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Mattsson J, Ljungars A, Carlsson A, Svensson C, Nilsson B, Ohlin M, Frendéus B. Sequence enrichment profiles enable target-agnostic antibody generation for a broad range of antigens. CELL REPORTS METHODS 2023; 3:100475. [PMID: 37323567 PMCID: PMC10261905 DOI: 10.1016/j.crmeth.2023.100475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/27/2023] [Accepted: 04/17/2023] [Indexed: 06/17/2023]
Abstract
Phenotypic drug discovery (PDD) enables the target-agnostic generation of therapeutic drugs with novel mechanisms of action. However, realizing its full potential for biologics discovery requires new technologies to produce antibodies to all, a priori unknown, disease-associated biomolecules. We present a methodology that helps achieve this by integrating computational modeling, differential antibody display selection, and massive parallel sequencing. The method uses the law of mass action-based computational modeling to optimize antibody display selection and, by matching computationally modeled and experimentally selected sequence enrichment profiles, predict which antibody sequences encode specificity for disease-associated biomolecules. Applied to a phage display antibody library and cell-based antibody selection, ∼105 antibody sequences encoding specificity for tumor cell surface receptors expressed at 103-106 receptors/cell were discovered. We anticipate that this approach will be broadly applicable to molecular libraries coupling genotype to phenotype and to the screening of complex antigen populations for identification of antibodies to unknown disease-associated targets.
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Affiliation(s)
- Jenny Mattsson
- BioInvent, Research, Lund, Sweden
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anne Ljungars
- BioInvent, Research, Lund, Sweden
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | - Carolin Svensson
- BioInvent, Research, Lund, Sweden
- Section of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Björn Nilsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Broad Institute, 415 Main Street, Cambridge, MA, USA
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
- SciLifeLab Human Antibody Therapeutics, Lund University, Lund, Sweden
| | - Björn Frendéus
- BioInvent, Research, Lund, Sweden
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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2
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Chen L, Wei X, Gu D, Xu Y, Zhou H. Human liver cancer organoids: Biological applications, current challenges, and prospects in hepatoma therapy. Cancer Lett 2023; 555:216048. [PMID: 36603689 DOI: 10.1016/j.canlet.2022.216048] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023]
Abstract
Liver cancer and disease are among the most socially challenging global health concerns. Although organ transplantation, surgical resection and anticancer drugs are the main methods for the treatment of liver cancer, there are still no proven cures owing to the lack of donor livers and tumor heterogeneity. Recently, advances in tumor organoid technology have attracted considerable attention as they can simulate the spatial constructs and pathophysiological characteristics of tumorigenesis and metastasis in a more realistic manner. Organoids may further contribute to the development of tailored therapies. Combining organoids with other emerging techniques, such as CRISPR-HOT, organ-on-a-chip, and 3D bioprinting, may further develop organoids and address their bottlenecks to create more practical models that generalize different tissue or organ interactions in tumor progression. In this review, we summarize the various methods in which liver organoids may be generated and describe their biological and clinical applications, present challenges, and prospects for their integration with emerging technologies. These rapidly developing liver organoids may become the focus of in vitro clinical model development and therapeutic research for liver diseases in the near future.
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Affiliation(s)
- Lichan Chen
- Department of Laboratory Medicine, Inst Translat Med, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Xiafei Wei
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China.
| | - Dayong Gu
- Department of Laboratory Medicine, Inst Translat Med, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Yong Xu
- Department of Laboratory Medicine, Inst Translat Med, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Hongzhong Zhou
- Department of Laboratory Medicine, Inst Translat Med, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangzhou Medical University, Guangzhou, China.
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3
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Tulika T, Ljungars A. Deep Mining of Complex Antibody Phage Pools. Methods Mol Biol 2023; 2702:419-431. [PMID: 37679633 DOI: 10.1007/978-1-0716-3381-6_22] [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: 09/09/2023]
Abstract
An important, and rapidly growing class of drugs are antibodies which can be discovered through phage display technology. In this technique, antibodies are typically first enriched through consecutive rounds of selection on a target antigen with amplification in bacteria between each selection round. Thereafter, a subset of random individual clones is analyzed for binding in a screening procedure. This results in discovery of the most abundant antibodies in the pool. However, there are multiple factors affecting the enrichment of antibodies during the selection resulting in a very complex output pool of antibodies. A few antibodies are present in many copies and others only in a few copies, where the most abundant antibodies are not necessarily the functionally best ones. In order to utilize the full potential of the output from a phage display selection, and enable discovery of low abundant, potentially functionally important clones, deep mining technologies are needed. In this chapter, two methods for deep mining of an antibody pool are described, protein depletion and antibody blocking. The methods can be applied both when the target is a single antigen and on complex antigen mixtures such as whole cells and tissues.
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Affiliation(s)
- Tulika Tulika
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
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4
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CDCP1: A promising diagnostic biomarker and therapeutic target for human cancer. Life Sci 2022; 301:120600. [DOI: 10.1016/j.lfs.2022.120600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 12/25/2022]
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5
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Loss of E-cadherin leads to Id2-dependent inhibition of cell cycle progression in metastatic lobular breast cancer. Oncogene 2022; 41:2932-2944. [PMID: 35437308 PMCID: PMC9122823 DOI: 10.1038/s41388-022-02314-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 12/30/2022]
Abstract
Invasive lobular breast carcinoma (ILC) is characterized by proliferative indolence and long-term latency relapses. This study aimed to identify how disseminating ILC cells control the balance between quiescence and cell cycle re-entry. In the absence of anchorage, ILC cells undergo a sustained cell cycle arrest in G0/G1 while maintaining viability. From the genes that are upregulated in anchorage independent ILC cells, we selected Inhibitor of DNA binding 2 (Id2), a mediator of cell cycle progression. Using loss-of-function experiments, we demonstrate that Id2 is essential for anchorage independent survival (anoikis resistance) in vitro and lung colonization in mice. Importantly, we find that under anchorage independent conditions, E-cadherin loss promotes expression of Id2 in multiple mouse and (organotypic) human models of ILC, an event that is caused by a direct p120-catenin/Kaiso-dependent transcriptional de-repression of the canonical Kaiso binding sequence TCCTGCNA. Conversely, stable inducible restoration of E-cadherin expression in the ILC cell line SUM44PE inhibits Id2 expression and anoikis resistance. We show evidence that Id2 accumulates in the cytosol, where it induces a sustained and CDK4/6-dependent G0/G1 cell cycle arrest through interaction with hypo-phosphorylated Rb. Finally, we find that Id2 is indeed enriched in ILC when compared to other breast cancers, and confirm cytosolic Id2 protein expression in primary ILC samples. In sum, we have linked mutational inactivation of E-cadherin to direct inhibition of cell cycle progression. Our work indicates that loss of E-cadherin and subsequent expression of Id2 drive indolence and dissemination of ILC. As such, E-cadherin and Id2 are promising candidates to stratify low and intermediate grade invasive breast cancers for the use of clinical cell cycle intervention drugs.
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Herpers B, Eppink B, James MI, Cortina C, Cañellas-Socias A, Boj SF, Hernando-Momblona X, Glodzik D, Roovers RC, van de Wetering M, Bartelink-Clements C, Zondag-van der Zande V, Mateos JG, Yan K, Salinaro L, Basmeleh A, Fatrai S, Maussang D, Lammerts van Bueren JJ, Chicote I, Serna G, Cabellos L, Ramírez L, Nuciforo P, Salazar R, Santos C, Villanueva A, Stephan-Otto Attolini C, Sancho E, Palmer HG, Tabernero J, Stratton MR, de Kruif J, Logtenberg T, Clevers H, Price LS, Vries RGJ, Batlle E, Throsby M. Functional patient-derived organoid screenings identify MCLA-158 as a therapeutic EGFR × LGR5 bispecific antibody with efficacy in epithelial tumors. NATURE CANCER 2022; 3:418-436. [PMID: 35469014 DOI: 10.1038/s43018-022-00359-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/04/2022] [Indexed: 12/19/2022]
Abstract
Patient-derived organoids (PDOs) recapitulate tumor architecture, contain cancer stem cells and have predictive value supporting personalized medicine. Here we describe a large-scale functional screen of dual-targeting bispecific antibodies (bAbs) on a heterogeneous colorectal cancer PDO biobank and paired healthy colonic mucosa samples. More than 500 therapeutic bAbs generated against Wingless-related integration site (WNT) and receptor tyrosine kinase (RTK) targets were functionally evaluated by high-content imaging to capture the complexity of PDO responses. Our drug discovery strategy resulted in the generation of MCLA-158, a bAb that specifically triggers epidermal growth factor receptor degradation in leucine-rich repeat-containing G-protein-coupled receptor 5-positive (LGR5+) cancer stem cells but shows minimal toxicity toward healthy LGR5+ colon stem cells. MCLA-158 exhibits therapeutic properties such as growth inhibition of KRAS-mutant colorectal cancers, blockade of metastasis initiation and suppression of tumor outgrowth in preclinical models for several epithelial cancer types.
