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Sun T, Zhao H, Hu L, Shao X, Lu Z, Wang Y, Ling P, Li Y, Zeng K, Chen Q. Enhanced optical imaging and fluorescent labeling for visualizing drug molecules within living organisms. Acta Pharm Sin B 2024; 14:2428-2446. [PMID: 38828150 PMCID: PMC11143489 DOI: 10.1016/j.apsb.2024.01.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/07/2024] [Accepted: 01/25/2024] [Indexed: 06/05/2024] Open
Abstract
The visualization of drugs in living systems has become key techniques in modern therapeutics. Recent advancements in optical imaging technologies and molecular design strategies have revolutionized drug visualization. At the subcellular level, super-resolution microscopy has allowed exploration of the molecular landscape within individual cells and the cellular response to drugs. Moving beyond subcellular imaging, researchers have integrated multiple modes, like optical near-infrared II imaging, to study the complex spatiotemporal interactions between drugs and their surroundings. By combining these visualization approaches, researchers gain supplementary information on physiological parameters, metabolic activity, and tissue composition, leading to a comprehensive understanding of drug behavior. This review focuses on cutting-edge technologies in drug visualization, particularly fluorescence imaging, and the main types of fluorescent molecules used. Additionally, we discuss current challenges and prospects in targeted drug research, emphasizing the importance of multidisciplinary cooperation in advancing drug visualization. With the integration of advanced imaging technology and molecular design, drug visualization has the potential to redefine our understanding of pharmacology, enabling the analysis of drug micro-dynamics in subcellular environments from new perspectives and deepening pharmacological research to the levels of the cell and organelles.
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Affiliation(s)
- Ting Sun
- School of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
- Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Huanxin Zhao
- School of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Luyao Hu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xintian Shao
- School of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
- School of Life Sciences, Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Zhiyuan Lu
- School of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Yuli Wang
- Tianjin Pharmaceutical DA REN TANG Group Corporation Limited Traditional Chinese Pharmacy Research Institute, Tianjin 300457, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemistry Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Peixue Ling
- Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Key Laboratory of Biopharmaceuticals, Postdoctoral Scientific Research Workstation, Shandong Academy of Pharmaceutical Science, Jinan 250098, China
| | - Yubo Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Kewu Zeng
- School of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qixin Chen
- School of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore 119074, Singapore
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Vedeneeva E, Gursky V, Samsonova M, Neganova I. Morphological Signal Processing for Phenotype Recognition of Human Pluripotent Stem Cells Using Machine Learning Methods. Biomedicines 2023; 11:3005. [PMID: 38002005 PMCID: PMC10669716 DOI: 10.3390/biomedicines11113005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Human pluripotent stem cells have the potential for unlimited proliferation and controlled differentiation into various somatic cells, making them a unique tool for regenerative and personalized medicine. Determining the best clone selection is a challenging problem in this field and requires new sensing instruments and methods able to automatically assess the state of a growing colony ('phenotype') and make decisions about its destiny. One possible solution for such label-free, non-invasive assessment is to make phase-contrast images and/or videos of growing stem cell colonies, process the morphological parameters ('morphological portrait', or signal), link this information to the colony phenotype, and initiate an automated protocol for the colony selection. As a step in implementing this strategy, we used machine learning methods to find an effective model for classifying the human pluripotent stem cell colonies of three lines according to their morphological phenotype ('good' or 'bad'), using morphological parameters from the previously published data as predictors. We found that the model using cellular morphological parameters as predictors and artificial neural networks as the classification method produced the best average accuracy of phenotype prediction (67%). When morphological parameters of colonies were used as predictors, logistic regression was the most effective classification method (75% average accuracy). Combining the morphological parameters of cells and colonies resulted in the most effective model, with a 99% average accuracy of phenotype prediction. Random forest was the most efficient classification method for the combined data. We applied feature selection methods and showed that different morphological parameters were important for phenotype recognition via either cellular or colonial parameters. Our results indicate a necessity for retaining both cellular and colonial morphological information for predicting the phenotype and provide an optimal choice for the machine learning method. The classification models reported in this study could be used as a basis for developing and/or improving automated solutions to control the quality of human pluripotent stem cells for medical purposes.
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Affiliation(s)
- Ekaterina Vedeneeva
- Department of Physics and Mechanics & Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia; (E.V.); (M.S.)
| | - Vitaly Gursky
- Laboratory of Molecular Medicine, Institute of Cytology, 194064 Saint Petersburg, Russia;
- Theoretical Department, Ioffe Institute, 194021 Saint Petersburg, Russia
| | - Maria Samsonova
- Department of Physics and Mechanics & Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia; (E.V.); (M.S.)
| | - Irina Neganova
- Laboratory of Molecular Medicine, Institute of Cytology, 194064 Saint Petersburg, Russia;
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Strauß S, Grijalva Garces D, Hubbuch J. Analytics in Extrusion-Based Bioprinting: Standardized Methods Improving Quantification and Comparability of the Performance of Bioinks. Polymers (Basel) 2023; 15:polym15081829. [PMID: 37111976 PMCID: PMC10144221 DOI: 10.3390/polym15081829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/30/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Three-dimensional bioprinting and especially extrusion-based printing as a most frequently employed method in this field is constantly evolving as a discipline in regenerative medicine and tissue engineering. However, the lack of relevant standardized analytics does not yet allow an easy comparison and transfer of knowledge between laboratories regarding newly developed bioinks and printing processes. This work revolves around the establishment of a standardized method, which enables the comparability of printed structures by controlling for the extrusion rate based on the specific flow behavior of each bioink. Furthermore, printing performance was evaluated by image-processing tools to verify the printing accuracy for lines, circles, and angles. In addition, and complementary to the accuracy metrics, a dead/live staining of embedded cells was performed to investigate the effect of the process on cell viability. Two bioinks, based on alginate and gelatin methacryloyl, which differed in 1% (w/v) alginate content, were tested for printing performance. The automated image processing tool reduced the analytical time while increasing reproducibility and objectivity during the identification of printed objects. During evaluation of the processing effect of the mixing of cell viability, NIH 3T3 fibroblasts were stained and analyzed after the mixing procedure and after the extrusion process using a flow cytometer, which evaluated a high number of cells. It could be observed that the small increase in alginate content made little difference in the printing accuracy but had a considerable strong effect on cell viability after both processing steps.
