the promising perspectives of personalized metabolomics, there are currently no FDA-approved metabolomics tests. The well-known problem of complexity of personalized metabolomics data analysis and their interpretation for the end-users, in addition to a traditional need for analytical methods to address the quality control, standardization, and data treatment are reported in the review. Possible ways to solve the problems and change the situation with the introduction of metabolomics tests into clinical practice, are also discussed.
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Garcia-Pardo M, Czarnecka K, Law JH, Salvarrey A, Fernandes R, Fan J, Corke L, Waddell TK, Yasufuku K, Donahoe LL, Pierre A, Le LW, Ghumman N, Liu G, Shepherd FA, Bradbury P, Sacher A, Stockley T, Pal P, Rogalla P, Tsao MS, Leighl NB. Plasma-first: accelerating lung cancer diagnosis and molecular profiling through liquid biopsy. Ther Adv Med Oncol 2022; 14:17588359221126151. [PMID: 36158638 PMCID: PMC9500258 DOI: 10.1177/17588359221126151] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/26/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction: Molecular profiling of tumor tissue is the gold standard for treatment decision-making in advanced non-small cell lung cancer (NSCLC). Results may be delayed or unavailable due to insufficient tissue, prolonged wait times for biopsy, pathology assessment and testing. We piloted the use of plasma testing in the initial diagnostic workup for patients with suspected advanced lung cancer. Methods: Patients with ⩽15 pack-year smoking history and suspected advanced lung cancer referred to the lung cancer rapid diagnostic program underwent plasma circulating-tumor DNA testing using a DNA-based mutation panel. Tissue testing was performed per standard of care, including comprehensive next-generation sequencing (NGS). The primary endpoint was time from diagnostic program referral to cancer treatment in stage IV NSCLC patients (Cohort A) compared to a contemporary cohort not enrolled in the study (Cohort B) and an historical pre-COVID cohort referred to the program between 2018 and 2019 (Cohort C). Results: From January to June 2021, 20 patients were enrolled in Cohort A; median age was 70.5 years (range 33–87), 70% were female, 55% Caucasian, 85% never smokers, and 75% were diagnosed with NSCLC. Seven had actionable alterations detected in plasma or tissue (4/7 concordant). Fusions, not tested in plasma, were identified by immunohistochemistry for three patients. Mean result turnaround time was 17.8 days for plasma NGS and 23.6 days for tissue (p = 0.10). Mean time from referral to treatment initiation was significantly shorter in cohort A at 32.6 days (SD 13.1) versus 62.2 days (SD 31.2) in cohort B and 61.5 days (SD 29.1) in cohort C, both p < 0.0001. Conclusion: Liquid biopsy in the initial diagnostic workup of patients with suspected advanced NSCLC can lead to faster molecular results and shorten time to treatment even with smaller DNA panels. An expansion study using comprehensive NGS plasma testing with faster turnaround time is ongoing (NCT04862924).
