1
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Sharma MP, Shukla S, Misra G. Recent advances in breast cancer cell line research. Int J Cancer 2024; 154:1683-1693. [PMID: 38230499 DOI: 10.1002/ijc.34849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
Breast cancer, a formidable global health challenge, needs continuous translational research to understand the complexity of mechanisms and improve therapeutic and diagnostic strategies. Breast cancer cell lines are of paramount importance as they significantly contribute to the initial stage of research to understand cancer biology. This review provides insights into targeted therapies and immunotherapies that have emerged using in vitro models and microbiome analysis. It focuses on therapeutic development using cell lines and the limitations of tumor heterogeneity and microenvironment. We explore the evolving landscape of breast cancer cell lines from two-dimensional (2-D) cultures to patient-derived xenograft (PDX) models advancing both fundamental and translational research. Patient-derived xenografts, cell line-derived xenografts (CDX), three-dimensional (3-D) cultures, organoids, and circulating tumor cells (CTC) models provide promising alternatives that capture the intricacies of the tumor microenvironment. This review bridges the gap between traditional cell lines and newer developments exploring the therapeutic and diagnostic advancements and needs for cell lines to expedite the progress in breast cancer research and treatment.
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Affiliation(s)
- Manika P Sharma
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), Noida, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Supriya Shukla
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), Noida, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Gauri Misra
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), Noida, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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2
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Vaishnavi A, Kinsey CG, McMahon M. Preclinical Modeling of Pathway-Targeted Therapy of Human Lung Cancer in the Mouse. Cold Spring Harb Perspect Med 2024; 14:a041385. [PMID: 37788883 PMCID: PMC10760064 DOI: 10.1101/cshperspect.a041385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Animal models, particularly genetically engineered mouse models (GEMMs), continue to have a transformative impact on our understanding of the initiation and progression of hematological malignancies and solid tumors. Furthermore, GEMMs have been employed in the design and optimization of potent anticancer therapies. Increasingly, drug responses are assessed in mouse models either prior, or in parallel, to the implementation of precision medical oncology, in which groups of patients with genetically stratified cancers are treated with drugs that target the relevant oncoprotein such that mechanisms of drug sensitivity or resistance may be identified. Subsequently, this has led to the design and preclinical testing of combination therapies designed to forestall the onset of drug resistance. Indeed, mouse models of human lung cancer represent a paradigm for how a wide variety of GEMMs, driven by a variety of oncogenic drivers, have been generated to study initiation, progression, and maintenance of this disease as well as response to drugs. These studies have now expanded beyond targeted therapy to include immunotherapy. We highlight key aspects of the relationship between mouse models and the evolution of therapeutic approaches, including oncogene-targeted therapies, immunotherapies, acquired drug resistance, and ways in which successful antitumor strategies improve on efficiently translating preclinical approaches into successful antitumor strategies in patients.
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Affiliation(s)
- Aria Vaishnavi
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Conan G Kinsey
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah 84112, USA
| | - Martin McMahon
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
- Department of Dermatology, University of Utah, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah 84112, USA
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3
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Wu Z, Huang D, Wang J, Zhao Y, Sun W, Shen X. Engineering Heterogeneous Tumor Models for Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304160. [PMID: 37946674 PMCID: PMC10767453 DOI: 10.1002/advs.202304160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/16/2023] [Indexed: 11/12/2023]
Abstract
Tumor tissue engineering holds great promise for replicating the physiological and behavioral characteristics of tumors in vitro. Advances in this field have led to new opportunities for studying the tumor microenvironment and exploring potential anti-cancer therapeutics. However, the main obstacle to the widespread adoption of tumor models is the poor understanding and insufficient reconstruction of tumor heterogeneity. In this review, the current progress of engineering heterogeneous tumor models is discussed. First, the major components of tumor heterogeneity are summarized, which encompasses various signaling pathways, cell proliferations, and spatial configurations. Then, contemporary approaches are elucidated in tumor engineering that are guided by fundamental principles of tumor biology, and the potential of a bottom-up approach in tumor engineering is highlighted. Additionally, the characterization approaches and biomedical applications of tumor models are discussed, emphasizing the significant role of engineered tumor models in scientific research and clinical trials. Lastly, the challenges of heterogeneous tumor models in promoting oncology research and tumor therapy are described and key directions for future research are provided.
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Affiliation(s)
- Zhuhao Wu
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
| | - Danqing Huang
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
| | - Jinglin Wang
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
| | - Yuanjin Zhao
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
- Department of Gastrointestinal SurgeryThe First Affiliated HospitalWenzhou Medical UniversityWenzhou325035China
| | - Weijian Sun
- Department of Gastrointestinal SurgeryThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Xian Shen
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
- Department of Gastrointestinal SurgeryThe First Affiliated HospitalWenzhou Medical UniversityWenzhou325035China
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4
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Philp LK. Patient-Derived Xenograft Models for Translational Prostate Cancer Research and Drug Development. Methods Mol Biol 2024; 2806:153-185. [PMID: 38676802 DOI: 10.1007/978-1-0716-3858-3_12] [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
Patient-derived xenografts (PDXs) are a valuable preclinical research platform generated through transplantation of a patient's resected tumor into an immunodeficient or humanized mouse. PDXs serve as a high-fidelity avatar for both precision medicine and therapeutic testing against the cancer patient's disease state. While PDXs show mixed response to initial establishment, those that successfully engraft and can be sustained with serial passaging form a useful tool for basic and translational prostate cancer (PCa) research. While genetically engineered mouse (GEM) models and human cancer cell lines, and their xenografts, each play beneficial roles in discovery science and initial drug screening, PDX tumors are emerging as the gold standard approach for therapeutic proof-of-concept prior to entering clinical trial. PDXs are a powerful platform, with PCa PDXs shown to represent the original patient tumor cell population and architecture, histopathology, genomic and transcriptomic landscape, and heterogeneity. Furthermore, PDX response to anticancer drugs in mice has been closely correlated to the original patient's susceptibility to these treatments in the clinic. Several PDXs have been established and have undergone critical in-depth characterization at the cellular and molecular level across multiple PCa tumor subtypes representing both primary and metastatic patient tumors and their inherent levels of androgen responsiveness and/or treatment resistance, including androgen-sensitive, castration resistant, and neuroendocrine PCa. Multiple PDX networks and repositories have been generated for the collaborative and shared use of these vital translational cancer tools. Here we describe the creation of a PDX maintenance colony from an established well-characterized PDX, best practice for PDX maintenance in mice, and their subsequent application in preclinical drug testing. This chapter aims to serve as a go to resource for the preparation and adoption of PCa PDX models in the research laboratory and for their use as a valuable preclinical platform for translational research and therapeutic agent development.
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Affiliation(s)
- Lisa Kate Philp
- Australian Prostate Cancer Research Centre - Queensland, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD, Australia.
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5
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Feng Q, Chen J, Huang J, Li X, Liu X, Xiao C, Zheng X, Chen X, Li J, Gu Z, Luo K, Xiao K, Li W. A redox-responsive nanosystem to suppress chemoresistant lung cancer through targeting STAT3. J Control Release 2023; 363:349-360. [PMID: 37748583 DOI: 10.1016/j.jconrel.2023.09.044] [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: 06/02/2023] [Revised: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Cancer stem cells (CSCs) have been demonstrated to be involved in tumor initiation and relapse, and the presence of CSCs in the tumor tissue often leads to therapeutic failure. BBI608 has been identified to eliminate CSCs by inhibiting signal transducer and activator of transcription 3 (STAT3). In this study, we confirm that BBI608 can efficiently suppress the proliferation and migration of non-small cell lung cancer (NSCLC) cells, and specifically kill the stemness-high population in chemoresistant NSCLC cells. To improve its bioavailability and tumor accumulation, BBI608 is successfully encapsulated into redox-responsive PEGylated branched N-(2-hydroxypropyl) methacrylamide (HPMA)-deoxy cholic acid (DA) polymeric nanoparticles (BBI608-SS-NPs). The BBI608-SS-NPs can release the drug in response to high concentrations of intracellular glutathione, and exhibit cytotoxicity against lung cancer cells and CSCs comparable to the free drug BBI608. Furthermore, the BBI608-SS-NPs preferentially accumulate in tumor sites, resulting in a superior anti-tumor efficacy in both cisplatin-resistant cell line-derived xenograft (CDX) and patient-derived xenograft (PDX) models of NSCLC. Mechanistic studies demonstrate that BBI608-SS-NPs not only directly inhibit the downstream genes of the STAT3 pathway, but also indirectly inhibit the Wnt pathway. Overall, this stimuli-responsive polymeric nanoformulation of BBI608 shows great potential in the treatment of chemoresistant NSCLC by targeting CSCs.
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Affiliation(s)
- Qiyi Feng
- Department of Pulmonary and Critical Care Medicine, Precision Medicine Center, Huaxi MR Research Center (HMRRC), Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, Department of Respiratory Medicine, and Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jie Chen
- Department of Pulmonary and Critical Care Medicine, Precision Medicine Center, Huaxi MR Research Center (HMRRC), Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, Department of Respiratory Medicine, and Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jinxing Huang
- Department of Pulmonary and Critical Care Medicine, Precision Medicine Center, Huaxi MR Research Center (HMRRC), Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, Department of Respiratory Medicine, and Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaojie Li
- Department of Pulmonary and Critical Care Medicine, Precision Medicine Center, Huaxi MR Research Center (HMRRC), Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, Department of Respiratory Medicine, and Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xinyi Liu
- Department of Pulmonary and Critical Care Medicine, Precision Medicine Center, Huaxi MR Research Center (HMRRC), Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, Department of Respiratory Medicine, and Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chunxiu Xiao
- Department of Pulmonary and Critical Care Medicine, Precision Medicine Center, Huaxi MR Research Center (HMRRC), Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, Department of Respiratory Medicine, and Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiuli Zheng
- Department of Pulmonary and Critical Care Medicine, Precision Medicine Center, Huaxi MR Research Center (HMRRC), Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, Department of Respiratory Medicine, and Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Frontier Medical Center, Tianfu Jincheng Laboratory, Sichuan Provincial Key Laboratory of Precision Medicine, Functional and Molecular Imaging Key Laboratory of Sichuan Province, and Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu 610041, China
| | - Xuanming Chen
- Department of Pulmonary and Critical Care Medicine, Precision Medicine Center, Huaxi MR Research Center (HMRRC), Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, Department of Respiratory Medicine, and Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jue Li
- Department of Pulmonary and Critical Care Medicine, Precision Medicine Center, Huaxi MR Research Center (HMRRC), Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, Department of Respiratory Medicine, and Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhongwei Gu
- Department of Pulmonary and Critical Care Medicine, Precision Medicine Center, Huaxi MR Research Center (HMRRC), Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, Department of Respiratory Medicine, and Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Frontier Medical Center, Tianfu Jincheng Laboratory, Sichuan Provincial Key Laboratory of Precision Medicine, Functional and Molecular Imaging Key Laboratory of Sichuan Province, and Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu 610041, China
| | - Kui Luo
- Department of Pulmonary and Critical Care Medicine, Precision Medicine Center, Huaxi MR Research Center (HMRRC), Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, Department of Respiratory Medicine, and Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Frontier Medical Center, Tianfu Jincheng Laboratory, Sichuan Provincial Key Laboratory of Precision Medicine, Functional and Molecular Imaging Key Laboratory of Sichuan Province, and Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu 610041, China.
| | - Kai Xiao
- Department of Pulmonary and Critical Care Medicine, Precision Medicine Center, Huaxi MR Research Center (HMRRC), Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, Department of Respiratory Medicine, and Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Frontier Medical Center, Tianfu Jincheng Laboratory, Sichuan Provincial Key Laboratory of Precision Medicine, Functional and Molecular Imaging Key Laboratory of Sichuan Province, and Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu 610041, China.
| | - Weimin Li
- Department of Pulmonary and Critical Care Medicine, Precision Medicine Center, Huaxi MR Research Center (HMRRC), Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, Department of Respiratory Medicine, and Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Frontier Medical Center, Tianfu Jincheng Laboratory, Sichuan Provincial Key Laboratory of Precision Medicine, Functional and Molecular Imaging Key Laboratory of Sichuan Province, and Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu 610041, China.
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6
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Wang W, Li Y, Lin K, Wang X, Tu Y, Zhuo Z. Progress in building clinically relevant patient-derived tumor xenograft models for cancer research. Animal Model Exp Med 2023; 6:381-398. [PMID: 37679891 PMCID: PMC10614132 DOI: 10.1002/ame2.12349] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/03/2023] [Indexed: 09/09/2023] Open
Abstract
Patient-derived tumor xenograft (PDX) models, a method involving the surgical extraction of tumor tissues from cancer patients and subsequent transplantation into immunodeficient mice, have emerged as a pivotal approach in translational research, particularly in advancing precision medicine. As the first stage of PDX development, the patient-derived orthotopic xenograft (PDOX) models implant tumor tissue in mice in the corresponding anatomical locations of the patient. The PDOX models have several advantages, including high fidelity to the original tumor, heightened drug sensitivity, and an elevated rate of successful transplantation. However, the PDOX models present significant challenges, requiring advanced surgical techniques and resource-intensive imaging technologies, which limit its application. And then, the humanized mouse models, as well as the zebrafish models, were developed. Humanized mouse models contain a human immune environment resembling the tumor and immune system interplay. The humanized mouse models are a hot topic in PDX model research. Regarding zebrafish patient-derived tumor xenografts (zPDX) and patient-derived organoids (PDO) as promising models for studying cancer and drug discovery, zPDX models are used to transplant tumors into zebrafish as novel personalized medical animal models with the advantage of reducing patient waiting time. PDO models provide a cost-effective approach for drug testing that replicates the in vivo environment and preserves important tumor-related information for patients. The present review highlights the functional characteristics of each new phase of PDX and provides insights into the challenges and prospective developments in this rapidly evolving field.