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Affiliation(s)
- Bram Herpers
- OcellO BV, Leiden, The Netherlands
- Crown Bioscience Netherlands BV, Leiden, The Netherlands
| | | | - Mark I James
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carme Cortina
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
- CIBERONC, Madrid, Spain
| | - Adrià Cañellas-Socias
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
- CIBERONC, Madrid, Spain
| | - Sylvia F Boj
- Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Xavier Hernando-Momblona
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
- CIBERONC, Madrid, Spain
| | - Dominik Glodzik
- Wellcome Sanger Institute, Hinxton, UK
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Marc van de Wetering
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | | | | | - Jara García Mateos
- OcellO BV, Leiden, The Netherlands
- Crown Bioscience Netherlands BV, Leiden, The Netherlands
| | - Kuan Yan
- OcellO BV, Leiden, The Netherlands
- Crown Bioscience Netherlands BV, Leiden, The Netherlands
| | | | | | | | | | | | - Irene Chicote
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Garazi Serna
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Laia Cabellos
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Barcelona, Spain
| | - Lorena Ramírez
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Barcelona, Spain
| | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ramon Salazar
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Alberto Villanueva
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
- Xenopat SL, Parc Cientific de Barcelona (PCB), Barcelona, Spain
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
- CIBERONC, Madrid, Spain
| | - Hector G Palmer
- CIBERONC, Madrid, Spain
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Barcelona, Spain
| | - Josep Tabernero
- CIBERONC, Madrid, Spain
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Barcelona, Spain
| | | | | | | | - Hans Clevers
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Leo S Price
- OcellO BV, Leiden, The Netherlands
- Crown Bioscience Netherlands BV, Leiden, The Netherlands
| | | | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain.
- CIBERONC, Madrid, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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7
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Ahmed-Cox A, Pandzic E, Johnston ST, Heu C, McGhee J, Mansfeld FM, Crampin EJ, Davis TP, Whan RM, Kavallaris M. Spatio-temporal analysis of nanoparticles in live tumor spheroids impacted by cell origin and density. J Control Release 2021; 341:661-675. [PMID: 34915071 DOI: 10.1016/j.jconrel.2021.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/18/2021] [Accepted: 12/08/2021] [Indexed: 12/18/2022]
Abstract
Nanoparticles hold great preclinical promise in cancer therapy but continue to suffer attrition through clinical trials. Advanced, three dimensional (3D) cellular models such as tumor spheroids can recapitulate elements of the tumor environment and are considered the superior model to evaluate nanoparticle designs. However, there is an important need to better understand nanoparticle penetration kinetics and determine how different cell characteristics may influence this nanoparticle uptake. A key challenge with current approaches for measuring nanoparticle accumulation in spheroids is that they are often static, losing spatial and temporal information which may be necessary for effective nanoparticle evaluation in 3D cell models. To overcome this challenge, we developed an analysis platform, termed the Determination of Nanoparticle Uptake in Tumor Spheroids (DONUTS), which retains spatial and temporal information during quantification, enabling evaluation of nanoparticle uptake in 3D tumor spheroids. Outperforming linear profiling methods, DONUTS was able to measure silica nanoparticle uptake to 10 μm accuracy in both isotropic and irregularly shaped cancer cell spheroids. This was then extended to determine penetration kinetics, first by a forward-in-time, center-in-space model, and then by mathematical modelling, which enabled the direct evaluation of nanoparticle penetration kinetics in different spheroid models. Nanoparticle uptake was shown to inversely relate to particle size and varied depending on the cell type, cell stiffness and density of the spheroid model. The automated analysis method we have developed can be applied to live spheroids in situ, for the advanced evaluation of nanoparticles as delivery agents in cancer therapy.
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Affiliation(s)
- Aria Ahmed-Cox
- Children's Cancer Institute, Lowy Cancer Research Center, UNSW Sydney, NSW 2031, Australia; ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Australian Center for NanoMedicine, UNSW Sydney, NSW 2031, Australia; School of Women and Children's Health, Faculty of Medicine and Health, UNSW Sydney, NSW 2031, Australia
| | - Elvis Pandzic
- Katharina Gaus Light Microscopy Facility, Mark Wainwright Analytical Center, UNSW Sydney, NSW 2031, Australia
| | - Stuart T Johnston
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Celine Heu
- Katharina Gaus Light Microscopy Facility, Mark Wainwright Analytical Center, UNSW Sydney, NSW 2031, Australia
| | - John McGhee
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Australian Center for NanoMedicine, UNSW Sydney, NSW 2031, Australia; 3D Visualisation Aesthetics Lab, UNSW Art & Design, UNSW Sydney, NSW 2021, Australia
| | - Friederike M Mansfeld
- Children's Cancer Institute, Lowy Cancer Research Center, UNSW Sydney, NSW 2031, Australia; ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Australian Center for NanoMedicine, UNSW Sydney, NSW 2031, Australia; School of Women and Children's Health, Faculty of Medicine and Health, UNSW Sydney, NSW 2031, Australia; ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Melbourne, Victoria, 3052, Australia
| | - Edmund J Crampin
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Parkville, Victoria 3010, Australia; School of Medicine, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Thomas P Davis
- Precision Medicine, Australian Institute of Bioengineering & Nanotechnology, University of Queensland, QLD, 40679, Australia
| | - Renee M Whan
- Katharina Gaus Light Microscopy Facility, Mark Wainwright Analytical Center, UNSW Sydney, NSW 2031, Australia
| | - Maria Kavallaris
- Children's Cancer Institute, Lowy Cancer Research Center, UNSW Sydney, NSW 2031, Australia; ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Australian Center for NanoMedicine, UNSW Sydney, NSW 2031, Australia; School of Women and Children's Health, Faculty of Medicine and Health, UNSW Sydney, NSW 2031, Australia.
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8
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Qu J, Kalyani FS, Liu L, Cheng T, Chen L. Tumor organoids: synergistic applications, current challenges, and future prospects in cancer therapy. Cancer Commun (Lond) 2021; 41:1331-1353. [PMID: 34713636 PMCID: PMC8696219 DOI: 10.1002/cac2.12224] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/29/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023] Open
Abstract
Patient-derived cancer cells (PDCs) and patient-derived xenografts (PDXs) are often used as tumor models, but have many shortcomings. PDCs not only lack diversity in terms of cell type, spatial organization, and microenvironment but also have adverse effects in stem cell cultures, whereas PDX are expensive with a low transplantation success rate and require a long culture time. In recent years, advances in three-dimensional (3D) organoid culture technology have led to the development of novel physiological systems that model the tissues of origin more precisely than traditional culture methods. Patient-derived cancer organoids bridge the conventional gaps in PDC and PDX models and closely reflect the pathophysiological features of natural tumorigenesis and metastasis, and have led to new patient-specific drug screening techniques, development of individualized treatment regimens, and discovery of prognostic biomarkers and mechanisms of resistance. Synergistic combinations of cancer organoids with other technologies, for example, organ-on-a-chip, 3D bio-printing, and CRISPR-Cas9-mediated homology-independent organoid transgenesis, and with treatments, such as immunotherapy, have been useful in overcoming their limitations and led to the development of more suitable model systems that recapitulate the complex stroma of cancer, inter-organ and intra-organ communications, and potentially multiorgan metastasis. In this review, we discuss various methods for the creation of organ-specific cancer organoids and summarize organ-specific advances and applications, synergistic technologies, and treatments as well as current limitations and future prospects for cancer organoids. Further advances will bring this novel 3D organoid culture technique closer to clinical practice in the future.
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Affiliation(s)
- Jingjing Qu
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, P. R. China.,Lung Cancer and Gastroenterology Department, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Farhin Shaheed Kalyani
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, P. R. China
| | - Li Liu
- Lung Cancer and Gastroenterology Department, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Tianli Cheng
- Thoracic Medicine Department 1, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Lijun Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, P. R. China
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9
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Carracedo-Reboredo P, Liñares-Blanco J, Rodríguez-Fernández N, Cedrón F, Novoa FJ, Carballal A, Maojo V, Pazos A, Fernandez-Lozano C. A review on machine learning approaches and trends in drug discovery. Comput Struct Biotechnol J 2021; 19:4538-4558. [PMID: 34471498 PMCID: PMC8387781 DOI: 10.1016/j.csbj.2021.08.011] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 12/30/2022] Open
Abstract
Drug discovery aims at finding new compounds with specific chemical properties for the treatment of diseases. In the last years, the approach used in this search presents an important component in computer science with the skyrocketing of machine learning techniques due to its democratization. With the objectives set by the Precision Medicine initiative and the new challenges generated, it is necessary to establish robust, standard and reproducible computational methodologies to achieve the objectives set. Currently, predictive models based on Machine Learning have gained great importance in the step prior to preclinical studies. This stage manages to drastically reduce costs and research times in the discovery of new drugs. This review article focuses on how these new methodologies are being used in recent years of research. Analyzing the state of the art in this field will give us an idea of where cheminformatics will be developed in the short term, the limitations it presents and the positive results it has achieved. This review will focus mainly on the methods used to model the molecular data, as well as the biological problems addressed and the Machine Learning algorithms used for drug discovery in recent years.
