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Temple J, Velliou E, Shehata M, Lévy R, Gupta P. Current strategies with implementation of three-dimensional cell culture: the challenge of quantification. Interface Focus 2022; 12:20220019. [PMID: 35992772 PMCID: PMC9372643 DOI: 10.1098/rsfs.2022.0019] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/20/2022] [Indexed: 12/14/2022] Open
Abstract
From growing cells in spheroids to arranging them on complex engineered scaffolds, three-dimensional cell culture protocols are rapidly expanding and diversifying. While these systems may often improve the physiological relevance of cell culture models, they come with technical challenges, as many of the analytical methods used to characterize traditional two-dimensional (2D) cells must be modified or replaced to be effective. Here we review the advantages and limitations of quantification methods based either on biochemical measurements or microscopy imaging. We focus on the most basic of parameters that one may want to measure, the number of cells. Precise determination of this number is essential for many analytical techniques where measured quantities are only meaningful when normalized to the number of cells (e.g. cytochrome p450 enzyme activity). Thus, accurate measurement of cell number is often a prerequisite to allowing comparisons across different conditions (culturing conditions or drug and treatment screening) or between cells in different spatial states. We note that this issue is often neglected in the literature with little or no information given regarding how normalization was performed, we highlight the pitfalls and complications of quantification and call for more accurate reporting to improve reproducibility.
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Affiliation(s)
- Jonathan Temple
- Bioscience building, University of Liverpool, Liverpool L69 3BX, UK
| | - Eirini Velliou
- Centre for 3D Models of Health and Disease, University College London, London, UK
| | - Mona Shehata
- Hutchison-MRC Research Centre, University of Cambridge, Cambridge CB2 1TN, UK
| | - Raphaël Lévy
- Bioscience building, University of Liverpool, Liverpool L69 3BX, UK
- Laboratoire for Vascular Translational Science, Université Sorbonne Paris Nord, Bobigny, France
| | - Priyanka Gupta
- Centre for 3D Models of Health and Disease, University College London, London, UK
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2
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Badr-Eldin SM, Aldawsari HM, Kotta S, Deb PK, Venugopala KN. Three-Dimensional In Vitro Cell Culture Models for Efficient Drug Discovery: Progress So Far and Future Prospects. Pharmaceuticals (Basel) 2022; 15:926. [PMID: 36015074 PMCID: PMC9412659 DOI: 10.3390/ph15080926] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 12/13/2022] Open
Abstract
Despite tremendous advancements in technologies and resources, drug discovery still remains a tedious and expensive process. Though most cells are cultured using 2D monolayer cultures, due to lack of specificity, biochemical incompatibility, and cell-to-cell/matrix communications, they often lag behind in the race of modern drug discovery. There exists compelling evidence that 3D cell culture models are quite promising and advantageous in mimicking in vivo conditions. It is anticipated that these 3D cell culture methods will bridge the translation of data from 2D cell culture to animal models. Although 3D technologies have been adopted widely these days, they still have certain challenges associated with them, such as the maintenance of a micro-tissue environment similar to in vivo models and a lack of reproducibility. However, newer 3D cell culture models are able to bypass these issues to a maximum extent. This review summarizes the basic principles of 3D cell culture approaches and emphasizes different 3D techniques such as hydrogels, spheroids, microfluidic devices, organoids, and 3D bioprinting methods. Besides the progress made so far in 3D cell culture systems, the article emphasizes the various challenges associated with these models and their potential role in drug repositioning, including perspectives from the COVID-19 pandemic.
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Affiliation(s)
- Shaimaa M. Badr-Eldin
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (H.M.A.); (S.K.)
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hibah M. Aldawsari
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (H.M.A.); (S.K.)
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sabna Kotta
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (H.M.A.); (S.K.)
