1
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Cases-Cunillera S, Friker LL, Müller P, Becker AJ, Gielen GH. From bedside to bench: New insights in epilepsy-associated tumors based on recent classification updates and animal models on brain tumor networks. Mol Oncol 2024. [PMID: 38899375 DOI: 10.1002/1878-0261.13680] [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: 12/28/2023] [Revised: 12/28/2023] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Low-grade neuroepithelial tumors (LGNTs), particularly those with glioneuronal histology, are highly associated with pharmacoresistant epilepsy. Increasing research focused on these neoplastic lesions did not translate into drug discovery; and anticonvulsant or antitumor therapies are not available yet. During the last years, animal modeling has improved, thereby leading to the possibility of generating brain tumors in mice mimicking crucial genetic, molecular and immunohistological features. Among them, intraventricular in utero electroporation (IUE) has been proven to be a valuable tool for the generation of animal models for LGNTs allowing endogenous tumor growth within the mouse brain parenchyma. Epileptogenicity is mostly determined by the slow-growing patterns of these tumors, thus mirroring intrinsic interactions between tumor cells and surrounding neurons is crucial to investigate the mechanisms underlying convulsive activity. In this review, we provide an updated classification of the human LGNT and summarize the most recent data from human and animal models, with a focus on the crosstalk between brain tumors and neuronal function.
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Affiliation(s)
- Silvia Cases-Cunillera
- INSERM U1266, Neuronal Signaling in Epilepsy and Glioma, Institute of Psychiatry and Neuroscience of Paris (IPNP), Université Paris Cité, Paris, France
- Section for Translational Epilepsy Research, Institute of Neuropathology, University Hospital Bonn, Bonn, Germany
| | - Lea L Friker
- Institute of Neuropathology, University Hospital Bonn, Bonn, Germany
| | - Philipp Müller
- Section for Translational Epilepsy Research, Institute of Neuropathology, University Hospital Bonn, Bonn, Germany
| | - Albert J Becker
- Section for Translational Epilepsy Research, Institute of Neuropathology, University Hospital Bonn, Bonn, Germany
| | - Gerrit H Gielen
- Institute of Neuropathology, University Hospital Bonn, Bonn, Germany
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2
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Hasham MG, Sargent JK, Warner MA, Farley SR, Hoffmann BR, Stodola TJ, Brunton CJ, Munger SC. Methods to study xenografted human cancer in genetically diverse mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576906. [PMID: 38328145 PMCID: PMC10849620 DOI: 10.1101/2024.01.23.576906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Xenografting human cancer tissues into mice to test new cures against cancers is critical for understanding and treating the disease. However, only a few inbred strains of mice are used to study cancers, and derivatives of mainly one strain, mostly NOD/ShiLtJ, are used for therapy efficacy studies. As it has been demonstrated when human cancer cell lines or patient-derived tissues (PDX) are xenografted into mice, the neoplastic cells are human but the supporting cells that comprise the tumor (the stroma) are from the mouse. Therefore, results of studies of xenografted tissues are influenced by the host strain. We previously published that when the same neoplastic cells are xenografted into different mouse strains, the pattern of tumor growth, histology of the tumor, number of immune cells infiltrating the tumor, and types of circulating cytokines differ depending on the strain. Therefore, to better comprehend the behavior of cancer in vivo, one must xenograft multiple mouse strains. Here we describe and report a series of methods that we used to reveal the genes and proteins expressed when the same cancer cell line, MDA-MB-231, is xenografted in different hosts. First, using proteomic analysis, we show how to use the same cell line in vivo to reveal the protein changes in the neoplastic cell that help it adapt to its host. Then, we show how different hosts respond molecularly to the same cell line. We also find that using multiple strains can reveal a more suitable host than those traditionally used for a "difficult to xenograft" PDX. In addition, using complex trait genetics, we illustrate a feasible method for uncovering the alleles of the host that support tumor growth. Finally, we demonstrate that Diversity Outbred mice, the epitome of a model of mouse-strain genetic diversity, can be xenografted with human cell lines or PDX using 2-deoxy-D-glucose treatment.
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3
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Weng T, Jenkins BJ, Saad MI. Patient-Derived Xenografts: A Valuable Preclinical Model for Drug Development and Biomarker Discovery. Methods Mol Biol 2024; 2806:19-30. [PMID: 38676793 DOI: 10.1007/978-1-0716-3858-3_3] [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), established by implanting patient tumor cells into immunodeficient mice, offer a platform for faithfully replicating human tumors. They closely mimic the histopathology, genomics, and drug sensitivity of patient tumors. This chapter highlights the versatile applications of PDXs, including studying tumor biology, metastasis, and chemoresistance, as well as their use in biomarker identification, drug screening, and personalized medicine. It also addresses challenges in using PDXs in cancer research, including variations in metastatic potential, lengthy establishment timelines, stromal changes, and limitations in immunocompromised models. Despite these challenges, PDXs remain invaluable tools guiding patient treatment and advancing preclinical drug development.