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Key Words
- ADMET, Absorption, distribution, metabolism, elimination and toxicity
- ADR, Adverse Drug Reaction
- AI, Artificial Intelligence
- ANN, Artificial Neural Networks
- APFP, Atom Pairs 2d FingerPrint
- AUC, Area under the Curve
- BBB, Blood–Brain barrier
- CDK, Chemical Development Kit
- CNN, Convolutional Neural Networks
- CNS, Central Nervous System
- CPI, Compound-protein interaction
- CV, Cross Validation
- Cheminformatics
- DL, Deep Learning
- DNA, Deoxyribonucleic acid
- Deep Learning
- Drug Discovery
- ECFP, Extended Connectivity Fingerprints
- FDA, Food and Drug Administration
- FNN, Fully Connected Neural Networks
- FP, Fringerprints
- FS, Feature Selection
- GCN, Graph Convolutional Networks
- GEO, Gene Expression Omnibus
- GNN, Graph Neural Networks
- GO, Gene Ontology
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MACCS, Molecular ACCess System
- MCC, Matthews correlation coefficient
- MD, Molecular Descriptors
- MKL, Multiple Kernel Learning
- ML, Machine Learning
- Machine Learning
- Molecular Descriptors
- NB, Naive Bayes
- OOB, Out of Bag
- PCA, Principal Component Analyisis
- QSAR
- QSAR, Quantitative structure–activity relationship
- RF, Random Forest
- RNA, Ribonucleic Acid
- SMILES, simplified molecular-input line-entry system
- SVM, Support Vector Machines
- TCGA, The Cancer Genome Atlas
- WHO, World Health Organization
- t-SNE, t-Distributed Stochastic Neighbor Embedding
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Affiliation(s)
- Paula Carracedo-Reboredo
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
| | - Jose Liñares-Blanco
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
- CITIC-Research Center of Information and Communication Technologies, Universidade da Coruna, A Coruña 15071, Spain
| | - Nereida Rodríguez-Fernández
- CITIC-Research Center of Information and Communication Technologies, Universidade da Coruna, A Coruña 15071, Spain
- Department of Computer Science and Information Technologies, Faculty of Communication Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
| | - Francisco Cedrón
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
| | - Francisco J. Novoa
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
| | - Adrian Carballal
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
- CITIC-Research Center of Information and Communication Technologies, Universidade da Coruna, A Coruña 15071, Spain
- Department of Computer Science and Information Technologies, Faculty of Communication Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
| | - Victor Maojo
- Biomedical Informatics Group, Artificial Intelligence Department, Polytechnic University of Madrid, Calle de los Ciruelos, Boadilla del Monte, Madrid 28660, Spain
| | - Alejandro Pazos
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
- CITIC-Research Center of Information and Communication Technologies, Universidade da Coruna, A Coruña 15071, Spain
- Grupo de Redes de Neuronas Artificiales y Sistemas Adaptativos. Imagen Médica y Diagnóstico Radiológico (RNASA-IMEDIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
| | - Carlos Fernandez-Lozano
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
- CITIC-Research Center of Information and Communication Technologies, Universidade da Coruna, A Coruña 15071, Spain
- Grupo de Redes de Neuronas Artificiales y Sistemas Adaptativos. Imagen Médica y Diagnóstico Radiológico (RNASA-IMEDIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
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10
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Azar J, Bahmad HF, Daher D, Moubarak MM, Hadadeh O, Monzer A, Al Bitar S, Jamal M, Al-Sayegh M, Abou-Kheir W. The Use of Stem Cell-Derived Organoids in Disease Modeling: An Update. Int J Mol Sci 2021; 22:7667. [PMID: 34299287 PMCID: PMC8303386 DOI: 10.3390/ijms22147667] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023] Open
Abstract
Organoids represent one of the most important advancements in the field of stem cells during the past decade. They are three-dimensional in vitro culturing models that originate from self-organizing stem cells and can mimic the in vivo structural and functional specificities of body organs. Organoids have been established from multiple adult tissues as well as pluripotent stem cells and have recently become a powerful tool for studying development and diseases in vitro, drug screening, and host-microbe interaction. The use of stem cells-that have self-renewal capacity to proliferate and differentiate into specialized cell types-for organoids culturing represents a major advancement in biomedical research. Indeed, this new technology has a great potential to be used in a multitude of fields, including cancer research, hereditary and infectious diseases. Nevertheless, organoid culturing is still rife with many challenges, not limited to being costly and time consuming, having variable rates of efficiency in generation and maintenance, genetic stability, and clinical applications. In this review, we aim to provide a synopsis of pluripotent stem cell-derived organoids and their use for disease modeling and other clinical applications.
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Affiliation(s)
- Joseph Azar
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2260, Lebanon; (J.A.); (H.F.B.); (D.D.); (M.M.M.); (O.H.); (A.M.); (S.A.B.)
| | - Hisham F. Bahmad
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2260, Lebanon; (J.A.); (H.F.B.); (D.D.); (M.M.M.); (O.H.); (A.M.); (S.A.B.)
- Arkadi M. Rywlin M.D. Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA
| | - Darine Daher
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2260, Lebanon; (J.A.); (H.F.B.); (D.D.); (M.M.M.); (O.H.); (A.M.); (S.A.B.)
| | - Maya M. Moubarak
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2260, Lebanon; (J.A.); (H.F.B.); (D.D.); (M.M.M.); (O.H.); (A.M.); (S.A.B.)
| | - Ola Hadadeh
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2260, Lebanon; (J.A.); (H.F.B.); (D.D.); (M.M.M.); (O.H.); (A.M.); (S.A.B.)
| | - Alissar Monzer
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2260, Lebanon; (J.A.); (H.F.B.); (D.D.); (M.M.M.); (O.H.); (A.M.); (S.A.B.)
| | - Samar Al Bitar
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2260, Lebanon; (J.A.); (H.F.B.); (D.D.); (M.M.M.); (O.H.); (A.M.); (S.A.B.)
| | - Mohamed Jamal
- Hamdan Bin Mohammed College of Dental Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 66566, United Arab Emirates
| | - Mohamed Al-Sayegh
- Biology Division, New York University Abu Dhabi, Abu Dhabi 2460, United Arab Emirates
| | - Wassim Abou-Kheir
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2260, Lebanon; (J.A.); (H.F.B.); (D.D.); (M.M.M.); (O.H.); (A.M.); (S.A.B.)
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11
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Zatreanu D, Robinson HMR, Alkhatib O, Boursier M, Finch H, Geo L, Grande D, Grinkevich V, Heald RA, Langdon S, Majithiya J, McWhirter C, Martin NMB, Moore S, Neves J, Rajendra E, Ranzani M, Schaedler T, Stockley M, Wiggins K, Brough R, Sridhar S, Gulati A, Shao N, Badder LM, Novo D, Knight EG, Marlow R, Haider S, Callen E, Hewitt G, Schimmel J, Prevo R, Alli C, Ferdinand A, Bell C, Blencowe P, Bot C, Calder M, Charles M, Curry J, Ekwuru T, Ewings K, Krajewski W, MacDonald E, McCarron H, Pang L, Pedder C, Rigoreau L, Swarbrick M, Wheatley E, Willis S, Wong AC, Nussenzweig A, Tijsterman M, Tutt A, Boulton SJ, Higgins GS, Pettitt SJ, Smith GCM, Lord CJ. Polθ inhibitors elicit BRCA-gene synthetic lethality and target PARP inhibitor resistance. Nat Commun 2021; 12:3636. [PMID: 34140467 PMCID: PMC8211653 DOI: 10.1038/s41467-021-23463-8] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/30/2021] [Indexed: 02/05/2023] Open
Abstract
To identify approaches to target DNA repair vulnerabilities in cancer, we discovered nanomolar potent, selective, low molecular weight (MW), allosteric inhibitors of the polymerase function of DNA polymerase Polθ, including ART558. ART558 inhibits the major Polθ-mediated DNA repair process, Theta-Mediated End Joining, without targeting Non-Homologous End Joining. In addition, ART558 elicits DNA damage and synthetic lethality in BRCA1- or BRCA2-mutant tumour cells and enhances the effects of a PARP inhibitor. Genetic perturbation screening revealed that defects in the 53BP1/Shieldin complex, which cause PARP inhibitor resistance, result in in vitro and in vivo sensitivity to small molecule Polθ polymerase inhibitors. Mechanistically, ART558 increases biomarkers of single-stranded DNA and synthetic lethality in 53BP1-defective cells whilst the inhibition of DNA nucleases that promote end-resection reversed these effects, implicating these in the synthetic lethal mechanism-of-action. Taken together, these observations describe a drug class that elicits BRCA-gene synthetic lethality and PARP inhibitor synergy, as well as targeting a biomarker-defined mechanism of PARPi-resistance.
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Affiliation(s)
- Diana Zatreanu
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Helen M R Robinson
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Omar Alkhatib
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Marie Boursier
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Harry Finch
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Lerin Geo
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Diego Grande
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Vera Grinkevich
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Robert A Heald
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Sophie Langdon
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Jayesh Majithiya
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Claire McWhirter
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Niall M B Martin
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Shaun Moore
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Joana Neves
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Eeson Rajendra
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Marco Ranzani
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Theresia Schaedler
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Martin Stockley
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Kimberley Wiggins
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Rachel Brough
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Sandhya Sridhar
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Aditi Gulati
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Nan Shao
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Luned M Badder
- The Breast Cancer Now Research Unit, King's College London, London, UK
| | - Daniela Novo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Eleanor G Knight
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rebecca Marlow
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Research Unit, King's College London, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Remko Prevo
- Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Christina Alli
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Amanda Ferdinand
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Cameron Bell
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Peter Blencowe
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Chris Bot
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Mathew Calder
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Mark Charles
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Jayne Curry
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Tennyson Ekwuru
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Katherine Ewings
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Wojciech Krajewski
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Ellen MacDonald
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Hollie McCarron
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Leon Pang
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Chris Pedder
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Laurent Rigoreau
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Martin Swarbrick
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Ed Wheatley
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Simon Willis
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Ai Ching Wong
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Andrew Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Research Unit, King's College London, London, UK
| | - Simon J Boulton
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
- The Francis Crick Institute, London, UK
| | - Geoff S Higgins
- Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Stephen J Pettitt
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Graeme C M Smith
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK.
| | - Christopher J Lord
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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12
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Yeow ZY, Lambrus BG, Marlow R, Zhan KH, Durin MA, Evans LT, Scott PM, Phan T, Park E, Ruiz LA, Moralli D, Knight EG, Badder LM, Novo D, Haider S, Green CM, Tutt ANJ, Lord CJ, Chapman JR, Holland AJ. Targeting TRIM37-driven centrosome dysfunction in 17q23-amplified breast cancer. Nature 2020; 585:447-452. [PMID: 32908313 PMCID: PMC7597367 DOI: 10.1038/s41586-020-2690-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 06/17/2020] [Indexed: 01/01/2023]
Abstract
Genomic instability is a hallmark of cancer, and has a central role in the initiation and development of breast cancer1,2. The success of poly-ADP ribose polymerase inhibitors in the treatment of breast cancers that are deficient in homologous recombination exemplifies the utility of synthetically lethal genetic interactions in the treatment of breast cancers that are driven by genomic instability3. Given that defects in homologous recombination are present in only a subset of breast cancers, there is a need to identify additional driver mechanisms for genomic instability and targeted strategies to exploit these defects in the treatment of cancer. Here we show that centrosome depletion induces synthetic lethality in cancer cells that contain the 17q23 amplicon, a recurrent copy number aberration that defines about 9% of all primary breast cancer tumours and is associated with high levels of genomic instability4-6. Specifically, inhibition of polo-like kinase 4 (PLK4) using small molecules leads to centrosome depletion, which triggers mitotic catastrophe in cells that exhibit amplicon-directed overexpression of TRIM37. To explain this effect, we identify TRIM37 as a negative regulator of centrosomal pericentriolar material. In 17q23-amplified cells that lack centrosomes, increased levels of TRIM37 block the formation of foci that comprise pericentriolar material-these foci are structures with a microtubule-nucleating capacity that are required for successful cell division in the absence of centrosomes. Finally, we find that the overexpression of TRIM37 causes genomic instability by delaying centrosome maturation and separation at mitotic entry, and thereby increases the frequency of mitotic errors. Collectively, these findings highlight TRIM37-dependent genomic instability as a putative driver event in 17q23-amplified breast cancer and provide a rationale for the use of centrosome-targeting therapeutic agents in treating these cancers.
