1
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Ng J, Pan E, Johnston A, Ribera NT, Kersbergen A, Hess JB, Best SA, Tsui E, Steinfort D, Sutherland KD. A Multiplexed Approach to Assess Small Cell Lung Cancer Subtype Heterogeneity in Primary and Patient-Derived Tumor Samples. Methods Mol Biol 2024; 2806:117-138. [PMID: 38676800 DOI: 10.1007/978-1-0716-3858-3_10] [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] [Indexed: 04/29/2024]
Abstract
Unlocking the heterogeneity of cancers is crucial for developing therapeutic approaches that effectively eradicate disease. As our understanding of markers specific to cancer subclones or subtypes expands, there is a growing demand for advanced technologies that enable the simultaneous investigation of multiple targets within an individual tumor sample. Indeed, multiplex approaches offer distinct benefits, particularly when tumor specimens are small and scarce. Here we describe the utility of two fluorescence-based multiplex approaches; fluorescent Western blots, and multiplex immunohistochemistry (Opal™) staining to interrogate heterogeneity, using small cell lung cancer as an example. Critically, the coupling of Opal™ staining with advanced image quantitation, permits the dissection of cancer cell phenotypes at a single cell level. These approaches can be applied to patient biopsies and/or patient-derived xenograft (PDX) models and serve as powerful methodologies for assessing tumor cell heterogeneity in response to therapy or between metastatic lesions across diverse tissue sites.
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Affiliation(s)
- Jin Ng
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Emma Pan
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Alex Johnston
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Nina Tubau Ribera
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Ariena Kersbergen
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jonas B Hess
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Sarah A Best
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Ellen Tsui
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Daniel Steinfort
- Department of Medicine, The University of Melbourne, Parkville, VIC, Australia
- Department of Respiratory Medicine, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Kate D Sutherland
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
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2
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Malchers F, Nogova L, van Attekum MH, Maas L, Brägelmann J, Bartenhagen C, Girard L, Bosco G, Dahmen I, Michels S, Weeden CE, Scheel AH, Meder L, Golfmann K, Schuldt P, Siemanowski J, Rehker J, Merkelbach-Bruse S, Menon R, Gautschi O, Heuckmann JM, Brambilla E, Asselin-Labat ML, Persigehl T, Minna JD, Walczak H, Ullrich RT, Fischer M, Reinhardt HC, Wolf J, Büttner R, Peifer M, George J, Thomas RK. Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer. J Clin Invest 2023; 133:e170217. [PMID: 37606995 PMCID: PMC10617767 DOI: 10.1172/jci170217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/17/2023] [Indexed: 08/23/2023] Open
Abstract
The discovery of frequent 8p11-p12 amplifications in squamous cell lung cancer (SQLC) has fueled hopes that FGFR1, located inside this amplicon, might be a therapeutic target. In a clinical trial, only 11% of patients with 8p11 amplification (detected by FISH) responded to FGFR kinase inhibitor treatment. To understand the mechanism of FGFR1 dependency, we performed deep genomic characterization of 52 SQLCs with 8p11-p12 amplification, including 10 tumors obtained from patients who had been treated with FGFR inhibitors. We discovered somatically altered variants of FGFR1 with deletion of exons 1-8 that resulted from intragenic tail-to-tail rearrangements. These ectodomain-deficient FGFR1 variants (ΔEC-FGFR1) were expressed in the affected tumors and were tumorigenic in both in vitro and in vivo models of lung cancer. Mechanistically, breakage-fusion-bridges were the source of 8p11-p12 amplification, resulting from frequent head-to-head and tail-to-tail rearrangements. Generally, tail-to-tail rearrangements within or in close proximity upstream of FGFR1 were associated with FGFR1 dependency. Thus, the genomic events shaping the architecture of the 8p11-p12 amplicon provide a mechanistic explanation for the emergence of FGFR1-driven SQLC. Specifically, we believe that FGFR1 ectodomain-deficient and FGFR1-centered amplifications caused by tail-to-tail rearrangements are a novel somatic genomic event that might be predictive of therapeutically relevant FGFR1 dependency.
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Affiliation(s)
- Florian Malchers
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Lucia Nogova
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Martijn H.A. van Attekum
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Lukas Maas
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Johannes Brägelmann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- Mildred Scheel School of Oncology, Cologne, University Hospital Cologne, Medical Faculty, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, University Hospital Cologne, Medical Faculty, Cologne, Germany
| | - Luc Girard
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Graziella Bosco
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Ilona Dahmen
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Sebastian Michels
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Clare E. Weeden
- Personalized Oncology Division, Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andreas H. Scheel
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Lydia Meder
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Kristina Golfmann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Philipp Schuldt
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Janna Siemanowski
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Jan Rehker
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Sabine Merkelbach-Bruse
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | | | - Oliver Gautschi
- University of Berne and Cantonal Hospital of Lucerne, Cantonal Hospital of Lucerne, Lucerne, Switzerland
| | | | | | - Marie-Liesse Asselin-Labat
- Personalized Oncology Division, Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Thorsten Persigehl
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - John D. Minna
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Henning Walczak
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- CECAD Cluster of Excellence, University of Cologne, Cologne, Germany
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, United Kingdom
| | - Roland T. Ullrich
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, University Hospital Cologne, Medical Faculty, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Jürgen Wolf
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Reinhard Büttner
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Martin Peifer
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Julie George
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- Department of Head and Neck Surgery, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Roman K. Thomas
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
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3
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Sahu P, Donovan C, Paudel KR, Pickles S, Chimankar V, Kim RY, Horvart JC, Dua K, Ieni A, Nucera F, Bielefeldt-Ohmann H, Mazilli S, Caramori G, Lyons JG, Hansbro PM. Pre-clinical lung squamous cell carcinoma mouse models to identify novel biomarkers and therapeutic interventions. Front Oncol 2023; 13:1260411. [PMID: 37817767 PMCID: PMC10560855 DOI: 10.3389/fonc.2023.1260411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/29/2023] [Indexed: 10/12/2023] Open
Abstract
Primary lung carcinoma or lung cancer (LC) is classified into small-cell or non-small-cell (NSCLC) lung carcinoma. Lung squamous cell carcinoma (LSCC) is the second most common subtype of NSCLC responsible for 30% of all LCs, and its survival remains low with only 24% of patients living for five years or longer post-diagnosis primarily due to the advanced stage of tumors at the time of diagnosis. The pathogenesis of LSCC is still poorly understood and has hampered the development of effective diagnostics and therapies. This review highlights the known risk factors, genetic and epigenetic alterations, miRNA biomarkers linked to the development and diagnosis of LSCC and the lack of therapeutic strategies to target specifically LSCC. We will also discuss existing animal models of LSCC including carcinogen induced, transgenic and xenograft mouse models, and their advantages and limitations along with the chemopreventive studies and molecular studies conducted using them. The importance of developing new and improved mouse models will also be discussed that will provide further insights into the initiation and progression of LSCC, and enable the identification of new biomarkers and therapeutic targets.