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Affiliation(s)
- Teresa Weng
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Brendan J Jenkins
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, SA, Australia
| | - Mohamed I Saad
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.
- Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia.
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, SA, Australia.
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4
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Coriu D, Stancioaica MC. Moving low-risk myelodysplastic syndromes from humans to mice: is it truly that simple? Haematologica 2024; 109:8-10. [PMID: 37534538 PMCID: PMC10772490 DOI: 10.3324/haematol.2023.283652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 07/27/2023] [Indexed: 08/04/2023] Open
Abstract
Not available.
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Affiliation(s)
- Daniel Coriu
- Center of Hematology and Bone Marrow Transplantation, Fundeni Clinical Institute, University of Medicine and Pharmacy "Carol Davila", Bucharest.
| | - Maria-Camelia Stancioaica
- Center of Hematology and Bone Marrow Transplantation, Fundeni Clinical Institute, University of Medicine and Pharmacy "Carol Davila", Bucharest
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5
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Forsythe SD, Pu T, Andrews SG, Madigan JP, Sadowski SM. Models in Pancreatic Neuroendocrine Neoplasms: Current Perspectives and Future Directions. Cancers (Basel) 2023; 15:3756. [PMID: 37568572 PMCID: PMC10416968 DOI: 10.3390/cancers15153756] [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: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/13/2023] Open
Abstract
Pancreatic neuroendocrine neoplasms (pNENs) are a heterogeneous group of tumors derived from multiple neuroendocrine origin cell subtypes. Incidence rates for pNENs have steadily risen over the last decade, and outcomes continue to vary widely due to inability to properly screen. These tumors encompass a wide range of functional and non-functional subtypes, with their rarity and slow growth making therapeutic development difficult as most clinically used therapeutics are derived from retrospective analyses. Improved molecular understanding of these cancers has increased our knowledge of the tumor biology for pNENs. Despite these advances in our understanding of pNENs, there remains a dearth of models for further investigation. In this review, we will cover the current field of pNEN models, which include established cell lines, animal models such as mice and zebrafish, and three-dimensional (3D) cell models, and compare their uses in modeling various disease aspects. While no study model is a complete representation of pNEN biology, each has advantages which allow for new scientific understanding of these rare tumors. Future efforts and advancements in technology will continue to create new options in modeling these cancers.
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Affiliation(s)
- Steven D. Forsythe
- Neuroendocrine Cancer Therapy Section, Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (S.D.F.); (S.G.A.); (J.P.M.)
| | - Tracey Pu
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Stephen G. Andrews
- Neuroendocrine Cancer Therapy Section, Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (S.D.F.); (S.G.A.); (J.P.M.)
| | - James P. Madigan
- Neuroendocrine Cancer Therapy Section, Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (S.D.F.); (S.G.A.); (J.P.M.)
| | - Samira M. Sadowski
- Neuroendocrine Cancer Therapy Section, Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (S.D.F.); (S.G.A.); (J.P.M.)
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6
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Zeng M, Ruan Z, Tang J, Liu M, Hu C, Fan P, Dai X. Generation, evolution, interfering factors, applications, and challenges of patient-derived xenograft models in immunodeficient mice. Cancer Cell Int 2023; 23:120. [PMID: 37344821 DOI: 10.1186/s12935-023-02953-3] [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: 03/09/2023] [Accepted: 05/24/2023] [Indexed: 06/23/2023] Open
Abstract
Establishing appropriate preclinical models is essential for cancer research. Evidence suggests that cancer is a highly heterogeneous disease. This follows the growing use of cancer models in cancer research to avoid these differences between xenograft tumor models and patient tumors. In recent years, a patient-derived xenograft (PDX) tumor model has been actively generated and applied, which preserves both cell-cell interactions and the microenvironment of tumors by directly transplanting cancer tissue from tumors into immunodeficient mice. In addition to this, the advent of alternative hosts, such as zebrafish hosts, or in vitro models (organoids and microfluidics), has also facilitated the advancement of cancer research. However, they still have a long way to go before they become reliable models. The development of immunodeficient mice has enabled PDX to become more mature and radiate new vitality. As one of the most reliable and standard preclinical models, the PDX model in immunodeficient mice (PDX-IM) exerts important effects in drug screening, biomarker development, personalized medicine, co-clinical trials, and immunotherapy. Here, we focus on the development procedures and application of PDX-IM in detail, summarize the implications that the evolution of immunodeficient mice has brought to PDX-IM, and cover the key issues in developing PDX-IM in preclinical studies.
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Affiliation(s)
- Mingtang Zeng
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zijing Ruan
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jiaxi Tang
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Maozhu Liu
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Chengji Hu
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ping Fan
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Xinhua Dai
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China.