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Affiliation(s)
- Zhong Y Yeow
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Bramwell G Lambrus
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca Marlow
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Unit, King's College London, London, UK
| | - Kevin H Zhan
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mary-Anne Durin
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lauren T Evans
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Phillip M Scott
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thao Phan
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Park
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lorena A Ruiz
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniela Moralli
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Eleanor G Knight
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Luned M Badder
- The Breast Cancer Now Unit, King's College London, London, UK
| | - Daniela Novo
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Catherine M Green
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Andrew N J Tutt
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Unit, King's College London, London, UK
| | - Christopher J Lord
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - J Ross Chapman
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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13
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Badder LM, Hollins AJ, Herpers B, Yan K, Ewan KB, Thomas M, Shone JR, Badder DA, Naven M, Ashelford KE, Hargest R, Clarke AR, Esdar C, Buchstaller HP, Treherne JM, Boj S, Ramezanpour B, Wienke D, Price LS, Shaw PH, Dale TC. 3D imaging of colorectal cancer organoids identifies responses to Tankyrase inhibitors. PLoS One 2020; 15:e0235319. [PMID: 32810173 PMCID: PMC7433887 DOI: 10.1371/journal.pone.0235319] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 06/12/2020] [Indexed: 12/30/2022] Open
Abstract
Aberrant activation of the Wnt signalling pathway is required for tumour initiation and survival in the majority of colorectal cancers. The development of inhibitors of Wnt signalling has been the focus of multiple drug discovery programs targeting colorectal cancer and other malignancies associated with aberrant pathway activation. However, progression of new clinical entities targeting the Wnt pathway has been slow. One challenge lies with the limited predictive power of 2D cancer cell lines because they fail to fully recapitulate intratumoural phenotypic heterogeneity. In particular, the relationship between 2D cancer cell biology and cancer stem cell function is poorly understood. By contrast, 3D tumour organoids provide a platform in which complex cell-cell interactions can be studied. However, complex 3D models provide a challenging platform for the quantitative analysis of drug responses of therapies that have differential effects on tumour cell subpopulations. Here, we generated tumour organoids from colorectal cancer patients and tested their responses to inhibitors of Tankyrase (TNKSi) which are known to modulate Wnt signalling. Using compounds with 3 orders of magnitude difference in cellular mechanistic potency together with image-based assays, we demonstrate that morphometric analyses can capture subtle alterations in organoid responses to Wnt inhibitors that are consistent with activity against a cancer stem cell subpopulation. Overall our study highlights the value of phenotypic readouts as a quantitative method to asses drug-induced effects in a relevant preclinical model.
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Affiliation(s)
- Luned M. Badder
- Cardiff University School of Biosciences, Cardiff, Wales, United Kingdom
- European Cancer Stem Cell Research Institute (ECSCRI), Cardiff University, Cardiff, Wales, United Kingdom
| | - Andrew J. Hollins
- Cardiff University School of Biosciences, Cardiff, Wales, United Kingdom
- European Cancer Stem Cell Research Institute (ECSCRI), Cardiff University, Cardiff, Wales, United Kingdom
| | | | - Kuan Yan
- OcellO B.V., Leiden, The Netherlands
| | - Kenneth B. Ewan
- Cardiff University School of Biosciences, Cardiff, Wales, United Kingdom
| | - Mairian Thomas
- Cellesce Ltd, Cardiff Medicentre, Heath Park, Cardiff, United Kingdom
| | - Jennifer R. Shone
- Cardiff University School of Biosciences, Cardiff, Wales, United Kingdom
| | - Delyth A. Badder
- Cellular Pathology Department, University Hospital for Wales, Cardiff, United Kingdom
| | - Marc Naven
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Kevin E. Ashelford
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Rachel Hargest
- Department of Colorectal Surgery, University Hospital of Wales, Cardiff, United Kingdom
- Division of Cancer and Genetics, CCMRC, Henry Wellcome Building, Cardiff University, Cardiff, United Kingdom
| | - Alan R. Clarke
- European Cancer Stem Cell Research Institute (ECSCRI), Cardiff University, Cardiff, Wales, United Kingdom
| | - Christina Esdar
- Biopharma, Merck Healthcare KGaA, Research & Development, Darmstadt, Germany
| | | | - J. Mark Treherne
- Cellesce Ltd, Cardiff Medicentre, Heath Park, Cardiff, United Kingdom
| | - Sylvia Boj
- Hubrecht Organoid Technology, Utrecht, The Netherlands
| | | | - Dirk Wienke
- Biopharma, Merck Healthcare KGaA, Research & Development, Darmstadt, Germany
| | | | - Paul H. Shaw
- Velindre Cancer Centre, Cardiff, Wales, United Kingdom
| | - Trevor C. Dale
- European Cancer Stem Cell Research Institute (ECSCRI), Cardiff University, Cardiff, Wales, United Kingdom
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14
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Harrington BS, He Y, Khan T, Puttick S, Conroy PJ, Kryza T, Cuda T, Sokolowski KA, Tse BWC, Robbins KK, Arachchige BJ, Stehbens SJ, Pollock PM, Reed S, Weroha SJ, Haluska P, Salomon C, Lourie R, Perrin LC, Law RHP, Whisstock JC, Hooper JD. Anti-CDCP1 immuno-conjugates for detection and inhibition of ovarian cancer. Am J Cancer Res 2020; 10:2095-2114. [PMID: 32104500 PMCID: PMC7019151 DOI: 10.7150/thno.30736] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
CUB-domain containing protein 1 (CDCP1) is a cancer associated cell surface protein that amplifies pro-tumorigenic signalling by other receptors including EGFR and HER2. Its potential as a cancer target is supported by studies showing that anti-CDCP1 antibodies inhibit cell migration and survival in vitro, and tumor growth and metastasis in vivo. Here we characterize two anti-CDCP1 antibodies, focusing on immuno-conjugates of one of these as a tool to detect and inhibit ovarian cancer. Methods: A panel of ovarian cancer cell lines was examined for cell surface expression of CDCP1 and loss of expression induced by anti-CDCP1 antibodies 10D7 and 41-2 using flow cytometry and Western blot analysis. Surface plasmon resonance analysis and examination of truncation mutants was used to analyse the binding properties of the antibodies for CDCP1. Live-cell spinning-disk confocal microscopy of GFP-tagged CDCP1 was used to track internalization and intracellular trafficking of CDCP1/antibody complexes. In vivo, zirconium 89-labelled 10D7 was detected by positron-emission tomography imaging, of an ovarian cancer patient-derived xenograft grown intraperitoneally in mice. The efficacy of cytotoxin-conjugated 10D7 was examined against ovarian cancer cells in vitro and in vivo. Results: Our data indicate that each antibody binds with high affinity to the extracellular domain of CDCP1 causing rapid internalization of the receptor/antibody complex and degradation of CDCP1 via processes mediated by the kinase Src. Highlighting the potential clinical utility of CDCP1, positron-emission tomography imaging, using zirconium 89-labelled 10D7, was able to detect subcutaneous and intraperitoneal xenograft ovarian cancers in mice, including small (diameter <3 mm) tumor deposits of an ovarian cancer patient-derived xenograft grown intraperitoneally in mice. Furthermore, cytotoxin-conjugated 10D7 was effective at inhibiting growth of CDCP1-expressing ovarian cancer cells in vitro and in vivo. Conclusions: These data demonstrate that CDCP1 internalizing antibodies have potential for killing and detection of CDCP1 expressing ovarian cancer cells.
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15
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Freeth J, Soden J. New Advances in Cell Microarray Technology to Expand Applications in Target Deconvolution and Off-Target Screening. SLAS DISCOVERY 2019; 25:223-230. [PMID: 31885307 DOI: 10.1177/2472555219897567] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Identifying the cell surface receptors of natural ligands, and deconvoluting the receptor targets of candidate drug leads, presents a challenge in medical research and drug discovery. Traditionally, success rates have been low, and screening efforts often generate numerous false-positive hits that require extensive follow-up to either validate or disregard. If successful, receptor identification enables the discovery of previously unknown, disease-relevant targets, provides critical insights into biological pathways and disease processes, and allows for secondary targets to be uncovered. By expressing the majority of the human plasma membrane proteome in human cells on glass slides in situ, human cell microarray technology provides a powerful approach for identifying receptor target interactions. This approach significantly increases the success rates in identifying specific primary receptor targets and off-targets while limiting the number of false-positive hits. Here we describe cell microarray technology, focusing on new advances including the use of whole cells as bait for receptor interactions, and the inclusion of secreted proteins that widens the utility of the technology in off-target screening.