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Affiliation(s)
- Priyanka Sahu
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
| | - Chantal Donovan
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
- University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Sophie Pickles
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Vrushali Chimankar
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Richard Y. Kim
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
- University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Jay C. Horvart
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Antonio Ieni
- Department of Human Pathology in Adult and Developmental Age “Gaetano Barresi”, Section of Anatomic Pathology, University of Messina, Messina, Italy
| | - Francesco Nucera
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Messina, Italy
| | - Helle Bielefeldt-Ohmann
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Sarah Mazilli
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Messina, Italy
| | - J. Guy Lyons
- Department of Dermatology, The University of Sydney at Royal Prince Alfred Hospital, Sydney, Australia, and Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | - Philip M. Hansbro
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
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4
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Wang RC, Wang Z. Precision Medicine: Disease Subtyping and Tailored Treatment. Cancers (Basel) 2023; 15:3837. [PMID: 37568653 PMCID: PMC10417651 DOI: 10.3390/cancers15153837] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
The genomics-based concept of precision medicine began to emerge following the completion of the Human Genome Project. In contrast to evidence-based medicine, precision medicine will allow doctors and scientists to tailor the treatment of different subpopulations of patients who differ in their susceptibility to specific diseases or responsiveness to specific therapies. The current precision medicine model was proposed to precisely classify patients into subgroups sharing a common biological basis of diseases for more effective tailored treatment to achieve improved outcomes. Precision medicine has become a term that symbolizes the new age of medicine. In this review, we examine the history, development, and future perspective of precision medicine. We also discuss the concepts, principles, tools, and applications of precision medicine and related fields. In our view, for precision medicine to work, two essential objectives need to be achieved. First, diseases need to be classified into various subtypes. Second, targeted therapies must be available for each specific disease subtype. Therefore, we focused this review on the progress in meeting these two objectives.
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Affiliation(s)
- Richard C. Wang
- Department of Radiology and Radiological Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA;
| | - Zhixiang Wang
- Department of Medical Genetics, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB T6J 5H4, Canada
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5
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Xue Y, Morris JL, Yang K, Fu Z, Zhu X, Johnson F, Meehan B, Witkowski L, Yasmeen A, Golenar T, Coatham M, Morin G, Monast A, Pilon V, Fiset PO, Jung S, Gonzalez AV, Camilleri-Broet S, Fu L, Postovit LM, Spicer J, Gotlieb WH, Guiot MC, Rak J, Park M, Lockwood W, Foulkes WD, Prudent J, Huang S. SMARCA4/2 loss inhibits chemotherapy-induced apoptosis by restricting IP3R3-mediated Ca 2+ flux to mitochondria. Nat Commun 2021; 12:5404. [PMID: 34518526 PMCID: PMC8438089 DOI: 10.1038/s41467-021-25260-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 07/27/2021] [Indexed: 12/25/2022] Open
Abstract
Inactivating mutations in SMARCA4 and concurrent epigenetic silencing of SMARCA2 characterize subsets of ovarian and lung cancers. Concomitant loss of these key subunits of SWI/SNF chromatin remodeling complexes in both cancers is associated with chemotherapy resistance and poor prognosis. Here, we discover that SMARCA4/2 loss inhibits chemotherapy-induced apoptosis through disrupting intracellular organelle calcium ion (Ca2+) release in these cancers. By restricting chromatin accessibility to ITPR3, encoding Ca2+ channel IP3R3, SMARCA4/2 deficiency causes reduced IP3R3 expression leading to impaired Ca2+ transfer from the endoplasmic reticulum to mitochondria required for apoptosis induction. Reactivation of SMARCA2 by a histone deacetylase inhibitor rescues IP3R3 expression and enhances cisplatin response in SMARCA4/2-deficient cancer cells both in vitro and in vivo. Our findings elucidate the contribution of SMARCA4/2 to Ca2+-dependent apoptosis induction, which may be exploited to enhance chemotherapy response in SMARCA4/2-deficient cancers.