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7
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Henderson CJ, McLaren AW, Kapelyukh Y, Wolf CR. Improving the predictive power of xenograft and syngeneic anti-tumour studies using mice humanised for pathways of drug metabolism. F1000Res 2023; 11:1081. [PMID: 37065929 PMCID: PMC10090862 DOI: 10.12688/f1000research.122987.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
Drug development is an expensive and time-consuming process, with only a small fraction of drugs gaining regulatory approval from the often many thousands of candidates identified during target validation. Once a lead compound has been identified and optimised, they are subject to intensive pre-clinical research to determine their pharmacodynamic, pharmacokinetic and toxicological properties, procedures which inevitably involve significant numbers of animals - mainly mice and rats, but also dogs and monkeys in much smaller numbers and for specific types of drug candidates. Many compounds that emerge from this process, having been shown to be safe and efficacious in pre-clinical studies, subsequently fail to replicate this outcome in clinical trials, therefore wasting time, money and, most importantly, animals. Due to high rates of metabolism and a differing spectrum of metabolites (some pharmacologically active) in rodents, species differences in drug metabolism can be a major impediment to drug discovery programmes and confound the extrapolation of animal data to humans. To circumvent this, we have developed a complex transgenic mouse model – 8HUM - which faithfully replicates human Phase I drug metabolism (and its regulation), and which will generate more human-relevant data from fewer animals in a pre-clinical setting and reduce attrition in the clinic. One key area for the pre-clinical application of animals in an oncology setting – almost exclusively mice - is their use in anti-tumour studies. We now further demonstrate the utility of the 8HUM mouse using a murine melanoma cell line as a syngeneic tumour and also present an immunodeficient version 8HUM_Rag2 -/- - for use in xenograft studies. These models will be of significant benefit not only to Pharma for pre-clinical drug development work, but also throughout the drug efficacy, toxicology, pharmacology, and drug metabolism communities, where fewer animals will be needed to generate more human-relevant data.
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Affiliation(s)
- Colin J. Henderson
- Division of Systems Medicine, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, Tayside, DD1 9SY, UK
| | - Aileen W. McLaren
- Division of Systems Medicine, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, Tayside, DD1 9SY, UK
| | - Yury Kapelyukh
- Division of Systems Medicine, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, Tayside, DD1 9SY, UK
| | - C. Roland Wolf
- Division of Systems Medicine, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, Tayside, DD1 9SY, UK
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8
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Partin A, Brettin T, Zhu Y, Dolezal JM, Kochanny S, Pearson AT, Shukla M, Evrard YA, Doroshow JH, Stevens RL. Data augmentation and multimodal learning for predicting drug response in patient-derived xenografts from gene expressions and histology images. Front Med (Lausanne) 2023; 10:1058919. [PMID: 36960342 PMCID: PMC10027779 DOI: 10.3389/fmed.2023.1058919] [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: 09/30/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
Patient-derived xenografts (PDXs) are an appealing platform for preclinical drug studies. A primary challenge in modeling drug response prediction (DRP) with PDXs and neural networks (NNs) is the limited number of drug response samples. We investigate multimodal neural network (MM-Net) and data augmentation for DRP in PDXs. The MM-Net learns to predict response using drug descriptors, gene expressions (GE), and histology whole-slide images (WSIs). We explore whether combining WSIs with GE improves predictions as compared with models that use GE alone. We propose two data augmentation methods which allow us training multimodal and unimodal NNs without changing architectures with a single larger dataset: 1) combine single-drug and drug-pair treatments by homogenizing drug representations, and 2) augment drug-pairs which doubles the sample size of all drug-pair samples. Unimodal NNs which use GE are compared to assess the contribution of data augmentation. The NN that uses the original and the augmented drug-pair treatments as well as single-drug treatments outperforms NNs that ignore either the augmented drug-pairs or the single-drug treatments. In assessing the multimodal learning based on the MCC metric, MM-Net outperforms all the baselines. Our results show that data augmentation and integration of histology images with GE can improve prediction performance of drug response in PDXs.
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Affiliation(s)
- Alexander Partin
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL, United States
| | - Thomas Brettin
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL, United States
| | - Yitan Zhu
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL, United States
| | - James M. Dolezal
- Section of Hematology/Oncology, Department of Medicine, University of Chicago Medical Center, Chicago, IL, United States
| | - Sara Kochanny
- Section of Hematology/Oncology, Department of Medicine, University of Chicago Medical Center, Chicago, IL, United States
| | - Alexander T. Pearson
- Section of Hematology/Oncology, Department of Medicine, University of Chicago Medical Center, Chicago, IL, United States
| | - Maulik Shukla
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL, United States
| | - Yvonne A. Evrard
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - James H. Doroshow
- Division of Cancer Therapeutics and Diagnosis, National Cancer Institute, Bethesda, MD, United States
| | - Rick L. Stevens
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL, United States
- Department of Computer Science, The University of Chicago, Chicago, IL, United States
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9
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Li X, Li M. The application of zebrafish patient-derived xenograft tumor models in the development of antitumor agents. Med Res Rev 2023; 43:212-236. [PMID: 36029178 DOI: 10.1002/med.21924] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/09/2022] [Accepted: 07/28/2022] [Indexed: 02/04/2023]
Abstract
The cost of antitumor drug development is enormous, yet the clinical outcomes are less than satisfactory. Therefore, it is of great importance to develop effective drug screening methods that enable accurate, rapid, and high-throughput discovery of lead compounds in the process of preclinical antitumor drug research. An effective solution is to use the patient-derived xenograft (PDX) tumor animal models, which are applicable for the elucidation of tumor pathogenesis and the preclinical testing of novel antitumor compounds. As a promising screening model organism, zebrafish has been widely applied in the construction of the PDX tumor model and the discovery of antineoplastic agents. Herein, we systematically survey the recent cutting-edge advances in zebrafish PDX models (zPDX) for studies of pathogenesis mechanisms and drug screening. In addition, the techniques used in the construction of zPDX are summarized. The advantages and limitations of the zPDX are also discussed in detail. Finally, the prospects of zPDX in drug discovery, translational medicine, and clinical precision medicine treatment are well presented.