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Pran Kishore Deb
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Philadelphia University, P.O. Box 1, Amman 19392, Jordan
| | - Katharigatta N. Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4001, South Africa
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3
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Ayvaz I, Sunay D, Sariyar E, Erdal E, Karagonlar ZF. Three-Dimensional Cell Culture Models of Hepatocellular Carcinoma - a Review. J Gastrointest Cancer 2021; 52:1294-1308. [PMID: 34927218 DOI: 10.1007/s12029-021-00772-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2021] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Three-dimensional (3D) cell culture studies are becoming extremely common because of their capability to mimic tumor architecture, such as cell-cell and cell-ECM interactions, more efficiently than 2D monolayer systems. These interactions have important roles in defining the tumor cell behaviors, such as proliferation, differentiation, and most importantly, tumor drug response. OBJECTIVE This review aims to provide an overview of the methods for 3D tumor spheroid formation to model human tumors, specifically concentrated on studies using hepatocellular carcinoma (HCC) cells. METHOD We obtained information from previously published articles. In this review, there is discussion of the scaffold and non-scaffold-based approaches, including hanging drop, bioreactors and 3D bioprinting. RESULTS AND CONCLUSION The mimicking of the tumor microenvironment (TME) as tumor spheroids could provide a valuable platform for studying tumor biology. Multicellular tumor spheroids are self-assembled cultures of mixed cells (tumor and stromal cells) organized in a 3D arrangement. These spheroids closely mimic the main features of human solid tumors, such as structural organization, central hypoxia, and overall oxygen and nutrient gradients. Hepatocellular carcinoma (HCC) is the most common liver malignancy, and most difficult to overcome because of its drug resistance and tumor heterogeneity. In order to mimic this highly heterogeneous environment, 3D cell culture systems are needed.
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Affiliation(s)
- Irmak Ayvaz
- Genetics and Bioengineering Department, Izmir University of Economics, Izmir, 35330, Turkey
| | - Dilara Sunay
- Genetics and Bioengineering Department, Izmir University of Economics, Izmir, 35330, Turkey
| | - Ece Sariyar
- Genetics and Bioengineering Department, Izmir University of Economics, Izmir, 35330, Turkey
| | - Esra Erdal
- Department of Medical Biology and Genetics, FacultyofMedicine, Dokuz Eylul University, Izmir, 35340, Turkey.,Izmir Biomedicine and Genome Center, Izmir, 35340, Turkey
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Tucker LH, Hamm GR, Sargeant RJE, Goodwin RJA, Mackay CL, Campbell CJ, Clarke DJ. Untargeted Metabolite Mapping in 3D Cell Culture Models Using High Spectral Resolution FT-ICR Mass Spectrometry Imaging. Anal Chem 2019; 91:9522-9529. [DOI: 10.1021/acs.analchem.9b00661] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lulu H. Tucker
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - Gregory R. Hamm
- Pathology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Rebecca J. E. Sargeant
- Pathology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Richard J. A. Goodwin
- Pathology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - C. Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - Colin J. Campbell
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - David J. Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
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Kim YE, Jeon HJ, Kim D, Lee SY, Kim KY, Hong J, Maeng PJ, Kim KR, Kang D. Quantitative Proteomic Analysis of 2D and 3D Cultured Colorectal Cancer Cells: Profiling of Tankyrase Inhibitor XAV939-Induced Proteome. Sci Rep 2018; 8:13255. [PMID: 30185973 PMCID: PMC6125324 DOI: 10.1038/s41598-018-31564-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/20/2018] [Indexed: 12/21/2022] Open
Abstract
Recently there has been a growing interest in three-dimensional (3D) cell culture systems for drug discovery and development. These 3D culture systems better represent the in vivo cellular environment compared to two-dimensional (2D) cell culture, thereby providing more physiologically reliable information on drug screening and testing. Here we present the quantitative profiling of a drug-induced proteome in 2D- and 3D-cultured colorectal cancer SW480 cells using 2D nanoflow liquid chromatography-tandem mass spectrometry (2D-nLC-MS/MS) integrated with isobaric tags for relative and absolute quantitation (iTRAQ). We identified a total of 4854 shared proteins between 2D- and 3D-cultured SW480 cells and 136/247 differentially expressed proteins (up/down-regulated in 3D compared to 2D). These up/down-regulated proteins were mainly involved in energy metabolism, cell growth, and cell-cell interactions. We also investigated the XAV939 (tankyrase inhibitor)-induced proteome to reveal factors involved in the 3D culture-selective growth inhibitory effect of XAV939 on SW480 cells. We identified novel XAV939-induced proteins, including gelsolin (a possible tumor suppressor) and lactate dehydrogenase A (a key enzyme of glycolysis), which were differentially expressed between 2D- and 3D-cultured SW480 cells. These results provide a promising informative protein dataset to determine the effect of XAV939 on the expression levels of proteins involved in SW480 cell growth.