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Affiliation(s)
- Weijing Wang
- Department of Clinical MedicineShantou University Medical CollegeShantouChina
| | - Yongshu Li
- College of Life SciencesHubei Normal UniversityHuangshiChina
- Shenzhen Institute for Technology InnovationNational Institute of MetrologyShenzhenChina
| | - Kaida Lin
- Department of Clinical MedicineShantou University Medical CollegeShantouChina
| | - Xiaokang Wang
- Department of PharmacyShenzhen Longhua District Central HospitalShenzhenChina
| | - Yanyang Tu
- Research Center, Huizhou Central People's HospitalGuangdong Medical UniversityHuizhou CityChina
| | - Zhenjian Zhuo
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate SchoolShenzhenChina
- Laboratory Animal Center, School of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate SchoolShenzhenChina
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7
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Croft D, Lodhia P, Lourenco S, MacKay C. Effectively utilizing publicly available databases for cancer target evaluation. NAR Cancer 2023; 5:zcad035. [PMID: 37457379 PMCID: PMC10346432 DOI: 10.1093/narcan/zcad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/12/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
The majority of compounds designed against cancer drug targets do not progress to become approved drugs, mainly due to lack of efficacy and/or unmanageable toxicity. Robust target evaluation is therefore required before progressing through the drug discovery process to reduce the high attrition rate. There are a wealth of publicly available databases that can be mined to generate data as part of a target evaluation. It can, however, be challenging to learn what databases are available, how and when they should be used, and to understand the associated limitations. Here, we have compiled and present key, freely accessible and easy-to-use databases that house informative datasets from in vitro, in vivo and clinical studies. We also highlight comprehensive target review databases that aim to bring together information from multiple sources into one-stop portals. In the post-genomics era, a key objective is to exploit the extensive cell, animal and patient characterization datasets in order to deliver precision medicine on a patient-specific basis. Effective utilization of the highlighted databases will go some way towards supporting the cancer research community achieve these aims.
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Affiliation(s)
- Daniel Croft
- Cancer Research Horizons, The Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Puja Lodhia
- Cancer Research Horizons, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sofia Lourenco
- Cancer Research Horizons, The Francis Crick Institute, London, NW1 1AT, UK
| | - Craig MacKay
- Cancer Research Horizons, The Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
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8
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Lawrence MG, Taylor RA, Cuffe GB, Ang LS, Clark AK, Goode DL, Porter LH, Le Magnen C, Navone NM, Schalken JA, Wang Y, van Weerden WM, Corey E, Isaacs JT, Nelson PS, Risbridger GP. The future of patient-derived xenografts in prostate cancer research. Nat Rev Urol 2023; 20:371-384. [PMID: 36650259 PMCID: PMC10789487 DOI: 10.1038/s41585-022-00706-x] [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] [Accepted: 12/09/2022] [Indexed: 01/19/2023]
Abstract
Patient-derived xenografts (PDXs) are generated by engrafting human tumours into mice. Serially transplantable PDXs are used to study tumour biology and test therapeutics, linking the laboratory to the clinic. Although few prostate cancer PDXs are available in large repositories, over 330 prostate cancer PDXs have been established, spanning broad clinical stages, genotypes and phenotypes. Nevertheless, more PDXs are needed to reflect patient diversity, and to study new treatments and emerging mechanisms of resistance. We can maximize the use of PDXs by exchanging models and datasets, and by depositing PDXs into biorepositories, but we must address the impediments to accessing PDXs, such as institutional, ethical and legal agreements. Through collaboration, researchers will gain greater access to PDXs representing diverse features of prostate cancer.
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Affiliation(s)
- Mitchell G Lawrence
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
- Melbourne Urological Research Alliance, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia.
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.
- Cabrini Institute, Cabrini Health, Malvern, Victoria, Australia.
| | - Renea A Taylor
- Melbourne Urological Research Alliance, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Cabrini Institute, Cabrini Health, Malvern, Victoria, Australia
- Department of Physiology, Monash University, Clayton, Victoria, Australia
| | - Georgia B Cuffe
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Lisa S Ang
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ashlee K Clark
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Department of Urology, Radboud University Medical Center, Nijmegen, Netherlands
| | - David L Goode
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Laura H Porter
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Clémentine Le Magnen
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- Department of Urology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Nora M Navone
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jack A Schalken
- Department of Urology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
- Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - John T Isaacs
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (SKCCC), Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pharmacology and Molecular Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Gail P Risbridger
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
- Melbourne Urological Research Alliance, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia.
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.
- Cabrini Institute, Cabrini Health, Malvern, Victoria, Australia.
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9
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Liu Y, Wu W, Cai C, Zhang H, Shen H, Han Y. Patient-derived xenograft models in cancer therapy: technologies and applications. Signal Transduct Target Ther 2023; 8:160. [PMID: 37045827 PMCID: PMC10097874 DOI: 10.1038/s41392-023-01419-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Patient-derived xenograft (PDX) models, in which tumor tissues from patients are implanted into immunocompromised or humanized mice, have shown superiority in recapitulating the characteristics of cancer, such as the spatial structure of cancer and the intratumor heterogeneity of cancer. Moreover, PDX models retain the genomic features of patients across different stages, subtypes, and diversified treatment backgrounds. Optimized PDX engraftment procedures and modern technologies such as multi-omics and deep learning have enabled a more comprehensive depiction of the PDX molecular landscape and boosted the utilization of PDX models. These irreplaceable advantages make PDX models an ideal choice in cancer treatment studies, such as preclinical trials of novel drugs, validating novel drug combinations, screening drug-sensitive patients, and exploring drug resistance mechanisms. In this review, we gave an overview of the history of PDX models and the process of PDX model establishment. Subsequently, the review presents the strengths and weaknesses of PDX models and highlights the integration of novel technologies in PDX model research. Finally, we delineated the broad application of PDX models in chemotherapy, targeted therapy, immunotherapy, and other novel therapies.
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Affiliation(s)
- Yihan Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Wantao Wu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China.
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China.
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10
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Goncharova AS, Kolesnikov EN, Egorov GY, Maksimov AY, Shevchenko AN, Nepomnyashchaya EM, Gvaldin DY, Kurbanova LZ, Khodakova DV, Kit SO, Kaymakchi OY, Snezhko AV. Development and characterization of patient-derived xenograft models of colorectal cancer for testing new pharmacological substances. BULLETIN OF SIBERIAN MEDICINE 2023. [DOI: 10.20538/1682-0363-2022-4-37-43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The aim of the study was to create a patient-derived xenograft (PDX) model of human colorectal cancer and to determine its histologic and molecular characteristics, such as the status of KRAS, NRAS, and BRAF genes and the presence of microsatellite instability.Materials and methods. First generation xenograft models in vivo were created using tumors from patients with colorectal cancer (n = 4) and immunodeficient Balb/c Nude mice (n = 20); second, third, and fourth generation models were created in the same mouse line (n = 3 for each generation). A caliper was used to measure subcutaneous xenografts; their size was calculated by the ellipsoid formula. Cryopreservation involved immersing the samples in a freezing medium (80% RPMI 1640, 10% fetal bovine serum, 10% dimethyl sulfoxide (DMSO)) and storing them at –80 °C. The histologic analysis was performed according to the standard technique (preparation of paraffin blocks and staining of microsections with hematoxylin and eosin). Mutations in the KRAS, NRAS, and BRAF genes were determined by direct Sanger sequencing; microsatellite instability was determined by the fragment analysis at five loci: Bat-25, Bat-26, NR21, NR24, and NR27.Results. Stable, transplantable xenografts of colorectal cancer were obtained from two out of four patients. The average waiting time from the implantation to the growth of the first generation xenograft was 28 days. The latency phase after cryopreservation was comparable to that at the creation of the first generation PDX model. The model reproduced the histotype, grade and mutational status of the KRAS, NRAS, and BRAF genes, as well as microsatellite instability of the donor tumor.Conclusion. The developed model of human colorectal cancer was characterized in terms of growth dynamics, cryopreservation tolerance, and histologic and molecular genetic parameters.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - S. O. Kit
- National Medical Research Center for Oncology
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11
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Landuzzi L, Ruzzi F, Lollini PL, Scotlandi K. Synovial Sarcoma Preclinical Modeling: Integrating Transgenic Mouse Models and Patient-Derived Models for Translational Research. Cancers (Basel) 2023; 15:cancers15030588. [PMID: 36765545 PMCID: PMC9913760 DOI: 10.3390/cancers15030588] [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: 12/20/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Synovial sarcomas (SyS) are rare malignant tumors predominantly affecting children, adolescents, and young adults. The genetic hallmark of SyS is the t(X;18) translocation encoding the SS18-SSX fusion gene. The fusion protein interacts with both the BAF enhancer and polycomb repressor complexes, and either activates or represses target gene transcription, resulting in genome-wide epigenetic perturbations and altered gene expression. Several experimental in in vivo models, including conditional transgenic mouse models expressing the SS18-SSX fusion protein and spontaneously developing SyS, are available. In addition, patient-derived xenografts have been estab-lished in immunodeficient mice, faithfully reproducing the complex clinical heterogeneity. This review focuses on the main molecular features of SyS and the related preclinical in vivo and in vitro models. We will analyze the different conditional SyS mouse models that, after combination with some of the few other recurrent alterations, such as gains in BCL2, Wnt-β-catenin signaling, FGFR family, or loss of PTEN and SMARCB1, have provided additional insight into the mechanisms of synovial sarcomagenesis. The recent advancements in the understanding of SyS biology and improvements in preclinical modeling pave the way to the development of new epigenetic drugs and immunotherapeutic approaches conducive to new treatment options.
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Affiliation(s)
- Lorena Landuzzi
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
- Correspondence: (L.L.); (P.-L.L.); Tel.: +39-051-2094796 (L.L.); +39-051-2094786 (P.-L.L.)
| | - Francesca Ruzzi
- Laboratory of Immunology and Biology of Metastasis, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Pier-Luigi Lollini
- Laboratory of Immunology and Biology of Metastasis, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
- Correspondence: (L.L.); (P.-L.L.); Tel.: +39-051-2094796 (L.L.); +39-051-2094786 (P.-L.L.)
| | - Katia Scotlandi
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
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12
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Serra-Camprubí Q, Verdaguer H, Oliveros W, Lupión-Garcia N, Llop-Guevara A, Molina C, Vila-Casadesús M, Turpin A, Neuzillet C, Frigola J, Querol J, Yáñez-Bartolomé M, Castet F, Fabregat-Franco C, Escudero-Iriarte C, Escorihuela M, Arenas EJ, Bernadó-Morales C, Haro N, Giles FJ, Pozo ÓJ, Miquel JM, Nuciforo PG, Vivancos A, Melé M, Serra V, Arribas J, Tabernero J, Peiró S, Macarulla T, Tian TV. Human Metastatic Cholangiocarcinoma Patient-Derived Xenografts and Tumoroids for Preclinical Drug Evaluation. Clin Cancer Res 2023; 29:432-445. [PMID: 36374558 PMCID: PMC9873249 DOI: 10.1158/1078-0432.ccr-22-2551] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/14/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Cholangiocarcinoma (CCA) is usually diagnosed at advanced stages, with limited therapeutic options. Preclinical models focused on unresectable metastatic CCA are necessary to develop rational treatments. Pathogenic mutations in IDH1/2, ARID1A/B, BAP1, and BRCA1/2 have been identified in 30%-50% of patients with CCA. Several types of tumor cells harboring these mutations exhibit homologous recombination deficiency (HRD) phenotype with enhanced sensitivity to PARP inhibitors (PARPi). However, PARPi treatment has not yet been tested for effectiveness in patient-derived models of advanced CCA. EXPERIMENTAL DESIGN We have established a collection of patient-derived xenografts from patients with unresectable metastatic CCA (CCA_PDX). The CCA_PDXs were characterized at both histopathologic and genomic levels. We optimized a protocol to generate CCA tumoroids from CCA_PDXs. We tested the effects of PARPis in both CCA tumoroids and CCA_PDXs. Finally, we used the RAD51 assay to evaluate the HRD status of CCA tissues. RESULTS This collection of CCA_PDXs recapitulates the histopathologic and molecular features of their original tumors. PARPi treatments inhibited the growth of CCA tumoroids and CCA_PDXs with pathogenic mutations of BRCA2, but not those with mutations of IDH1, ARID1A, or BAP1. In line with these findings, only CCA_PDX and CCA patient biopsy samples with mutations of BRCA2 showed RAD51 scores compatible with HRD. CONCLUSIONS Our results suggest that patients with advanced CCA with pathogenic mutations of BRCA2, but not those with mutations of IDH1, ARID1A, or BAP1, are likely to benefit from PARPi therapy. This collection of CCA_PDXs provides new opportunities for evaluating drug response and prioritizing clinical trials.
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Affiliation(s)
- Queralt Serra-Camprubí
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Helena Verdaguer
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Gastrointestinal and Endocrine Tumor Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Winona Oliveros
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Núria Lupión-Garcia
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Alba Llop-Guevara
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Cristina Molina
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Maria Vila-Casadesús
- Cancer Genomics Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Anthony Turpin
- Université de Lille, CNRS INSERM UMR9020-U1277, CANTHER Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, France.,Medical Oncology Department, CHRU Lille, Lille, France
| | - Cindy Neuzillet
- Gastrointestinal Oncology, Medical Oncology Department, Curie Institute, Versailles St-Quentin-Paris Saclay University, Saint-Cloud, France
| | - Joan Frigola
- Clinical Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Jessica Querol
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Mariana Yáñez-Bartolomé
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Florian Castet
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Gastrointestinal and Endocrine Tumor Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carles Fabregat-Franco
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Gastrointestinal and Endocrine Tumor Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carmen Escudero-Iriarte
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Marta Escorihuela
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Enrique J. Arenas
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Cristina Bernadó-Morales
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Noemí Haro
- Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | | | - Óscar J. Pozo
- Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Josep M. Miquel
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Paolo G. Nuciforo
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Violeta Serra
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Joaquín Arribas
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Monforte de Lemos, Madrid, Spain.,Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Josep Tabernero
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Gastrointestinal and Endocrine Tumor Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Sandra Peiró
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Corresponding Authors: Tian V. Tian, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain. Phone: (34)932543450, ext. 8656; E-mail: ; Teresa Macarulla, ; and Sandra Peiró,
| | - Teresa Macarulla
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Gastrointestinal and Endocrine Tumor Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Corresponding Authors: Tian V. Tian, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain. Phone: (34)932543450, ext. 8656; E-mail: ; Teresa Macarulla, ; and Sandra Peiró,
| | - Tian V. Tian
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Corresponding Authors: Tian V. Tian, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain. Phone: (34)932543450, ext. 8656; E-mail: ; Teresa Macarulla, ; and Sandra Peiró,
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13
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Xu H, Zheng H, Zhang Q, Song H, Wang Q, Xiao J, Dong Y, Shen Z, Wang S, Wu S, Wei Y, Lu W, Zhu Y, Niu X. A Multicentre Clinical Study of Sarcoma Personalised Treatment Using Patient-Derived Tumour Xenografts. Clin Oncol (R Coll Radiol) 2023; 35:e48-e59. [PMID: 35781406 DOI: 10.1016/j.clon.2022.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/21/2022] [Accepted: 06/09/2022] [Indexed: 01/04/2023]
Abstract
AIMS Medication for advanced sarcomas has not improved for three decades. Patient-derived tumour xenografts (PDTX) are a promising solution for developing new therapies and real-time personalised medicine because of their highly effective prediction of drug efficacy. However, there is a dearth of PDTX models for sarcomas due to the scarcity and heterogeneity of the disease. MATERIALS AND METHODS A multicentre clinical collaborative study (ChiCTR-OOC-17013617) was carried out. Fresh patient tumour tissues via resection or biopsy were used for the PDTX set-up. The standard medical care chosen by the physician was given to the patient, in parallel with testing on multiple regimens. The outcomes of patients' responses and PDTX tests were compared. Comprehensive analyses were carried out to assess the clinical value of PDTX for the treatment of sarcomas. Living tissues from successfully engrafted cases were deposited into a repository. RESULTS Forty-two cases, including 36 bone sarcomas and six soft-tissue sarcomas, were enrolled; the overall engraftment rate was 73.8%. Histopathological examination showed a 100% consistency between primary tumours and tumour grafts. The engraftment rate was independent of age, gender and sampling methods, but was associated with subtypes of tumour. The outgrowth time of tumour grafts could be associated with prognosis. Major somatic mutations in tumour grafts occurred primarily in common tumour driver genes. Poor prognosis was associated with the KMT2C mutation. A drug efficacy test showed complete concordance between the PDTX model and patients' responses in 17 regimens. CONCLUSION PDTX is an ideal preclinical model for sarcomas because of its faithful preservation of the heterogeneity of the disease, a satisfactory engraftment rate and high accuracy in its prediction of drug efficacy.