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Affiliation(s)
- Miguel Garcia-Pardo
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Kasia Czarnecka
- Division of Respirology, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Jennifer H Law
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Alexandra Salvarrey
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, CanadaDivision of Thoracic Surgery, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Roxanne Fernandes
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jason Fan
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lucy Corke
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Thomas K Waddell
- Division of Thoracic Surgery, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Kazuhiro Yasufuku
- Division of Thoracic Surgery, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Laura L Donahoe
- Division of Thoracic Surgery, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Andrew Pierre
- Division of Thoracic Surgery, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Lisa W Le
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Noor Ghumman
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Geoffrey Liu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Frances A Shepherd
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Penelope Bradbury
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Adrian Sacher
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Tracy Stockley
- Department of Laboratory Medicine and Pathobiology, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Prodipto Pal
- Department of Laboratory Medicine and Pathobiology, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Patrik Rogalla
- Joint Department of Medical Imaging, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Ming Sound Tsao
- Department of Laboratory Medicine and Pathobiology, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Natasha B Leighl
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, 7-913 700 University Avenue, Toronto, ON M5G 1Z5, Canada
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4
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Upfront Next Generation Sequencing in Non-Small Cell Lung Cancer. Curr Oncol 2022; 29:4428-4437. [PMID: 35877212 PMCID: PMC9319994 DOI: 10.3390/curroncol29070352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 12/04/2022] Open
Abstract
In advanced non-small cell lung cancer (NSCLC), patients with actionable genomic alterations may derive additional clinical benefit from targeted treatment compared to cytotoxic chemotherapy. Current guidelines recommend extensive testing with next generation sequencing (NGS) panels. We investigated the impact of using a targeted NGS panel (TruSight Tumor 15, Illumina) as reflex testing for NSCLC samples at a single institution. Molecular analysis examined 15 genes for hotspot mutation variants, including AKT1, BRAF, EGFR, ERBB2, FOXL2, GNA11, GNAQ, KIT, KRAS, MET, NRAS, PDGFRA, PIK3CA, RET and TP53 genes. Between February 2017 and October 2020, 1460 samples from 1395 patients were analyzed. 1201 patients (86.1%) had at least one variant identified, most frequently TP53 (47.5%), KRAS (32.2%) or EGFR (24.2%). Among these, 994 patients (71.3%) had clinically relevant variants eligible for treatment with approved therapies or clinical trial enrollment. The incremental cost of NGS beyond single gene testing (EGFR, ALK) was CAD $233 per case. Reflex upfront NGS identified at least one actionable variant in more than 70% of patients with NSCLC, with minimal increase in testing cost. Implementation of NGS panels remains essential as treatment paradigms continue to evolve.
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Makarem M, Ezeife DA, Smith AC, Li JJN, Law JH, Tsao MS, Leighl NB. Reflex ROS1 IHC Screening with FISH Confirmation for Advanced Non-Small Cell Lung Cancer-A Cost-Efficient Strategy in a Public Healthcare System. Curr Oncol 2021; 28:3268-3279. [PMID: 34449580 PMCID: PMC8395515 DOI: 10.3390/curroncol28050284] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 12/11/2022] Open
Abstract
ROS1 rearrangements are identified in 1-2% of lung adenocarcinoma cases, and reflex testing is guideline-recommended. We developed a decision model for population-based ROS1 testing from a Canadian public healthcare perspective to determine the strategy that optimized detection of true-positive (TP) cases while minimizing costs and turnaround time (TAT). Eight diagnostic strategies were compared, including reflex single gene testing via immunohistochemistry (IHC) screening, fluorescence in-situ hybridization (FISH), next-generation sequencing (NGS), and biomarker-informed (EGFR/ALK/KRAS wildtype) testing initiated by pathologists and clinician-initiated strategies. Reflex IHC screening with FISH confirmation of positive cases yielded the best results for TAT, TP detection rate, and cost. IHC screening saved CAD 1,000,000 versus reflex FISH testing. NGS was the costliest reflex strategy. Biomarker-informed testing was cost-efficient but delayed TAT. Clinician-initiated testing was the least costly but resulted in long TAT and missed TP cases, highlighting the importance of reflex testing. Thus, reflex IHC screening for ROS1 with FISH confirmation provides a cost-efficient strategy with short TAT and maximizes the number of TP cases detected.
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Affiliation(s)
- Maisam Makarem
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; (M.M.); (A.C.S.); (J.J.N.L.); (J.H.L.); (M.-S.T.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Doreen A. Ezeife
- Tom Baker Cancer Centre, University of Calgary, Calgary, AB T2N 4N2, Canada;
| | - Adam C. Smith
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; (M.M.); (A.C.S.); (J.J.N.L.); (J.H.L.); (M.-S.T.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Janice J. N. Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; (M.M.); (A.C.S.); (J.J.N.L.); (J.H.L.); (M.-S.T.)
| | - Jennifer H. Law
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; (M.M.); (A.C.S.); (J.J.N.L.); (J.H.L.); (M.-S.T.)