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Affiliation(s)
- Young Eun Kim
- Center for Bioanalysis, Division of Chemical and Medical Metrology, Korea Research Institute of Standards and Science, Daejeon, 34113, Korea
| | - Hyo Jin Jeon
- Therapeutic & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea.,Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Dahee Kim
- Therapeutic & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Sun Young Lee
- Center for Bioanalysis, Division of Chemical and Medical Metrology, Korea Research Institute of Standards and Science, Daejeon, 34113, Korea.,College of Pharmacy, Kyung Hee University, Seoul, 02447, Korea
| | - Ki Young Kim
- Therapeutic & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Jongki Hong
- College of Pharmacy, Kyung Hee University, Seoul, 02447, Korea
| | - Pil Jae Maeng
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Kwang-Rok Kim
- Therapeutic & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea.
| | - Dukjin Kang
- Center for Bioanalysis, Division of Chemical and Medical Metrology, Korea Research Institute of Standards and Science, Daejeon, 34113, Korea.
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Acland M, Mittal P, Lokman NA, Klingler-Hoffmann M, Oehler MK, Hoffmann P. Mass Spectrometry Analyses of Multicellular Tumor Spheroids. Proteomics Clin Appl 2018; 12:e1700124. [PMID: 29227035 DOI: 10.1002/prca.201700124] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/13/2017] [Indexed: 12/21/2022]
Abstract
Multicellular tumor spheroids (MCTS) are a powerful biological in vitro model, which closely mimics the 3D structure of primary avascularized tumors. Mass spectrometry (MS) has established itself as a powerful analytical tool, not only to better understand and describe the complex structure of MCTS, but also to monitor their response to cancer therapeutics. The first part of this review focuses on traditional mass spectrometry approaches with an emphasis on elucidating the molecular characteristics of these structures. Then the mass spectrometry imaging (MSI) approaches used to obtain spatially defined information from MCTS is described. Finally the analysis of primary spheroids, such as those present in ovarian cancer, and the great potential that mass spectrometry analysis of these structures has for improved understanding of cancer progression and for personalized in vitro therapeutic testing is discussed.
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Affiliation(s)
- Mitchell Acland
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Institute of Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, South Australia, Australia
| | - Parul Mittal
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Institute of Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, South Australia, Australia
| | - Noor A Lokman
- Discipline of Obstetrics and Gynaecology, School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Manuela Klingler-Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Martin K Oehler
- Discipline of Obstetrics and Gynaecology, School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia.,Department of Gynaecological Oncology, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Peter Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
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Gupta D, Grant DM, Zakir Hossain KM, Ahmed I, Sottile V. Role of geometrical cues in bone marrow-derived mesenchymal stem cell survival, growth and osteogenic differentiation. J Biomater Appl 2017; 32:906-919. [DOI: 10.1177/0885328217745699] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Dhanak Gupta
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Medicine, University of Nottingham, Nottingham, UK
- Advanced Materials Research Group, Faculty of Engineering, University of Nottingham, UK
| | - David M Grant
- Advanced Materials Research Group, Faculty of Engineering, University of Nottingham, UK
| | - Kazi M Zakir Hossain
- Advanced Materials Research Group, Faculty of Engineering, University of Nottingham, UK
| | - Ifty Ahmed
- Advanced Materials Research Group, Faculty of Engineering, University of Nottingham, UK
| | - Virginie Sottile
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Medicine, University of Nottingham, Nottingham, UK
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8
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Ravi M, Ramesh A, Pattabhi A. Contributions of 3D Cell Cultures for Cancer Research. J Cell Physiol 2017; 232:2679-2697. [PMID: 27791270 DOI: 10.1002/jcp.25664] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 10/26/2016] [Indexed: 12/24/2022]
Abstract
Cancer cell lines have contributed immensely in understanding the complex physiology of cancers. They are excellent material for studies as they offer homogenous samples without individual variations and can be utilised with ease and flexibility. Also, the number of assays and end-points one can study is almost limitless; with the advantage of improvising, modifying or altering several variables and methods. Literally, a new dimension to cancer research has been achieved by the advent of 3Dimensional (3D) cell culture techniques. This approach increased many folds the ways in which cancer cell lines can be utilised for understanding complex cancer biology. 3D cell culture techniques are now the preferred way of using cancer cell lines to bridge the gap between the 'absolute in vitro' and 'true in vivo'. The aspects of cancer biology that 3D cell culture systems have contributed include morphology, microenvironment, gene and protein expression, invasion/migration/metastasis, angiogenesis, tumour metabolism and drug discovery, testing chemotherapeutic agents, adaptive responses and cancer stem cells. We present here, a comprehensive review on the applications of 3D cell culture systems for these aspects of cancers. J. Cell. Physiol. 232: 2679-2697, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Maddaly Ravi