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Affiliation(s)
- Yibo Xue
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Division of Medical Genetics, McGill University Health Centre, and Cancer Research Program, Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - Jordan L Morris
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Kangning Yang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Zheng Fu
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Xianbing Zhu
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Fraser Johnson
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Brian Meehan
- Department of Pediatrics, Research Institute of the McGill University Health Centre, Montreal Children's Hospital, McGill University, Montreal, QC, Canada
| | - Leora Witkowski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Amber Yasmeen
- Division of Gynecologic Oncology, Segal Cancer Center, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Tunde Golenar
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Mackenzie Coatham
- Department of Oncology, Department of Obstetrics and Gynecology, University of Alberta, Edmonton, AB, Canada
| | - Geneviève Morin
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Anie Monast
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Virginie Pilon
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | | | - Sungmi Jung
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Anne V Gonzalez
- Department of Medicine, Division of Respiratory Medicine, McGill University Health Centre, Montreal Chest Institute, Montreal, QC, Canada
| | | | - Lili Fu
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Lynne-Marie Postovit
- Department of Oncology, Department of Obstetrics and Gynecology, University of Alberta, Edmonton, AB, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Jonathan Spicer
- Department of Surgery, McGill University Health Center, Montreal, QC, Canada
| | - Walter H Gotlieb
- Division of Gynecologic Oncology, Segal Cancer Center, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Marie-Christine Guiot
- Department of Pathology, Montreal Neurological Hospital/Institute, McGill University Health Centre, Montreal, QC, Canada
| | - Janusz Rak
- Department of Pediatrics, Research Institute of the McGill University Health Centre, Montreal Children's Hospital, McGill University, Montreal, QC, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - William Lockwood
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Division of Medical Genetics, McGill University Health Centre, and Cancer Research Program, Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Julien Prudent
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, QC, Canada.
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada.
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6
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Mapping lung squamous cell carcinoma pathogenesis through in vitro and in vivo models. Commun Biol 2021; 4:937. [PMID: 34354223 PMCID: PMC8342622 DOI: 10.1038/s42003-021-02470-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is the main cause of cancer death worldwide, with lung squamous cell carcinoma (LUSC) being the second most frequent subtype. Preclinical LUSC models recapitulating human disease pathogenesis are key for the development of early intervention approaches and improved therapies. Here, we review advances and challenges in the generation of LUSC models, from 2D and 3D cultures, to murine models. We discuss how molecular profiling of premalignant lesions and invasive LUSC has contributed to the refinement of in vitro and in vivo models, and in turn, how these systems have increased our understanding of LUSC biology and therapeutic vulnerabilities.
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7
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Bogatyrova O, Mattsson JSM, Ross EM, Sanderson MP, Backman M, Botling J, Brunnström H, Kurppa P, La Fleur L, Strell C, Wilm C, Zimmermann A, Esdar C, Micke P. FGFR1 overexpression in non-small cell lung cancer is mediated by genetic and epigenetic mechanisms and is a determinant of FGFR1 inhibitor response. Eur J Cancer 2021; 151:136-149. [PMID: 33984662 DOI: 10.1016/j.ejca.2021.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/11/2021] [Accepted: 04/06/2021] [Indexed: 02/06/2023]
Abstract
Amplification of fibroblast growth factor receptor 1 (FGFR1) in non-small cell lung cancer (NSCLC) has been considered as an actionable drug target. However, pan-FGFR tyrosine kinase inhibitors did not demonstrate convincing clinical efficacy in FGFR1-amplified NSCLC patients. This study aimed to characterise the molecular context of FGFR1 expression and to define biomarkers predictive of FGFR1 inhibitor response. In this study, 635 NSCLC samples were characterised for FGFR1 protein expression by immunohistochemistry and copy number gain (CNG) by in situ hybridisation (n = 298) or DNA microarray (n = 189). FGFR1 gene expression (n = 369) and immune cell profiles (n = 309) were also examined. Furthermore, gene expression, methylation and microRNA data from The Cancer Genome Atlas (TCGA) were compared. A panel of FGFR1-amplified NSCLC patient-derived xenograft (PDX) models were tested for response to the selective FGFR1 antagonist M6123. A minority of patients demonstrated FGFR1 CNG (10.5%) or increased FGFR1 mRNA (8.7%) and protein expression (4.4%). FGFR1 CNG correlated weakly with FGFR1 gene and protein expression. Tumours overexpressing FGFR1 protein were typically devoid of driver alterations (e.g. EGFR, KRAS) and showed reduced infiltration of T-lymphocytes and lower PD-L1 expression. Promoter methylation and microRNA were identified as regulators of FGFR1 expression in NSCLC and other cancers. Finally, NSCLC PDX models demonstrating FGFR1 amplification and FGFR1 protein overexpression were sensitive to M6123. The unique molecular and immune features of tumours with high FGFR1 expression provide a rationale to stratify patients in future clinical trials of FGFR1 pathway-targeting agents.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- B7-H1 Antigen/metabolism
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/metabolism
- DNA Methylation
- Epigenesis, Genetic
- Female
- Gene Amplification
- Gene Expression Regulation, Neoplastic
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/immunology
- Lung Neoplasms/metabolism
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Mice, Inbred NOD
- Mice, SCID
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Molecular Targeted Therapy
- Receptor, Fibroblast Growth Factor, Type 1/antagonists & inhibitors
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Tumor Microenvironment
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Olga Bogatyrova
- Translational Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Johanna S M Mattsson
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Edith M Ross
- Translational Medicine, Merck KGaA, Darmstadt, Germany
| | - Michael P Sanderson
- Translational Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Max Backman
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Johan Botling
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Hans Brunnström
- Division of Pathology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Pinja Kurppa
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Linnéa La Fleur
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Carina Strell
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Claudia Wilm
- Translational Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Astrid Zimmermann
- Translational Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Christina Esdar
- Translational Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Patrick Micke
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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8
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Li Z, Zheng W, Wang H, Cheng Y, Fang Y, Wu F, Sun G, Sun G, Lv C, Hui B. Application of Animal Models in Cancer Research: Recent Progress and Future Prospects. Cancer Manag Res 2021; 13:2455-2475. [PMID: 33758544 PMCID: PMC7979343 DOI: 10.2147/cmar.s302565] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/25/2021] [Indexed: 12/18/2022] Open
Abstract
Animal models refers to the animal experimental objects and related materials that can simulate human body established in medical research. As the second-largest disease in terms of morbidity and mortality after cardiovascular disease, cancer has always been the focus of human attention all over the world, which makes it a research hotspot in the medical field. At the same time, more and more animal models have been constructed and used in cancer research. With the deepening of research, the construction methods of cancer animal models are becoming more and more diverse, including chemical induction, xenotransplantation, gene programming, and so on. In recent years, patient-derived xenotransplantation (PDX) model has become a research hotspot because it can retain the microenvironment of the primary tumor and the basic characteristics of cells. Animal models can be used not only to study the biochemical and physiological processes of the occurrence and development of cancer in objects but also for the screening of cancer drugs and the exploration of gene therapy. In this paper, several main tumor animal models and the application progress of animal models in tumor research are systematically reviewed. Finally, combined with the latest progress and development trend in this field, the future research of tumor animal model was prospected.