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Affiliation(s)
- Xiang Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Minyong Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
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10
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Dao V, Yuki K, Lo YH, Nakano M, Kuo CJ. Immune organoids: from tumor modeling to precision oncology. Trends Cancer 2022; 8:870-880. [PMID: 35773148 PMCID: PMC9704769 DOI: 10.1016/j.trecan.2022.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 12/31/2022]
Abstract
Cancer immunotherapies, particularly immune checkpoint inhibitors, are rapidly becoming standard-of-care for many cancers. The ascendance of immune checkpoint inhibitor treatment and limitations in the accurate prediction of clinical response thereof have provided significant impetus to develop preclinical models that can guide therapeutic intervention. Traditional organoid culture methods that exclusively grow tumor epithelium as patient-derived organoids are under investigation as a personalized platform for drug discovery and for predicting clinical efficacy of chemotherapies and targeted agents. Recently, the patient-derived tumor organoid platform has evolved to contain more complex stromal and immune compartments needed to assess immunotherapeutic efficacy. We review the different methodologies for developing a more holistic patient-derived tumor organoid platform and for modeling the native immune tumor microenvironment.
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Affiliation(s)
- Vinh Dao
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA; Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kanako Yuki
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yuan-Hung Lo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michitaka Nakano
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA.
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11
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Henderson CJ, McLaren AW, Kapelyukh Y, Wolf CR. Improving the predictive power of xenograft and syngeneic anti-tumour studies using mice humanised for pathways of drug metabolism. F1000Res 2022; 11:1081. [PMID: 37065929 PMCID: PMC10090862 DOI: 10.12688/f1000research.122987.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/13/2022] [Indexed: 11/20/2022] Open
Abstract
Drug development is an expensive and time-consuming process, with only a small fraction of drugs gaining regulatory approval from the often many thousands of candidates identified during target validation. Once a lead compound has been identified and optimised, they are subject to intensive pre-clinical research to determine their pharmacodynamic, pharmacokinetic and toxicological properties, procedures which inevitably involve significant numbers of animals - mainly mice and rats, but also dogs and monkeys in much smaller numbers and for specific types of drug candidates. Many compounds that emerge from this process, having been shown to be safe and efficacious in pre-clinical studies, subsequently fail to replicate this outcome in clinical trials, therefore wasting time, money and, most importantly, animals. The poor predictive power of animal models in pre-clinical studies is predominantly due to lack of efficacy or safety reasons, which in turn can be attributed mainly to the significant species differences in drug metabolism between humans and animals. To circumvent this, we have developed a complex transgenic mouse model – 8HUM - which faithfully replicates human Phase I drug metabolism (and its regulation), and which will generate more human-relevant data [REFINEMENT] from fewer animals [REDUCTION] in a pre-clinical setting and reduce attrition in the clinic. One key area for the pre-clinical application of animals in an oncology setting – almost exclusively mice - is their use in anti-tumour studies. We now further demonstrate the utility of the 8HUM mouse using a murine melanoma cell line as a syngeneic tumour and also present an immunodeficient version 8HUM_Rag2-/- - for use in xenograft studies. These models will be of significant benefit not only to Pharma for pre-clinical drug development work, but also throughout the drug efficacy, toxicology, pharmacology, and drug metabolism communities, where fewer animals will be needed to generate more human-relevant data.
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Affiliation(s)
- Colin J. Henderson
- Division of Systems Medicine, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, Tayside, DD1 9SY, UK
| | - Aileen W. McLaren
- Division of Systems Medicine, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, Tayside, DD1 9SY, UK
| | - Yury Kapelyukh
- Division of Systems Medicine, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, Tayside, DD1 9SY, UK
| | - C. Roland Wolf
- Division of Systems Medicine, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, Tayside, DD1 9SY, UK
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12
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Chava S, Bugide S, Malvi P, Gupta R. Co-targeting of specific epigenetic regulators in combination with CDC7 potently inhibit melanoma growth. iScience 2022; 25:104752. [PMID: 35942091 PMCID: PMC9356103 DOI: 10.1016/j.isci.2022.104752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/31/2022] [Accepted: 07/08/2022] [Indexed: 12/14/2022] Open
Abstract
Melanoma is a highly aggressive skin cancer that frequently metastasizes, but current therapies only benefit some patients. Here, we demonstrate that the serine/threonine kinase cell division cycle 7 (CDC7) is overexpressed in melanoma, and patients with higher expression have shorter survival. Transcription factor ELK1 regulates CDC7 expression, and CDC7 inhibition promotes cell cycle arrest, senescence, and apoptosis, leading to inhibition of melanoma tumor growth and metastasis. Our chemical genetics screen with epigenetic inhibitors revealed stronger melanoma tumor growth inhibition when XL413 is combined with the EZH2 inhibitor GSK343 or BRPF1/2/3 inhibitor OF1. Mechanistically, XL413 with GSK343 or OF1 synergistically altered the expression of tumor-suppressive genes, leading to higher apoptosis than the single agent alone. Collectively, these results identify CDC7 as a driver of melanoma tumor growth and metastasis that can be targeted alone or in combination with EZH2 or BRPF1/2/3 inhibitors.