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Affiliation(s)
- Svenja Strauß
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - David Grijalva Garces
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Jürgen Hubbuch
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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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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Powell RT, Moussalli MJ, Guo L, Bae G, Singh P, Stephan C, Shureiqi I, Davies PJ. deepOrganoid: A brightfield cell viability model for screening matrix-embedded organoids. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:175-184. [PMID: 35314378 DOI: 10.1016/j.slasd.2022.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
High-throughput viability screens are commonly used in the identification and development of chemotherapeutic drugs. These systems rely on the fidelity of the cellular model systems to recapitulate the drug response that occurs in vivo. In recent years, there has been an expansion in the utilization of patient-derived materials as well as advanced cell culture techniques, such as multi-cellular tumor organoids, to further enhance the translational relevance of cellular model systems. Simple quantitative analysis remains a challenge, primarily due to the difficulties of robust image segmentation in heterogenous 3D cultures. However, explicit segmentation is not required with the advancement of deep learning, and it can be used for both continuous (regression) or categorical classification problems. Deep learning approaches are additionally benefited by being fully data-driven and highly automatable, thus they can be established and run with minimal to no user-defined parameters. In this article, we describe the development and implementation of a regressive deep learning model trained on brightfield images of patient-derived organoids and use the terminal viability readout (CellTiter-Glo) as training labels. Ultimately, this has led to the generation of a non-invasive and label-free tool to evaluate changes in organoid viability.
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Affiliation(s)
- Reid T Powell
- Center for Translational Cancer Research, Texas A&M University, 2121 W. Holcombe Blvd. Rm 911, Houston, TX 77030, United States.
| | - Micheline J Moussalli
- Department of Gastrointestinal Medical Oncology, UT MDACC, Houston, TX, United States
| | - Lei Guo
- Center for Translational Cancer Research, Texas A&M University, 2121 W. Holcombe Blvd. Rm 911, Houston, TX 77030, United States
| | - Goeun Bae
- Center for Translational Cancer Research, Texas A&M University, 2121 W. Holcombe Blvd. Rm 911, Houston, TX 77030, United States
| | - Pankaj Singh
- Center for Translational Cancer Research, Texas A&M University, 2121 W. Holcombe Blvd. Rm 911, Houston, TX 77030, United States
| | - Clifford Stephan
- Center for Translational Cancer Research, Texas A&M University, 2121 W. Holcombe Blvd. Rm 911, Houston, TX 77030, United States
| | - Imad Shureiqi
- Department of Gastrointestinal Medical Oncology, UT MDACC, Houston, TX, United States
| | - Peter J Davies
- Center for Translational Cancer Research, Texas A&M University, 2121 W. Holcombe Blvd. Rm 911, Houston, TX 77030, United States
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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: 43] [Impact Index Per Article: 21.5] [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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Rodrigues D, Herpers B, Ferreira S, Jo H, Fisher C, Coyle L, Chung SW, Kleinjans JCS, Jennen DGJ, de Kok TM. A Transcriptomic Approach to Elucidate the Mechanisms of Gefitinib-Induced Toxicity in Healthy Human Intestinal Organoids. Int J Mol Sci 2022; 23:ijms23042213. [PMID: 35216325 PMCID: PMC8876167 DOI: 10.3390/ijms23042213] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 02/01/2023] Open
Abstract
Gefitinib is a tyrosine kinase inhibitor (TKI) that selectively inhibits the epidermal growth factor receptor (EGFR), hampering cell growth and proliferation. Due to its action, gefitinib has been used in the treatment of cancers that present abnormally increased expression of EGFR. However, side effects from gefitinib therapy may occur, among which diarrhoea is most common, that can lead to interruption of the planned therapy in the more severe cases. The mechanisms underlying intestinal toxicity induced by gefitinib are not well understood. Therefore, this study aims at providing insight into these mechanisms based on transcriptomic responses induced in vitro. A 3D culture of healthy human colon and small intestine (SI) organoids was exposed to 0.1, 1, 10 and 30 µM of gefitinib, for a maximum of three days. These drug concentrations were selected using physiologically-based pharmacokinetic simulation considering patient dosing regimens. Samples were used for the analysis of viability and caspase 3/7 activation, image-based analysis of structural changes, as well as RNA isolation and sequencing via high-throughput techniques. Differential gene expression analysis showed that gefitinib perturbed signal transduction pathways, apoptosis, cell cycle, FOXO-mediated transcription, p53 signalling pathway, and metabolic pathways. Remarkably, opposite expression patterns of genes associated with metabolism of lipids and cholesterol biosynthesis were observed in colon versus SI organoids in response to gefitinib. These differences in the organoids’ responses could be linked to increased activated protein kinase (AMPK) activity in colon, which can influence the sensitivity of the colon to the drug. Therefore, this study sheds light on how gefitinib induces toxicity in intestinal organoids and provides an avenue towards the development of a potential tool for drug screening and development.
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Affiliation(s)
- Daniela Rodrigues
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands; (J.C.S.K.); (D.G.J.J.); (T.M.d.K.)
- Correspondence:
| | - Bram Herpers
- Crown Bioscience Netherlands B.V., J.H. Oortweg 21, 2333 CH Leiden, The Netherlands;
| | - Sofia Ferreira
- Simcyp Division, Certara UK Limited, Sheffield S1 2BJ, UK; (S.F.); (H.J.); (C.F.)
| | - Heeseung Jo
- Simcyp Division, Certara UK Limited, Sheffield S1 2BJ, UK; (S.F.); (H.J.); (C.F.)
| | - Ciarán Fisher
- Simcyp Division, Certara UK Limited, Sheffield S1 2BJ, UK; (S.F.); (H.J.); (C.F.)
| | - Luke Coyle
- Boehringer Ingelheim International GmbH, Pharmaceuticals Inc., Ridgefield, CT 06877, USA; (L.C.); (S.-W.C.)
| | - Seung-Wook Chung
- Boehringer Ingelheim International GmbH, Pharmaceuticals Inc., Ridgefield, CT 06877, USA; (L.C.); (S.-W.C.)
| | - Jos C. S. Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands; (J.C.S.K.); (D.G.J.J.); (T.M.d.K.)
| | - Danyel G. J. Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands; (J.C.S.K.); (D.G.J.J.); (T.M.d.K.)
| | - Theo M. de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands; (J.C.S.K.); (D.G.J.J.); (T.M.d.K.)
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8
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Rodrigues D, Coyle L, Füzi B, Ferreira S, Jo H, Herpers B, Chung SW, Fisher C, Kleinjans JCS, Jennen D, de Kok TM. Unravelling Mechanisms of Doxorubicin-Induced Toxicity in 3D Human Intestinal Organoids. Int J Mol Sci 2022; 23:ijms23031286. [PMID: 35163210 PMCID: PMC8836276 DOI: 10.3390/ijms23031286] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/12/2022] Open
Abstract
Doxorubicin is widely used in the treatment of different cancers, and its side effects can be severe in many tissues, including the intestines. Symptoms such as diarrhoea and abdominal pain caused by intestinal inflammation lead to the interruption of chemotherapy. Nevertheless, the molecular mechanisms associated with doxorubicin intestinal toxicity have been poorly explored. This study aims to investigate such mechanisms by exposing 3D small intestine and colon organoids to doxorubicin and to evaluate transcriptomic responses in relation to viability and apoptosis as physiological endpoints. The in vitro concentrations and dosing regimens of doxorubicin were selected based on physiologically based pharmacokinetic model simulations of treatment regimens recommended for cancer patients. Cytotoxicity and cell morphology were evaluated as well as gene expression and biological pathways affected by doxorubicin. In both types of organoids, cell cycle, the p53 signalling pathway, and oxidative stress were the most affected pathways. However, significant differences between colon and SI organoids were evident, particularly in essential metabolic pathways. Short time-series expression miner was used to further explore temporal changes in gene profiles, which identified distinct tissue responses. Finally, in silico proteomics revealed important proteins involved in doxorubicin metabolism and cellular processes that were in line with the transcriptomic responses, including cell cycle and senescence, transport of molecules, and mitochondria impairment. This study provides new insight into doxorubicin-induced effects on the gene expression levels in the intestines. Currently, we are exploring the potential use of these data in establishing quantitative systems toxicology models for the prediction of drug-induced gastrointestinal toxicity.