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Affiliation(s)
- H Xu
- Beijing Jishuitan Hospital, Beijing, China
| | - H Zheng
- Nanjing Personal Oncology Biological Technology Co. Ltd, Nanjing, China
| | - Q Zhang
- Beijing Jishuitan Hospital, Beijing, China
| | - H Song
- Nanjing Personal Oncology Biological Technology Co. Ltd, Nanjing, China
| | - Q Wang
- Nanjing Personal Oncology Biological Technology Co. Ltd, Nanjing, China
| | - J Xiao
- Changzheng Hospital, Shanghai, China
| | - Y Dong
- The Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Z Shen
- The Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - S Wang
- Spine Surgery, Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - S Wu
- Jinling Hospital, Nanjing, Jiangsu, China
| | - Y Wei
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - W Lu
- Zhongshan Hospital, Fudan University, Shanghai, China
| | - Y Zhu
- Nanjing Personal Oncology Biological Technology Co. Ltd, Nanjing, China
| | - X Niu
- Beijing Jishuitan Hospital, Beijing, China.
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14
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Perova Z, Martinez M, Mandloi T, Gomez F, Halmagyi C, Follette A, Mason J, Newhauser S, Begley D, Krupke D, Bult C, Parkinson H, Groza T. PDCM Finder: an open global research platform for patient-derived cancer models. Nucleic Acids Res 2022; 51:D1360-D1366. [PMID: 36399494 PMCID: PMC9825610 DOI: 10.1093/nar/gkac1021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
PDCM Finder (www.cancermodels.org) is a cancer research platform that aggregates clinical, genomic and functional data from patient-derived xenografts, organoids and cell lines. It was launched in April 2022 as a successor of the PDX Finder portal, which focused solely on patient-derived xenograft models. Currently the portal has over 6200 models across 13 cancer types, including rare paediatric models (17%) and models from minority ethnic backgrounds (33%), making it the largest free to consumer and open access resource of this kind. The PDCM Finder standardises, harmonises and integrates the complex and diverse data associated with PDCMs for the cancer community and displays over 90 million data points across a variety of data types (clinical metadata, molecular and treatment-based). PDCM data is FAIR and underpins the generation and testing of new hypotheses in cancer mechanisms and personalised medicine development.
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Affiliation(s)
- Zinaida Perova
- To whom correspondence should be addressed. Tel: +44 1223 494 121; Fax: +44 1223 494 468;
| | - Mauricio Martinez
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tushar Mandloi
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Federico Lopez Gomez
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Csaba Halmagyi
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alex Follette
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steven Newhauser
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Dale A Begley
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Debra M Krupke
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Carol Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Helen Parkinson
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tudor Groza
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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15
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Woo XY, Srivastava A, Mack PC, Graber JH, Sanderson BJ, Lloyd MW, Chen M, Domanskyi S, Gandour-Edwards R, Tsai RA, Keck J, Cheng M, Bundy M, Jocoy EL, Riess JW, Holland W, Grubb SC, Peterson JG, Stafford GA, Paisie C, Neuhauser SB, Karuturi RKM, George J, Simons AK, Chavaree M, Tepper CG, Goodwin N, Airhart SD, Lara PN, Openshaw TH, Liu ET, Gandara DR, Bult CJ. A Genomically and Clinically Annotated Patient-Derived Xenograft Resource for Preclinical Research in Non-Small Cell Lung Cancer. Cancer Res 2022; 82:4126-4138. [PMID: 36069866 PMCID: PMC9664138 DOI: 10.1158/0008-5472.can-22-0948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/22/2022] [Accepted: 09/01/2022] [Indexed: 12/14/2022]
Abstract
Patient-derived xenograft (PDX) models are an effective preclinical in vivo platform for testing the efficacy of novel drugs and drug combinations for cancer therapeutics. Here we describe a repository of 79 genomically and clinically annotated lung cancer PDXs available from The Jackson Laboratory that have been extensively characterized for histopathologic features, mutational profiles, gene expression, and copy-number aberrations. Most of the PDXs are models of non-small cell lung cancer (NSCLC), including 37 lung adenocarcinoma (LUAD) and 33 lung squamous cell carcinoma (LUSC) models. Other lung cancer models in the repository include four small cell carcinomas, two large cell neuroendocrine carcinomas, two adenosquamous carcinomas, and one pleomorphic carcinoma. Models with both de novo and acquired resistance to targeted therapies with tyrosine kinase inhibitors are available in the collection. The genomic profiles of the LUAD and LUSC PDX models are consistent with those observed in patient tumors from The Cancer Genome Atlas and previously characterized gene expression-based molecular subtypes. Clinically relevant mutations identified in the original patient tumors were confirmed in engrafted PDX tumors. Treatment studies performed in a subset of the models recapitulated the responses expected on the basis of the observed genomic profiles. These models therefore serve as a valuable preclinical platform for translational cancer research. SIGNIFICANCE Patient-derived xenografts of lung cancer retain key features observed in the originating patient tumors and show expected responses to treatment with standard-of-care agents, providing experimentally tractable and reproducible models for preclinical investigations.
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Affiliation(s)
- Xing Yi Woo
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA,Current affiliation: Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Anuj Srivastava
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Philip C. Mack
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA,Current affiliation: Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joel H. Graber
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA,Current affiliation: MDI Biological Laboratory, Bar Harbor, Maine, USA
| | - Brian J. Sanderson
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Michael W. Lloyd
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - Mandy Chen
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - Sergii Domanskyi
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | | | - Rebekah A. Tsai
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - James Keck
- The Jackson Laboratory, Sacramento, California, USA
| | | | | | | | - Jonathan W. Riess
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - William Holland
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Stephen C. Grubb
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - James G. Peterson
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - Grace A. Stafford
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - Carolyn Paisie
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | | | | | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Allen K. Simons
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - Margaret Chavaree
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA,Eastern Maine Medical Center, Lafayette Family Cancer Center, Brewer, Maine, USA
| | - Clifford G. Tepper
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Neal Goodwin
- The Jackson Laboratory, Sacramento, California, USA,Current affiliation: Teknova, Hollister, California USA
| | - Susan D. Airhart
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - Primo N. Lara
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Thomas H. Openshaw
- Eastern Maine Medical Center, Lafayette Family Cancer Center, Brewer, Maine, USA,Current affiliation: Cape Cod Hospital, Hyannis, Massachusetts, USA
| | - Edison T. Liu
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - David R. Gandara
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Carol J. Bult
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA,Corresponding author: Carol J. Bult, The Jackson Laboratory, 600 Main Street, RL13, Bar Harbor, ME 04609; (tel) 207-288-6324,
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16
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Schueler J, Borenstein J, Buti L, Dong M, Masmoudi F, Hribar K, Anderson E, Sommergruber W. How to build a tumor: An industry perspective. Drug Discov Today 2022; 27:103329. [PMID: 35908685 PMCID: PMC9585375 DOI: 10.1016/j.drudis.2022.07.014] [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: 03/23/2022] [Revised: 06/23/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
During the past 15 years, a plethora of innovative 3D in vitro systems has been developed. They offer the possibility of identifying crucial cellular and molecular contributors to the disease by permitting manipulation of each in isolation. However, improvements are needed particularly with respect to the predictivity and validity of those models. The major challenge now is to identify which assay and readout combination(s) best suits the current scientific question(s). A deep understanding of the different platforms along with their pros and cons is a prerequisite to make this decision. This review aims to give an overview of the most prominent systems with a focus on applications, translational relevance and adoption drivers from an industry perspective.
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Affiliation(s)
- Julia Schueler
- Charles River Discovery Research Services Germany GmbH, Freiburg, Germany,Corresponding author.
| | | | | | - Meng Dong
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology and University of Tuebingen, Stuttgart, Germany
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17
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Zanella ER, Grassi E, Trusolino L. Towards precision oncology with patient-derived xenografts. Nat Rev Clin Oncol 2022; 19:719-732. [PMID: 36151307 DOI: 10.1038/s41571-022-00682-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2022] [Indexed: 11/09/2022]
Abstract
Under the selective pressure of therapy, tumours dynamically evolve multiple adaptive mechanisms that make static interrogation of genomic alterations insufficient to guide treatment decisions. Clinical research does not enable the assessment of how various regulatory circuits in tumours are affected by therapeutic insults over time and space. Likewise, testing different precision oncology approaches informed by composite and ever-changing molecular information is hard to achieve in patients. Therefore, preclinical models that incorporate the biology and genetics of human cancers, facilitate analyses of complex variables and enable adequate population throughput are needed to pinpoint randomly distributed response predictors. Patient-derived xenograft (PDX) models are dynamic entities in which cancer evolution can be monitored through serial propagation in mice. PDX models can also recapitulate interpatient diversity, thus enabling the identification of response biomarkers and therapeutic targets for molecularly defined tumour subgroups. In this Review, we discuss examples from the past decade of the use of PDX models for precision oncology, from translational research to drug discovery. We elaborate on how and to what extent preclinical observations in PDX models have confirmed and/or anticipated findings in patients. Finally, we illustrate emerging methodological efforts that could broaden the application of PDX models by honing their predictive accuracy or improving their versatility.
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Affiliation(s)
| | - Elena Grassi
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Italy.,Department of Oncology, University of Torino, Candiolo, Italy
| | - Livio Trusolino
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Italy. .,Department of Oncology, University of Torino, Candiolo, Italy.
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18
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Qin T, Fan J, Lu F, Zhang L, Liu C, Xiong Q, Zhao Y, Chen G, Sun C. Harnessing preclinical models for the interrogation of ovarian cancer. J Exp Clin Cancer Res 2022; 41:277. [PMID: 36114548 PMCID: PMC9479310 DOI: 10.1186/s13046-022-02486-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/05/2022] [Indexed: 12/24/2022] Open
Abstract
Ovarian cancer (OC) is a heterogeneous malignancy with various etiology, histopathology, and biological feature. Despite accumulating understanding of OC in the post-genomic era, the preclinical knowledge still undergoes limited translation from bench to beside, and the prognosis of ovarian cancer has remained dismal over the past 30 years. Henceforth, reliable preclinical model systems are warranted to bridge the gap between laboratory experiments and clinical practice. In this review, we discuss the status quo of ovarian cancer preclinical models which includes conventional cell line models, patient-derived xenografts (PDXs), patient-derived organoids (PDOs), patient-derived explants (PDEs), and genetically engineered mouse models (GEMMs). Each model has its own strengths and drawbacks. We focus on the potentials and challenges of using these valuable tools, either alone or in combination, to interrogate critical issues with OC.
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19
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Gasparini P, Casanova M, Centonze G, Borzi C, Bergamaschi L, Collini P, Testi A, Chiaravalli S, Massimino M, Sozzi G, Ferrari A, Moro M. Establishment of 6 pediatric rhabdomyosarcoma patient’s derived xenograft models closely recapitulating patients’ tumor characteristics. TUMORI JOURNAL 2022:3008916221110266. [PMID: 36114629 DOI: 10.1177/03008916221110266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Introduction: The prognosis for patients with metastatic and recurrent pediatric rhabdomyosarcoma (RMS) remains poor. The availability of preclinical models is essential to identify promising treatments We established a series of pediatric RMS patient derived xenografts (PDXs), all faithfully mirroring primary tumor characteristics and representing a unique tool for clarifying the biological processes underlying RMS progression and relapse. Methods: Fresh tumor samples from 12 RMS patients were implanted subcutaneously in both flanks of immunocompromised mice. PDXs were considered as grafted after accomplishing three passages in mice. Characterization of tumor tissues and models was performed by comparing both morphology and immunoistochemical and fluorescence in situ hybridization (FISH) characteristics. Results: Six PDXs were established, with a successful take rate of 50%. All models closely mirrored parental tumor characteristics. An increased grafting rate for tumors derived from patients with worse outcome (p = 0.006) was detected. For 50% PDXs grafting occurred when the corresponding patient was still alive. Conclusion: Our findings increase the number of available RMS PDX models and strengthen the role of PDXs as useful preclinical tools for patients with unmet medical needs and to develop personalized therapies.