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; (M.M.); (A.C.S.); (J.J.N.L.); (J.H.L.); (M.-S.T.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Natasha B. Leighl
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; (M.M.); (A.C.S.); (J.J.N.L.); (J.H.L.); (M.-S.T.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
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Lichtenberg S, Trifonova OP, Maslov DL, Balashova EE, Lokhov PG. Metabolomic Laboratory-Developed Tests: Current Status and Perspectives. Metabolites 2021; 11:423. [PMID: 34206934 PMCID: PMC8305461 DOI: 10.3390/metabo11070423] [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: 05/31/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
Laboratory-developed tests (LDTs) are a subset of in vitro diagnostic devices, which the US Food and Drug Administration defines as "tests that are manufactured by and used within a single laboratory". The review describes the emergence and history of LDTs. The current state and development prospects of LDTs based on metabolomics are analyzed. By comparing LDTs with the scientific metabolomics study of human bio samples, the characteristic features of metabolomic LDT are shown, revealing its essence, strengths, and limitations. The possibilities for further developments and scaling of metabolomic LDTs and their potential significance for healthcare are discussed. The legal aspects of LDT regulation in the United States, European Union, and Singapore, demonstrating different approaches to this issue, are also provided. Based on the data presented in the review, recommendations were made on the feasibility and ways of further introducing metabolomic LDTs into practice.
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Affiliation(s)
- Steven Lichtenberg
- Metabometrics, Inc., 651 N Broad St, Suite 205 #1370, Middletown, DE 19709, USA
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Oxana P. Trifonova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Dmitry L. Maslov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Elena E. Balashova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Petr G. Lokhov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
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7
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Hwang DM, Albaqer T, Santiago RC, Weiss J, Tanguay J, Cabanero M, Leung Y, Pal P, Khan Z, Lau SCM, Sacher A, Torlakovic E, Cheung C, Tsao MS. Prevalence and Heterogeneity of PD-L1 Expression by 22C3 Assay in Routine Population-Based and Reflexive Clinical Testing in Lung Cancer. J Thorac Oncol 2021; 16:1490-1500. [PMID: 33915250 DOI: 10.1016/j.jtho.2021.03.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/22/2021] [Accepted: 03/30/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Programmed death-ligand 1 (PD-L1) is used as a biomarker for anti-programmed cell death protein-1 (PD-1) or anti-PD-L1 immunotherapies in NSCLC. We report here the results of population-based PD-L1 testing using the 22C3 IHC pharmDx Assay (Agilent Technologies) in a large Canadian regional reference pathology laboratory. METHODS Testing was conducted reflexively on biopsies and resections for NSCLC during an 8-month period. Tumor proportion score (TPS) cutoffs for low and high expression were 1% and 50%, respectively. RESULTS Altogether, 2031 PD-L1 tests were performed on specimens from 1795 patients, with 107 inconclusive results (5.3%). Excluding cases with inconclusive/missing data, proportions for the remaining 1713 patients were 41.6% for TPS less than 1%, 28.6% for TPS 1% to 49%, and 29.8% for TPS greater than or equal to 50%. Higher PD-L1 expression rates were noted in EGFR wild-type versus mutant tumors (p < 0.001), squamous versus adenocarcinoma (p < 0.001), and metastatic versus primary tumors (p < 0.001). PD-L1 among 103 patients with paired biopsy and resection specimens revealed moderate concordance (κ = 0.67). A total of 52% (25 of 48) of biopsies with TPS less than 1% had TPS greater than 1% in resection, whereas 84.6% (22 of 26) of biopsies with TPS greater than or equal to 50% were concordant in resected tumors. Discordance rates between biopsy and resection were 71.4% for biopsies with less than 8 mm2 total area, compared with 33.3% for biopsies with greater than or equal to 8 mm2 area (p < 0.026). Concordance among 27 patients with paired primary lung and metastatic tumor biopsies revealed only weak concordance (κ = 0.48). CONCLUSIONS Intratumoral heterogeneity of PD-L1 expression may result in misclassification of PD-L1 status in a substantial proportion of PD-L1-negative small biopsy samples. Biopsy of metastatic site may increase proportion of patients with high PD-L1 expression.