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Affiliation(s)
- Daniela Rodrigues
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands; (J.C.S.K.); (D.J.); (T.M.d.K.)
- Correspondence:
| | - Luke Coyle
- Boehringer Ingelheim International GmbH, Pharmaceuticals Inc., Ridgefield, CT 06877, USA; (L.C.); (S.-W.C.)
| | - Barbara Füzi
- Department of Pharmaceutical Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria;
| | - Sofia Ferreira
- Certara UK Limited, Simcyp Division, Sheffield S1 2BJ, UK; (S.F.); (H.J.); (C.F.)
| | - Heeseung Jo
- Certara UK Limited, Simcyp Division, Sheffield S1 2BJ, UK; (S.F.); (H.J.); (C.F.)
| | - Bram Herpers
- Crown Bioscience Netherlands B.V., J.H. Oortweg 21, 2333 CH Leiden, The Netherlands;
| | - Seung-Wook Chung
- Boehringer Ingelheim International GmbH, Pharmaceuticals Inc., Ridgefield, CT 06877, USA; (L.C.); (S.-W.C.)
| | - Ciarán Fisher
- Certara UK Limited, Simcyp Division, Sheffield S1 2BJ, UK; (S.F.); (H.J.); (C.F.)
| | - Jos C. S. Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands; (J.C.S.K.); (D.J.); (T.M.d.K.)
| | - Danyel Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands; (J.C.S.K.); (D.J.); (T.M.d.K.)
| | - Theo M. de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands; (J.C.S.K.); (D.J.); (T.M.d.K.)
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9
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Rodrigues D, de Souza T, Coyle L, Di Piazza M, Herpers B, Ferreira S, Zhang M, Vappiani J, Sévin DC, Gabor A, Lynch A, Chung SW, Saez-Rodriguez J, Jennen DGJ, Kleinjans JCS, de Kok TM. New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids. Arch Toxicol 2021; 95:2691-2718. [PMID: 34151400 PMCID: PMC8298376 DOI: 10.1007/s00204-021-03092-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022]
Abstract
5-Fluorouracil (5-FU) is a widely used chemotherapeutical that induces acute toxicity in the small and large intestine of patients. Symptoms can be severe and lead to the interruption of cancer treatments. However, there is limited understanding of the molecular mechanisms underlying 5-FU-induced intestinal toxicity. In this study, well-established 3D organoid models of human colon and small intestine (SI) were used to characterize 5-FU transcriptomic and metabolomic responses. Clinically relevant 5-FU concentrations for in vitro testing in organoids were established using physiologically based pharmacokinetic simulation of dosing regimens recommended for cancer patients, resulting in exposures to 10, 100 and 1000 µM. After treatment, different measurements were performed: cell viability and apoptosis; image analysis of cell morphological changes; RNA sequencing; and metabolome analysis of supernatant from organoids cultures. Based on analysis of the differentially expressed genes, the most prominent molecular pathways affected by 5-FU included cell cycle, p53 signalling, mitochondrial ATP synthesis and apoptosis. Short time-series expression miner demonstrated tissue-specific mechanisms affected by 5-FU, namely biosynthesis and transport of small molecules, and mRNA translation for colon; cell signalling mediated by Rho GTPases and fork-head box transcription factors for SI. Metabolomic analysis showed that in addition to the effects on TCA cycle and oxidative stress in both organoids, tissue-specific metabolic alterations were also induced by 5-FU. Multi-omics integration identified transcription factor E2F1, a regulator of cell cycle and apoptosis, as the best key node across all samples. These results provide new insights into 5-FU toxicity mechanisms and underline the relevance of human organoid models in the safety assessment in drug development.
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Affiliation(s)
- Daniela Rodrigues
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands.
| | - Terezinha de Souza
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Luke Coyle
- Departmnet of Nonclinical Drug Safety, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Matteo Di Piazza
- Departmnet of Nonclinical Drug Safety, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
- F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Bram Herpers
- OcellO B.V., BioPartner Center, Leiden, the Netherlands
| | - Sofia Ferreira
- Certara UK Limited, Simcyp Division, Sheffield, S1 2BJ, UK
| | - Mian Zhang
- Certara UK Limited, Simcyp Division, Sheffield, S1 2BJ, UK
| | | | - Daniel C Sévin
- GSK Functional Genomics/Cellzome, 69117, Heidelberg, Germany
| | - Attila Gabor
- Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
| | | | - Seung-Wook Chung
- Departmnet of Nonclinical Drug Safety, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Julio Saez-Rodriguez
- GSK Non-Clinical Safety, Ware, SG12 0DP, UK
- Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, Heidelberg University, Heidelberg, Germany
| | - Danyel G J Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Theo M de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
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10
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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: 144] [Impact Index Per Article: 48.0] [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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11
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Lürig MD, Donoughe S, Svensson EI, Porto A, Tsuboi M. Computer Vision, Machine Learning, and the Promise of Phenomics in Ecology and Evolutionary Biology. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.642774] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
For centuries, ecologists and evolutionary biologists have used images such as drawings, paintings and photographs to record and quantify the shapes and patterns of life. With the advent of digital imaging, biologists continue to collect image data at an ever-increasing rate. This immense body of data provides insight into a wide range of biological phenomena, including phenotypic diversity, population dynamics, mechanisms of divergence and adaptation, and evolutionary change. However, the rate of image acquisition frequently outpaces our capacity to manually extract meaningful information from images. Moreover, manual image analysis is low-throughput, difficult to reproduce, and typically measures only a few traits at a time. This has proven to be an impediment to the growing field of phenomics – the study of many phenotypic dimensions together. Computer vision (CV), the automated extraction and processing of information from digital images, provides the opportunity to alleviate this longstanding analytical bottleneck. In this review, we illustrate the capabilities of CV as an efficient and comprehensive method to collect phenomic data in ecological and evolutionary research. First, we briefly review phenomics, arguing that ecologists and evolutionary biologists can effectively capture phenomic-level data by taking pictures and analyzing them using CV. Next we describe the primary types of image-based data, review CV approaches for extracting them (including techniques that entail machine learning and others that do not), and identify the most common hurdles and pitfalls. Finally, we highlight recent successful implementations and promising future applications of CV in the study of phenotypes. In anticipation that CV will become a basic component of the biologist’s toolkit, our review is intended as an entry point for ecologists and evolutionary biologists that are interested in extracting phenotypic information from digital images.