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Affiliation(s)
- Patrizia Gasparini
- Tumor Genomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Michela Casanova
- Paediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Giovanni Centonze
- First Pathology Division, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Cristina Borzi
- Tumor Genomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Luca Bergamaschi
- Paediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Paola Collini
- Soft Tissue and Bone Pathology, Histopathology and Pediatric Pathology Unit, Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Adele Testi
- Laboratory of Molecular Pathology, Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Stefano Chiaravalli
- Paediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Maura Massimino
- Paediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Gabriella Sozzi
- Tumor Genomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Ferrari
- Paediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Massimo Moro
- Tumor Genomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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20
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Poulos RC, Cai Z, Robinson PJ, Reddel RR, Zhong Q. Opportunities for pharmacoproteomics in biomarker discovery. Proteomics 2022; 23:e2200031. [PMID: 36086888 DOI: 10.1002/pmic.202200031] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/30/2022] [Accepted: 09/06/2022] [Indexed: 11/08/2022]
Abstract
Proteomic data are a uniquely valuable resource for drug response prediction and biomarker discovery because most drugs interact directly with proteins in target cells rather than with DNA or RNA. Recent advances in mass spectrometry and associated processing methods have enabled the generation of large-scale proteomic datasets. Here we review the significant opportunities that currently exist to combine large-scale proteomic data with drug-related research, a field termed pharmacoproteomics. We describe successful applications of drug response prediction using molecular data, with an emphasis on oncology. We focus on technical advances in data-independent acquisition mass spectrometry (DIA-MS) that can facilitate the discovery of protein biomarkers for drug responses, alongside the increased availability of big biomedical data. We spotlight new opportunities for machine learning in pharmacoproteomics, driven by the combination of these large datasets and improved high-performance computing. Finally, we explore the value of pre-clinical models for pharmacoproteomic studies and the accompanying challenges of clinical validation. We propose that pharmacoproteomics offers the potential for novel discovery and innovation within the cancer landscape. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Rebecca C Poulos
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Zhaoxiang Cai
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Phillip J Robinson
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Roger R Reddel
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Qing Zhong
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
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21
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Genta S, Coburn B, Cescon DW, Spreafico A. Patient-derived cancer models: Valuable platforms for anticancer drug testing. Front Oncol 2022; 12:976065. [PMID: 36033445 PMCID: PMC9413077 DOI: 10.3389/fonc.2022.976065] [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: 06/23/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Molecularly targeted treatments and immunotherapy are cornerstones in oncology, with demonstrated efficacy across different tumor types. Nevertheless, the overwhelming majority metastatic disease is incurable due to the onset of drug resistance. Preclinical models including genetically engineered mouse models, patient-derived xenografts and two- and three-dimensional cell cultures have emerged as a useful resource to study mechanisms of cancer progression and predict efficacy of anticancer drugs. However, variables including tumor heterogeneity and the complexities of the microenvironment can impair the faithfulness of these platforms. Here, we will discuss advantages and limitations of these preclinical models, their applicability for drug testing and in co-clinical trials and potential strategies to increase their reliability in predicting responsiveness to anticancer medications.
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Affiliation(s)
- Sofia Genta
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - David W. Cescon
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Anna Spreafico
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
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22
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Huang L, Wang J, Fang B, Meric-Bernstam F, Roth JA, Ha MJ. CombPDX: a unified statistical framework for evaluating drug synergism in patient-derived xenografts. Sci Rep 2022; 12:12984. [PMID: 35906256 PMCID: PMC9338066 DOI: 10.1038/s41598-022-16933-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/18/2022] [Indexed: 12/14/2022] Open
Abstract
Anticancer combination therapy has been developed to increase efficacy by enhancing synergy. Patient-derived xenografts (PDXs) have emerged as reliable preclinical models to develop effective treatments in translational cancer research. However, most PDX combination study designs focus on single dose levels, and dose-response surface models are not appropriate for testing synergism. We propose a comprehensive statistical framework to assess joint action of drug combinations from PDX tumor growth curve data. We provide various metrics and robust statistical inference procedures that locally (at a fixed time) and globally (across time) access combination effects under classical drug interaction models. Integrating genomic and pharmacological profiles in non-small-cell lung cancer (NSCLC), we have shown the utilities of combPDX in discovering effective therapeutic combinations and relevant biological mechanisms. We provide an interactive web server, combPDX ( https://licaih.shinyapps.io/CombPDX/ ), to analyze PDX tumor growth curve data and perform power analyses.
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Affiliation(s)
- Licai Huang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Quantitative Sciences Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Jing Wang
- Departments of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Bingliang Fang
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jack A Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Min Jin Ha
- Department of Biostatistics, Graduate School of Public Health, Yonsei University, Seoul, South Korea.
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23
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Tanaka K, Kato I, Dobashi Y, Imai JI, Mikami T, Kubota H, Ueno H, Ito M, Ogawa S, Nakahata T, Takita J, Toyoda H, Ogawa C, Adachi S, Watanabe S, Goto H. The first Japanese biobank of patient-derived pediatric acute lymphoblastic leukemia xenograft models. Cancer Sci 2022; 113:3814-3825. [PMID: 35879192 DOI: 10.1111/cas.15506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/11/2022] [Accepted: 07/19/2022] [Indexed: 11/28/2022] Open
Abstract
A lack of practical resources in Japan has limited preclinical discovery and testing of therapies for pediatric relapsed and refractory acute lymphoblastic leukemia (ALL), which has poor outcomes. Here, we established 57 patient-derived xenografts (PDXs) in NOD.Cg-Prkdcscid ll2rgtm1Sug /ShiJic (NOG) mice and created a biobank by preserving PDX cells including 3 extramedullary relapsed ALL PDXs. We demonstrated that our PDX mice and PDX cells mimicked the biological features of relapsed ALL and that PDX models reproduced treatment-mediated clonal selection. Our PDX biobank is a useful scientific resource for capturing drug sensitivity features of pediatric patients with ALL, providing an essential tool for the development of targeted therapies.
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Affiliation(s)
- Kuniaki Tanaka
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Japan Children's Cancer Group, Relapsed ALL Committee
| | - Yuu Dobashi
- Medical-Industrial Translational Research Center, Fukushima Medical University, Fukushima, Japan
| | - Jun-Ichi Imai
- Medical-Industrial Translational Research Center, Fukushima Medical University, Fukushima, Japan
| | - Takashi Mikami
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hirohito Kubota
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroo Ueno
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Pathology and Tumor Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Mamoru Ito
- Central Institute for Experimental Animals, Kawasaki, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tatsutoshi Nakahata
- Central Institute for Experimental Animals, Kawasaki, Japan.,Department of Fundamental Cell Technology, Center for iPS Cell Research and Application, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hidemi Toyoda
- Japan Children's Cancer Group, Relapsed ALL Committee.,Department of Pediatrics, Mie University Graduate School of Medicine, Mie, Japan
| | - Chitose Ogawa
- Japan Children's Cancer Group, Relapsed ALL Committee.,Department of Pediatric Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Souichi Adachi
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinya Watanabe
- Medical-Industrial Translational Research Center, Fukushima Medical University, Fukushima, Japan
| | - Hiroaki Goto
- Japan Children's Cancer Group, Relapsed ALL Committee.,Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
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24
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Theranostic Potentials of Gold Nanomaterials in Hematological Malignancies. Cancers (Basel) 2022; 14:cancers14133047. [PMID: 35804818 PMCID: PMC9264814 DOI: 10.3390/cancers14133047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/03/2022] [Accepted: 06/17/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Hematological malignancies (HMs) cover 50% of all malignancies, and people of all ages can be affected by these deadly diseases. In many cases, conventional diagnostic tools fail to diagnose HMs at an early stage, due to heterogeneity and the long-term indolent phase of HMs. Therefore, many patients start their treatment at the late stage of HMs and have poor survival. Gold nanomaterials (GNMs) have shown promise as a cancer theranostic agent. GNMs are 1 nm to 100 nm materials having magnetic resonance and surface-plasmon-resonance properties. GNMs conjugated with antibodies, nucleic acids, peptides, photosensitizers, chemotherapeutic drugs, synthetic-drug candidates, bioactive compounds, and other theranostic biomolecules may enhance the efficacy and efficiency of both traditional and advanced theranostic approaches to combat HMs. Abstract Hematological malignancies (HMs) are a heterogeneous group of blood neoplasia generally characterized by abnormal blood-cell production. Detection of HMs-specific molecular biomarkers (e.g., surface antigens, nucleic acid, and proteomic biomarkers) is crucial in determining clinical states and monitoring disease progression. Early diagnosis of HMs, followed by an effective treatment, can remarkably extend overall survival of patients. However, traditional and advanced HMs’ diagnostic strategies still lack selectivity and sensitivity. More importantly, commercially available chemotherapeutic drugs are losing their efficacy due to adverse effects, and many patients develop resistance against these drugs. To overcome these limitations, the development of novel potent and reliable theranostic agents is urgently needed to diagnose and combat HMs at an early stage. Recently, gold nanomaterials (GNMs) have shown promise in the diagnosis and treatment of HMs. Magnetic resonance and the surface-plasmon-resonance properties of GNMs have made them a suitable candidate in the diagnosis of HMs via magnetic-resonance imaging and colorimetric or electrochemical sensing of cancer-specific biomarkers. Furthermore, GNMs-based photodynamic therapy, photothermal therapy, radiation therapy, and targeted drug delivery enhanced the selectivity and efficacy of anticancer drugs or drug candidates. Therefore, surface-tuned GNMs could be used as sensitive, reliable, and accurate early HMs, metastatic HMs, and MRD-detection tools, as well as selective, potent anticancer agents. However, GNMs may induce endothelial leakage to exacerbate cancer metastasis. Studies using clinical patient samples, patient-derived HMs models, or healthy-animal models could give a precise idea about their theranostic potential as well as biocompatibility. The present review will investigate the theranostic potential of vectorized GNMs in HMs and future challenges before clinical theranostic applications in HMs.
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25
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Giansanti P, Samaras P, Bian Y, Meng C, Coluccio A, Frejno M, Jakubowsky H, Dobiasch S, Hazarika RR, Rechenberger J, Calzada-Wack J, Krumm J, Mueller S, Lee CY, Wimberger N, Lautenbacher L, Hassan Z, Chang YC, Falcomatà C, Bayer FP, Bärthel S, Schmidt T, Rad R, Combs SE, The M, Johannes F, Saur D, de Angelis MH, Wilhelm M, Schneider G, Kuster B. Mass spectrometry-based draft of the mouse proteome. Nat Methods 2022; 19:803-811. [PMID: 35710609 DOI: 10.1038/s41592-022-01526-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/17/2022] [Indexed: 01/06/2023]
Abstract
The laboratory mouse ranks among the most important experimental systems for biomedical research and molecular reference maps of such models are essential informational tools. Here, we present a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues and several lines of analyses exemplify which insights can be gleaned from the data. For instance, tissue- and cell-type resolved profiles provide protein evidence for the expression of 17,000 genes, thousands of isoforms and 50,000 phosphorylation sites in vivo. Proteogenomic comparison of mouse, human and Arabidopsis reveal common and distinct mechanisms of gene expression regulation and, despite many similarities, numerous differentially abundant orthologs that likely serve species-specific functions. We leverage the mouse proteome by integrating phenotypic drug (n > 400) and radiation response data with the proteomes of 66 pancreatic ductal adenocarcinoma (PDAC) cell lines to reveal molecular markers for sensitivity and resistance. This unique atlas complements other molecular resources for the mouse and can be explored online via ProteomicsDB and PACiFIC.
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Affiliation(s)
- Piero Giansanti
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Yangyang Bian
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,College of Life Science, Northwest University, Xi'an, China
| | - Chen Meng
- Bavarian Biomolecular Mass Spectrometry Center, Technical University of Munich, Freising, Germany
| | - Andrea Coluccio
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Martin Frejno
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Hannah Jakubowsky
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Sophie Dobiasch
- Department of Radiation Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Radiation Medicine, Department of Radiation Sciences, Helmholtz Zentrum München, Neuherberg, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rashmi R Hazarika
- Population epigenetics and epigenomics, Technical University of Munich, Freising, Germany.,Institute of Advanced Study (IAS), Technical University of Munich, Freising, Germany
| | - Julia Rechenberger
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Julia Calzada-Wack
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Krumm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Sebastian Mueller
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Chien-Yun Lee
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Nicole Wimberger
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Ludwig Lautenbacher
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Zonera Hassan
- Medical Clinic and Policlinic II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Yun-Chien Chang
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Chiara Falcomatà
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Stefanie Bärthel
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Tobias Schmidt
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Roland Rad
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Stephanie E Combs
- Department of Radiation Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Radiation Medicine, Department of Radiation Sciences, Helmholtz Zentrum München, Neuherberg, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Frank Johannes
- Population epigenetics and epigenomics, Technical University of Munich, Freising, Germany.,Institute of Advanced Study (IAS), Technical University of Munich, Freising, Germany
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Experimental Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,Computational Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Günter Schneider
- Medical Clinic and Policlinic II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,University Medical Center Göttingen, Department of General, Visceral and Pediatric Surgery, Göttingen, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany. .,Bavarian Biomolecular Mass Spectrometry Center, Technical University of Munich, Freising, Germany. .,German Cancer Consortium (DKTK), Munich, Germany. .,German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Institute of Advanced Study (IAS), Technical University of Munich, Freising, Germany.
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26
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Preclinical models of epithelial ovarian cancer: practical considerations and challenges for a meaningful application. Cell Mol Life Sci 2022; 79:364. [PMID: 35705879 PMCID: PMC9200670 DOI: 10.1007/s00018-022-04395-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/05/2022] [Accepted: 05/23/2022] [Indexed: 12/14/2022]
Abstract
Despite many improvements in ovarian cancer diagnosis and treatment, until now, conventional chemotherapy and new biological drugs have not been shown to cure the disease, and the overall prognosis remains poor. Over 90% of ovarian malignancies are categorized as epithelial ovarian cancers (EOC), a collection of different types of neoplasms with distinctive disease biology, response to chemotherapy, and outcome. Advances in our understanding of the histopathology and molecular features of EOC subtypes, as well as the cellular origins of these cancers, have given a boost to the development of clinically relevant experimental models. The overall goal of this review is to provide a comprehensive description of the available preclinical investigational approaches aimed at better characterizing disease development and progression and at identifying new therapeutic strategies. Systems discussed comprise monolayer (2D) and three-dimensional (3D) cultures of established and primary cancer cell lines, organoids and patient-derived explants, animal models, including carcinogen-induced, syngeneic, genetically engineered mouse, xenografts, patient-derived xenografts (PDX), humanized PDX, and the zebrafish and the laying hen models. Recent advances in tumour-on-a-chip platforms are also detailed. The critical analysis of strengths and weaknesses of each experimental model will aid in identifying opportunities to optimize their translational value.