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Affiliation(s)
- Jim Freeth
- Retrogenix Limited, Chinley, High Peak, UK
| | - Jo Soden
- Retrogenix Limited, Chinley, High Peak, UK
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16
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Ljungars A, Svensson C, Carlsson A, Birgersson E, Tornberg UC, Frendéus B, Ohlin M, Mattsson M. Deep Mining of Complex Antibody Phage Pools Generated by Cell Panning Enables Discovery of Rare Antibodies Binding New Targets and Epitopes. Front Pharmacol 2019; 10:847. [PMID: 31417405 PMCID: PMC6683657 DOI: 10.3389/fphar.2019.00847] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/02/2019] [Indexed: 01/11/2023] Open
Abstract
Phage display technology is a common approach for discovery of therapeutic antibodies. Drug candidates are typically isolated in two steps: First, a pool of antibodies is enriched through consecutive rounds of selection on a target antigen, and then individual clones are characterized in a screening procedure. When whole cells are used as targets, as in phenotypic discovery, the output phage pool typically contains thousands of antibodies, binding, in theory, hundreds of different cell surface receptors. Clonal expansion throughout the phage display enrichment process is affected by multiple factors resulting in extremely complex output phage pools where a few antibodies are highly abundant and the majority is very rare. This is a huge challenge in the screening where only a fraction of the antibodies can be tested using a conventional binding analysis, identifying mainly the most abundant clones typically binding only one or a few targets. As the expected number of antibodies and specificities in the pool is much higher, complementing methods, to reach deeper into the pool, are required, called deep mining methods. In this study, four deep mining methods were evaluated: 1) isolation of rare sub-pools of specific antibodies through selection on recombinant proteins predicted to be expressed on the target cells, 2) isolation of a sub-pool enriched for antibodies of unknown specificities through depletion of the primary phage pool on recombinant proteins corresponding to receptors known to generate many binders, 3) isolation of a sub-pool enriched for antibodies through selection on cells blocked with antibodies dominating the primary phage pool, and 4) next-generation sequencing-based analysis of isolated antibody pools followed by antibody gene synthesis and production of rare but enriched clones. We demonstrate that antibodies binding new targets and epitopes, not discovered through screening alone, can be discovered using described deep mining methods. Overall, we demonstrate the complexity of phage pools generated through selection on cells and show that a combination of conventional screening and deep mining methods are needed to fully utilize such pools. Deep mining will be important in future phenotypic antibody drug discovery efforts to increase the diversity of identified antibodies and targets.
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Affiliation(s)
- Anne Ljungars
- BioInvent International AB, Lund, Sweden
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | | | | | | | | | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
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Booij TH, Price LS, Danen EHJ. 3D Cell-Based Assays for Drug Screens: Challenges in Imaging, Image Analysis, and High-Content Analysis. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2019; 24:615-627. [PMID: 30817892 PMCID: PMC6589915 DOI: 10.1177/2472555219830087] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/17/2019] [Accepted: 01/21/2019] [Indexed: 12/13/2022]
Abstract
The introduction of more relevant cell models in early preclinical drug discovery, combined with high-content imaging and automated analysis, is expected to increase the quality of compounds progressing to preclinical stages in the drug development pipeline. In this review we discuss the current switch to more relevant 3D cell culture models and associated challenges for high-throughput screening and high-content analysis. We propose that overcoming these challenges will enable front-loading the drug discovery pipeline with better biology, extracting the most from that biology, and, in general, improving translation between in vitro and in vivo models. This is expected to reduce the proportion of compounds that fail in vivo testing due to a lack of efficacy or to toxicity.
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Affiliation(s)
- Tijmen H. Booij
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- NEXUS Personalized Health Technologies, ETH Zürich, Switzerland
| | - Leo S. Price
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- OcellO B.V., Leiden, The Netherlands
| | - Erik H. J. Danen
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
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18
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A platform for phenotypic discovery of therapeutic antibodies and targets applied on Chronic Lymphocytic Leukemia. NPJ Precis Oncol 2018; 2:18. [PMID: 30182064 PMCID: PMC6120912 DOI: 10.1038/s41698-018-0061-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/27/2018] [Accepted: 07/03/2018] [Indexed: 11/17/2022] Open
Abstract
Development of antibody drugs against novel targets and pathways offers great opportunities to improve current cancer treatment. We here describe a phenotypic discovery platform enabling efficient identification of therapeutic antibody-target combinations. The platform utilizes primary patient cells throughout the discovery process and includes methods for differential phage display cell panning, high-throughput cell-based specificity screening, phenotypic in vitro screening, target deconvolution, and confirmatory in vivo screening. In this study the platform was applied on cancer cells from patients with Chronic Lymphocytic Leukemia resulting in discovery of antibodies with improved cytotoxicity in vitro compared to the standard of care, the CD20-specific monoclonal antibody rituximab. Isolated antibodies were found to target six different receptors on Chronic Lymphocytic Leukemia cells; CD21, CD23, CD32, CD72, CD200, and HLA-DR of which CD32, CD200, and HLA-DR appeared as the most potent targets for antibody-based cytotoxicity treatment. Enhanced antibody efficacy was confirmed in vivo using a patient-derived xenograft model.
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19
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Comess KM, McLoughlin SM, Oyer JA, Richardson PL, Stöckmann H, Vasudevan A, Warder SE. Emerging Approaches for the Identification of Protein Targets of Small Molecules - A Practitioners’ Perspective. J Med Chem 2018; 61:8504-8535. [DOI: 10.1021/acs.jmedchem.7b01921] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kenneth M. Comess
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Shaun M. McLoughlin
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Jon A. Oyer
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Paul L. Richardson
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Henning Stöckmann
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Anil Vasudevan
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Scott E. Warder
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
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20
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Jackson SJ, Thomas GJ. Human tissue models in cancer research: looking beyond the mouse. Dis Model Mech 2018; 10:939-942. [PMID: 28768734 PMCID: PMC5560067 DOI: 10.1242/dmm.031260] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Mouse models, including patient-derived xenograft mice, are widely used to address questions in cancer research. However, there are documented flaws in these models that can result in the misrepresentation of human tumour biology and limit the suitability of the model for translational research. A coordinated effort to promote the more widespread development and use of ‘non-animal human tissue’ models could provide a clinically relevant platform for many cancer studies, maximising the opportunities presented by human tissue resources such as biobanks. A number of key factors limit the wide adoption of non-animal human tissue models in cancer research, including deficiencies in the infrastructure and the technical tools required to collect, transport, store and maintain human tissue for lab use. Another obstacle is the long-standing cultural reliance on animal models, which can make researchers resistant to change, often because of concerns about historical data compatibility and losing ground in a competitive environment while new approaches are embedded in lab practice. There are a wide range of initiatives that aim to address these issues by facilitating data sharing and promoting collaborations between organisations and researchers who work with human tissue. The importance of coordinating biobanks and introducing quality standards is gaining momentum. There is an exciting opportunity to transform cancer drug discovery by optimising the use of human tissue and reducing the reliance on potentially less predictive animal models. Summary: Samuel Jackson and Gareth Thomas discuss the limitations of patient-derived xenograft mouse models and highlight initiatives to maximise the use of human tissue in cancer research, with the goal of improving translation and reducing animal experimentation.
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Affiliation(s)
- Samuel J Jackson
- National Centre for the Replacement, Refinement and Reduction of Animals in Research, Gibbs Building, 215 Euston Road, London NW1 2BE, UK
| | - Gareth J Thomas
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Somers Building, MP 824 Tremona Road, Southampton SO16 6YD, UK
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Hydrophilic Auristatin Glycoside Payload Enables Improved Antibody-Drug Conjugate Efficacy and Biocompatibility. Antibodies (Basel) 2018; 7:antib7020015. [PMID: 31544867 PMCID: PMC6698876 DOI: 10.3390/antib7020015] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/01/2018] [Accepted: 03/05/2018] [Indexed: 11/17/2022] Open
Abstract
Antibody-drug conjugates (ADCs) offer a combination of antibody therapy and specific delivery of potent small-molecule payloads to target cells. The properties of the ADC molecule are determined by the balance of its components. The efficacy of the payload component increases with higher drug-to-antibody ratio (DAR), while homogeneous DAR = 8 ADCs are easily prepared by conjugation to the four accessible antibody hinge cystines. However, use of hydrophobic payloads has permitted only DAR = 2-4, due to poor pharmacokinetics and aggregation problems. Here, we describe generation and characterization of homogeneous DAR = 8 ADCs carrying a novel auristatin β-D-glucuronide, MMAU. The glycoside payload contributed to overall hydrophilicity of the ADC reducing aggregation. Compared to standard DAR = 2-4 ADCs, cytotoxicity of the homogeneous DAR = 8 ADCs was improved to low-picomolar IC50 values against cancer cells in vitro. Bystander efficacy was restored after ADC internalization and subsequent cleavage of the glycoside, although unconjugated MMAU was relatively non-toxic to cells. DAR = 8 MMAU ADCs were effective against target antigen-expressing xenograft tumors. The ADCs were also studied in 3D in vitro patient-derived xenograft (PDX) assays where they outperformed clinically used ADC. In conclusion, increased hydrophilicity of the payload contributed to the ADC's hydrophilicity, stability and safety to non-target cells, while significantly improving cytotoxicity and enabling bystander efficacy.