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12
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Differential reprogramming of breast cancer subtypes in 3D cultures and implications for sensitivity to targeted therapy. Sci Rep 2021; 11:7259. [PMID: 33790333 PMCID: PMC8012355 DOI: 10.1038/s41598-021-86664-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 03/15/2021] [Indexed: 02/06/2023] Open
Abstract
Screening for effective candidate drugs for breast cancer has shifted from two-dimensional (2D) to three-dimensional (3D) cultures. Here we systematically compared the transcriptomes of these different culture conditions by RNAseq of 14 BC cell lines cultured in both 2D and 3D conditions. All 3D BC cell cultures demonstrated increased mitochondrial metabolism and downregulated cell cycle programs. Luminal BC cells in 3D demonstrated overall limited reprogramming. 3D basal B BC cells showed increased expression of extracellular matrix (ECM) interaction genes, which coincides with an invasive phenotype not observed in other BC cells. Genes downregulated in 3D were associated with metastatic disease progression in BC patients, including cyclin dependent kinases and aurora kinases. Furthermore, the overall correlation of the cell line transcriptome to the BC patient transcriptome was increased in 3D cultures for all TNBC cell lines. To define the most optimal culture conditions to study the oncogenic pathway of interest, an open source bioinformatics strategy was established.
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13
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Paidi SK, Shah V, Raj P, Glunde K, Pandey R, Barman I. Coarse Raman and optical diffraction tomographic imaging enable label-free phenotyping of isogenic breast cancer cells of varying metastatic potential. Biosens Bioelectron 2021; 175:112863. [PMID: 33272866 PMCID: PMC7847362 DOI: 10.1016/j.bios.2020.112863] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022]
Abstract
Identification of the metastatic potential represents one of the most important tasks for molecular imaging of cancer. While molecular imaging of metastases has witnessed substantial progress as an area of clinical inquiry, determining precisely what differentiates the metastatic phenotype has proven to be more elusive. In this study, we utilize both the morphological and molecular information provided by 3D optical diffraction tomography and Raman spectroscopy, respectively, to propose a label-free route for optical phenotyping of cancer cells at single-cell resolution. By using an isogenic panel of cell lines derived from MDA-MB-231 breast cancer cells that vary in their metastatic potential, we show that 3D refractive index tomograms can capture subtle morphological differences among the parental, circulating tumor cells, and lung metastatic cells. By leveraging its molecular specificity, we demonstrate that coarse Raman microscopy is capable of rapidly mapping a sufficient number of cells for training a random forest classifier that can accurately predict the metastatic potential of cells at a single-cell level. We also perform multivariate curve resolution alternating least squares decomposition of the spectral dataset to demarcate spectra from cytoplasm and nucleus, and test the feasibility of identifying metastatic phenotypes using the spectra only from the cytoplasmic and nuclear regions. Overall, our study provides a rationale for employing coarse Raman mapping to substantially reduce measurement time thereby enabling the acquisition of reasonably large training datasets that hold the key for label-free single-cell analysis and, consequently, for differentiation of indolent from aggressive phenotypes.
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Affiliation(s)
- Santosh Kumar Paidi
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Vaani Shah
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Piyush Raj
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kristine Glunde
- The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Rishikesh Pandey
- CytoVeris Inc, Farmington, CT, 06032, USA; Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA; The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; Department of Oncology, Johns Hopkins University, Baltimore, MD, 21287, USA.
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14
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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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15
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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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16
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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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17
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Verschuuren M, Verstraelen P, García-Díaz Barriga G, Cilissen I, Coninx E, Verslegers M, Larsen PH, Nuydens R, De Vos WH. High-throughput microscopy exposes a pharmacological window in which dual leucine zipper kinase inhibition preserves neuronal network connectivity. Acta Neuropathol Commun 2019; 7:93. [PMID: 31164177 PMCID: PMC6549294 DOI: 10.1186/s40478-019-0741-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/16/2019] [Indexed: 12/13/2022] Open
Abstract
Therapeutic developments for neurodegenerative disorders are redirecting their focus to the mechanisms that contribute to neuronal connectivity and the loss thereof. Using a high-throughput microscopy pipeline that integrates morphological and functional measurements, we found that inhibition of dual leucine zipper kinase (DLK) increased neuronal connectivity in primary cortical cultures. This neuroprotective effect was not only observed in basal conditions but also in cultures depleted from antioxidants and in cultures in which microtubule stability was genetically perturbed. Based on the morphofunctional connectivity signature, we further showed that the effects were limited to a specific dose and time range. Thus, our results illustrate that profiling microscopy images with deep coverage enables sensitive interrogation of neuronal connectivity and allows exposing a pharmacological window for targeted treatments. In doing so, we revealed a broad-spectrum neuroprotective effect of DLK inhibition, which may have relevance to pathological conditions that ar.e associated with compromised neuronal connectivity.
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18
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Mahbub SB, Guller A, Campbell JM, Anwer AG, Gosnell ME, Vesey G, Goldys EM. Non-Invasive Monitoring of Functional State of Articular Cartilage Tissue with Label-Free Unsupervised Hyperspectral Imaging. Sci Rep 2019; 9:4398. [PMID: 30867549 PMCID: PMC6416344 DOI: 10.1038/s41598-019-40942-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/26/2019] [Indexed: 01/19/2023] Open
Abstract
Damage and degradation of articular cartilage leads to severe pain and loss of mobility. The development of new therapies for cartilage regeneration for monitoring their effect requires further study of cartilage, ideally at a molecular level and in a minimally invasive way. Hyperspectral microscopy is a novel technology which utilises endogenous fluorophores to non-invasively assess the molecular composition of cells and tissue. In this study, we applied hyperspectral microscopy to healthy bovine articular cartilage and osteoarthritic human articular cartilage to investigate its capacity to generate informative molecular data and characterise disease state and treatment effects. We successfully demonstrated label-free fluorescence identification of collagen type I and II - isolated in cartilage here for the first time and the co-enzymes free NADH and FAD which together give the optical redox ratio that is an important measure of metabolic activity. The intracellular composition of chondrocytes was also examined. Differences were observed in the molecular ratios within the superficial and transitional zones of the articular cartilage which appeared to be influenced by disease state and treatment. These findings show that hyperspectral microscopy could be useful for investigating the molecular underpinnings of articular cartilage degradation and repair. As it is non-invasive and non-destructive, samples can be repeatedly assessed over time, enabling true time-course experiments with in-depth molecular data. Additionally, there is potential for the hyperspectral approach to be adapted for patient examination to allow the investigation of cartilage state. This could be of advantage for assessment and diagnosis as well as treatment monitoring.
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Affiliation(s)
- Saabah B Mahbub
- ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW, Australia.