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27
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Koc S, Lloyd M, Grover J, Xiao N, Seepo S, Subramanian S, Ray M, Frech C, DiGiovanna J, Webster P, Neuhauser S, Srivastava A, Woo XY, Sanderson B, White B, Lott P, Dobrolecki L, Dowst H, Evrard Y, Wallace T, Moscow J, Doroshow J, Mitsiades N, Kaochar S, Pan CX, Chen M, Carvajal-Carmona L, Welm A, Welm B, Lewis M, Govindan R, Ding L, Li S, Herlyn M, Davies M, Roth J, Meric-Bernstam F, Robinson P, Bult C, Davis-Dusenbery B, Dean DA, Chuang J. PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery. NAR Cancer 2022; 4:zcac014. [PMID: 35475145 PMCID: PMC9026194 DOI: 10.1093/narcan/zcac014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/04/2022] [Accepted: 04/07/2022] [Indexed: 01/26/2023] Open
Abstract
We created the PDX Network (PDXNet) portal (https://portal.pdxnetwork.org/) to centralize access to the National Cancer Institute-funded PDXNet consortium resources, to facilitate collaboration among researchers and to make these data easily available for research. The portal includes sections for resources, analysis results, metrics for PDXNet activities, data processing protocols and training materials for processing PDX data. Currently, the portal contains PDXNet model information and data resources from 334 new models across 33 cancer types. Tissue samples of these models were deposited in the NCI's Patient-Derived Model Repository (PDMR) for public access. These models have 2134 associated sequencing files from 873 samples across 308 patients, which are hosted on the Cancer Genomics Cloud powered by Seven Bridges and the NCI Cancer Data Service for long-term storage and access with dbGaP permissions. The portal includes results from freely available, robust, validated and standardized analysis workflows on PDXNet sequencing files and PDMR data (3857 samples from 629 patients across 85 disease types). The PDXNet portal is continuously updated with new data and is of significant utility to the cancer research community as it provides a centralized location for PDXNet resources, which support multi-agent treatment studies, determination of sensitivity and resistance mechanisms, and preclinical trials.
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Affiliation(s)
- Soner Koc
- Seven Bridges, Charlestown, MA 02129, USA
| | | | | | - Nan Xiao
- Seven Bridges, Charlestown, MA 02129, USA
| | - Sara Seepo
- Seven Bridges, Charlestown, MA 02129, USA
| | | | | | | | | | | | | | - Anuj Srivastava
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Xing Yi Woo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Brian J Sanderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Brian White
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Paul Lott
- University of California - Davis, Davis, CA 95616, USA
| | | | - Heidi Dowst
- Baylor College of Medicine, Houston, TX 77030, USA
| | - Yvonne A Evrard
- Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Tiffany A Wallace
- Center to Reduce Health Disparities, National Cancer Institute, Bethesda, MD 20814, USA
| | - Jeffrey A Moscow
- Investigational Drug Branch, National Cancer Institute, Bethesda, MD 20814, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20814, USA
| | | | | | - Chong-xian Pan
- University of California - Davis, Davis, CA 95616, USA
- Harvard Medical School, West Roxbury, MA 02115, USA
| | - Moon S Chen
- University of California - Davis, Davis, CA 95616, USA
| | | | - Alana L Welm
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Bryan E Welm
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | | | | | - Li Ding
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shunqiang Li
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Michael A Davies
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jack Roth
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Carol J Bult
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | | | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
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Sun M, Wang Z, Sun W, Chen M, Ma X, Shen J, Fu Z, Zuo D, Wang G, Wang H, Wang C, Yin F, Wang Z, Zhang C, Hua Y, Cai Z. Correlation between Patient-Derived Xenograft Modeling and Prognosis in Osteosarcoma. Orthop Surg 2022; 14:1161-1166. [PMID: 35538733 PMCID: PMC9163969 DOI: 10.1111/os.13211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022] Open
Abstract
Objective To retrospectively analyze and compare the relationship between the success rate of patient‐derived xenograft (PDX) modeling of osteosarcoma and prognosis (3‐year overall survival rate and disease‐free survival rate) and incidence of lung metastasis. Methods The sample group consisted of 57 osteosarcoma patients with definite pathological diagnoses from Shanghai General Hospital from 2015–2017. PDX models in 57 patients were analyzed by retrospective analyses. Among the patients currently inoculated, 20 were tumorigenic in the PDX model, and 37 were nontumorigenic. According to the tumorigenicity of PDXs, the corresponding osteosarcoma patients were divided into two groups. The effects of clinically related indicators on the model were retrospectively compared. The patients were followed, and the 3‐year survival, 3‐year disease‐free survival (DFS), and lung metastasis rates were collected. The relationship between the modeling success and patient prognosis was investigated. Results In the chemotherapy‐treated group, the PDX modeling success rate was 17.4%, and in the nonchemotherapy group, the success rate was 47.1%. The success of PDX modeling was related to whether patients received chemotherapy. The success rate of PDX modeling is significantly reduced after receiving chemotherapy. The 3‐year overall survival rate of the PDX‐grafted group was 49.23%, and that of the PDX‐nongrafted group was 65.71%. There was a significant difference between the two groups, showing a strong negative correlation between the 3‐year survival rate and the success rate of the PDX model. The 3‐year disease‐free survival rate of the PDX‐grafted group was 29.54%. The 3‐year DFS of the PDX‐nongrafted group was 50.34%. There was a significant difference between the two groups. Lower grafted rates indicate a higher DFS rate. The incidence of lung metastasis in the PDX‐grafted group was 32.4%, and that in the nongrafted group was 13.1%. There was a significant difference between the two groups. The successful establishment of the PDX model indicates that patients are more likely to have lung metastases. Conclusions The success of PDX modeling often indicates poor prognosis (low 3‐year overall survival rate and disease‐free survival rate) and a greater possibility of lung metastasis. Therefore, PDX modeling in osteosarcoma patients can accurately predict the prognosis of patients and the risk of lung metastasis in advance to help us develop better therapeutic strategies.
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Affiliation(s)
- Mengxiong Sun
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Zongyi Wang
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Wei Sun
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Ming Chen
- Department of Orthopaedics, Qingpu Branch of Zhongshan Hospital Affiliated with Fudan University, Shanghai, China
| | - Xiaojun Ma
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Jiakang Shen
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Zeze Fu
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Dongqing Zuo
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Gangyang Wang
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Hongsheng Wang
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Chongren Wang
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Fei Yin
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Zhuoying Wang
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | | | - Yingqi Hua
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Zhengdong Cai
- Department of Orthopaedics, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
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Oswald E, Bug D, Grote A, Lashuk K, Bouteldja N, Lenhard D, Löhr A, Behnke A, Knauff V, Edinger A, Klingner K, Gaedicke S, Niedermann G, Merhof D, Feuerhake F, Schueler J. Immune cell infiltration pattern in non-small cell lung cancer PDX models is a model immanent feature and correlates with a distinct molecular and phenotypic make-up. J Immunother Cancer 2022; 10:jitc-2021-004412. [PMID: 35483746 PMCID: PMC9052060 DOI: 10.1136/jitc-2021-004412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The field of cancer immunology is rapidly moving towards innovative therapeutic strategies, resulting in the need for robust and predictive preclinical platforms reflecting the immunological response to cancer. Well characterized preclinical models are essential for the development of predictive biomarkers in the oncology as well as the immune-oncology space. In the current study, gold standard preclinical models are being refined and combined with novel image analysis tools to meet those requirements. METHODS A panel of 14 non-small cell lung cancer patient-derived xenograft models (NSCLC PDX) was propagated in humanized NOD/Shi-scid/IL-2Rnull mice. The models were comprehensively characterized for relevant phenotypic and molecular features, including flow cytometry, immunohistochemistry, histology, whole exome sequencing and cytokine secretion. RESULTS Models reflecting hot (>5% tumor-infiltrating lymphocytes/TILs) as opposed to cold tumors (<5% TILs) significantly differed regarding their cytokine profiles, molecular genetic aberrations, stroma content, and programmed cell death ligand-1 status. Treatment experiments including anti cytotoxic T-lymphocyte-associated protein 4, anti-programmed cell death 1 or the combination thereof across all 14 models in the single mouse trial format showed distinctive tumor growth response and spatial immune cell patterns as monitored by computerized analysis of digitized whole-slide images. Image analysis provided for the first time qualitative evaluation of the extent to which PDX models retain the histological features from their original human donors. CONCLUSIONS Deep phenotyping of PDX models in a humanized setting by combinations of computational pathology, immunohistochemistry, flow cytometry and proteomics enables the exhaustive analysis of innovative preclinical models and paves the way towards the development of translational biomarkers for immuno-oncology drugs.
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Affiliation(s)
- Eva Oswald
- Charles River Discovery Research Services Gemany GmbH, Charles River Laboratories Inc, Freiburg, Germany
| | - Daniel Bug
- Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
| | - Anne Grote
- Department of Pathology, Hannover Medical School, Hannover, Germany
| | - Kanstantsin Lashuk
- Charles River Discovery Research Services Gemany GmbH, Charles River Laboratories Inc, Freiburg, Germany
| | - Nassim Bouteldja
- Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
| | - Dorothee Lenhard
- Charles River Discovery Research Services Gemany GmbH, Charles River Laboratories Inc, Freiburg, Germany
| | - Anne Löhr
- Charles River Discovery Research Services Gemany GmbH, Charles River Laboratories Inc, Freiburg, Germany
| | - Anke Behnke
- Charles River Discovery Research Services Gemany GmbH, Charles River Laboratories Inc, Freiburg, Germany
| | - Volker Knauff
- Charles River Discovery Research Services Gemany GmbH, Charles River Laboratories Inc, Freiburg, Germany
| | - Anna Edinger
- Charles River Discovery Research Services Gemany GmbH, Charles River Laboratories Inc, Freiburg, Germany
| | - Kerstin Klingner
- Charles River Discovery Research Services Gemany GmbH, Charles River Laboratories Inc, Freiburg, Germany
| | - Simone Gaedicke
- Department of Radiation Oncology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Gabriele Niedermann
- Department of Radiation Oncology, Medical Center-University of Freiburg, Freiburg, Germany.,German Cancer Consortium, Heidelberg, Germany
| | - Dorit Merhof
- Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
| | | | - Julia Schueler
- Charles River Discovery Research Services Gemany GmbH, Charles River Laboratories Inc, Freiburg, Germany
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30
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Biomimetic hydrogel supports initiation and growth of patient-derived breast tumor organoids. Nat Commun 2022; 13:1466. [PMID: 35304464 PMCID: PMC8933543 DOI: 10.1038/s41467-022-28788-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
Patient-derived tumor organoids (PDOs) are a highly promising preclinical model that recapitulates the histology, gene expression, and drug response of the donor patient tumor. Currently, PDO culture relies on basement-membrane extract (BME), which suffers from batch-to-batch variability, the presence of xenogeneic compounds and residual growth factors, and poor control of mechanical properties. Additionally, for the development of new organoid lines from patient-derived xenografts, contamination of murine host cells poses a problem. We propose a nanofibrillar hydrogel (EKGel) for the initiation and growth of breast cancer PDOs. PDOs grown in EKGel have histopathologic features, gene expression, and drug response that are similar to those of their parental tumors and PDOs in BME. In addition, EKGel offers reduced batch-to-batch variability, a range of mechanical properties, and suppressed contamination from murine cells. These results show that EKGel is an improved alternative to BME matrices for the initiation, growth, and maintenance of breast cancer PDOs. Patient-derived tumour organoids are important preclinical models but suffer from variability from the use of basement-membrane extract and cell contamination. Here, the authors report on the development of mimetic nanofibrilar hydrogel which supports tumour organoid growth with reduced batch variability and cell contamination.
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31
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Dudová Z, Conte N, Mason J, Stuchlík D, Peša R, Halmagyi C, Perova Z, Mosaku A, Thorne R, Follette A, Pivarč Ľ, Šašinka R, Usman M, Neuhauser S, Begley DA, Krupke DM, Frassà M, Fiori A, Corsi R, Vezzadini L, Isella C, Bertotti A, Bult C, Parkinson H, Medico E, Meehan T, Křenek A. The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization. BMC Genomics 2022; 23:156. [PMID: 35193494 PMCID: PMC8862363 DOI: 10.1186/s12864-022-08367-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/03/2022] [Indexed: 01/05/2023] Open
Abstract
Background Patient-derived xenografts (PDX) mice models play an important role in preclinical trials and personalized medicine. Sharing data on the models is highly valuable for numerous reasons – ethical, economical, research cross validation etc. The EurOPDX Consortium was established 8 years ago to share such information and avoid duplicating efforts in developing new PDX mice models and unify approaches to support preclinical research. EurOPDX Data Portal is the unified data sharing platform adopted by the Consortium. Main body In this paper we describe the main features of the EurOPDX Data Portal (https://dataportal.europdx.eu/), its architecture and possible utilization by researchers who look for PDX mice models for their research. The Portal offers a catalogue of European models accessible on a cooperative basis. The models are searchable by metadata, and a detailed view provides molecular profiles (gene expression, mutation, copy number alteration) and treatment studies. The Portal displays the data in multiple tools (PDX Finder, cBioPortal, and GenomeCruzer in future), which are populated from a common database displaying strictly mutually consistent views. (Short) Conclusion EurOPDX Data Portal is an entry point to the EurOPDX Research Infrastructure offering PDX mice models for collaborative research, (meta)data describing their features and deep molecular data analysis according to users’ interests.
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Affiliation(s)
- Zdenka Dudová
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic
| | - Nathalie Conte
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Dalibor Stuchlík
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic
| | - Radim Peša
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic
| | - Csaba Halmagyi
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Zinaida Perova
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Abayomi Mosaku
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ross Thorne
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alex Follette
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ľuboslav Pivarč
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic
| | - Radim Šašinka
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic
| | - Muhammad Usman
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic
| | - Steven Neuhauser
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Dale A Begley
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Debra M Krupke
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | | | - Alessandro Fiori
- Department of Oncology, University of Torino, 10060, Candiolo, TO, Italy
| | - Riccardo Corsi
- Kairos3D, via Agostino da Montefeltro 2, 10134, Turin, Italy
| | - Luca Vezzadini
- Kairos3D, via Agostino da Montefeltro 2, 10134, Turin, Italy
| | - Claudio Isella
- Department of Oncology, University of Torino, 10060, Candiolo, TO, Italy.,Candiolo Cancer Institute, FPO-IRCCS, S.P. 142, km 3,95, 10060, Candiolo, TO, Italy
| | - Andrea Bertotti
- Department of Oncology, University of Torino, 10060, Candiolo, TO, Italy
| | - Carol Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Helen Parkinson
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Enzo Medico
- Department of Oncology, University of Torino, 10060, Candiolo, TO, Italy.,Candiolo Cancer Institute, FPO-IRCCS, S.P. 142, km 3,95, 10060, Candiolo, TO, Italy
| | - Terrence Meehan
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Aleš Křenek
- Institute of Computer Science, Masaryk University, Šumavská 15, 60200, Brno, Czech Republic.