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Affiliation(s)
- David M Hwang
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine & Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Tahani Albaqer
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Pathology, Kuwait Cancer Control Center, Kuwait City, Kuwait
| | - Rex C Santiago
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Institute of Pathology, St. Luke's Medical Center, Quezon City, Philippines
| | - Jessica Weiss
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jeffrey Tanguay
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Michael Cabanero
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Yuki Leung
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Prodipto Pal
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Zanobia Khan
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Sally C M Lau
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Adrian Sacher
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Emina Torlakovic
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Pathology and Laboratory Medicine, Saskatchewan Health Authority and College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Carol Cheung
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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8
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Lokhov PG, Maslov DL, Lichtenberg S, Trifonova OP, Balashova EE. Holistic Metabolomic Laboratory-Developed Test (LDT): Development and Use for the Diagnosis of Early-Stage Parkinson's Disease. Metabolites 2020; 11:metabo11010014. [PMID: 33383698 PMCID: PMC7824177 DOI: 10.3390/metabo11010014] [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: 10/09/2020] [Revised: 12/24/2020] [Accepted: 12/24/2020] [Indexed: 02/04/2023] Open
Abstract
A laboratory-developed test (LDT) is a type of in vitro diagnostic test that is developed and used within a single laboratory. The holistic metabolomic LDT integrating the currently available data on human metabolic pathways, changes in the concentrations of low-molecular-weight compounds in the human blood during diseases and other conditions, and their prevalent location in the body was developed. That is, the LDT uses all of the accumulated metabolic data relevant for disease diagnosis and high-resolution mass spectrometry with data processing by in-house software. In this study, the LDT was applied to diagnose early-stage Parkinson's disease (PD), which currently lacks available laboratory tests. The use of the LDT for blood plasma samples confirmed its ability for such diagnostics with 73% accuracy. The diagnosis was based on relevant data, such as the detection of overrepresented metabolite sets associated with PD and other neurodegenerative diseases. Additionally, the ability of the LDT to detect normal composition of low-molecular-weight compounds in blood was demonstrated, thus providing a definition of healthy at the molecular level. This LDT approach as a screening tool can be used for the further widespread testing for other diseases, since 'omics' tests, to which the metabolomic LDT belongs, cover a variety of them.
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Affiliation(s)
- Petr G. Lokhov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (D.L.M.); (O.P.T.); (E.E.B.)
- Correspondence:
| | - Dmitry L. Maslov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (D.L.M.); (O.P.T.); (E.E.B.)
| | - Steven Lichtenberg
- Metabometrics, Inc, 651 N Broad St, Suite 205 #1370, Middletown, DE 19709, USA;
| | - Oxana P. Trifonova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (D.L.M.); (O.P.T.); (E.E.B.)
| | - Elena E. Balashova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (D.L.M.); (O.P.T.); (E.E.B.)
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9
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Shi R, Filho SNM, Li M, Fares A, Weiss J, Pham NA, Ludkovski O, Raghavan V, Li Q, Ravi D, Cabanero M, Moghal N, Leighl NB, Bradbury P, Sacher A, Shepherd FA, Yasufuku K, Tsao MS, Liu G. BRAF V600E mutation and MET amplification as resistance pathways of the second-generation anaplastic lymphoma kinase (ALK) inhibitor alectinib in lung cancer. Lung Cancer 2020; 146:78-85. [PMID: 32521388 DOI: 10.1016/j.lungcan.2020.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/02/2020] [Accepted: 05/12/2020] [Indexed: 01/28/2023]
Abstract
BACKGROUND Anaplastic lymphoma kinase (ALK) targeted therapies have demonstrated remarkable efficacy in ALK-positive lung adenocarcinomas. However, patients inevitably develop resistance to such therapies. To investigate novel mechanisms of resistance to second generation ALK inhibitors, we characterized and modeled ALK inhibitor resistance of ALK-positive patient-derived xenograft (PDX) models established from advanced-stage lung adenocarcinoma patients who have progressed on one or more ALK inhibitors. METHODS Whole exome sequencing was performed to identify resistance mechanisms to ALK inhibitors in PDXs generated from biopsies at the time of relapse. ALK fusion status was confirmed using fluorescent in situ hybridization, immunohistochemistry, RNA-sequencing, RT-qPCR and western blot. Targeted therapies to overcome acquired resistance were then tested on the PDX models. RESULTS Three PDX models were successfully established from biopsies of two patients who had progressed on crizotinib and/or alectinib. The PDX models recapitulated the histology and ALK status of their patient tumors, as well as their matched patients' clinical treatment outcome to ALK inhibitors. Whole exome sequencing identified MET amplification and previously unreported BRAF V600E mutation as independent mechanisms of resistance to alectinib. Importantly, PDX treatment of inhibitors specific for these targets combined with ALK inhibitor overcame resistance. CONCLUSIONS Bypass signaling pathway through c-MET and BRAF are independent mechanisms of resistance to alectinib. Individualized intervention against these resistance pathways could be viable therapeutic options in alectinib-refractory lung adenocarcinoma.