- Faculty of Biomedical Sciences, Technology and Research, Department of Human Genetics, Sri Ramachandra University, Porur, Chennai, India
| | - Aarthi Ramesh
- Faculty of Biomedical Sciences, Technology and Research, Department of Human Genetics, Sri Ramachandra University, Porur, Chennai, India
| | - Aishwarya Pattabhi
- Faculty of Biomedical Sciences, Technology and Research, Department of Human Genetics, Sri Ramachandra University, Porur, Chennai, India
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Stankevicius V, Vasauskas G, Bulotiene D, Butkyte S, Jarmalaite S, Rotomskis R, Suziedelis K. Gene and miRNA expression signature of Lewis lung carcinoma LLC1 cells in extracellular matrix enriched microenvironment. BMC Cancer 2016; 16:789. [PMID: 27729023 PMCID: PMC5057255 DOI: 10.1186/s12885-016-2825-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/30/2016] [Indexed: 12/15/2022] Open
Abstract
Background The extracellular matrix (ECM), one of the key components of tumor microenvironment, has a tremendous impact on cancer development and highly influences tumor cell features. ECM affects vital cellular functions such as cell differentiation, migration, survival and proliferation. Gene and protein expression levels are regulated in cell-ECM interaction dependent manner as well. The rate of unsuccessful clinical trials, based on cell culture research models lacking the ECM microenvironment, indicates the need for alternative models and determines the shift to three-dimensional (3D) laminin rich ECM models, better simulating tissue organization. Recognized advantages of 3D models suggest the development of new anticancer treatment strategies. This is among the most promising directions of 3D cell cultures application. However, detailed analysis at the molecular level of 2D/3D cell cultures and tumors in vivo is still needed to elucidate cellular pathways most promising for the development of targeted therapies. In order to elucidate which biological pathways are altered during microenvironmental shift we have analyzed whole genome mRNA and miRNA expression differences in LLC1 cells cultured in 2D or 3D culture conditions. Methods In our study we used DNA microarrays for whole genome analysis of mRNA and miRNA expression differences in LLC1 cells cultivated in 2D or 3D culture conditions. Next, we indicated the most common enriched functional categories using KEGG pathway enrichment analysis. Finally, we validated the microarray data by quantitative PCR in LLC1 cells cultured under 2D or 3D conditions or LLC1 tumors implanted in experimental animals. Results Microarray gene expression analysis revealed that 1884 genes and 77 miRNAs were significantly altered in LLC1 cells after 48 h cell growth under 2D and ECM based 3D cell growth conditions. Pathway enrichment results indicated metabolic pathway, MAP kinase, cell adhesion and immune response as the most significantly altered functional categories in LLC1 cells due to the microenvironmental shift from 2D to 3D. Comparison of the expression levels of selected genes and miRNA between LLC1 cells grown in 3D cell culture and LLC1 tumors implanted in the mouse model indicated correspondence between both model systems. Conclusions Global gene and miRNA expression analysis in LLC1 cells under ECM microenvironment indicated altered immune response, adhesion and MAP kinase pathways. All these processes are related to tumor development, progression and treatment response, suggesting the most promising directions for the development of targeted therapies using the 3D cell culture models. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2825-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vaidotas Stankevicius
- National Cancer Institute, Vilnius, Lithuania.,Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Joint Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gintautas Vasauskas
- National Cancer Institute, Vilnius, Lithuania.,Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Joint Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Stase Butkyte
- Vilnius University Institute of Biotechnology, Joint Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Sonata Jarmalaite
- National Cancer Institute, Vilnius, Lithuania.,Human Genome Research Centre, Department Botany & Genetics, Faculty of Natural Sciences, Joint Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ricardas Rotomskis
- National Cancer Institute, Vilnius, Lithuania.,Biophotonics Group of Laser Research Centre, Vilnius University, Vilnius, Lithuania
| | - Kestutis Suziedelis
- National Cancer Institute, Vilnius, Lithuania. .,Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Joint Life Sciences Center, Vilnius University, Vilnius, Lithuania. .,Laboratory of Molecular Oncology, National Cancer Institute, Santariskiu 1, Vilnius, LT-08660, Lithuania.