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32
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Ali Z, Vildevall M, Rodriguez GV, Tandiono D, Vamvakaris I, Evangelou G, Lolas G, Syrigos KN, Villanueva A, Wick M, Omar S, Erkstam A, Schueler J, Fahlgren A, Jensen LD. Zebrafish patient-derived xenograft models predict lymph node involvement and treatment outcome in non-small cell lung cancer. J Exp Clin Cancer Res 2022; 41:58. [PMID: 35139880 PMCID: PMC8827197 DOI: 10.1186/s13046-022-02280-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/31/2022] [Indexed: 11/25/2022] Open
Abstract
Background Accurate predictions of tumor dissemination risks and medical treatment outcomes are critical to personalize therapy. Patient-derived xenograft (PDX) models in mice have demonstrated high accuracy in predicting therapeutic outcomes, but methods for predicting tumor invasiveness and early stages of vascular/lymphatic dissemination are still lacking. Here we show that a zebrafish tumor xenograft (ZTX) platform based on implantation of PDX tissue fragments recapitulate both treatment outcome and tumor invasiveness/dissemination in patients, within an assay time of only 3 days. Methods Using a panel of 39 non-small cell lung cancer PDX models, we developed a combined mouse-zebrafish PDX platform based on direct implantation of cryopreserved PDX tissue fragments into zebrafish embryos, without the need for pre-culturing or expansion. Clinical proof-of-principle was established by direct implantation of tumor samples from four patients. Results The resulting ZTX models responded to Erlotinib and Paclitaxel, with similar potency as in mouse-PDX models and the patients themselves, and resistant tumors similarly failed to respond to these drugs in the ZTX system. Drug response was coupled to elevated expression of EGFR, Mdm2, Ptch1 and Tsc1 (Erlotinib), or Nras and Ptch1 (Paclitaxel) and reduced expression of Egfr, Erbb2 and Foxa (Paclitaxel). Importantly, ZTX models retained the invasive phenotypes of the tumors and predicted lymph node involvement of the patients with 91% sensitivity and 62% specificity, which was superior to clinically used tests. The biopsies from all four patient tested implanted successfully, and treatment outcome and dissemination were quantified for all patients in only 3 days. Conclusions We conclude that the ZTX platform provide a fast, accurate, and clinically relevant system for evaluation of treatment outcome and invasion/dissemination of PDX models, providing an attractive platform for combined mouse-zebrafish PDX trials and personalized medicine. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02280-x.
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Affiliation(s)
| | | | | | | | | | - Georgios Evangelou
- 3rd Department of Internal Medicine and Laboratory, National & Kapodistrian University of Athens, Athens, Greece
| | - Georgios Lolas
- 3rd Department of Internal Medicine and Laboratory, National & Kapodistrian University of Athens, Athens, Greece.,InCELLiA P.C, Athens, Greece
| | - Konstantinos N Syrigos
- 3rd Department of Internal Medicine and Laboratory, National & Kapodistrian University of Athens, Athens, Greece
| | - Alberto Villanueva
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), Oncobell Program, L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain.,Xenopat S.L., Parc Cientific de Barcelona (PCB), Barcelona, Spain
| | | | - Shenga Omar
- Division of Cardiovascular Medicine, Department of Medical and Health Sciences, Linköping University, Campus US, Entrance 68, Pl. 08, SE-58185, Linköping, Sweden
| | | | | | - Anna Fahlgren
- BioReperia AB, Linköping, Sweden.,Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linköping University, Linöping, Sweden
| | - Lasse D Jensen
- BioReperia AB, Linköping, Sweden. .,Division of Cardiovascular Medicine, Department of Medical and Health Sciences, Linköping University, Campus US, Entrance 68, Pl. 08, SE-58185, Linköping, Sweden.
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Noguchi R, Yoshimatsu Y, Ono T, Sei A, Motoi N, Yatabe Y, Yoshida Y, Watanabe S, Kondo T. Establishment and characterization of NCC‑DMM1‑C1, a novel patient‑derived cell line of desmoplastic malignant pleural mesothelioma. Oncol Lett 2021; 23:64. [PMID: 35069873 PMCID: PMC8756558 DOI: 10.3892/ol.2021.13182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/27/2021] [Indexed: 12/05/2022] Open
Abstract
Desmoplastic malignant pleural mesothelioma (DMM) is a rare histological variant of malignant pleural mesothelioma, which is a highly aggressive neoplasm of the mesothelium. DMM is associated with distant metastases and short survival. Effective treatments for DMM are not established and the development of histotype-tailored treatments is difficult due to the rarity of the disease. Although patient-derived cancer models are crucial tools for the development of novel therapeutics, they are difficult to obtain for DMM; no DMM cell lines or xenografts are available from public biobanks and only two cell lines have been reported. Thus, the present study aimed to establish a novel cell line of DMM as a resource for drug screening. A cell line of DMM was established, designated as NCC-DMM1-C1, using surgically resected tumor tissues from a 73-year-old male patient with DMM. Characteristics of NCC-DMM1-C1 cells were examined, such as growth, spheroid formation and invasion capability. Drug targets and anti-cancer drugs with anti-proliferative efficacy were examined using a comprehensive kinase activity assay and drug screening of 213 anti-cancer agents, respectively. NCC-DMM1-C1 exhibited fast growth, spheroid formation and invasion capability, suggesting that the NCC-DMM1-C1 cells retained the aggressive features of DMM. NCC-DMM1-C1 cells and the tumor tissue shared common activity profiles of kinases, which included FES, Wee1, platelet-derived growth factor receptor-β and Src. The drug screening revealed that bortezomib, fostamatinib, gemcitabine, homoharringtonine and vinorelbine had anti-proliferative effects, which have not been previously reported for DMM. It was concluded that NCC-DMM1-C1 cells may be a useful tool for the study of DMM.
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Affiliation(s)
- Rei Noguchi
- Division of Rare Cancer Research, National Cancer Center Research Institute, Chuo‑ku, Tokyo 104‑0045, Japan
| | - Yuki Yoshimatsu
- Division of Rare Cancer Research, National Cancer Center Research Institute, Chuo‑ku, Tokyo 104‑0045, Japan
| | - Takuya Ono
- Division of Rare Cancer Research, National Cancer Center Research Institute, Chuo‑ku, Tokyo 104‑0045, Japan
| | - Akane Sei
- Division of Rare Cancer Research, National Cancer Center Research Institute, Chuo‑ku, Tokyo 104‑0045, Japan
| | - Noriko Motoi
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Chuo‑ku, Tokyo 104‑0045, Japan
| | - Yasushi Yatabe
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Chuo‑ku, Tokyo 104‑0045, Japan
| | - Yukihiro Yoshida
- Department of Thoracic Surgery, National Cancer Center Hospital, Chuo‑ku, Tokyo 104‑0045, Japan
| | - Shunichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Chuo‑ku, Tokyo 104‑0045, Japan
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, Chuo‑ku, Tokyo 104‑0045, Japan
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Sueyoshi K, Komura D, Katoh H, Yamamoto A, Onoyama T, Chijiwa T, Isagawa T, Tanaka M, Suemizu H, Nakamura M, Miyagi Y, Aburatani H, Ishikawa S. Multi-tumor analysis of cancer-stroma interactomes of patient-derived xenografts unveils the unique homeostatic process in renal cell carcinomas. iScience 2021; 24:103322. [PMID: 35079698 PMCID: PMC8767947 DOI: 10.1016/j.isci.2021.103322] [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: 11/12/2020] [Revised: 06/22/2021] [Accepted: 10/19/2021] [Indexed: 12/22/2022] Open
Abstract
The patient-derived xenograft (PDX) model is a versatile tool used to study the tumor microenvironment (TME). However, limited studies have described multi-tumor PDX screening strategies to detect hub regulators during cancer-stroma interaction. Transcriptomes of cancer (human) and stroma (mouse) components of 70 PDX samples comprising 9 distinctive tumor types were analyzed in this study. PDX models recapitulated the original tumors' features, including tumor composition and putative signaling. Particularly, kidney renal clear cell carcinoma (KIRC) stood out, with altered hypoxia-related pathways and a high proportion of endothelial cells in the TME. Furthermore, an integrated analysis conducted to predict paracrine effectors in the KIRC cancer-to-stroma communication detected well-established soluble factors responsible for the hypoxia-related reaction and the so-far unestablished soluble factor, apelin (APLN). Subsequent experiments also supported the potential role of APLN in KIRC tumor progression. Therefore, this paper hereby provides an analytical workflow to find hub regulators in cancer-stroma interactions.
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Affiliation(s)
- Kuniyo Sueyoshi
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Experimental Research Buliding, 12Floor, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Department of Thoracic Surgery, Tokyo Medical and Dental University, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Daisuke Komura
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Experimental Research Buliding, 12Floor, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroto Katoh
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Experimental Research Buliding, 12Floor, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Asami Yamamoto
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Experimental Research Buliding, 12Floor, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Takumi Onoyama
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Experimental Research Buliding, 12Floor, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Division of Gastroenterology and Nephrology, Department of Multidisciplinary Internal Medicine, School of Medicine, Faculty of Medicine, Tottori University, Tottori 683-8504, Japan
| | - Tsuyoshi Chijiwa
- Central Institute for Experimental Animals, Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210–0821, Japan
| | - Takayuki Isagawa
- Data Science Center, Jichi Medical University, Yakushiji, Shimotsuke-shi, Tochigi 329–0498, Japan
| | - Mariko Tanaka
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113–8654, Japan
| | - Hiroshi Suemizu
- Central Institute for Experimental Animals, Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210–0821, Japan
| | - Masato Nakamura
- Department of Regenerative Medicine, Tokai University School of Medicine, Shimokasuya, Isehara, Kanagawa 259–1193, Japan
| | - Yohei Miyagi
- Research Institute, Kanagawa Cancer Center, Nakao, Asahi-ku, Yokohama 241–8515, Japan
| | - Hiroyuki Aburatani
- Division of Genome Sciences, RCAST, The University of Tokyo, Tokyo 113–8654, Japan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Experimental Research Buliding, 12Floor, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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De Marco M, Del Papa N, Reppucci F, Iorio V, Basile A, Falco A, Iaccarino R, Brongo S, De Caro F, Capunzo M, Turco MC, Rosati A, Marzullo L. BAG3 induces α-SMA expression in human fibroblasts and its over-expression correlates with poorer survival in fibrotic cancer patients. J Cell Biochem 2021; 123:91-101. [PMID: 34741483 PMCID: PMC9297854 DOI: 10.1002/jcb.30171] [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: 04/13/2021] [Revised: 09/28/2021] [Accepted: 10/23/2021] [Indexed: 02/06/2023]
Abstract
Hypoxia and angiogenesis in solid tumors are often strictly linked to the development of fibrotic tissues, a detrimental event that compromises the antitumor immunity. As a consequence, tumor aggressiveness and poor patient prognosis relate to higher incidence of tissue fibrosis and stromal stiffness. The molecular pathways through which normal fibroblasts are converted in cancer-associated fibroblasts (CAFs) have a central role in the onset of fibrosis in tumor stroma, thus emerging as a strategic target of novel therapeutic approaches for cancer disease. Several studies addressed the role of BAG3 in sustaining growth and survival of cancer cell and also shed light on the different mechanisms in which the intracellular protein is involved. More recently, new pieces of evidence revealed a pivotal role of extracellular BAG3 in pro-tumor cell signaling in the tumor microenvironment, as well as its involvement in the development of fibrosis in tumor tissues. Here we report further data showing the presence of the BAG3 receptor (Interferon-induced transmembrane protein [IFITM]-2) on the plasma membrane of normal dermal fibroblasts and the activity of BAG3 as a factor able to induce the expression of α-smooth muscle actin and the phosphorylation of AKT and focal adhesion kinase, that sustain CAF functions in tumor microenvironment. Furthermore, in agreement with these findings, bag3 gene expression has been analyzed by high throughput RNA sequencing databases from patients-derived xenografts. A strong correlation between bag3 gene expression and patients' survival was found in several types of fibrotic tumors. The results obtained provide encouraging data that identify BAG3 as a promising therapeutic target to counteract fibrosis in tumors.
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Affiliation(s)
- Margot De Marco
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy.,R&D Division, BIOUNIVERSA s.r.l., Baronissi, Salerno, Italy
| | - Nicoletta Del Papa
- Rheumatology Department, Scleroderma Unit, G. Pini Hospital, Milano, Italy
| | - Francesca Reppucci
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy
| | - Vittoria Iorio
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy
| | - Anna Basile
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy.,R&D Division, BIOUNIVERSA s.r.l., Baronissi, Salerno, Italy
| | - Antonia Falco
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy.,R&D Division, BIOUNIVERSA s.r.l., Baronissi, Salerno, Italy
| | - Roberta Iaccarino
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy
| | - Sergio Brongo
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy
| | - Francesco De Caro
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy
| | - Mario Capunzo
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy
| | - Maria Caterina Turco
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy.,R&D Division, BIOUNIVERSA s.r.l., Baronissi, Salerno, Italy
| | - Alessandra Rosati
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy.,R&D Division, BIOUNIVERSA s.r.l., Baronissi, Salerno, Italy
| | - Liberato Marzullo
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy.,R&D Division, BIOUNIVERSA s.r.l., Baronissi, Salerno, Italy
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Zeng Z, Wong CJ, Yang L, Ouardaoui N, Li D, Zhang W, Gu S, Zhang Y, Liu Y, Wang X, Fu J, Zhou L, Zhang B, Kim S, Yates KB, Brown M, Freeman GJ, Uppaluri R, Manguso R, Liu XS. TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response. Nucleic Acids Res 2021; 50:D1391-D1397. [PMID: 34534350 PMCID: PMC8728303 DOI: 10.1093/nar/gkab804] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/28/2021] [Accepted: 09/16/2021] [Indexed: 01/11/2023] Open
Abstract
Syngeneic mouse models are tumors derived from murine cancer cells engrafted on genetically identical mouse strains. They are widely used tools for studying tumor immunity and immunotherapy response in the context of a fully functional murine immune system. Large volumes of syngeneic mouse tumor expression profiles under different immunotherapy treatments have been generated, although a lack of systematic collection and analysis makes data reuse challenging. We present Tumor Immune Syngeneic MOuse (TISMO), a database with an extensive collection of syngeneic mouse model profiles with interactive visualization features. TISMO contains 605 in vitro RNA-seq samples from 49 syngeneic cancer cell lines across 23 cancer types, of which 195 underwent cytokine treatment. TISMO also includes 1518 in vivo RNA-seq samples from 68 syngeneic mouse tumor models across 19 cancer types, of which 832 were from immune checkpoint blockade (ICB) studies. We manually annotated the sample metadata, such as cell line, mouse strain, transplantation site, treatment, and response status, and uniformly processed and quality-controlled the RNA-seq data. Besides data download, TISMO provides interactive web interfaces to investigate whether specific gene expression, pathway enrichment, or immune infiltration level is associated with differential immunotherapy response. TISMO is available at http://tismo.cistrome.org.