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Affiliation(s)
- Ruoshi Shi
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Sebastiao N Martins Filho
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ming Li
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Aline Fares
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jessica Weiss
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Nhu-An Pham
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Olga Ludkovski
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Vibha Raghavan
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Quan Li
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Deepti Ravi
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Michael Cabanero
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Nadeem Moghal
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Natasha B Leighl
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Penelope Bradbury
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Adrian Sacher
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Frances A Shepherd
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kazuhiro Yasufuku
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Geoffrey Liu
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada; Dalla Lana School of Public Health and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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10
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Lokhov PG, Trifonova OP, Maslov DL, Lichtenberg S, Balashova EE. Diagnosis of Parkinson's Disease by A Metabolomics-Based Laboratory-Developed Test (LDT). Diagnostics (Basel) 2020; 10:diagnostics10050332. [PMID: 32455603 PMCID: PMC7277951 DOI: 10.3390/diagnostics10050332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/29/2020] [Accepted: 05/19/2020] [Indexed: 01/02/2023] Open
Abstract
A laboratory-developed test (LDT) is a type of in vitro diagnostic test that is designed, manufactured and used in the same laboratory (i.e., an in-house test). In this study, a metabolomics-based LDT was developed. This test involves a blood plasma preparation, direct-infusion mass spectrometry analysis with a high-resolution mass spectrometer, alignment and normalization of mass peaks using original algorithms, metabolite annotation by a biochemical context-driven algorithm, detection of overrepresented metabolic pathways and results in a visualization in the form of a pathway names cloud. The LDT was applied to detect early stage Parkinson’s disease (PD)—the diagnosis of which currently requires great effort due to the lack of available laboratory tests. In a case–control study (n = 56), the LDT revealed a statistically sound pattern in the PD-relevant pathways. Usage of the LDT for individuals confirmed its ability to reveal this pattern and thus diagnose PD at the early-stage (1–2.5 stages, according to Hoehn and Yahr scale). The detection of this pattern by LDT could diagnose PD with a specificity of 64%, sensitivity of 86% and an accuracy of 75%. Thus, this LDT can be used for further widespread testing.
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Affiliation(s)
- Petr G. Lokhov
- Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
- Correspondence:
| | - Oxana P. Trifonova
- Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Dmitry L. Maslov
- Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Steven Lichtenberg
- Metabometrics, Inc., 651 N Broad St., Suite 205 #1370, Middletown, DE 19709, USA;
| | - Elena E. Balashova
- Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
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11
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Tsao MS, Yatabe Y. Old Soldiers Never Die: Is There Still a Role for Immunohistochemistry in the Era of Next-Generation Sequencing Panel Testing? J Thorac Oncol 2020; 14:2035-2038. [PMID: 31757371 DOI: 10.1016/j.jtho.2019.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Ming Sound Tsao
- Laboratory Medicine Program, Department of Pathology, University Health Network, Princess Margaret Cancer Centre and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center, Tokyo, Japan
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