- Graduate School of Biomedical Engineering, UNSW Australia, Sydney, NSW, 2052, Australia.
| | - Anna Guller
- Graduate School of Biomedical Engineering, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Jared M Campbell
- Graduate School of Biomedical Engineering, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Ayad G Anwer
- Graduate School of Biomedical Engineering, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Martin E Gosnell
- ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW, Australia
- Quantitative Pty Ltd, 116-118 Great Western Highway, Mt. Victoria, NSW, 2786, Australia
| | - Graham Vesey
- Regeneus Pty Ltd, 25 Bridge Street, Pymble, NSW, 2073, Australia
| | - Ewa M Goldys
- Graduate School of Biomedical Engineering, UNSW Australia, Sydney, NSW, 2052, Australia.
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19
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Parrish J, Lim KS, Baer K, Hooper GJ, Woodfield TBF. A 96-well microplate bioreactor platform supporting individual dual perfusion and high-throughput assessment of simple or biofabricated 3D tissue models. LAB ON A CHIP 2018; 18:2757-2775. [PMID: 30117514 DOI: 10.1039/c8lc00485d] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Traditional 2D monolayer cell cultures and submillimeter 3D tissue construct cultures used widely in tissue engineering are limited in their ability to extrapolate experimental data to predict in vivo responses due to their simplistic organization and lack of stimuli. The rise of biofabrication and bioreactor technologies has sought to address this through the development of techniques to spatially organize components of a tissue construct, and devices to supply these tissue constructs with an increasingly in vivo-like environment. Current bioreactors supporting both parenchymal and barrier tissue constructs in interconnected systems for body-on-a-chip platforms have chosen to emphasize study throughput or system/tissue complexity. Here, we report a platform to address this disparity in throughput and both system complexity (by supporting multiple in situ assessment methods) and tissue complexity (by adopting a construct-agnostic format). We introduce an ANSI/SLAS-compliant microplate and docking station fabricated via stereolithography (SLA), or precision machining, to provide up to 96 samples (Ø6 × 10 mm) with two individually-addressable fluid circuits (192 total), loading access, and inspection window for imaging during perfusion. Biofabricated ovarian cancer models were developed to demonstrate the in situ assessment capabilities via microscopy and a perfused resazurin-based metabolic activity assay. In situ microscopy highlighted flexibility of the sample housing to accommodate a range of sample geometries. Utility for drug screening was demonstrated by exposing the ovarian cancer models to an anticancer drug (doxorubicin) and generating the dose-response curve in situ, while achieving an assay quality similar to static wellplate culture. The potential for quantitative analysis of temporal tissue development and screening studies was confirmed by imaging soft- (gelatin) and hard-tissue (calcium chloride) analogs inside the bioreactor via spectral computed tomography (CT) scanning. As a proof-of-concept for particle tracing studies, flowing microparticles were visualized to inform the design of hydrogel constructs. Finally, the ability for mechanistic yet high-throughput screening was demonstrated in a vascular coculture model adopting endothelial and mesenchymal stem cells (HUVEC-MSC), encapsulated in gelatin-norbornene (gel-NOR) hydrogel cast into SLA-printed well inserts. This study illustrates the potential of a scalable dual perfusion bioreactor platform for parenchymal and barrier tissue constructs to support a broad range of multi-organ-on-a-chip applications.
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Affiliation(s)
- J Parrish
- Christchurch Regenerative Medicine and Tissue Engineering (CReaTE) Group, Department of Orthopaedic Surgery & Musculoskeletal Medicine, Centre for Bioengineering & Nanomedicine, University of Otago Christchurch, Christchurch 8140, New Zealand.
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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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21
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Joshi P, Datar A, Yu KN, Kang SY, Lee MY. High-content imaging assays on a miniaturized 3D cell culture platform. Toxicol In Vitro 2018; 50:147-159. [PMID: 29501531 DOI: 10.1016/j.tiv.2018.02.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 12/17/2022]
Abstract
The majority of high-content imaging (HCI) assays have been performed on two-dimensional (2D) cell monolayers for its convenience and throughput. However, 2D-cultured cell models often do not represent the in vivo characteristics accurately and therefore reduce the predictability of drug toxicity/efficacy in vivo. Recently, three-dimensional (3D) cell-based HCI assays have been demonstrated to improve predictability, but its use is limited due to difficulty in maneuverability and low throughput in cell imaging. To alleviate these issues, we have developed miniaturized 3D cell culture on a micropillar/microwell chip and demonstrated high-throughput HCI assays for mechanistic toxicity. Briefly, Hep3B human hepatoma cell line was encapsulated in a mixture of alginate and fibrin gel on the micropillar chip, cultured in 3D, and exposed to six model compounds in the microwell chip for rapidly assessing mechanistic hepatotoxicity. Several toxicity parameters, including DNA damage, mitochondrial impairment, intracellular glutathione level, and cell membrane integrity were measured on the chip, and the IC50 values of the compounds at different readouts were determined to investigate the mechanism of toxicity. Overall, the Z' factors were between 0.6 and 0.8 for the HCI assays, and the coefficient of variation (CV) were below 20%. These results indicate high robustness and reproducibility of the HCI assays established on the miniaturized 3D cell culture chip. In addition, it was possible to determine the predominant mechanism of toxicity using the 3D HCI assays. Therefore, our miniaturized 3D cell culture coupled with HCI assays has great potential for high-throughput screening (HTS) of compounds and mechanistic toxicity profiling.
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Affiliation(s)
- Pranav Joshi
- Department of Chemical and Biomedical Engineering, Cleveland State University, 455 Fenn Hall, 1960 East 24th Street, Cleveland, OH 44115-2214, USA
| | - Akshata Datar
- Department of Chemical and Biomedical Engineering, Cleveland State University, 455 Fenn Hall, 1960 East 24th Street, Cleveland, OH 44115-2214, USA
| | - Kyeong-Nam Yu
- Department of Chemical and Biomedical Engineering, Cleveland State University, 455 Fenn Hall, 1960 East 24th Street, Cleveland, OH 44115-2214, USA
| | - Soo-Yeon Kang
- Department of Chemical and Biomedical Engineering, Cleveland State University, 455 Fenn Hall, 1960 East 24th Street, Cleveland, OH 44115-2214, USA
| | - Moo-Yeal Lee
- Department of Chemical and Biomedical Engineering, Cleveland State University, 455 Fenn Hall, 1960 East 24th Street, Cleveland, OH 44115-2214, USA.