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Affiliation(s)
- Zexian Zeng
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Cheryl J Wong
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115 USA
| | - Lin Yang
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Nofal Ouardaoui
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Dian Li
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Wubing Zhang
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA.,School of Life Science and Technology, Tongji University, Shanghai, 200060, China
| | - Shengqing Gu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Yi Zhang
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Yang Liu
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Xiaoqing Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Jingxin Fu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02129, USA
| | - Liye Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Boning Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Sarah Kim
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02129, USA
| | - Kathleen B Yates
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02129, USA.,Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02114, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ravindra Uppaluri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Surgery, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Robert Manguso
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02129, USA.,Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02114, USA
| | - X Shirley Liu
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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37
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Chen F, Wendl MC, Wyczalkowski MA, Bailey MH, Li Y, Ding L. Moving pan-cancer studies from basic research toward the clinic. NATURE CANCER 2021; 2:879-890. [PMID: 35121865 DOI: 10.1038/s43018-021-00250-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 07/21/2021] [Indexed: 06/14/2023]
Abstract
Although all cancers share common hallmarks, we have long realized that there is no silver-bullet treatment for the disease. Many clinical oncologists specialize in a single cancer type, based predominantly on the tissue of origin. With advances brought by genetics and cancer genomic research, we now know that cancers are profoundly different, both in origins and in genetic alterations. At the same time, commonalities such as key driver mutations, altered pathways, mutational, immune and microbial signatures and other areas (many revealed by pan-cancer studies) point to the intriguing possibility of targeting common traits across diverse cancer types with the same therapeutic strategies. Studies designed to delineate differences and similarities across cancer types are thus critical in discerning the basic dynamics of oncogenesis, as well as informing diagnoses, prognoses and therapies. We anticipate growing emphases on the development and application of therapies targeting underlying commonalities of different cancer types, while tailoring to the unique tissue environment and intrinsic molecular fingerprints of each cancer type and subtype. Here we summarize the facets of pan-cancer research and how they are pushing progress toward personalized medicine.
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Affiliation(s)
- Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael C Wendl
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
- Department of Mathematics, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Matthew H Bailey
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA.
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38
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Sun H, Cao S, Mashl RJ, Mo CK, Zaccaria S, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA, Patidar R, Chen L, Wyczalkowski MA, Jayasinghe RG, Rodrigues FM, Terekhanova NV, Li Y, Lim KH, Wang-Gillam A, Van Tine BA, Ma CX, Aft R, Fuh KC, Schwarz JK, Zevallos JP, Puram SV, Dipersio JF, Davis-Dusenbery B, Ellis MJ, Lewis MT, Davies MA, Herlyn M, Fang B, Roth JA, Welm AL, Welm BE, Meric-Bernstam F, Chen F, Fields RC, Li S, Govindan R, Doroshow JH, Moscow JA, Evrard YA, Chuang JH, Raphael BJ, Ding L. Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment. Nat Commun 2021; 12:5086. [PMID: 34429404 PMCID: PMC8384880 DOI: 10.1038/s41467-021-25177-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs' recapitulation of human tumors.
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Affiliation(s)
- Hua Sun
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - R Jay Mashl
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Chia-Kuei Mo
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Simone Zaccaria
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Computational Cancer Genomics Research Group and Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
- Department of Mathematics, Washington University in St. Louis, St. Louis, MO, USA
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Sherri R Davies
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Matthew H Bailey
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Tina M Primeau
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Jeremy Hoog
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Jacqueline L Mudd
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Dennis A Dean
- Seven Bridges Genomics, Inc., Cambridge, Charlestown, MA, USA
| | - Rajesh Patidar
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Li Chen
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Reyka G Jayasinghe
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Fernanda Martins Rodrigues
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Nadezhda V Terekhanova
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Kian-Huat Lim
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrea Wang-Gillam
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Brian A Van Tine
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Cynthia X Ma
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Rebecca Aft
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Katherine C Fuh
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Julie K Schwarz
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, MO, USA
| | - Jose P Zevallos
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Otolaryngology, Washington University St. Louis, St. Louis, MO, USA
| | - Sidharth V Puram
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Otolaryngology, Washington University St. Louis, St. Louis, MO, USA
| | - John F Dipersio
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael T Lewis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael A Davies
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Bingliang Fang
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jack A Roth
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alana L Welm
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Bryan E Welm
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | | | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryan C Fields
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Shunqiang Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Ramaswamy Govindan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - Jeffrey A Moscow
- Investigational Drug Branch, National Cancer Institute, Bethesda, MD, USA
| | - Yvonne A Evrard
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.
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Piyawajanusorn C, Nguyen LC, Ghislat G, Ballester PJ. A gentle introduction to understanding preclinical data for cancer pharmaco-omic modeling. Brief Bioinform 2021; 22:6343527. [PMID: 34368843 DOI: 10.1093/bib/bbab312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/25/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022] Open
Abstract
A central goal of precision oncology is to administer an optimal drug treatment to each cancer patient. A common preclinical approach to tackle this problem has been to characterize the tumors of patients at the molecular and drug response levels, and employ the resulting datasets for predictive in silico modeling (mostly using machine learning). Understanding how and why the different variants of these datasets are generated is an important component of this process. This review focuses on providing such introduction aimed at scientists with little previous exposure to this research area.
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Affiliation(s)
- Chayanit Piyawajanusorn
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France.,Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Linh C Nguyen
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France.,Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ghita Ghislat
- U1104, CNRS UMR7280, Centre d'Immunologie de Marseille-Luminy, Inserm, Marseille, France
| | - Pedro J Ballester
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France
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40
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Wu J, Sheng J, Qin H, Cui M, Yang Y, Zhang X. The Application Progress of Patient-Derived Tumor Xenograft Models After Cholangiocarcinoma Surgeries. Front Oncol 2021; 11:628636. [PMID: 34367944 PMCID: PMC8339899 DOI: 10.3389/fonc.2021.628636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 06/30/2021] [Indexed: 12/29/2022] Open
Abstract
Surgical treatment is the only possible cure for cholangiocarcinoma (CCA) at present. However, the high recurrence rate of postoperative CCA leads to a very poor prognosis for patients, effective postoperative chemotherapy is hence the key to preventing the recurrence of CCA. The sensitivity of CCA to cytotoxic chemotherapy drugs and targeted drugs varies from person to person, and therefore, the screening of sensitive drugs has become an important topic after CCA surgeries. Patient-Derived tumor Xenograft models (PDX) can stably retain the genetic and pathological characteristics of primary tumors, and better simulate the tumor microenvironment of CCA. The model is also of great significance in screening therapeutic targeted drugs after CCA, analyzing predictive biomarkers, and improving signal pathways in prognosis and basic research. This paper will review the current established methods and applications of the patient-derived tumor xenograft model of cholangiocarcinoma, aiming to provide new ideas for basic research and individualized treatment of cholangiocarcinoma after surgery.
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Affiliation(s)
- Jun Wu
- Department of Hepatopancreatobiliary Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Jiyao Sheng
- Department of Hepatopancreatobiliary Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Hanjiao Qin
- Department of Radiotherapy, The Second Hospital of Jilin University, Changchun, China
| | - Mengying Cui
- Department of Hepatopancreatobiliary Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yongsheng Yang
- Department of Hepatopancreatobiliary Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Xuewen Zhang
- Department of Hepatopancreatobiliary Surgery, The Second Hospital of Jilin University, Changchun, China
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41
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Annaratone L, De Palma G, Bonizzi G, Sapino A, Botti G, Berrino E, Mannelli C, Arcella P, Di Martino S, Steffan A, Daidone MG, Canzonieri V, Parodi B, Paradiso AV, Barberis M, Marchiò C. Basic principles of biobanking: from biological samples to precision medicine for patients. Virchows Arch 2021; 479:233-246. [PMID: 34255145 PMCID: PMC8275637 DOI: 10.1007/s00428-021-03151-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/24/2021] [Accepted: 06/30/2021] [Indexed: 12/15/2022]
Abstract
The term "biobanking" is often misapplied to any collection of human biological materials (biospecimens) regardless of requirements related to ethical and legal issues or the standardization of different processes involved in tissue collection. A proper definition of biobanks is large collections of biospecimens linked to relevant personal and health information (health records, family history, lifestyle, genetic information) that are held predominantly for use in health and medical research. In addition, the International Organization for Standardization, in illustrating the requirements for biobanking (ISO 20387:2018), stresses the concept of biobanks being legal entities driving the process of acquisition and storage together with some or all of the activities related to collection, preparation, preservation, testing, analysing and distributing defined biological material as well as related information and data. In this review article, we aim to discuss the basic principles of biobanking, spanning from definitions to classification systems, standardization processes and documents, sustainability and ethical and legal requirements. We also deal with emerging specimens that are currently being generated and shaping the so-called next-generation biobanking, and we provide pragmatic examples of cancer-associated biobanking by discussing the process behind the construction of a biobank and the infrastructures supporting the implementation of biobanking in scientific research.
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Affiliation(s)
- Laura Annaratone
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Giuseppe De Palma
- Institutional BioBank, Experimental Oncology and Biobank Management Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Giuseppina Bonizzi
- Unit of Histopathology and Molecular Diagnostics, Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Anna Sapino
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Gerardo Botti
- Istituto Nazionale Tumori, Fondazione G. Pascale, IRCCS, Naples, Italy
| | - Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Pamela Arcella
- Department of Oncology, University of Turin, Turin, Italy
| | - Simona Di Martino
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy
| | | | - Vincenzo Canzonieri
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy
| | | | - Angelo Virgilio Paradiso
- Institutional BioBank, Experimental Oncology and Biobank Management Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Massimo Barberis
- Unit of Histopathology and Molecular Diagnostics, Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy. .,Department of Medical Sciences, University of Turin, Turin, Italy.
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42
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Rafique R, Islam SR, Kazi JU. Machine learning in the prediction of cancer therapy. Comput Struct Biotechnol J 2021; 19:4003-4017. [PMID: 34377366 PMCID: PMC8321893 DOI: 10.1016/j.csbj.2021.07.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022] Open
Abstract
Resistance to therapy remains a major cause of cancer treatment failures, resulting in many cancer-related deaths. Resistance can occur at any time during the treatment, even at the beginning. The current treatment plan is dependent mainly on cancer subtypes and the presence of genetic mutations. Evidently, the presence of a genetic mutation does not always predict the therapeutic response and can vary for different cancer subtypes. Therefore, there is an unmet need for predictive models to match a cancer patient with a specific drug or drug combination. Recent advancements in predictive models using artificial intelligence have shown great promise in preclinical settings. However, despite massive improvements in computational power, building clinically useable models remains challenging due to a lack of clinically meaningful pharmacogenomic data. In this review, we provide an overview of recent advancements in therapeutic response prediction using machine learning, which is the most widely used branch of artificial intelligence. We describe the basics of machine learning algorithms, illustrate their use, and highlight the current challenges in therapy response prediction for clinical practice.
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Affiliation(s)
| | - S.M. Riazul Islam
- Department of Computer Science and Engineering, Sejong University, Seoul, South Korea
| | - Julhash U. Kazi
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Corresponding author at: Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon village Building 404:C3, Scheelevägen 8, 22363 Lund, Sweden.
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43
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Pham NA, Radulovich N, Ibrahimov E, Martins-Filho SN, Li Q, Pintilie M, Weiss J, Raghavan V, Cabanero M, Denroche RE, Wilson JM, Metran-Nascente C, Borgida A, Hutchinson S, Dodd A, Begora M, Chadwick D, Serra S, Knox JJ, Gallinger S, Hedley DW, Muthuswamy L, Tsao MS. Patient-derived tumor xenograft and organoid models established from resected pancreatic, duodenal and biliary cancers. Sci Rep 2021; 11:10619. [PMID: 34011980 PMCID: PMC8134568 DOI: 10.1038/s41598-021-90049-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
Patient-derived xenograft (PDX) and their xenograft-derived organoid (XDO) models that recapitulate the genotypic and phenotypic landscape of patient cancers could help to advance research and lead to improved clinical management. PDX models were established from 276 pancreato-duodenal and biliary cancer resections. Initial, passage 0 (P0) engraftment rates were 59% (118/199) for pancreatic, 86% (25/29) for duodenal, and 35% (17/48) for biliary ductal tumors. Pancreatic ductal adenocarcinoma (PDAC), had a P0 engraftment rate of 62% (105/169). KRAS mutant and wild-type PDAC models were molecularly profiled, and XDO models were generated to perform initial drug response evaluations. Subsets of PDAC PDX models showed global copy number variants and gene expression profiles that were retained with serial passaging, and they showed a spectrum of somatic mutations represented in patient tumors. PDAC XDO models were established, with a success rate of 71% (10/14). Pathway activation of KRAS-MAPK in PDXs was independent of KRAS mutational status. Four wild-type KRAS models were characterized by one with EGFR (L747-P753 del), two with BRAF alterations (N486_P490del or V600E), and one with triple negative KRAS/EGFR/BRAF. Model OCIP256, characterized by BRAF (N486-P490 del), had activated phospho-ERK. A combination treatment of a pan-RAF inhibitor (LY3009120) and a MEK inhibitor (trametinib) effectively suppressed phospho-ERK and inhibited growth of OCIP256 XDO and PDX models. PDAC/duodenal adenocarcinoma have high success rates forming PDX/organoid and retaining their phenotypic and genotypic features. These models may be effective tools to evaluate novel drug combination therapies.
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Affiliation(s)
- Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Emin Ibrahimov
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Quan Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Melania Pintilie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jessica Weiss
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Vibha Raghavan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michael Cabanero
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Julie M Wilson
- Ontario Institute of Cancer Research (OICR), Toronto, ON, Canada
| | | | - Ayelet Borgida
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Shawn Hutchinson
- Division of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Anna Dodd
- Division of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michael Begora
- Department of Pathology, UHN Program in BioSpecimen Sciences, University Health Network, Toronto, ON, Canada
| | - Dianne Chadwick
- Department of Pathology, UHN Program in BioSpecimen Sciences, University Health Network, Toronto, ON, Canada
| | - Stefano Serra
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jennifer J Knox
- Division of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Steven Gallinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Division of General Surgery, University of Toronto, Toronto, ON, Canada
| | - David W Hedley
- Division of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lakshmi Muthuswamy
- Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
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44
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Feng F, Shen B, Mou X, Li Y, Li H. Large-scale pharmacogenomic studies and drug response prediction for personalized cancer medicine. J Genet Genomics 2021; 48:540-551. [PMID: 34023295 DOI: 10.1016/j.jgg.2021.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 12/26/2022]
Abstract
The response rate of most anti-cancer drugs is limited because of the high heterogeneity of cancer and the complex mechanism of drug action. Personalized treatment that stratifies patients into subgroups using molecular biomarkers is promising to improve clinical benefit. With the accumulation of preclinical models and advances in computational approaches of drug response prediction, pharmacogenomics has made great success over the last 20 years and is increasingly used in the clinical practice of personalized cancer medicine. In this article, we first summarize FDA-approved pharmacogenomic biomarkers and large-scale pharmacogenomic studies of preclinical cancer models such as patient-derived cell lines, organoids, and xenografts. Furthermore, we comprehensively review the recent developments of computational methods in drug response prediction, covering network, machine learning, and deep learning technologies and strategies to evaluate immunotherapy response. In the end, we discuss challenges and propose possible solutions for further improvement.