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Affiliation(s)
- Zhitao Li
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Wubin Zheng
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Hanjin Wang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Ye Cheng
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yijiao Fang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
| | - Fan Wu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Guoqiang Sun
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Guangshun Sun
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Chengyu Lv
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Bingqing Hui
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
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9
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Grohmann C, Walker F, Devlin M, Luo MX, Chüeh AC, Doherty J, Vaillant F, Ho GY, Wakefield MJ, Weeden CE, Kamili A, Murray J, Po'uha ST, Weinstock J, Kane SR, Faux MC, Broekhuizen E, Zheng Y, Shield-Artin K, Kershaw NJ, Tan CW, Witchard HM, Ebert G, Charman SA, Street I, Kavallaris M, Haber M, Fletcher JI, Asselin-Labat ML, Scott CL, Visvader JE, Lindeman GJ, Watson KG, Burgess AW, Lessene G. Preclinical small molecule WEHI-7326 overcomes drug resistance and elicits response in patient-derived xenograft models of human treatment-refractory tumors. Cell Death Dis 2021; 12:268. [PMID: 33712556 PMCID: PMC7955127 DOI: 10.1038/s41419-020-03269-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/29/2022]
Abstract
Targeting cell division by chemotherapy is a highly effective strategy to treat a wide range of cancers. However, there are limitations of many standard-of-care chemotherapies: undesirable drug toxicity, side-effects, resistance and high cost. New small molecules which kill a wide range of cancer subtypes, with good therapeutic window in vivo, have the potential to complement the current arsenal of anti-cancer agents and deliver improved safety profiles for cancer patients. We describe results with a new anti-cancer small molecule, WEHI-7326, which causes cell cycle arrest in G2/M, cell death in vitro, and displays efficacious anti-tumor activity in vivo. WEHI-7326 induces cell death in a broad range of cancer cell lines, including taxane-resistant cells, and inhibits growth of human colon, brain, lung, prostate and breast tumors in mice xenografts. Importantly, the compound elicits tumor responses as a single agent in patient-derived xenografts of clinically aggressive, treatment-refractory neuroblastoma, breast, lung and ovarian cancer. In combination with standard-of-care, WEHI-7326 induces a remarkable complete response in a mouse model of high-risk neuroblastoma. WEHI-7326 is mechanistically distinct from known microtubule-targeting agents and blocks cells early in mitosis to inhibit cell division, ultimately leading to apoptotic cell death. The compound is simple to produce and possesses favorable pharmacokinetic and toxicity profiles in rodents. It represents a novel class of anti-cancer therapeutics with excellent potential for further development due to the ease of synthesis, simple formulation, moderate side effects and potent in vivo activity. WEHI-7326 has the potential to complement current frontline anti-cancer drugs and to overcome drug resistance in a wide range of cancers.
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Affiliation(s)
- Christoph Grohmann
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia.
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia.
| | - Francesca Walker
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- Ludwig Institute for Cancer Research, Melbourne, VIC, 3000, Australia
| | - Mark Devlin
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre building, Melbourne, 3000, Australia
- Cancer Therapeutics CRC, Melbourne, VIC, 3000, Australia
| | - Meng-Xiao Luo
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Anderly C Chüeh
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- Cancer Therapeutics CRC, Melbourne, VIC, 3000, Australia
| | - Judy Doherty
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre building, Melbourne, 3000, Australia
- Cancer Therapeutics CRC, Melbourne, VIC, 3000, Australia
| | - François Vaillant
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Gwo-Yaw Ho
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- The University of Melbourne, Department of Obstetrics and Gynaecology, Parkville, VIC, 3050, Australia
| | - Clare E Weeden
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Alvin Kamili
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
- School of Women's and Children's Health, UNSW, Sydney, NSW, 2052, Australia
| | - Jayne Murray
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
| | - Sela T Po'uha
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
| | - Janet Weinstock
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- Ludwig Institute for Cancer Research, Melbourne, VIC, 3000, Australia
| | - Serena R Kane
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Maree C Faux
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Esmee Broekhuizen
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Ye Zheng
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Kristy Shield-Artin
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Nadia J Kershaw
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- Ludwig Institute for Cancer Research, Melbourne, VIC, 3000, Australia
| | - Chin Wee Tan
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Helen M Witchard
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
| | - Gregor Ebert
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Clayton, VIC, 3052, Australia
| | - Ian Street
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- Cancer Therapeutics CRC, Melbourne, VIC, 3000, Australia
| | - Maria Kavallaris
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
- ARC Centre of Excellence in Convergent Bionano Science and Technology, Australian Centre for Nanomedicine, UNSW, Sydney, NSW, 2052, Australia
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
| | - Jamie I Fletcher
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
- School of Women's and Children's Health, UNSW, Sydney, NSW, 2052, Australia
| | - Marie-Liesse Asselin-Labat
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Clare L Scott
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre building, Melbourne, 3000, Australia
- The University of Melbourne, Department of Obstetrics and Gynaecology, Parkville, VIC, 3050, Australia
| | - Jane E Visvader
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Geoffrey J Lindeman
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre building, Melbourne, 3000, Australia
- The University of Melbourne, Department of Medicine, Parkville, VIC, 3000, Australia
| | - Keith G Watson
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Antony W Burgess
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia.