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Affiliation(s)
- Suresh Chava
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Suresh Bugide
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Parmanand Malvi
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Romi Gupta
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
- O’Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
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13
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Abdolahi S, Ghazvinian Z, Muhammadnejad S, Saleh M, Asadzadeh Aghdaei H, Baghaei K. Patient-derived xenograft (PDX) models, applications and challenges in cancer research. J Transl Med 2022; 20:206. [PMID: 35538576 PMCID: PMC9088152 DOI: 10.1186/s12967-022-03405-8] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/24/2022] [Indexed: 12/12/2022] Open
Abstract
The establishing of the first cancer models created a new perspective on the identification and evaluation of new anti-cancer therapies in preclinical studies. Patient-derived xenograft models are created by tumor tissue engraftment. These models accurately represent the biology and heterogeneity of different cancers and recapitulate tumor microenvironment. These features have made it a reliable model along with the development of humanized models. Therefore, they are used in many studies, such as the development of anti-cancer drugs, co-clinical trials, personalized medicine, immunotherapy, and PDX biobanks. This review summarizes patient-derived xenograft models development procedures, drug development applications in various cancers, challenges and limitations.
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Affiliation(s)
- Shahrokh Abdolahi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Ghazvinian
- Department of Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Samad Muhammadnejad
- Cell-Based Therapies Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahshid Saleh
- Department of Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Baghaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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14
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Shin HY, Lee EJ, Yang W, Kim HS, Chung D, Cho H, Kim JH. Identification of Prognostic Markers of Gynecologic Cancers Utilizing Patient-Derived Xenograft Mouse Models. Cancers (Basel) 2022; 14:cancers14030829. [PMID: 35159096 PMCID: PMC8834149 DOI: 10.3390/cancers14030829] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 02/04/2023] Open
Abstract
Patient-derived xenografts (PDXs) are important in vivo models for the development of precision medicine. However, challenges exist regarding genetic alterations and relapse after primary treatment. Thus, PDX models are required as a new approach for preclinical and clinical studies. We established PDX models of gynecologic cancers and analyzed their clinical information. We subcutaneously transplanted 207 tumor tissues from patients with gynecologic cancer into nude mice from 2014 to 2019. The successful engraftment rate of ovarian, cervical, and uterine cancer was 47%, 64%, and 56%, respectively. The subsequent passages (P2 and P3) showed higher success and faster growth rates than the first passage (P1). Using gynecologic cancer PDX models, the tumor grade is a common clinical factor affecting PDX establishment. We found that the PDX success rate correlated with the patient’s prognosis, and also that ovarian cancer patients with a poor prognosis had a faster PDX growth rate (p < 0.0001). Next, the gene sets associated with inflammation and immune responses were shown in high-ranking successful PDX engraftment through gene set enrichment analysis and RNA sequencing. Up-regulated genes in successful engraftment were found to correlate with ovarian clear cell cancer patient outcomes via Gene Expression Omnibus dataset analysis.
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Affiliation(s)
- Ha-Yeon Shin
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea; (H.-Y.S.); (E.-j.L.); (H.S.K.); (D.C.); (H.C.)
| | - Eun-ju Lee
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea; (H.-Y.S.); (E.-j.L.); (H.S.K.); (D.C.); (H.C.)
| | - Wookyeom Yang
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Hyo Sun Kim
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea; (H.-Y.S.); (E.-j.L.); (H.S.K.); (D.C.); (H.C.)
| | - Dawn Chung
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea; (H.-Y.S.); (E.-j.L.); (H.S.K.); (D.C.); (H.C.)
| | - Hanbyoul Cho
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea; (H.-Y.S.); (E.-j.L.); (H.S.K.); (D.C.); (H.C.)
| | - Jae-Hoon Kim
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea; (H.-Y.S.); (E.-j.L.); (H.S.K.); (D.C.); (H.C.)