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22
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Zhang Z, Wang H, Ding Q, Xing Y, Xu Z, Lu C, Luo D, Xu L, Xia W, Zhou C, Shi M. Establishment of patient-derived tumor spheroids for non-small cell lung cancer. PLoS One 2018; 13:e0194016. [PMID: 29543851 PMCID: PMC5854348 DOI: 10.1371/journal.pone.0194016] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/22/2018] [Indexed: 12/19/2022] Open
Abstract
The prognosis of advanced non-small cell lung cancer (NSCLC) patients is poor. One of the reasons for this hampered progress has been a lack of in vitro models that would faithfully recapitulate the heterogeneity of tumors and response to treatment. In this study, surgically resected tumors were obtained from patients with stage I/II NSCLC during curative-intent surgery. Using a 3D patient-derived tumor spheroids culture system, our results demonstrate successful long-term expansion of primary NSCLC cells in vitro (> 120 days). Patient-derived tumor spheroid (PDS) cultures could be established with a success rate of 100% (3 out of 3 samples). Consistent with their growth in culture and their cancer type, many cells within the tumor spheroids were stained positive for Ki67 and thyroid transcription factor-1. The result of this study supports the establishment of an expandable 3D in vitro NSCLC model for drug screening, and enables the potential long term studies such as the establishment of drug resistant models.
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Affiliation(s)
- Zengli Zhang
- Department of Respiration, The Second Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Huiqian Wang
- Invitrocue Biomedical Service Suzhou, Suzhou, P.R. China
| | - Qifeng Ding
- Department of Thoracic & Cardiac Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Yufei Xing
- Department of Respiration, The Second Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Zhonghua Xu
- Department of Thoracic & Cardiac Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Chun Lu
- Invitrocue Biomedical Service Suzhou, Suzhou, P.R. China
| | - Dongdong Luo
- Invitrocue Biomedical Service Suzhou, Suzhou, P.R. China
| | - Longjiang Xu
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Wei Xia
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, P.R. China
- * E-mail: (MS); (CZ)
| | - Minhua Shi
- Department of Respiration, The Second Affiliated Hospital of Soochow University, Suzhou, P.R. China
- * E-mail: (MS); (CZ)
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23
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Novel 3D Liquid Cell Culture Method for Anchorage-independent Cell Growth, Cell Imaging and Automated Drug Screening. Sci Rep 2018; 8:3627. [PMID: 29483620 PMCID: PMC5827526 DOI: 10.1038/s41598-018-21950-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/13/2018] [Indexed: 12/21/2022] Open
Abstract
Cells grown in three-dimensional (3D) cultures are more likely to have native cell-cell and cell-matrix interactions than in 2D cultures that impose mechanical constraints to cells. However, most 3D cultures utilise gel matrix which, while serving as a scaffold, limits application due to its solid and opaque nature and inconsistency in cell exposure to exogenous signals. In 3D culture without gel matrix, cells tend to adhere to each other and form clumps with necrotic zone at the centre, making them unsuitable for analyses. Here we report that addition of low-molecular-weight agar named LA717 to culture media allows cells to grow as dispersed clonal spheroids in 3D. LA717 maintains cells dispersed and settled to the bottom of the medium while keeping the medium clear with little additional viscosity, making it suitable for microscopic observation. Importantly, cancer spheroids formed in LA717-containing medium show higher sensitivity to anti-cancer drugs such as Trametinib and MK-2206 that are not as effective in 2D. Because of the small and consistent size of spheroids, cell viability and drug toxicity are readily detectable in automated imaging analysis. These results demonstrate that LA717 offers a novel 3D culture system with great in vivo reflection and practicality.
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24
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Williams GS, Mistry B, Guillard S, Ulrichsen JC, Sandercock AM, Wang J, González-Muñoz A, Parmentier J, Black C, Soden J, Freeth J, Jovanović J, Leyland R, Al-Lamki RS, Leishman AJ, Rust SJ, Stewart R, Jermutus L, Bradley JR, Bedian V, Valge-Archer V, Minter R, Wilkinson RW. Phenotypic screening reveals TNFR2 as a promising target for cancer immunotherapy. Oncotarget 2018; 7:68278-68291. [PMID: 27626702 PMCID: PMC5356554 DOI: 10.18632/oncotarget.11943] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/13/2016] [Indexed: 01/22/2023] Open
Abstract
Antibodies that target cell-surface molecules on T cells can enhance anti-tumor immune responses, resulting in sustained immune-mediated control of cancer. We set out to find new cancer immunotherapy targets by phenotypic screening on human regulatory T (Treg) cells and report the discovery of novel activators of tumor necrosis factor receptor 2 (TNFR2) and a potential role for this target in immunotherapy. A diverse phage display library was screened to find antibody mimetics with preferential binding to Treg cells, the most Treg-selective of which were all, without exception, found to bind specifically to TNFR2. A subset of these TNFR2 binders were found to agonise the receptor, inducing iκ-B degradation and NF-κB pathway signalling in vitro. TNFR2 was found to be expressed by tumor-infiltrating Treg cells, and to a lesser extent Teff cells, from three lung cancer patients, and a similar pattern was also observed in mice implanted with CT26 syngeneic tumors. In such animals, TNFR2-specific agonists inhibited tumor growth, enhanced tumor infiltration by CD8+ T cells and increased CD8+ T cell IFN-γ synthesis. Together, these data indicate a novel mechanism for TNF-α-independent TNFR2 agonism in cancer immunotherapy, and demonstrate the utility of target-agnostic screening in highlighting important targets during drug discovery.
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Affiliation(s)
| | - Bina Mistry
- MedImmune Ltd., Granta Park, Cambridge, CB21 6GH, UK
| | | | | | | | - Jun Wang
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | | | | | | | - Jo Soden
- Retrogenix Ltd, Whaley Bridge, High Peak, SK23 7LY, UK
| | - Jim Freeth
- Retrogenix Ltd, Whaley Bridge, High Peak, SK23 7LY, UK
| | | | | | - Rafia S Al-Lamki
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | | | - Steven J Rust
- MedImmune Ltd., Granta Park, Cambridge, CB21 6GH, UK
| | - Ross Stewart
- MedImmune Ltd., Granta Park, Cambridge, CB21 6GH, UK
| | - Lutz Jermutus
- MedImmune Ltd., Granta Park, Cambridge, CB21 6GH, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Vahe Bedian
- Oncology iMED, AstraZeneca-R&D Boston, Waltham, MA 02451, USA
| | | | - Ralph Minter
- MedImmune Ltd., Granta Park, Cambridge, CB21 6GH, UK
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25
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O'Sullivan D, Dowling P, Joyce H, McAuley E, McCann A, Henry M, McGovern B, Barham P, Kelleher FC, Murphy J, Kennedy S, Swan N, Moriarty M, Clynes M, Larkin A. A novel inhibitory anti-invasive MAb isolated using phenotypic screening highlights AnxA6 as a functionally relevant target protein in pancreatic cancer. Br J Cancer 2017; 117:1326-1335. [PMID: 28881357 PMCID: PMC5672937 DOI: 10.1038/bjc.2017.306] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/17/2017] [Accepted: 08/07/2017] [Indexed: 12/20/2022] Open
Abstract
Background: Discovery and validation of new antibody tractable targets is critical for the development of new antibody therapeutics to address unmet needs in oncology. Methods: A highly invasive clonal variant of the MDA-MB-435S cell line was used to generate monoclonal antibodies (MAbs), which were screened for anti-invasive activity against aggressive cancer cells in vitro. The molecular target of selected inhibitory MAb 9E1 was identified using immunoprecipitation/liquid chromatography-tandem mass spectrometry. The potential anti-tumour effects of MAb 9E1 were investigated in vitro together with immunohistochemical analysis of the 9E1 target antigen in normal and cancer tissues. Results: MAb 9E1 significantly decreases invasion in pancreatic, lung squamous and breast cancer cells and silencing of its target antigen, which was revealed as AnxA6, leads to markedly reduced invasive capacity of pancreatic and lung squamous cancer in vitro. IHC using MAb 9E1 revealed that AnxA6 exhibits a high prevalence of membrane immunoreactivity across aggressive tumour types with restricted expression observed in the majority of normal tissues. In pancreatic ductal adenocarcinoma, high AnxA6 IHC score correlated with the presence of tumour budding at the invasive front of tumours (P=0.082), the presence of perineural invasion (P= <0.0001) and showed a weak correlation with reduced survival (P=0.2242). Conclusions: This study highlights the use of phenotypic hybridoma screening as an effective strategy to select a novel function-blocking MAb, 9E1 with anti-cancer activity in vitro. Moreover, through characterisation of the 9E1 target antigen, AnxA6, our findings support further investigation of AnxA6 as a potential candidate target for antibody-mediated inhibition of pancreatic cancer.
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Affiliation(s)
- Dermot O'Sullivan
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paul Dowling
- Department of Biology, National University of Ireland - Maynooth, Co. Kildare, Ireland
| | - Helena Joyce
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Edel McAuley
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Andrew McCann
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Brianan McGovern
- Department of Histopathology, St. Vincents' University Hospital, Elm Park, Dublin 4, Ireland
| | - Paul Barham
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Fergal C Kelleher
- Department of Medical Oncology, St. Vincents' University Hospital, Elm Park, Dublin 4, Ireland
| | - Jean Murphy
- Department of Histopathology, St. Vincents' University Hospital, Elm Park, Dublin 4, Ireland
| | - Susan Kennedy
- Department of Histopathology, St. Vincents' University Hospital, Elm Park, Dublin 4, Ireland
| | - Niall Swan
- Department of Histopathology, St. Vincents' University Hospital, Elm Park, Dublin 4, Ireland
| | - Michael Moriarty
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Annemarie Larkin
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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Minter RR, Sandercock AM, Rust SJ. Phenotypic screening-the fast track to novel antibody discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2017. [PMID: 28647091 DOI: 10.1016/j.ddtec.2017.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The majority of antibody therapeutics have been isolated from target-led drug discovery, where many years of target research preceded drug program initiation. However, as the search for validated targets becomes more challenging and target space becomes increasingly competitive, alternative strategies, such as phenotypic drug discovery, are gaining favour. This review highlights successful examples of antibody phenotypic screens that have led to clinical drug candidates. We also review the requirements for performing an effective antibody phenotypic screen, including antibody enrichment and target identification strategies. Finally, the future impact of phenotypic drug discovery on antibody drug pipelines will be discussed.