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22
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Ahonen I, Åkerfelt M, Toriseva M, Oswald E, Schüler J, Nees M. A high-content image analysis approach for quantitative measurements of chemosensitivity in patient-derived tumor microtissues. Sci Rep 2017; 7:6600. [PMID: 28747710 PMCID: PMC5529420 DOI: 10.1038/s41598-017-06544-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/14/2017] [Indexed: 11/17/2022] Open
Abstract
Organotypic, three-dimensional (3D) cancer models have enabled investigations of complex microtissues in increasingly realistic conditions. However, a drawback of these advanced models remains the poor biological relevance of cancer cell lines, while higher clinical significance would be obtainable with patient-derived cell cultures. Here, we describe the generation and data analysis of 3D microtissue models from patient-derived xenografts (PDX) of non-small cell lung carcinoma (NSCLC). Standard of care anti-cancer drugs were applied and the altered multicellular morphologies were captured by confocal microscopy, followed by automated image analyses to quantitatively measure phenotypic features for high-content chemosensitivity tests. The obtained image data were thresholded using a local entropy filter after which the image foreground was split into local regions, for a supervised classification into tumor or fibroblast cell types. Robust statistical methods were applied to evaluate treatment effects on growth and morphology. Both novel and existing computational approaches were compared at each step, while prioritizing high experimental throughput. Docetaxel was found to be the most effective drug that blocked both tumor growth and invasion. These effects were also validated in PDX tumors in vivo. Our research opens new avenues for high-content drug screening based on patient-derived cell cultures, and for personalized chemosensitivity testing.
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Affiliation(s)
- Ilmari Ahonen
- Department of Mathematics and Statistics, University of Turku, Turku, Finland. .,Institute of Biomedicine, University of Turku, Turku, Finland.
| | - Malin Åkerfelt
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Mervi Toriseva
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Eva Oswald
- Discovery Services, Charles River, Freiburg, Germany
| | - Julia Schüler
- Discovery Services, Charles River, Freiburg, Germany
| | - Matthias Nees
- Institute of Biomedicine, University of Turku, Turku, Finland
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23
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Booij TH, Bange H, Leonhard WN, Yan K, Fokkelman M, Kunnen SJ, Dauwerse JG, Qin Y, van de Water B, van Westen GJP, Peters DJM, Price LS. High-Throughput Phenotypic Screening of Kinase Inhibitors to Identify Drug Targets for Polycystic Kidney Disease. SLAS DISCOVERY 2017. [PMID: 28644734 PMCID: PMC5574491 DOI: 10.1177/2472555217716056] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Polycystic kidney disease (PKD) is a prevalent disorder characterized by renal cysts that lead to kidney failure. Various signaling pathways have been targeted to stop disease progression, but most interventions still focus on alleviating PKD-associated symptoms. The mechanistic complexity of the disease, as well as the lack of functional in vitro assays for compound testing, has made drug discovery for PKD challenging. To identify modulators of PKD, Pkd1–/– kidney tubule epithelial cells were applied to a scalable and automated 3D cyst culture model for compound screening, followed by phenotypic profiling to determine compound efficacy. We used this screening platform to screen a library of 273 kinase inhibitors to probe various signaling pathways involved in cyst growth. We show that inhibition of several targets, including aurora kinase, CDK, Chk, IGF-1R, Syk, and mTOR, but, surprisingly, not PI3K, prevented forskolin-induced cyst swelling. Additionally, we show that multiparametric phenotypic classification discriminated potentially undesirable (i.e., cytotoxic) compounds from molecules inducing the desired phenotypic change, greatly facilitating hit selection and validation. Our findings show that a pathophysiologically relevant 3D cyst culture model of PKD coupled to phenotypic profiling can be used to identify potentially therapeutic compounds and predict and validate molecular targets for PKD.
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Affiliation(s)
- Tijmen H Booij
- 1 Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden, Netherlands
| | - Hester Bange
- 1 Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden, Netherlands
| | - Wouter N Leonhard
- 2 Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Kuan Yan
- 3 OcellO B.V., Leiden, Netherlands
| | - Michiel Fokkelman
- 1 Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden, Netherlands
| | - Steven J Kunnen
- 2 Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Yu Qin
- 1 Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden, Netherlands
| | - Bob van de Water
- 1 Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden, Netherlands
| | - Gerard J P van Westen
- 4 Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden, Netherlands
| | | | - Leo S Price
- 1 Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden, Netherlands.,3 OcellO B.V., Leiden, Netherlands
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24
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Lovitt CJ, Shelper TB, Avery VM. Cancer drug discovery: recent innovative approaches to tumor modeling. Expert Opin Drug Discov 2017; 11:885-94. [PMID: 27454169 DOI: 10.1080/17460441.2016.1214562] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
INTRODUCTION Cell culture models have been at the heart of anti-cancer drug discovery programs for over half a century. Advancements in cell culture techniques have seen the rapid evolution of more complex in vitro cell culture models investigated for use in drug discovery. Three-dimensional (3D) cell culture research has become a strong focal point, as this technique permits the recapitulation of the tumor microenvironment. Biologically relevant 3D cellular models have demonstrated significant promise in advancing cancer drug discovery, and will continue to play an increasing role in the future. AREAS COVERED In this review, recent advances in 3D cell culture techniques and their application in tumor modeling and anti-cancer drug discovery programs are discussed. The topics include selection of cancer cells, 3D cell culture assays (associated endpoint measurements and analysis), 3D microfluidic systems and 3D bio-printing. EXPERT OPINION Although advanced cancer cell culture models and techniques are becoming commonplace in many research groups, the use of these approaches has yet to be fully embraced in anti-cancer drug applications. Furthermore, limitations associated with analyzing information-rich biological data remain unaddressed.
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Affiliation(s)
- Carrie J Lovitt
- a Discovery Biology, Eskitis Institute for Drug Discovery , Griffith University , Nathan , Australia
| | - Todd B Shelper
- a Discovery Biology, Eskitis Institute for Drug Discovery , Griffith University , Nathan , Australia
| | - Vicky M Avery
- a Discovery Biology, Eskitis Institute for Drug Discovery , Griffith University , Nathan , Australia
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25
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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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26
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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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27
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Booij TH, Klop MJD, Yan K, Szántai-Kis C, Szokol B, Orfi L, van de Water B, Keri G, Price LS. Development of a 3D Tissue Culture-Based High-Content Screening Platform That Uses Phenotypic Profiling to Discriminate Selective Inhibitors of Receptor Tyrosine Kinases. ACTA ACUST UNITED AC 2016; 21:912-22. [PMID: 27412535 PMCID: PMC5030728 DOI: 10.1177/1087057116657269] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/01/2016] [Indexed: 11/17/2022]
Abstract
3D tissue cultures provide a more physiologically relevant context for the screening of compounds, compared with 2D cell cultures. Cells cultured in 3D hydrogels also show complex phenotypes, increasing the scope for phenotypic profiling. Here we describe a high-content screening platform that uses invasive human prostate cancer cells cultured in 3D in standard 384-well assay plates to study the activity of potential therapeutic small molecules and antibody biologics. Image analysis tools were developed to process 3D image data to measure over 800 phenotypic parameters. Multiparametric analysis was used to evaluate the effect of compounds on tissue morphology. We applied this screening platform to measure the activity and selectivity of inhibitors of the c-Met and epidermal growth factor (EGF) receptor (EGFR) tyrosine kinases in 3D cultured prostate carcinoma cells. c-Met and EGFR activity was quantified based on the phenotypic profiles induced by their respective ligands, hepatocyte growth factor and EGF. The screening method was applied to a novel collection of 80 putative inhibitors of c-Met and EGFR. Compounds were identified that induced phenotypic profiles indicative of selective inhibition of c-Met, EGFR, or bispecific inhibition of both targets. In conclusion, we describe a fully scalable high-content screening platform that uses phenotypic profiling to discriminate selective and nonselective (off-target) inhibitors in a physiologically relevant 3D cell culture setting.