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10
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Dubiak-Szepietowska M, Karczmarczyk A, Winckler T, Feller KH. A cell-based biosensor for nanomaterials cytotoxicity assessment in three dimensional cell culture. Toxicology 2016; 370:60-69. [PMID: 27693313 DOI: 10.1016/j.tox.2016.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/22/2016] [Accepted: 09/26/2016] [Indexed: 12/17/2022]
Abstract
Nanoparticles (NPs) are widely used in consumer and medicinal products. The high prevalence of nanoparticles in the environment raises concerns regarding their effects on human health, but there is limited knowledge about how NPs interact with cells or tissues. Because the European Union has called for a substantial reduction of animal experiments for scientific purposes (Directive 2010/63), increased efforts are required to develop in vitro models to evaluate potentially hazardous agents. Here, we describe a new cell-based biosensor for the evaluation of NPs cytotoxicity. The new biosensor is based on transgenic human hepatoblastoma cells (HepG2) that express a secreted form of alkaline phosphatase (SEAP) as a reporter protein whose expression is induced upon activation of a stress response pathway controlled by the transcription regulator nuclear factor-κB (NF-κB). The NF-κB_HepG2 sensor cells were cultured in a Matrigel-based three dimensional environment to simulate the in vivo situation. The new biosensor cells offer the advantage of generating fast and reproducible readout at lower concentrations and shorter incubation time than conventional viability assays, avoid possible interaction between nanomaterials and assay compounds, therefore, minimize generation of false positive or negative results and indicate mechanism of toxicity through NF-κB signaling.
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Affiliation(s)
- Monika Dubiak-Szepietowska
- Department of Medical Engineering and Biotechnology, Ernst-Abbe-University of Applied Sciences Jena, Carl-Zeiss Promenade 2, 07745 Jena, Germany.