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Affiliation(s)
- Fangyoumin Feng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bihan Shen
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoqin Mou
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yixue Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 330106, China
| | - Hong Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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45
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Preclinical In Vivo Modeling of Pediatric Sarcoma-Promises and Limitations. J Clin Med 2021; 10:jcm10081578. [PMID: 33918045 PMCID: PMC8069549 DOI: 10.3390/jcm10081578] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 02/07/2023] Open
Abstract
Pediatric sarcomas are an extremely heterogeneous group of genetically distinct diseases. Despite the increasing knowledge on their molecular makeup in recent years, true therapeutic advancements are largely lacking and prognosis often remains dim, particularly for relapsed and metastasized patients. Since this is largely due to the lack of suitable model systems as a prerequisite to develop and assess novel therapeutics, we here review the available approaches to model sarcoma in vivo. We focused on genetically engineered and patient-derived mouse models, compared strengths and weaknesses, and finally explored possibilities and limitations to utilize these models to advance both biological understanding as well as clinical diagnosis and therapy.
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46
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Green S, Dam MS, Svendsen MN. Mouse avatars of human cancers: the temporality of translation in precision oncology. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2021; 43:27. [PMID: 33620596 DOI: 10.1007/s40656-021-00383-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Patient-derived xenografts (PDXs) are currently promoted as new translational models in precision oncology. PDXs are immunodeficient mice with human tumors that are used as surrogate models to represent specific types of cancer. By accounting for the genetic heterogeneity of cancer tumors, PDXs are hoped to provide more clinically relevant results in preclinical research. Further, in the function of so-called "mouse avatars", PDXs are hoped to allow for patient-specific drug testing in real-time (in parallel to treatment of the corresponding cancer patient). This paper examines the circulation of knowledge and bodily material across the species boundary of human and personalized mouse model, historically as well as in contemporary practices. PDXs raise interesting questions about the relation between animal model and human patient, and about the capacity of hybrid or interspecies models to close existing translational gaps. We highlight that the translational potential of PDXs not only depends on representational matching of model and target, but also on temporal alignment between model development and practical uses. Aside from the importance of ensuring temporal stability of human tumors in a murine body, the mouse avatar concept rests on the possibility of aligning the temporal horizons of the clinic and the lab. We examine strategies to address temporal challenges, including cryopreservation and biobanking, as well as attempts to speed up translation through modification and use of faster developing organisms. We discuss how featured model virtues change with precision oncology, and contend that temporality is a model feature that deserves more philosophical attention.
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Affiliation(s)
- Sara Green
- Section for History and Philosophy of Science, Department of Science Education, University of Copenhagen, Niels Bohr Building (NBB), Universitetsparken 5, 2100, Copenhagen Ø, Denmark.
- Department of Public Health, Centre for Medical Science and Technology Studies, University of Copenhagen, Oester Farimagsgade 5, opg. B, Postboks 2099, 1014, Copenhagen, Denmark.
| | - Mie S Dam
- Department of Public Health, Centre for Medical Science and Technology Studies, University of Copenhagen, Oester Farimagsgade 5, opg. B, Postboks 2099, 1014, Copenhagen, Denmark
| | - Mette N Svendsen
- Department of Public Health, Centre for Medical Science and Technology Studies, University of Copenhagen, Oester Farimagsgade 5, opg. B, Postboks 2099, 1014, Copenhagen, Denmark
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47
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Patient Derived Xenografts for Genome-Driven Therapy of Osteosarcoma. Cells 2021; 10:cells10020416. [PMID: 33671173 PMCID: PMC7922432 DOI: 10.3390/cells10020416] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 02/06/2023] Open
Abstract
Osteosarcoma (OS) is a rare malignant primary tumor of mesenchymal origin affecting bone. It is characterized by a complex genotype, mainly due to the high frequency of chromothripsis, which leads to multiple somatic copy number alterations and structural rearrangements. Any effort to design genome-driven therapies must therefore consider such high inter- and intra-tumor heterogeneity. Therefore, many laboratories and international networks are developing and sharing OS patient-derived xenografts (OS PDX) to broaden the availability of models that reproduce OS complex clinical heterogeneity. OS PDXs, and new cell lines derived from PDXs, faithfully preserve tumor heterogeneity, genetic, and epigenetic features and are thus valuable tools for predicting drug responses. Here, we review recent achievements concerning OS PDXs, summarizing the methods used to obtain ectopic and orthotopic xenografts and to fully characterize these models. The availability of OS PDXs across the many international PDX platforms and their possible use in PDX clinical trials are also described. We recommend the coupling of next-generation sequencing (NGS) data analysis with functional studies in OS PDXs, as well as the setup of OS PDX clinical trials and co-clinical trials, to enhance the predictive power of experimental evidence and to accelerate the clinical translation of effective genome-guided therapies for this aggressive disease.
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48
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Kondo T. Current status and future outlook for patient-derived cancer models from a rare cancer research perspective. Cancer Sci 2021; 112:953-961. [PMID: 32986888 PMCID: PMC7935796 DOI: 10.1111/cas.14669] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 12/19/2022] Open
Abstract
Rare cancers are a group of approximately 200 malignancies with extremely low incidences and with a wide variety of genotypes and phenotypes. Collectively, they are more common than any single malignancy. However, given the small numbers of individuals diagnosed with rare cancers, it is difficult to design clinical trials with sufficient patient numbers. Therefore, few effective anticancer drugs have been developed, and evidence‐based medicine is not always feasible for rare cancers. Consequently, their clinical outcomes are generally poorer. Cancer research requires adequate models that faithfully recapitulate molecular features and reproduce treatment responses of the original tumors. Such models allow us to focus on more efficacious drugs in the clinical studies. For rare cancers, patient‐derived cancer models are particularly important because the enrollment of sufficient patients is rarely attainable within a reasonable period of time. However, extremely few models are available for rare cancers. For example, cell lines and xenografts are available for only a limited number of histological subtypes of sarcomas; therefore, most sarcoma research is performed without such models, and a lack of adequate cancer models causes a lag in therapeutic development. The establishment of novel rare cancer models will dramatically facilitate rare cancer research and treatment development in the near future. This review focuses on the status of patient‐derived rare cancer models and discusses their pivotal problems and possibilities, using sarcomas as a representative rare cancer type. Multi‐institutional collaboration will help address the scarcity of patient‐derived rare cancer models.
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Affiliation(s)
- Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, Chuo-ku, Japan
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49
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Yang J, Li Q, Noureen N, Fang Y, Kurmasheva R, Houghton PJ, Wang X, Zheng S. PCAT: an integrated portal for genomic and preclinical testing data of pediatric cancer patient-derived xenograft models. Nucleic Acids Res 2021; 49:D1321-D1327. [PMID: 32810235 PMCID: PMC7778893 DOI: 10.1093/nar/gkaa698] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 12/30/2022] Open
Abstract
Although cancer is the leading cause of disease-related mortality in children, the relative rarity of pediatric cancers poses a significant challenge for developing novel therapeutics to further improve prognosis. Patient-derived xenograft (PDX) models, which are usually developed from high-risk tumors, are a useful platform to study molecular driver events, identify biomarkers and prioritize therapeutic agents. Here, we develop PDX for Childhood Cancer Therapeutics (PCAT), a new integrated portal for pediatric cancer PDX models. Distinct from previously reported PDX portals, PCAT is focused on pediatric cancer models and provides intuitive interfaces for querying and data mining. The current release comprises 324 models and their associated clinical and genomic data, including gene expression, mutation and copy number alteration. Importantly, PCAT curates preclinical testing results for 68 models and 79 therapeutic agents manually collected from individual agent testing studies published since 2008. To facilitate comparisons of patterns between patient tumors and PDX models, PCAT curates clinical and molecular data of patient tumors from the TARGET project. In addition, PCAT provides access to gene fusions identified in nearly 1000 TARGET samples. PCAT was built using R-shiny and MySQL. The portal can be accessed at http://pcat.zhenglab.info or http://www.pedtranscriptome.org.
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Affiliation(s)
- Juechen Yang
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Qilin Li
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Nighat Noureen
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Yanbing Fang
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA.,School of Natural Science, University of Texas at Austin, Austin, TX 78712, USA
| | - Raushan Kurmasheva
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA.,Department of Molecular Medicine, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA.,Department of Molecular Medicine, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Xiaojing Wang
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA.,Department of Population Health Sciences, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA.,Department of Population Health Sciences, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
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50
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Golebiewska A, Hau AC, Oudin A, Stieber D, Yabo YA, Baus V, Barthelemy V, Klein E, Bougnaud S, Keunen O, Wantz M, Michelucci A, Neirinckx V, Muller A, Kaoma T, Nazarov PV, Azuaje F, De Falco A, Flies B, Richart L, Poovathingal S, Arns T, Grzyb K, Mock A, Herold-Mende C, Steino A, Brown D, May P, Miletic H, Malta TM, Noushmehr H, Kwon YJ, Jahn W, Klink B, Tanner G, Stead LF, Mittelbronn M, Skupin A, Hertel F, Bjerkvig R, Niclou SP. Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology. Acta Neuropathol 2020; 140:919-949. [PMID: 33009951 PMCID: PMC7666297 DOI: 10.1007/s00401-020-02226-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 11/29/2022]
Abstract
Patient-based cancer models are essential tools for studying tumor biology and for the assessment of drug responses in a translational context. We report the establishment a large cohort of unique organoids and patient-derived orthotopic xenografts (PDOX) of various glioma subtypes, including gliomas with mutations in IDH1, and paired longitudinal PDOX from primary and recurrent tumors of the same patient. We show that glioma PDOXs enable long-term propagation of patient tumors and represent clinically relevant patient avatars that retain histopathological, genetic, epigenetic, and transcriptomic features of parental tumors. We find no evidence of mouse-specific clonal evolution in glioma PDOXs. Our cohort captures individual molecular genotypes for precision medicine including mutations in IDH1, ATRX, TP53, MDM2/4, amplification of EGFR, PDGFRA, MET, CDK4/6, MDM2/4, and deletion of CDKN2A/B, PTCH, and PTEN. Matched longitudinal PDOX recapitulate the limited genetic evolution of gliomas observed in patients following treatment. At the histological level, we observe increased vascularization in the rat host as compared to mice. PDOX-derived standardized glioma organoids are amenable to high-throughput drug screens that can be validated in mice. We show clinically relevant responses to temozolomide (TMZ) and to targeted treatments, such as EGFR and CDK4/6 inhibitors in (epi)genetically defined subgroups, according to MGMT promoter and EGFR/CDK status, respectively. Dianhydrogalactitol (VAL-083), a promising bifunctional alkylating agent in the current clinical trial, displayed high therapeutic efficacy, and was able to overcome TMZ resistance in glioblastoma. Our work underscores the clinical relevance of glioma organoids and PDOX models for translational research and personalized treatment studies and represents a unique publicly available resource for precision oncology.
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Affiliation(s)
- Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Ann-Christin Hau
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Anaïs Oudin
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Daniel Stieber
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
- National Center of Genetics, Laboratoire National de Santé, 3555, Dudelange, Luxembourg
| | - Yahaya A Yabo
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Virginie Baus
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Vanessa Barthelemy
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Eliane Klein
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Sébastien Bougnaud
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Olivier Keunen
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
- Quantitative Biology Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - May Wantz
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Alessandro Michelucci
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
- Neuro-Immunology Group, Department of Oncology, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Virginie Neirinckx
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Arnaud Muller
- Quantitative Biology Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Tony Kaoma
- Quantitative Biology Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Francisco Azuaje
- Quantitative Biology Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Alfonso De Falco
- National Center of Genetics, Laboratoire National de Santé, 3555, Dudelange, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4367, Belvaux, Luxembourg
- Luxembourg Center of Neuropathology, Luxembourg, Luxembourg
| | - Ben Flies
- National Center of Genetics, Laboratoire National de Santé, 3555, Dudelange, Luxembourg
| | - Lorraine Richart
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4367, Belvaux, Luxembourg
- Luxembourg Center of Neuropathology, Luxembourg, Luxembourg
- National Center of Pathology, Laboratoire National de Santé, 3555, Dudelange, Luxembourg
- Department of Oncology, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Suresh Poovathingal
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Thais Arns
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Andreas Mock
- Division of Experimental Neurosurgery, Department of Neurosurgery, University of Heidelberg, 69120, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, 69120, Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University of Heidelberg, 69120, Heidelberg, Germany
| | - Anne Steino
- DelMar Pharmaceuticals, Inc., Vancouver, BC, Canada
- DelMar Pharmaceuticals, Inc., Menlo Park, CA, USA
| | - Dennis Brown
- DelMar Pharmaceuticals, Inc., Vancouver, BC, Canada
- DelMar Pharmaceuticals, Inc., Menlo Park, CA, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Hrvoje Miletic
- Department of Biomedicine, University of Bergen, 5019, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Yong-Jun Kwon
- Department of Oncology, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Winnie Jahn
- German Cancer Consortium (DKTK), 01307, Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
| | - Barbara Klink
- National Center of Genetics, Laboratoire National de Santé, 3555, Dudelange, Luxembourg
- Department of Oncology, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
- German Cancer Consortium (DKTK), 01307, Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Georgette Tanner
- Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Lucy F Stead
- Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
- Luxembourg Center of Neuropathology, Luxembourg, Luxembourg
- National Center of Pathology, Laboratoire National de Santé, 3555, Dudelange, Luxembourg
- Department of Oncology, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Frank Hertel
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
- Department of Neurosurgery, Centre Hospitalier Luxembourg, 1210, Luxembourg, Luxembourg
| | - Rolf Bjerkvig
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
- Department of Biomedicine, University of Bergen, 5019, Bergen, Norway
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg.
- Department of Biomedicine, University of Bergen, 5019, Bergen, Norway.
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