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia.
- Ludwig Institute for Cancer Research, Melbourne, VIC, 3000, Australia.
| | - Guillaume Lessene
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia.
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia.
- The University of Melbourne, Department of Pharmacology and Therapeutics, Parkville, VIC, 3050, Australia.
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10
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Jung HY, Kim TH, Lee JE, Kim HK, Cho JH, Choi YS, Shin S, Lee SH, Rhee H, Lee HK, Choi HJ, Jang HY, Lee S, Kang JH, Choi YA, Lee S, Lee J, Choi YL, Kim J. PDX models of human lung squamous cell carcinoma: consideration of factors in preclinical and co-clinical applications. J Transl Med 2020; 18:307. [PMID: 32762722 PMCID: PMC7409653 DOI: 10.1186/s12967-020-02473-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/28/2020] [Indexed: 12/20/2022] Open
Abstract
Background Treatment of human lung squamous cell carcinoma (LUSC) using current targeted therapies is limited because of their diverse somatic mutations without any specific dominant driver mutations. These mutational diversities preventing the use of common targeted therapies or the combination of available therapeutic modalities would require a preclinical animal model of this tumor to acquire improved clinical responses. Patient-derived xenograft (PDX) models have been recognized as a potentially useful preclinical model for personalized precision medicine. However, whether the use of LUSC PDX models would be appropriate enough for clinical application is still controversial. Methods In the process of developing PDX models from Korean patients with LUSC, the authors investigated the factors influencing the successful initial engraftment of tumors in NOD scid gamma mice and the retainability of the pathological and genomic characteristics of the parental patient tumors in PDX tumors. Conclusions The authors have developed 62 LUSC PDX models that retained the pathological and genomic features of parental patient tumors, which could be used in preclinical and co-clinical studies. Trial registration Tumor samples were obtained from 139 patients with LUSC between November 2014 and January 2019. All the patients provided signed informed consents. This study was approved by the institutional review board (IRB) of Samsung Medical Center (2018-03-110)
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Affiliation(s)
- Hae-Yun Jung
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Tae Ho Kim
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | - Hong Kwan Kim
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jong Ho Cho
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Yong Soo Choi
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sumin Shin
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | | | | | | | | | - Jung Hee Kang
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Young Ae Choi
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sanghyuk Lee
- Ewha Research Center for Systems Biology (ERCSB) and Department of Life Science, Ewha Womans University, Seoul, South Korea
| | - Jinseon Lee
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Yoon La Choi
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Jhingook Kim
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
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11
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SuperFreq: Integrated mutation detection and clonal tracking in cancer. PLoS Comput Biol 2020; 16:e1007603. [PMID: 32053599 PMCID: PMC7043783 DOI: 10.1371/journal.pcbi.1007603] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 02/26/2020] [Accepted: 12/11/2019] [Indexed: 01/28/2023] Open
Abstract
Analysing multiple cancer samples from an individual patient can provide insight into the way the disease evolves. Monitoring the expansion and contraction of distinct clones helps to reveal the mutations that initiate the disease and those that drive progression. Existing approaches for clonal tracking from sequencing data typically require the user to combine multiple tools that are not purpose-built for this task. Furthermore, most methods require a matched normal (non-tumour) sample, which limits the scope of application. We developed SuperFreq, a cancer exome sequencing analysis pipeline that integrates identification of somatic single nucleotide variants (SNVs) and copy number alterations (CNAs) and clonal tracking for both. SuperFreq does not require a matched normal and instead relies on unrelated controls. When analysing multiple samples from a single patient, SuperFreq cross checks variant calls to improve clonal tracking, which helps to separate somatic from germline variants, and to resolve overlapping CNA calls. To demonstrate our software we analysed 304 cancer-normal exome samples across 33 cancer types in The Cancer Genome Atlas (TCGA) and evaluated the quality of the SNV and CNA calls. We simulated clonal evolution through in silico mixing of cancer and normal samples in known proportion. We found that SuperFreq identified 93% of clones with a cellular fraction of at least 50% and mutations were assigned to the correct clone with high recall and precision. In addition, SuperFreq maintained a similar level of performance for most aspects of the analysis when run without a matched normal. SuperFreq is highly versatile and can be applied in many different experimental settings for the analysis of exomes and other capture libraries. We demonstrate an application of SuperFreq to leukaemia patients with diagnosis and relapse samples. Cancer is a disease that continues to evolve. Understanding how it changes can provide key biological insights; for example, it can help to identify recurrent patterns associated with therapy resistance. However, tracking clonal evolution in a cancer from sequencing data is a major analytical challenge. We have developed SuperFreq, an analysis framework purpose built for the detection of intra-tumoural heterogeneity and clonal evolution. SuperFreq encapsulates mutation detection, quality assessment, clonal tracking and phylogeny, for both point mutations and copy number alterations. To demonstrate the major advance that SuperFreq offers, we developed a test dataset with engineered clones, made by blending data from cancer and normal samples from The Cancer Genome Atlas. We demonstrate that SuperFreq exhibits robust performance, both for detecting clones and for assigning mutations to clones. SuperFreq is a powerful and adaptable analysis framework that can be applied to address many research questions. We include an example application, where we identify both early and relapse-specific driver mutations in an acute myeloid leukaemia.