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Affiliation(s)
- Tijmen H Booij
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | | | - Kuan Yan
- OcellO B.V., Leiden, The Netherlands
| | | | | | - Laszlo Orfi
- Vichem Chemie Research Ltd., Budapest, Hungary Department of Pharmaceutical Chemistry, Semmelweis University, Budapest, Hungary
| | - Bob van de Water
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Gyorgy Keri
- Vichem Chemie Research Ltd., Budapest, Hungary MTA-SE Pathobiochemistry Research Group, Department of Medical Chemistry, Semmelweis University, Budapest, Hungary
| | - Leo S Price
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands OcellO B.V., Leiden, The Netherlands
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Gosnell ME, Anwer AG, Mahbub SB, Menon Perinchery S, Inglis DW, Adhikary PP, Jazayeri JA, Cahill MA, Saad S, Pollock CA, Sutton-McDowall ML, Thompson JG, Goldys EM. Quantitative non-invasive cell characterisation and discrimination based on multispectral autofluorescence features. Sci Rep 2016; 6:23453. [PMID: 27029742 PMCID: PMC4814840 DOI: 10.1038/srep23453] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/07/2016] [Indexed: 02/08/2023] Open
Abstract
Automated and unbiased methods of non-invasive cell monitoring able to deal with complex biological heterogeneity are fundamentally important for biology and medicine. Label-free cell imaging provides information about endogenous autofluorescent metabolites, enzymes and cofactors in cells. However extracting high content information from autofluorescence imaging has been hitherto impossible. Here, we quantitatively characterise cell populations in different tissue types, live or fixed, by using novel image processing and a simple multispectral upgrade of a wide-field fluorescence microscope. Our optimal discrimination approach enables statistical hypothesis testing and intuitive visualisations where previously undetectable differences become clearly apparent. Label-free classifications are validated by the analysis of Classification Determinant (CD) antigen expression. The versatility of our method is illustrated by detecting genetic mutations in cancer, non-invasive monitoring of CD90 expression, label-free tracking of stem cell differentiation, identifying stem cell subpopulations with varying functional characteristics, tissue diagnostics in diabetes, and assessing the condition of preimplantation embryos.
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Affiliation(s)
- Martin E. Gosnell
- Quantitative Pty Ltd ABN 17165684186, Beaumont Hills NSW 2155, Australia.
- ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, North Ryde 2109, NSW Australia
| | - Ayad G. Anwer
- ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, North Ryde 2109, NSW Australia
| | - Saabah B. Mahbub
- ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, North Ryde 2109, NSW Australia
| | - Sandeep Menon Perinchery
- ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, North Ryde 2109, NSW Australia
| | - David W. Inglis
- ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, North Ryde 2109, NSW Australia
| | - Partho P. Adhikary
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Jalal A. Jazayeri
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Michael A. Cahill
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Sonia Saad
- Kolling Institute of Medical Research, Royal North Shore Hospital/Northern Clinical School, University of Sydney, Pacific Hwy, St Leonards NSW 2065, Australia
| | - Carol A. Pollock
- Kolling Institute of Medical Research, Royal North Shore Hospital/Northern Clinical School, University of Sydney, Pacific Hwy, St Leonards NSW 2065, Australia
| | - Melanie L. Sutton-McDowall
- Robinson Research Institute, School of Paediatrics and Reproductive Health, The University of Adelaide, Medical School, Frome Road, Adelaide, South Australia, 5005, Australia
- Australian Research Council Centre of Excellence for Nanoscale Biophotonics and Institute for Photonics and Advanced Sensing, The University of Adelaide, North Terrace, Adelaide, South Australia, 5005, Australia
| | - Jeremy G. Thompson
- Robinson Research Institute, School of Paediatrics and Reproductive Health, The University of Adelaide, Medical School, Frome Road, Adelaide, South Australia, 5005, Australia
- Australian Research Council Centre of Excellence for Nanoscale Biophotonics and Institute for Photonics and Advanced Sensing, The University of Adelaide, North Terrace, Adelaide, South Australia, 5005, Australia
| | - Ewa M. Goldys
- ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, North Ryde 2109, NSW Australia
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Joshi P, Lee MY. High Content Imaging (HCI) on Miniaturized Three-Dimensional (3D) Cell Cultures. BIOSENSORS 2015; 5:768-90. [PMID: 26694477 PMCID: PMC4697144 DOI: 10.3390/bios5040768] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 12/09/2015] [Accepted: 12/10/2015] [Indexed: 12/26/2022]
Abstract
High content imaging (HCI) is a multiplexed cell staining assay developed for better understanding of complex biological functions and mechanisms of drug action, and it has become an important tool for toxicity and efficacy screening of drug candidates. Conventional HCI assays have been carried out on two-dimensional (2D) cell monolayer cultures, which in turn limit predictability of drug toxicity/efficacy in vivo; thus, there has been an urgent need to perform HCI assays on three-dimensional (3D) cell cultures. Although 3D cell cultures better mimic in vivo microenvironments of human tissues and provide an in-depth understanding of the morphological and functional features of tissues, they are also limited by having relatively low throughput and thus are not amenable to high-throughput screening (HTS). One attempt of making 3D cell culture amenable for HTS is to utilize miniaturized cell culture platforms. This review aims to highlight miniaturized 3D cell culture platforms compatible with current HCI technology.
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Affiliation(s)
- Pranav Joshi
- Department of Chemical & Biomedical Engineering, Cleveland State University, 1960 East 24th Street Cleveland, Ohio, OH 44115-2214, USA.
| | - Moo-Yeal Lee
- Department of Chemical & Biomedical Engineering, Cleveland State University, 1960 East 24th Street Cleveland, Ohio, OH 44115-2214, USA.