- Correspondence: ; Tel.: +82-02-2019-3430
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15
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Wang B, Wu H, Hu C, Wang H, Liu J, Wang W, Liu Q. An overview of kinase downregulators and recent advances in discovery approaches. Signal Transduct Target Ther 2021; 6:423. [PMID: 34924565 PMCID: PMC8685278 DOI: 10.1038/s41392-021-00826-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/28/2021] [Accepted: 11/05/2021] [Indexed: 12/17/2022] Open
Abstract
Since the clinical approval of imatinib, the discovery of protein kinase downregulators entered a prosperous age. However, challenges still exist in the discovery of kinase downregulator drugs, such as the high failure rate during development, side effects, and drug-resistance problems. With the progress made through multidisciplinary efforts, an increasing number of new approaches have been applied to solve the above problems during the discovery process of kinase downregulators. In terms of in vitro and in vivo drug evaluation, progress was also made in cellular and animal model platforms for better and more clinically relevant drug assessment. Here, we review the advances in drug design strategies, drug property evaluation technologies, and efficacy evaluation models and technologies. Finally, we discuss the challenges and perspectives in the development of kinase downregulator drugs.
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Affiliation(s)
- Beilei Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Hong Wu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Chen Hu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Haizhen Wang
- Hefei PreceDo pharmaceuticals Co., Ltd, Hefei, Anhui, 230088, People's Republic of China
| | - Jing Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Wenchao Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
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16
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Zhuang P, Chiang YH, Fernanda MS, He M. Using Spheroids as Building Blocks Towards 3D Bioprinting of Tumor Microenvironment. Int J Bioprint 2021; 7:444. [PMID: 34805601 PMCID: PMC8600307 DOI: 10.18063/ijb.v7i4.444] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/02/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer still ranks as a leading cause of mortality worldwide. Although considerable efforts have been dedicated to anticancer therapeutics, progress is still slow, partially due to the absence of robust prediction models. Multicellular tumor spheroids, as a major three-dimensional (3D) culture model exhibiting features of avascular tumors, gained great popularity in pathophysiological studies and high throughput drug screening. However, limited control over cellular and structural organization is still the key challenge in achieving in vivo like tissue microenvironment. 3D bioprinting has made great strides toward tissue/organ mimicry, due to its outstanding spatial control through combining both cells and materials, scalability, and reproducibility. Prospectively, harnessing the power from both 3D bioprinting and multicellular spheroids would likely generate more faithful tumor models and advance our understanding on the mechanism of tumor progression. In this review, the emerging concept on using spheroids as a building block in 3D bioprinting for tumor modeling is illustrated. We begin by describing the context of the tumor microenvironment, followed by an introduction of various methodologies for tumor spheroid formation, with their specific merits and drawbacks. Thereafter, we present an overview of existing 3D printed tumor models using spheroids as a focus. We provide a compilation of the contemporary literature sources and summarize the overall advancements in technology and possibilities of using spheroids as building blocks in 3D printed tissue modeling, with a particular emphasis on tumor models. Future outlooks about the wonderous advancements of integrated 3D spheroidal printing conclude this review.
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Affiliation(s)
- Pei Zhuang
- Department of Pharmaceutics, University of Florida, Gainesville, Florida, 32610, USA
| | - Yi-Hua Chiang
- Department of Pharmaceutics, University of Florida, Gainesville, Florida, 32610, USA
| | | | - Mei He
- Department of Pharmaceutics, University of Florida, Gainesville, Florida, 32610, USA
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17
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Voutsadakis IA. Cell Models for Chromosome 20q11.21 Amplification and Drug Sensitivities in Colorectal Cancer. ACTA ACUST UNITED AC 2021; 57:medicina57090860. [PMID: 34577783 PMCID: PMC8465100 DOI: 10.3390/medicina57090860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/03/2021] [Accepted: 08/22/2021] [Indexed: 11/16/2022]
Abstract
Background and objectives: The chromosome locus 20q11.21 is a commonly amplified locus in colorectal cancer, with a prevalence of 8% to 9%. Several candidate cancer-associated genes are transcribed from the locus. The therapeutic implications of the amplification in colorectal cancer remain unclear. Materials and Methods: Preclinical cell line models of colorectal cancer included in the Cancer Cell Line Encyclopedia (CCLE) collection were examined for the presence of amplifications in 20q11.21 genes. Correlations of the presence of 20q11.21 amplifications with gene essentialities and drug sensitivities were surveyed on salient databases for determination of therapeutic leads. Results: A significant subset of colorectal cancer cell lines in the CCLE (12 of 63 cell lines, 19%) bear amplifications of genes located at 20q11.21. Cancer-associated genes of the locus include ASXL1, DNMT3B, BCL2L1, TPX2, KIF3B and POFUT1. These genes are all amplified in the 12 cell lines, but they are variably over-expressed at the mRNA level, compared to non-amplified lines. 20q11.21 amplified cell lines are sensitive to various tyrosine kinase inhibitors and are resistant to chemotherapy drugs targeting the mitotic apparatus and microtubules. CRISPR and RNAi dependencies screening revealed, besides the β-catenin and KRAS genes, a few recurrent gene dependencies in more than one cell line, including YAP1 and JUP. Conclusions: Cell line models of colorectal cancer with 20q11.21 gene amplifications display dependencies on the presence of specific genes and resistance or sensitivity to specific drugs and drug categories. Observations from in vitro models may form the basis for clinical drug development in this subtype of colorectal cancer. Genetic lesions conferring synthetic lethality to certain drugs or categories of drugs could be discovered with this approach.