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Affiliation(s)
- Ralph R Minter
- Department of Antibody Discovery and Protein Engineering, MedImmune, Milstein Building, Granta Park, Cambridge CB21 6GH, UK
| | - Alan M Sandercock
- Department of Antibody Discovery and Protein Engineering, MedImmune, Milstein Building, Granta Park, Cambridge CB21 6GH, UK
| | - Steven J Rust
- Department of Antibody Discovery and Protein Engineering, MedImmune, Milstein Building, Granta Park, Cambridge CB21 6GH, UK.
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27
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In vitro assays supporting the safety assessment of immunomodulatory monoclonal antibodies. Toxicol In Vitro 2017; 45:296-308. [PMID: 28263892 DOI: 10.1016/j.tiv.2017.02.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/08/2017] [Accepted: 02/28/2017] [Indexed: 01/11/2023]
Abstract
Many monoclonal antibodies (mAbs) licensed for human use or in clinical development for cancer and autoimmune disease directly interact with the immune system. These immunomodulatory mAbs have an inherent risk of adverse immune-mediated drug reactions, including infusion reactions, cytokine storms, immunosuppression and autoimmunity. A thorough understanding of the potential for immunotoxicity of a mAb is required to support administration to humans. This review will highlight the key role of in vitro assays in defining the immunopharmacology, immunotoxicity and immunogenicity of mAbs. A wide range of in vitro tests with multiple formats of different complexity can be utilized to characterize i) the antibody-binding domains of the mAb, such as on-target binding and downstream pharmacological effects (e.g. immunosuppression, immune activation, cytokine release) in both humans and animal species used for toxicology studies and off-target binding; ii) Fc-dependent effects such as Fc-mediated cellular activation (e.g. of leukocytes, platelets) and cytokine release, complement activation; and iii) product-related factors (sequence, physical-chemical properties and impurities) that can impact both pharmacological activity and immunogenicity potential of a mAb. These assays can be crucial to the selection of mAbs with an optimum balance of safety and efficacy, in defining whether a mAb is a high risk molecule, and together with animal data, can inform human safe starting doses and escalation schemes.
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28
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Alsehli H, Gari M, Abuzinadah M, Abuzenadah A. The emerging importance of high content screening for future therapeutics. J Microsc Ultrastruct 2017. [DOI: 10.1016/j.jmau.2017.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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29
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Dimasi N, Fleming R, Sachsenmeier KF, Bezabeh B, Hay C, Wu J, Sult E, Rajan S, Zhuang L, Cariuk P, Buchanan A, Bowen MA, Wu H, Gao C. Guiding bispecific monovalent antibody formation through proteolysis of IgG1 single-chain. MAbs 2017; 9:438-454. [PMID: 28055299 DOI: 10.1080/19420862.2016.1277301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We developed an IgG1 domain-tethering approach to guide the correct assembly of 2 light and 2 heavy chains, derived from 2 different antibodies, to form bispecific monovalent antibodies in IgG1 format. We show here that assembling 2 different light and heavy chains by sequentially connecting them with protease-cleavable polypeptide linkers results in the generation of monovalent bispecific antibodies that have IgG1 sequence, structure and functional properties. This approach was used to generate a bispecific monovalent antibody targeting the epidermal growth factor receptor and the type I insulin-like growth factor receptor that: 1) can be produced and purified using standard IgG1 techniques; 2) exhibits stability and structural features comparable to IgG1; 3) binds both targets simultaneously; and 4) has potent anti-tumor activity. Our strategy provides new engineering opportunities for bispecific antibody applications, and, most importantly, overcomes some of the limitations (e.g., half-antibody and homodimer formation, light chains mispairing, multi-step purification), inherent with some of the previously described IgG1-based bispecific monovalent antibodies.
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Affiliation(s)
- Nazzareno Dimasi
- a Antibody Discovery and Protein Engineering, MedImmune , Gaithersburg , MD , USA
| | - Ryan Fleming
- a Antibody Discovery and Protein Engineering, MedImmune , Gaithersburg , MD , USA
| | | | - Binyam Bezabeh
- a Antibody Discovery and Protein Engineering, MedImmune , Gaithersburg , MD , USA
| | - Carl Hay
- c Oncology Research, MedImmune , Gaithersburg , MD , USA
| | - Jincheng Wu
- d Research Bioinformatics, MedImmune , Gaithersburg , MD , USA
| | - Erin Sult
- c Oncology Research, MedImmune , Gaithersburg , MD , USA
| | - Saravanan Rajan
- a Antibody Discovery and Protein Engineering, MedImmune , Gaithersburg , MD , USA
| | - Li Zhuang
- a Antibody Discovery and Protein Engineering, MedImmune , Gaithersburg , MD , USA
| | - Peter Cariuk
- e Antibody Discovery and Protein Engineering, MedImmune , Cambridge , UK
| | - Andrew Buchanan
- e Antibody Discovery and Protein Engineering, MedImmune , Cambridge , UK
| | - Michael A Bowen
- a Antibody Discovery and Protein Engineering, MedImmune , Gaithersburg , MD , USA
| | - Herren Wu
- a Antibody Discovery and Protein Engineering, MedImmune , Gaithersburg , MD , USA
| | - Changshou Gao
- a Antibody Discovery and Protein Engineering, MedImmune , Gaithersburg , MD , USA
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Hollins AJ, Parry L. Long-Term Culture of Intestinal Cell Progenitors: An Overview of Their Development, Application, and Associated Technologies. CURRENT PATHOBIOLOGY REPORTS 2016; 4:209-219. [PMID: 27882268 PMCID: PMC5101250 DOI: 10.1007/s40139-016-0119-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE OF REVIEW Long-term culture of adult progenitor cells in 3D is a recently emerging technology that inhabits the space between 2D cell lines and organ slice culture. RECENT FINDINGS Adaptations to defined media components in the wake of advances in ES and iPS cell culture has led to the identification of conditions that maintained intestinal cell progenitors in culture. These conditions retain cellular heterogeneity of the normal or tumour tissue, and the cultures have been shown to be genetically stable, such that substantial biobanks are being created from patient derived material. This coupled with advances in analytical tools has generated a field, characterized by the term "organoid culture", that has huge potential for advancing drug discovery, regenerative medicine, and furthering the understanding of fundamental intestinal biology. SUMMARY In this review, we describe the approaches available for the long-term culture of intestinal cells from normal and diseased tissue, the current challenges, and how the technology is likely to develop further.
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Affiliation(s)
| | - Lee Parry
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, CF24 4HQ UK
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Ezrin Is Associated with Disease Progression in Ovarian Carcinoma. PLoS One 2016; 11:e0162502. [PMID: 27622508 PMCID: PMC5021292 DOI: 10.1371/journal.pone.0162502] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 08/23/2016] [Indexed: 12/24/2022] Open
Abstract
Objective Ezrin and p130Cas are structural proteins with an important role in signaling pathways and have been shown to promote cancer dissemination. We previously reported on overexpression of both ezrin and p130Cas in breast carcinoma effusions compared to primary carcinomas. Since ovarian and breast carcinomas share the ability to disseminate by forming malignant effusions, we sought to study the role of these molecules in ovarian carcinoma (OC). Methods OC cell lines were cultured in two different 3-dimensional conditions, on alginate scaffolds and as spheroids, which served as models for solid tumor and malignant effusions, respectively. shRNA was used to reduce protein expression in the cells. The malignant potential was evaluated by chemo-invasion assay, branching capacity on Matrigel and rate of proliferation. Subsequently, clinical specimens of high-grade serous carcinoma effusions, ovarian tumors and solid metastases were analyzed for ezrin and p130Cas expression. Results Higher ezrin expression was found in cells composing the spheroids compared to their counterparts cultured on alginate scaffold and in clinical samples of malignant effusions compared to solid tumors. In addition, reduced Ezrin expression impaired the invasion ability and the branching capacity of OC cells to a greater extent than reduced p130Cas expression. However, ezrin and p130Cas expression in effusions was unrelated to clinical outcome. Conclusions The 3-dimensional cell cultures were found to mimic the different tumor sites and be applicable as a model. The in vitro results concur with the clinical specimen analysis, suggesting that in OC, the role of ezrin in disease progression is more pronounced than that of p130Cas.
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Horvath P, Aulner N, Bickle M, Davies AM, Nery ED, Ebner D, Montoya MC, Östling P, Pietiäinen V, Price LS, Shorte SL, Turcatti G, von Schantz C, Carragher NO. Screening out irrelevant cell-based models of disease. Nat Rev Drug Discov 2016; 15:751-769. [PMID: 27616293 DOI: 10.1038/nrd.2016.175] [Citation(s) in RCA: 322] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The common and persistent failures to translate promising preclinical drug candidates into clinical success highlight the limited effectiveness of disease models currently used in drug discovery. An apparent reluctance to explore and adopt alternative cell- and tissue-based model systems, coupled with a detachment from clinical practice during assay validation, contributes to ineffective translational research. To help address these issues and stimulate debate, here we propose a set of principles to facilitate the definition and development of disease-relevant assays, and we discuss new opportunities for exploiting the latest advances in cell-based assay technologies in drug discovery, including induced pluripotent stem cells, three-dimensional (3D) co-culture and organ-on-a-chip systems, complemented by advances in single-cell imaging and gene editing technologies. Funding to support precompetitive, multidisciplinary collaborations to develop novel preclinical models and cell-based screening technologies could have a key role in improving their clinical relevance, and ultimately increase clinical success rates.