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Martinez NJ, Titus SA, Wagner AK, Simeonov A. High-throughput fluorescence imaging approaches for drug discovery using in vitro and in vivo three-dimensional models. Expert Opin Drug Discov 2015; 10:1347-61. [PMID: 26394277 DOI: 10.1517/17460441.2015.1091814] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION High-resolution microscopy using fluorescent probes is a powerful tool to investigate individual cell structure and function, cell subpopulations and mechanisms underlying cellular responses to drugs. Additionally, responses to drugs more closely resemble those seen in vivo when cells are physically connected in three-dimensional (3D) systems (either 3D cell cultures or whole organisms), as opposed to traditional monolayer cultures. Combined, the use of imaging-based 3D models in the early stages of drug development has the potential to generate biologically relevant data that will increase the likelihood of success for drug candidates in human studies. AREAS COVERED The authors discuss current methods for the culturing of cells in 3D as well as approaches for the imaging of whole-animal models and 3D cultures that are amenable to high-throughput settings and could be implemented to support drug discovery campaigns. Furthermore, they provide critical considerations when discussing imaging these 3D systems for high-throughput chemical screenings. EXPERT OPINION Despite widespread understanding of the limitations imposed by the two-dimensional versus the 3D cellular paradigm, imaging-based drug screening of 3D cellular models is still limited, with only a few screens found in the literature. Image acquisition in high throughput, accurate interpretation of fluorescent signal, and uptake of staining reagents can be challenging, as the samples are in essence large aggregates of cells. The authors recognize these shortcomings that need to be overcome before the field can accelerate the utilization of these technologies in large-scale chemical screens.
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Affiliation(s)
- Natalia J Martinez
- a National Institutes of Health, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA
| | - Steven A Titus
- a National Institutes of Health, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA
| | - Amanda K Wagner
- a National Institutes of Health, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA
| | - Anton Simeonov
- a National Institutes of Health, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA
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Monjaret F, Fernandes M, Duchemin-Pelletier E, Argento A, Degot S, Young J. Fully Automated One-Step Production of Functional 3D Tumor Spheroids for High-Content Screening. ACTA ACUST UNITED AC 2015; 21:268-80. [PMID: 26385905 DOI: 10.1177/2211068215607058] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Indexed: 11/15/2022]
Abstract
Adoption of spheroids within high-content screening (HCS) has lagged behind high-throughput screening (HTS) due to issues with running complex assays on large three-dimensional (3D) structures.To enable multiplexed imaging and analysis of spheroids, different cancer cell lines were grown in 3D on micropatterned 96-well plates with automated production of nine uniform spheroids per well. Spheroids achieve diameters of up to 600 µm, and reproducibility was experimentally validated (interwell and interplate CV(diameter) <5%). Biphoton imaging confirmed that micropatterned spheroids exhibit characteristic cell heterogeneity with distinct microregions. Furthermore, central necrosis appears at a consistent spheroid size, suggesting standardized growth.Using three reference compounds (fluorouracil, irinotecan, and staurosporine), we validated HT-29 micropatterned spheroids on an HCS platform, benchmarking against hanging-drop spheroids. Spheroid formation and imaging in a single plate accelerate assay workflow, and fixed positioning prevents structures from overlapping or sticking to the well wall, augmenting image processing reliability. Furthermore, multiple spheroids per well increase the statistical confidence sufficiently to discriminate compound mechanisms of action and generate EC50 values for endpoints of cell death, architectural change, and size within a single-pass read. Higher quality data and a more efficient HCS work chain should encourage integration of micropatterned spheroid models within fundamental research and drug discovery applications.
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Affiliation(s)
| | | | | | | | | | - Joanne Young
- CYTOO SA, Minatec-BHT-Bât 52, Grenoble, 38040, France
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Sandercock AM, Rust S, Guillard S, Sachsenmeier KF, Holoweckyj N, Hay C, Flynn M, Huang Q, Yan K, Herpers B, Price LS, Soden J, Freeth J, Jermutus L, Hollingsworth R, Minter R. Identification of anti-tumour biologics using primary tumour models, 3-D phenotypic screening and image-based multi-parametric profiling. Mol Cancer 2015; 14:147. [PMID: 26227951 PMCID: PMC4521473 DOI: 10.1186/s12943-015-0415-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 07/17/2015] [Indexed: 11/23/2022] Open
Abstract
Background Monolayer cultures of immortalised cell lines are a popular screening tool for novel anti-cancer therapeutics, but these methods can be a poor surrogate for disease states, and there is a need for drug screening platforms which are more predictive of clinical outcome. In this study, we describe a phenotypic antibody screen using three-dimensional cultures of primary cells, and image-based multi-parametric profiling in PC-3 cells, to identify anti-cancer biologics against new therapeutic targets. Methods ScFv Antibodies and designed ankyrin repeat proteins (DARPins) were isolated using phage display selections against primary non-small cell lung carcinoma cells. The selected molecules were screened for anti-proliferative and pro-apoptotic activity against primary cells grown in three-dimensional culture, and in an ultra-high content screen on a 3-D cultured cell line using multi-parametric profiling to detect treatment-induced phenotypic changes. The targets of molecules of interest were identified using a cell-surface membrane protein array. An anti-CUB domain containing protein 1 (CDCP1) antibody was tested for tumour growth inhibition in a patient-derived xenograft model, generated from a stage-IV non-small cell lung carcinoma, with and without cisplatin. Results Two primary non-small cell lung carcinoma cell models were established for antibody isolation and primary screening in anti-proliferative and apoptosis assays. These assays identified multiple antibodies demonstrating activity in specific culture formats. A subset of the DARPins was profiled in an ultra-high content multi-parametric screen, where 300 morphological features were measured per sample. Machine learning was used to select features to classify treatment responses, then antibodies were characterised based on the phenotypes that they induced. This method co-classified several DARPins that targeted CDCP1 into two sets with different phenotypes. Finally, an anti-CDCP1 antibody significantly enhanced the efficacy of cisplatin in a patient-derived NSCLC xenograft model. Conclusions Phenotypic profiling using complex 3-D cell cultures steers hit selection towards more relevant in vivo phenotypes, and may shed light on subtle mechanistic variations in drug candidates, enabling data-driven decisions for oncology target validation. CDCP1 was identified as a potential target for cisplatin combination therapy. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0415-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Steven Rust
- MedImmune, Granta Park, Cambridge, CB21 6GH, UK.
| | | | | | | | - Carl Hay
- MedImmune, One MedImmune Way, Gaithersburg, MD, 20287, USA.
| | - Matt Flynn
- MedImmune, One MedImmune Way, Gaithersburg, MD, 20287, USA.
| | - Qihui Huang
- MedImmune, One MedImmune Way, Gaithersburg, MD, 20287, USA.
| | - Kuan Yan
- OcellO, Leiden BioPartner Center, J. H Oortweg 21, 2333 CH, Leiden, The Netherlands.
| | - Bram Herpers
- OcellO, Leiden BioPartner Center, J. H Oortweg 21, 2333 CH, Leiden, The Netherlands.
| | - Leo S Price
- OcellO, Leiden BioPartner Center, J. H Oortweg 21, 2333 CH, Leiden, The Netherlands.
| | - Jo Soden
- Retrogenix, Crown House, Bingswood Estate, Whaley Bridge, High Peak, SK23 7LY, UK.
| | - Jim Freeth
- Retrogenix, Crown House, Bingswood Estate, Whaley Bridge, High Peak, SK23 7LY, UK.
| | | | | | - Ralph Minter
- MedImmune, Granta Park, Cambridge, CB21 6GH, UK.
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