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12
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Yoshida GJ. Applications of patient-derived tumor xenograft models and tumor organoids. J Hematol Oncol 2020; 13:4. [PMID: 31910904 PMCID: PMC6947974 DOI: 10.1186/s13045-019-0829-z] [Citation(s) in RCA: 243] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 11/13/2019] [Indexed: 12/16/2022] Open
Abstract
Patient-derived tumor xenografts (PDXs), in which tumor fragments surgically dissected from cancer patients are directly transplanted into immunodeficient mice, have emerged as a useful model for translational research aimed at facilitating precision medicine. PDX susceptibility to anti-cancer drugs is closely correlated with clinical data in patients, from whom PDX models have been derived. Accumulating evidence suggests that PDX models are highly effective in predicting the efficacy of both conventional and novel anti-cancer therapeutics. This also allows “co-clinical trials,” in which pre-clinical investigations in vivo and clinical trials could be performed in parallel or sequentially to assess drug efficacy in patients and PDXs. However, tumor heterogeneity present in PDX models and in the original tumor samples constitutes an obstacle for application of PDX models. Moreover, human stromal cells originally present in tumors dissected from patients are gradually replaced by host stromal cells as the xenograft grows. This replacement by murine stroma could preclude analysis of human tumor-stroma interactions, as some mouse stromal cytokines might not affect human carcinoma cells in PDX models. The present review highlights the biological and clinical significance of PDX models and three-dimensional patient-derived tumor organoid cultures of several kinds of solid tumors, such as those of the colon, pancreas, brain, breast, lung, skin, and ovary.
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Affiliation(s)
- Go J Yoshida
- Department of Pathology and Oncology, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8412, Japan. .,Department of Immunological Diagnosis, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8412, Japan.
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13
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Koga Y, Ochiai A. Systematic Review of Patient-Derived Xenograft Models for Preclinical Studies of Anti-Cancer Drugs in Solid Tumors. Cells 2019; 8:cells8050418. [PMID: 31064068 PMCID: PMC6562882 DOI: 10.3390/cells8050418] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 04/26/2019] [Accepted: 05/04/2019] [Indexed: 01/06/2023] Open
Abstract
Patient-derived xenograft (PDX) models are used as powerful tools for understanding cancer biology in PDX clinical trials and co-clinical trials. In this systematic review, we focus on PDX clinical trials or co-clinical trials for drug development in solid tumors and summarize the utility of PDX models in the development of anti-cancer drugs, as well as the challenges involved in this approach, following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. Recently, the assessment of drug efficacy by PDX clinical and co-clinical trials has become an important method. PDX clinical trials can be used for the development of anti-cancer drugs before clinical trials, with their efficacy assessed by the modified response evaluation criteria in solid tumors (mRECIST). A few dozen cases of PDX models have completed enrollment, and the efficacy of the drugs is assessed by 1 × 1 × 1 or 3 × 1 × 1 approaches in the PDX clinical trials. Furthermore, co-clinical trials can be used for personalized care or precision medicine with the evaluation of a new drug or a novel combination. Several PDX models from patients in clinical trials have been used to assess the efficacy of individual drugs or drug combinations in co-clinical trials.
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Affiliation(s)
- Yoshikatsu Koga
- Department of Strategic Programs, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa 277-8577, Japan.
| | - Atsushi Ochiai
- Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa 277-8577, Japan.
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14
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Expansion of cancer stem cell pool initiates lung cancer recurrence before angiogenesis. Proc Natl Acad Sci U S A 2018; 115:E8948-E8957. [PMID: 30158168 DOI: 10.1073/pnas.1806219115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Angiogenesis is essential in the early stage of solid tumor recurrence, but how a suspensive tumor is reactivated before angiogenesis is mostly unknown. Herein, we stumble across an interesting phenomenon that s.c. xenografting human lung cancer tissues can awaken the s.c. suspensive tumor in nude mice. We further found that a high level of insulin-like growth factor 1 (IGF1) was mainly responsible for triggering the transition from suspensive tumor to progressive tumor in this model. The s.c. suspensive tumor is characterized with growth arrest, avascularity, and a steady-state level of proliferating and apoptotic cells. Intriguingly, CD133+ lung cancer stem cells (LCSCs) are highly enriched in suspensive tumor compared with progressive tumor. Mechanistically, high IGF1 initiates LCSCs self-renewal from asymmetry to symmetry via the activation of a PI3K/Akt/β-catenin axis. Next, the expansion of LCSC pool promotes angiogenesis by increasing the production of CXCL1 and PlGF in CD133+ LCSCs, which results in lung cancer recurrence. Clinically, a high level of serum IGF1 in lung cancer patients after orthotopic lung cancer resection as an unfavorable factor is strongly correlated with the high rate of recurrence and indicates an adverse progression-free survival. Vice versa, blocking IGF1 or CXCL1/PlGF with neutralizing antibodies can prevent the reactivation of a suspensive tumor induced by IGF1 stimulation in the mouse model. Collectively, the expansion of LCSC pool before angiogenesis induced by IGF1 is a key checkpoint during the initiation of cancer relapse, and targeting serum IGF1 may be a promising treatment for preventing recurrence in lung cancer patients.