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Affiliation(s)
- Ioannis A. Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, 750 Great Northern Road, Sault Ste. Marie, ON P6B 0A8, Canada; or
- Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, ON P6B 0A8, Canada
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18
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Zebrafish Patient-Derived Xenografts Identify Chemo-Response in Pancreatic Ductal Adenocarcinoma Patients. Cancers (Basel) 2021; 13:cancers13164131. [PMID: 34439284 PMCID: PMC8394309 DOI: 10.3390/cancers13164131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/07/2021] [Accepted: 08/12/2021] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Treating the PDAC (pancreatic ductal adenocarcinoma) zPDXs (zebrafish patient-derived xenografts) with chemotherapy regimens commonly used, we performed a co-clinical trial testing the predictiveness of the model. We found that zPDX may predict patient outcomes, classifying them into responders (R) and non-responders (NR), reporting a statistically significant higher cancer recurrence rate at 1 year after surgery in the NR group: 66.7 versus 14.3%. Our zPDX model seems to be a promising tool for the stratification of PDAC patients. This is a crucial starting point for future study involving more patients to obtain a method to really personalize the oncological treatment of PDAC patients. Abstract It is increasingly evident the necessity of new predictive tools for the treatment of pancreatic ductal adenocarcinoma in a personalized manner. We present a co-clinical trial testing the predictiveness of zPDX (zebrafish patient-derived xenograft) for assessing if patients could benefit from a therapeutic strategy (ClinicalTrials.gov: XenoZ, NCT03668418). zPDX are generated xenografting tumor tissues in zebrafish embryos. zPDX were exposed to chemotherapy regimens commonly used. We considered a zPDX a responder (R) when a decrease ≥50% in the relative tumor area was reported; otherwise, we considered them a non-responder (NR). Patients were classified as Responder if their own zPDX was classified as an R for the chemotherapy scheme she/he received an adjuvant treatment; otherwise, we considered them a Non-Responder. We compared the cancer recurrence rate at 1 year after surgery and the disease-free survival (DFS) of patients of both groups. We reported a statistically significant higher recurrence rate in the Non-Responder group: 66.7% vs. 14.3% (p = 0.036), anticipating relapse/no relapse within 1 year after surgery in 12/16 patients. The mean DFS was longer in the R-group than the NR-group, even if not statistically significant: 19.2 months vs. 12.7 months, (p = 0.123). The proposed strategy could potentially improve preclinical evaluation of treatment modalities and may enable prospective therapeutic selection in everyday clinical practice.
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19
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VanderWalde A. Personalized Medicine in Oncology; a Special Issue of the Journal of Personalized Medicine. J Pers Med 2021; 11:jpm11070632. [PMID: 34357099 PMCID: PMC8303664 DOI: 10.3390/jpm11070632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 11/21/2022] Open
Affiliation(s)
- Ari VanderWalde
- West Cancer Center and Research Institute, Memphis, TN 38138, USA
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20
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Kanaki Z, Voutsina A, Markou A, Pateras IS, Potaris K, Avgeris M, Makrythanasis P, Athanasiadis EI, Vamvakaris I, Patsea E, Vachlas K, Lianidou E, Georgoulias V, Kotsakis A, Klinakis A. Generation of Non-Small Cell Lung Cancer Patient-Derived Xenografts to Study Intratumor Heterogeneity. Cancers (Basel) 2021; 13:cancers13102446. [PMID: 34070013 PMCID: PMC8157865 DOI: 10.3390/cancers13102446] [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: 04/05/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary It is widely thought that tumors are composed of different subpopulations of cancer cells carrying genetic alterations with some of them being common among all cells while others are unique for each subpopulation. This variable genetic profile of tumor cells is a component of what is collectively described as intratumor heterogeneity (ITH). Surviving the immune system and therapies, and establishing metastases are forces of natural selection that act upon ITH and drive tumor evolution and, eventually, the clinical presentation of patients. The aim of this prospective study was to investigate ITH in early-stage operable non-small cell lung cancer. We directly grafted human tumors in immunosuppressed mice and compared the genetic profile of the tumors grown in mice with that of the original human tumors. We identified clinical factors that affected the ability of human tumors to grow as mouse xenografts. Abstract Recent advances in sequencing technologies have allowed the in-depth molecular study of tumors, even at the single cell level. Sequencing efforts have uncovered a previously unappreciated heterogeneity among tumor cells, which has been postulated to be the driving force of tumor evolution and to facilitate recurrence, metastasis, and drug resistance. In the current study, focused on early-stage operable non-small cell lung cancer, we used tumor growth in patient-derived xenograft (PDX) models in mice as a fast-forward tumor evolution process to investigate the molecular characteristics of tumor cells that grow in mice, as well as the parameters that affect the grafting efficiency. We found that squamous cell carcinomas grafted significantly more efficiently compared with adenocarcinomas. Advanced stage, patient age and primary tumor size were positively correlated with grafting. Additionally, we isolated and characterized circulating tumor cells (CTC) from patients’ peripheral blood and found that the presence of CTCs expressing epithelial-to-mesenchymal (EMT) markers correlated with the grafting potential. Interestingly, exome sequencing of the PDX tumor identified genetic alterations in DNA repair and genome integrity genes that were under-represented in the human primary counterpart. In conclusion, through the generation of a PDX biobank of NSCLC, we identified the clinical and molecular properties of tumors that affected growth in mice.