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Affiliation(s)
- Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary; and at the Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland.,European Cell-Based Assays Interest Group
| | - Nathalie Aulner
- Imagopole-Citech, Institut Pasteur, Paris 75015, France.,European Cell-Based Assays Interest Group
| | - Marc Bickle
- Technology Development Studio, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.,European Cell-Based Assays Interest Group
| | - Anthony M Davies
- Translational Cell Imaging Queensland (TCIQ), Institute of Health Biomedical Innovation, Queensland University of Technology, Brisbane 4102 QLD, Australia; and The Irish National Centre for High Content Screening and Analysis, Trinity Translational Medicine Institute, Trinity College Dublin, Phase 3 Trinity Health Sciences 1.20, St James Hospital, Dublin D8, Republic of Ireland.,European Cell-Based Assays Interest Group
| | - Elaine Del Nery
- Institut Curie, PSL Research University, Department of Translational Research, The Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), F-75005, Paris, France.,European Cell-Based Assays Interest Group
| | - Daniel Ebner
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.,European Cell-Based Assays Interest Group
| | - Maria C Montoya
- Cellomics Unit, Cell Biology &Physiology Program, Cell &Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain.,European Cell-Based Assays Interest Group
| | - Päivi Östling
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland.,Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, Stockholm 17165, Sweden.,European Cell-Based Assays Interest Group
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland.,European Cell-Based Assays Interest Group
| | - Leo S Price
- Faculty of Science, Leiden Academic Centre for Drug Research, Toxicology, Universiteit Leiden, The Netherlands; and at OcellO, J.H Oortweg 21, 2333 CH, Leiden, The Netherlands.,European Cell-Based Assays Interest Group
| | - Spencer L Shorte
- Imagopole-Citech, Institut Pasteur, Paris 75015, France.,European Cell-Based Assays Interest Group
| | - Gerardo Turcatti
- Biomolecular Screening Facility, Swiss Federal Institute of Technology (EPFL), Lausanne CH-1015, Switzerland.,European Cell-Based Assays Interest Group
| | - Carina von Schantz
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland.,European Cell-Based Assays Interest Group
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK.,European Cell-Based Assays Interest Group
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Abstract
Modelling human diseases in in vitro systems is undisputedly an invaluable research tool, yet there are many limitations. Some of those limitations have been overcome through the introduction of organoid culture systems, which have revolutionised colorectal cancer research and enabled an array of new experimental techniques. This 3D system models the physiology, shape, dynamics and cell make-up of the intestinal epithelium producing a relevant and highly adaptable model system. The increased functional relevance of this model compared to the use of 2D cancer cell lines makes it an invaluable tool for both basic and translational research. As the limitations of this system are being overcome to make high-throughput assays possible, it is clear that organoids are becoming a mainstay of colorectal cancer research. This review aims to explore the advantages and limitations of this system and discusses the future directions enabled by this model.
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Affiliation(s)
- Madeleine Young
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
| | - Karen R. Reed
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
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Abstract
Phenotypic drug discovery (PDD) strategies are defined by screening and selection of hit or lead compounds based on quantifiable phenotypic endpoints without prior knowledge of the drug target. We outline the challenges associated with traditional phenotypic screening strategies and propose solutions and new opportunities to be gained by adopting modern PDD technologies. We highlight both historical and recent examples of approved drugs and new drug candidates discovered by modern phenotypic screening. Finally, we offer a prospective view of a new era of PDD underpinned by a wealth of technology advances in the areas of in vitro model development, high-content imaging and image informatics, mechanism-of-action profiling and target deconvolution.
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36
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Drug combination therapy increases successful drug repositioning. Drug Discov Today 2016; 21:1189-95. [PMID: 27240777 DOI: 10.1016/j.drudis.2016.05.015] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/28/2016] [Accepted: 05/23/2016] [Indexed: 11/21/2022]
Abstract
Repositioning of approved drugs has recently gained new momentum for rapid identification and development of new therapeutics for diseases that lack effective drug treatment. Reported repurposing screens have increased dramatically in number in the past five years. However, many newly identified compounds have low potency; this limits their immediate clinical applications because the known, tolerated plasma drug concentrations are lower than the required therapeutic drug concentrations. Drug combinations of two or more compounds with different mechanisms of action are an alternative approach to increase the success rate of drug repositioning.
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Generation of a monoclonal antibody recognizing the CEACAM glycan structure and inhibiting adhesion using cancer tissue-originated spheroid as an antigen. Sci Rep 2016; 6:24823. [PMID: 27098764 PMCID: PMC4838943 DOI: 10.1038/srep24823] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/05/2016] [Indexed: 02/06/2023] Open
Abstract
Spheroids cultured directly from tumours can better reflect in vivo tumour characteristics than two-dimensional monolayer culture or three-dimensional culture of established cell lines. In this study, we generated antibodies by directly immunizing mice with primary-cultured living spheroids from human colorectal cancer. We performed phenotypic screening via recognition of the surface of the spheroids and inhibition of their adhesion to extracellular matrices to identify a monoclonal antibody, clone 5G2. The antibody inhibited cell migration in two-dimensional culture and promoted cell detachment. Western blotting and immunohistochemistry detected the 5G2 signal in many colorectal cancer spheroids, as well as patient tumours, but failed to detect in various cell lines examined. We found that 5G2 recognized the Lea and Lec on N-glycan, and their major carrier proteins were CEACAM5 and CEACAM6. Pre-incubation of the spheroids with 5G2 impaired translocation of integrin β4 from the lateral membrane to the contact interface between the extracellular matrix when embedded in it. As we successfully obtained a functional antibody, which antigen was glycan structures and lost in cell lines, cancer tissue-originated spheroids can be a useful antigen for generating novel anti-cancer antibodies.
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Wright HJ, Arulmoli J, Motazedi M, Nelson LJ, Heinemann FS, Flanagan LA, Razorenova OV. CDCP1 cleavage is necessary for homodimerization-induced migration of triple-negative breast cancer. Oncogene 2016; 35:4762-72. [PMID: 26876198 DOI: 10.1038/onc.2016.7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 01/17/2023]
Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive and metastatic form of breast cancer that lacks the estrogen, progesterone and HER2 receptors and is resistant to targeted and hormone therapies. TNBCs express high levels of the transmembrane glycoprotein, complement C1r/C1s, Uegf, Bmp1 (CUB)-domain containing protein 1 (CDCP1), which has been correlated with the aggressiveness and poor prognosis of multiple carcinomas. Full-length CDCP1 (flCDCP1) can be proteolytically cleaved, resulting in a cleaved membrane-bound isoform (cCDCP1). CDCP1 is phosphorylated by Src family kinases in its full-length and cleaved states, which is important for its pro-metastatic signaling. We observed that cCDCP1, compared with flCDCP1, induced a dramatic increase in phosphorylation of the migration-associated proteins: PKCδ, ERK1/2 and p38 mitogen-activated protein kinase in HEK 293T. In addition, only cCDCP1 induced migration of HEK 293T cells and rescued migration of the TNBC cell lines expressing short hairpin RNA against CDCP1. Importantly, we found that only cCDCP1 is capable of dimerization, which can be blocked by expression of the extracellular portion of cCDCP1 (ECC), indicating that dimerization occurs through CDCP1's ectodomain. We found that ECC inhibited phosphorylation of PKCδ and migration of TNBC cells in two-dimensional culture. Furthermore, ECC decreased cell invasiveness, inhibited proliferation and stimulated apoptosis of TNBC cells in three-dimensional culture, indicating that the cCDCP1 dimer is an important contributor to TNBC aggressiveness. These studies have important implications for the development of a therapeutic to block CDCP1 activity and TNBC metastasis.
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Affiliation(s)
- H J Wright
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - J Arulmoli
- Department of Biomedical Engineering, University of California, Irvine, CA, USA
| | - M Motazedi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - L J Nelson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - F S Heinemann
- Department of Pathology, Hoag Memorial Hospital Presbyterian, Newport Beach, CA, USA
| | - L A Flanagan
- Department of Biomedical Engineering, University of California, Irvine, CA, USA.,Department of Neurology, University of California, Irvine, CA, USA
| | - O V Razorenova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
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Gonzalez-Munoz AL, Minter RR, Rust SJ. Phenotypic screening: the future of antibody discovery. Drug Discov Today 2015; 21:150-156. [PMID: 26440132 DOI: 10.1016/j.drudis.2015.09.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/22/2015] [Accepted: 09/29/2015] [Indexed: 10/22/2022]
Abstract
Most antibody therapeutics have been isolated from high throughput target-based screening. However, as the number of validated targets diminishes and the target space becomes increasingly competitive, alternative strategies, such as phenotypic screening, are gaining momentum. Here, we review successful phenotypic screens, including those used to isolate antibodies against cancer and infectious agents. We also consider exciting advances in the expression and phenotypic screening of antibody repertoires in single cell autocrine systems. As technologies continue to develop, we believe that antibody phenotypic screening will increase further in popularity and has the potential to provide the next generation of therapeutic antibodies.
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Affiliation(s)
- Andrea L Gonzalez-Munoz
- Department of Antibody Discovery and Protein Engineering, MedImmune, Milstein Building, Granta Park, Cambridge CB21 6GH, UK
| | - Ralph R Minter
- Department of Antibody Discovery and Protein Engineering, MedImmune, Milstein Building, Granta Park, Cambridge CB21 6GH, UK
| | - Steven J Rust
- Department of Antibody Discovery and Protein Engineering, MedImmune, Milstein Building, Granta Park, Cambridge CB21 6GH, UK.
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