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15
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Testa U, Castelli G, Pelosi E. Lung Cancers: Molecular Characterization, Clonal Heterogeneity and Evolution, and Cancer Stem Cells. Cancers (Basel) 2018; 10:E248. [PMID: 30060526 PMCID: PMC6116004 DOI: 10.3390/cancers10080248] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/21/2022] Open
Abstract
Lung cancer causes the largest number of cancer-related deaths in the world. Most (85%) of lung cancers are classified as non-small-cell lung cancer (NSCLC) and small-cell lung cancer (15%) (SCLC). The 5-year survival rate for NSCLC patients remains very low (about 16% at 5 years). The two predominant NSCLC histological phenotypes are adenocarcinoma (ADC) and squamous cell carcinoma (LSQCC). ADCs display several recurrent genetic alterations, including: KRAS, BRAF and EGFR mutations; recurrent mutations and amplifications of several oncogenes, including ERBB2, MET, FGFR1 and FGFR2; fusion oncogenes involving ALK, ROS1, Neuregulin1 (NRG1) and RET. In LSQCC recurrent mutations of TP53, FGFR1, FGFR2, FGFR3, DDR2 and genes of the PI3K pathway have been detected, quantitative gene abnormalities of PTEN and CDKN2A. Developments in the characterization of lung cancer molecular abnormalities provided a strong rationale for new therapeutic options and for understanding the mechanisms of drug resistance. However, the complexity of lung cancer genomes is particularly high, as shown by deep-sequencing studies supporting the heterogeneity of lung tumors at cellular level, with sub-clones exhibiting different combinations of mutations. Molecular studies performed on lung tumors during treatment have shown the phenomenon of clonal evolution, thus supporting the occurrence of a temporal tumor heterogeneity.
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Affiliation(s)
- Ugo Testa
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Germana Castelli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Elvira Pelosi
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
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16
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He D, Zhang J, Wu W, Yi N, He W, Lu P, Li B, Yang N, Wang D, Xue Z, Zhang P, Fan G, Zhu X. A novel immunodeficient rat model supports human lung cancer xenografts. FASEB J 2018; 33:140-150. [PMID: 29944447 DOI: 10.1096/fj.201800102rr] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Patient-derived xenograft (PDX) animal models allow the exogenous growth of human tumors, offering an irreplaceable preclinical tool for oncology research. Mice are the most commonly used host for human PDX models, however their small body size limits the xenograft growth, sample collection, and drug evaluation. Therefore, we sought to develop a novel rat model that could overcome many of these limitations. We knocked out Rag1, Rag2, and Il2rg in Sprague Dawley (SD) rats by clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 technology. The development of lymphoid organs is significantly impaired in Rag1-/-Rag2-/-Il2rg-/Y (designated as SD-RG) rats. Consequently, SD-RG rats are severely immunodeficient with an absence of mature T, B, and NK cells in the immune system. After subcutaneous injection of tumor cell lines of different origin, such as NCI-H460, U-87MG, and MDA-MB-231, the tumors grow significantly faster and larger in SD-RG rats than in nonobese diabetic- Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice. Most important of all, we successfully established a PDX model of lung squamous cell carcinoma in which the grafts recapitulate the histopathologic features of the primary tumor for several passages. In conclusion, the severely immunodeficient SD-RG rats support fast growth of PDX compared with mice, thus holding great potential to serve as a new model for oncology research.-He, D., Zhang, J., Wu, W., Yi, N., He, W., Lu, P., Li, B., Yang, N., Wang, D., Xue, Z., Zhang, P., Fan, G., Zhu, X. A novel immunodeficient rat model supports human lung cancer xenografts.
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Affiliation(s)
- Di He
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Junhui Zhang
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University Suzhou Institute, Tongji University School of Medicine, Shanghai, China
| | - Wanwan Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ning Yi
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University Suzhou Institute, Tongji University School of Medicine, Shanghai, China
| | - Wen He
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University Suzhou Institute, Tongji University School of Medicine, Shanghai, China
| | - Ping Lu
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University Suzhou Institute, Tongji University School of Medicine, Shanghai, China
| | - Bin Li
- Alphacait AL Biotech Company, Hangzhou, China
| | - Nan Yang
- PharmaLegacy Laboratories Company, Shanghai, China; and
| | - Di Wang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhigang Xue
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University Suzhou Institute, Tongji University School of Medicine, Shanghai, China
| | - Peng Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Guoping Fan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Xianmin Zhu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
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17
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Abstract
BACKGROUND Over the last 15 years, an estimated 3000 large centralized biobanks have been established worldwide, making important contributions to the further development of precision medicine. In many cases, these biobanks are affiliated with pathological institutes or work closely with them. OBJECTIVE In which translational research projects, and during which phases in the development of new drugs are human bioprobes being used and can their use be easily traced in the literature? METHODS PubMed, Internet research, and information from the German Biobank Alliance and the European initiative BBMRI-ERIC. RESULTS High-quality biosamples from centralized biobanks are increasingly used in clinical research and development projects. Success stories, where bioprobes have contributed to the further development of precision medicine, are shown in this paper using among others the example of RET gene fusion discovery in lung cancer. Interestingly enough, many key publications in the field of precision medicine do not contain exact references to the biobanks involved. CONCLUSIONS The importance of centralized biobanks in translational research and clinical development is constantly increasing. However, in order to ensure the acceptance and visibility of biobanks, their participation in success stories of biomedical progress must be systematically documented and published.