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Affiliation(s)
- Zoi Kanaki
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (Z.K.); (A.V.); (P.M.)
| | - Alexandra Voutsina
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (Z.K.); (A.V.); (P.M.)
| | - Athina Markou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.M.); (E.L.)
| | - Ioannis S. Pateras
- Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Konstantinos Potaris
- Department of Thoracic Surgery, Sotiria Hospital for Chest Diseases, 11527 Athens, Greece; (K.P.); (K.V.)
| | - Margaritis Avgeris
- Laboratory of Clinical Biochemistry–Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, “P. & A. Kyriakou” Children’s Hospital, 11527 Athens, Greece;
| | - Periklis Makrythanasis
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (Z.K.); (A.V.); (P.M.)
| | | | - Ioannis Vamvakaris
- Pathology Department, Athens Chest Hospital “Sotiria”, 11527 Athens, Greece;
| | - Eleni Patsea
- Department of Pathology, Metropolitan Hospital, 18547 Cholargos, Greece;
| | - Konstantinos Vachlas
- Department of Thoracic Surgery, Sotiria Hospital for Chest Diseases, 11527 Athens, Greece; (K.P.); (K.V.)
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.M.); (E.L.)
| | | | - Athanasios Kotsakis
- Department of Medical Oncology, General University Hospital of Larissa, 41110 Larissa, Greece;
| | - Apostolos Klinakis
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (Z.K.); (A.V.); (P.M.)
- Correspondence:
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21
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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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22
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Paran Y, Liron Y, Batsir S, Mabjeesh N, Geiger B, Kam Z. Multi-parametric characterization of drug effects on cells. F1000Res 2021; 9. [PMID: 33363713 PMCID: PMC7737707 DOI: 10.12688/f1000research.26254.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 12/28/2022] Open
Abstract
We present here a novel multi-parametric approach for the characterization of multiple cellular features, using images acquired by high-throughput and high-definition light microscopy. We specifically used this approach for deep and unbiased analysis of the effects of a drug library on five cultured cell lines. The presented method enables the acquisition and analysis of millions of images, of treated and control cells, followed by an automated identification of drugs inducing strong responses, evaluating the median effect concentrations and those cellular properties that are most highly affected by the drug. The tools described here provide standardized quantification of multiple attributes for systems level dissection of complex functions in normal and diseased cells, using multiple perturbations. Such analysis of cells, derived from pathological samples, may help in the diagnosis and follow-up of treatment in patients.
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Affiliation(s)
- Yael Paran
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel.,IDEA Biomedical Ltd., Rehovot, 76705, Israel
| | - Yuvalal Liron
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Sarit Batsir
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nicola Mabjeesh
- Department of Urology, Tel Aviv Sourasky Medical Center, Tel Aviv, 64239, Israel
| | - Benjamin Geiger
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel.,Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Zvi Kam
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel
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23
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Liang K, Liu Q, Kong Q. New technologies in developing recombinant-attenuated bacteria for cancer therapy. Biotechnol Bioeng 2020; 118:513-530. [PMID: 33038015 DOI: 10.1002/bit.27596] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/12/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
Cancer has always been a global problem, with more cases of cancer patients being diagnosed every year. Conventional cancer treatments, including radiotherapy, chemotherapy, and surgery, are still unable to bypass their obvious limitations, and developing effective targeted therapies is still required. More than one century ago, the doctor William B. Coley discovered that cancer patients had tumor regression by injection of Streptococcus bacteria. The studies of cancer therapy using bacterial microorganisms are now very widespread. In particular, the facultative anaerobic bacteria Salmonella typhimurium is widely investigated as it can selectively colonize different types of tumors, locally deliver various antitumor drugs, and inhibit tumor growth. The exciting antitumor efficacy and safety observed in animal tumor models prompted the well-known attenuated Salmonella bacterial strain VNP20009 to be tested in human clinical trials in the early 21st century. Regrettably, no patients showed significant therapeutic effects and even bacterial colonization in tumor tissue was undetectable in most patients. Salmonella bacteria are still considered as a promising agent or vehicle for cancer therapy. Recent efforts have been focused on the generation of attenuated bacterial strains with higher targeting for tumor tissue, and optimization of the delivery of therapeutic antitumor cargoes into the tumor microenvironment. This review will summarize new technologies or approaches that may improve bacteria-mediated cancer therapy.
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Affiliation(s)
- Kang Liang
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Qing Liu
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Qingke Kong
- College of Veterinary Medicine, Southwest University, Chongqing, China
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