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18
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Dual inhibition of BCL-XL and MCL-1 is required to induce tumour regression in lung squamous cell carcinomas sensitive to FGFR inhibition. Oncogene 2018; 37:4475-4488. [DOI: 10.1038/s41388-018-0268-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 03/19/2018] [Accepted: 03/29/2018] [Indexed: 12/17/2022]
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19
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Head and neck squamous cell carcinoma: Genomics and emerging biomarkers for immunomodulatory cancer treatments. Semin Cancer Biol 2018; 52:228-240. [PMID: 29355614 DOI: 10.1016/j.semcancer.2018.01.008] [Citation(s) in RCA: 254] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/29/2017] [Accepted: 01/13/2018] [Indexed: 12/30/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) comprises a heterogeneous group of tumors that arise from the squamous epithelium of the oral cavity, oropharynx, larynx and hypopharynx. While many HNSCCs are related to classical etiologic factors of smoking and alcohol, a clinically, genomically, and immunologically distinct subgroup of tumors arise from the epithelium of the tonsil and the base of tongue as a result of infection with Human Papilloma Virus (HPV). In this review we describe the genomic and immunologic landscape of HNSCC, highlighting differences between HPV-positive and HPV-negative HNSCC. While HPV-negative tumors are characterized by tobacco-associated mutations in genes including TP53 and CDKN2A, in HPV-positive HNSCC integration of viral genome from HPV into the host cellular genome results in expression of the E6 and E7 viral oncoproteins, with consequent degradation of p53 and functional inactivation of Rb. The immune microenvironment of HNSCC is characterized by changes in immune cell populations, immune checkpoints, as well as tumor or microenvironmental factors that alter the balance of the immune milieu in favor of immunosuppression, allowing tumor evasion and escape from immune surveillance. Immune therapies, in particular those targeting the PD1 receptor or its ligand PD-L1, including nivolumab, pembrolizumab, durvalumab, and atezolizumab have shown significant efficacy in subsets of patients with HNSCC. Current trials are evaluating the efficacy of these agents in combination with chemotherapy, radiotherapy and other immune therapies including CTLA-4 and IDO-1 inhibitors. While biomarkers including PD-L1 expression, PD-L2 expression and the interferon-gamma gene signature show potential to predict benefit from checkpoint inhibitor therapy - it is hoped that improved understanding of the genomic and immune landscape will lead to ways to improved strategies to stratify patients and to select which HNSCC are most likely to benefit from these therapies.
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20
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Flockerzi FA, Roggia C, Langer F, Holleczek B, Bohle RM. FGFR1 gene amplification in squamous cell carcinomas of the lung: a potential favorable prognostic marker for women and for patients with advanced cancer. Virchows Arch 2017; 472:759-769. [PMID: 29270870 DOI: 10.1007/s00428-017-2282-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/30/2017] [Accepted: 12/11/2017] [Indexed: 12/01/2022]
Abstract
In squamous cell carcinoma (SCC) of the lung, mutations within the genes of fibroblast growth factor receptors (FGFR) such as K660N/K660E in FGFR2 and R248C/S249C in FGFR3 and FGFR1 gene amplification have been described, but their prognostic relevance still remains unclear. In order to detect the mutation frequencies and to define their prognostic value for associated clinicopathologic features and survival of patients, resected ΔNp63/p40-positive SCC of the lung (n = 101) were screened for FGFR1 gene amplification by fluorescence in situ hybridization performed on formalin-fixed paraffin embedded tissues and for the presumed driver mutations in genes of FGFR2 and FGFR3 by PCR and Sanger sequencing. Twenty-two of 101 SCCs (22%) were positive for amplification based on a FGFR1/centromere (chromosome 8) ratio > 2.0 or higher. In advanced tumor stages (III-IV), the overall survival of patients carrying FGFR1 gene amplification was significantly higher (p = 0.006). Among women, FGFR1 gene amplification was significantly associated with longer overall survival (p = 0.023). The presence of FGFR1 gene amplification was associated with patient age (65 versus 69 years, p = 0.046), but not with gender, tumor stage, histologic subtype, tumor grade, or ΔNp63/p40 immunoreactivity. The S249C mutation in the FGFR3 gene was identified in one out of 101 SCCs (1%); the K600N, K660E, or R248C mutations were not identified. These results suggest that FGFR1 gene amplification is a frequent alteration in SCC of the lung and appears not to be a negative but rather a favorable prognostic marker for women and particularly for patients with advanced SCC of the lung (stage III-IV).
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Affiliation(s)
- Fidelis Andrea Flockerzi
- Department of Pathology, Saarland University Medical Center, Homburg, Building 26, 66421, Homburg, Germany.
| | - Cristiana Roggia
- Department of Pathology, Saarland University Medical Center, Homburg, Building 26, 66421, Homburg, Germany.,Department of Interdisciplinary Division of Neuro-Oncology, University Hospital Tübingen, Tübingen, Germany
| | - Frank Langer
- Department of Thoracic and Cardiovascular Surgery, Saarland University Medical Center, Homburg, Germany
| | | | - Rainer M Bohle
- Department of Pathology, Saarland University Medical Center, Homburg, Building 26, 66421, Homburg, Germany.,Cancer Center Saarland, Saarland University Medical Center, Homburg, Germany
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