| | - Aleksandra Karczmarczyk
- Department of Medical Engineering and Biotechnology, Ernst-Abbe-University of Applied Sciences Jena, Carl-Zeiss Promenade 2, 07745 Jena, Germany
| | - Thomas Winckler
- Institute of Pharmacy, Friedrich Schiller University Jena, Semmelweissstrasse 10, 07743 Jena, Germany
| | - Karl-Heinz Feller
- Department of Medical Engineering and Biotechnology, Ernst-Abbe-University of Applied Sciences Jena, Carl-Zeiss Promenade 2, 07745 Jena, Germany
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Pruksakorn D, Teeyakasem P, Klangjorhor J, Chaiyawat P, Settakorn J, Diskul-Na-Ayudthaya P, Chokchaichamnankit D, Pothacharoen P, Srisomsap C. Overexpression of KH-type splicing regulatory protein regulates proliferation, migration, and implantation ability of osteosarcoma. Int J Oncol 2016; 49:903-12. [PMID: 27573585 PMCID: PMC4948955 DOI: 10.3892/ijo.2016.3601] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/15/2016] [Indexed: 12/16/2022] Open
Abstract
Osteosarcoma is a common malignant bone tumor in children and adolescents. The current 5-year survival rate is ~60% and that seems to be reaching a plateau. In order to improve treatment outcomes of osteosarcoma, a better understanding of tumorigenesis and underlying molecular mechanisms is required for searching out possible new treatment targets. This study aimed to identify the potential proteins involving the pathogenesis of osteosarcoma using a proteomics approach. Proteins extracted from primary cell culture of osteosarcoma (n=7) and osteoblasts of cancellous bone (n=7) were studied. Using 2-DE based proteomics and LC-MS/MS analysis, we successfully determined seven differentially expressed protein spots. Four upregulated proteins and three downregulated proteins were observed in this study in which KH-type splicing regulatory protein (KSRP) was selected for further exploration. KSRP was significantly upregulated in osteosarcoma cells compared to osteoblasts using western blot assay. In addition, immunohistochemistry demonstrated that KSRP was also highly expressed in osteosarcoma tissue of independent cases from the experimental group. More importantly, KSRP silencing of osteosarcoma cell lines significantly decreased cell proliferation, migration ability, as well as implantation and growth ability in chick chorioallantoic membrane assay. Taken together, these findings demonstrate, that KSRP plays important roles in regulatory controls of osteosarcoma pathogenesis and serves as a potentially therapeutic target of osteosarcoma.
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Affiliation(s)
- Dumnoensun Pruksakorn
- Department of Orthopedics, Faculty of Medicine, Orthopedic Laboratory and Research Netting Center (OLARN Center), Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pimpisa Teeyakasem
- Department of Orthopedics, Faculty of Medicine, Orthopedic Laboratory and Research Netting Center (OLARN Center), Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jeerawan Klangjorhor
- Department of Orthopedics, Faculty of Medicine, Orthopedic Laboratory and Research Netting Center (OLARN Center), Chiang Mai University, Chiang Mai 50200, Thailand
| | - Parunya Chaiyawat
- Department of Orthopedics, Faculty of Medicine, Orthopedic Laboratory and Research Netting Center (OLARN Center), Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jongkolnee Settakorn
- Department of Pathology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | | | | | - Peraphan Pothacharoen
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
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12
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A method to investigate the anti-metabolic activity of anti-cancer agents on ovarian cancer cells cultured in a 96-well high throughput format. J Ovarian Res 2015; 8:43. [PMID: 26141064 PMCID: PMC4491427 DOI: 10.1186/s13048-015-0172-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 06/25/2015] [Indexed: 11/26/2022] Open
Abstract
Background An early step of advanced ovarian cancer begins when floating cancerous cells as single cells or small clusters grow on the peritoneal surface. This surface is rich in extracellular matrix (ECM) proteins, which have profound effects on cellular behaviour and can facilitate cancer progression. Subsequently, this ECM may alter cellular metabolism making cancer cells susceptible to chemotherapeutic agents differently. Therefore, generating a cell culture tool in vitro that includes the interaction between ECM and cancer cells will facilitate our understanding of how cancer cells behave during cancer treatment. There is some evidence to suggest that in an in vitro model that includes ECM components such as collagens will provide a better predictive tool for drug evaluation than a traditional cell monolayer (2D) culture model. Findings As a proof -of- concept, we made a collagen gel in a 96-well plate format and utilised this to evaluate the efficacy of clinical cytotoxic drugs, a targeted drug, and food compounds in single and combination treatments. The primary endpoints were to measure the reduction of cellular metabolism and secretion of vascular endothelial growth factor (VEGF). The invasive capacity of cancer cells was observed in collagen gels and it was cell line-dependent. The responses to drugs were prominently observed in collagen gels, but they had little effect on 2D cell monolayers. These responses were cell line- and type of drug-dependent. Conclusions The collagen gel in a 96 well plate format was easy to set up and could have potential to identify drug sensitivity in the clinical management of women with platinum resistant ovarian cancer.
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Feist P, Sun L, Liu X, Dovichi NJ, Hummon AB. Bottom-up proteomic analysis of single HCT 116 colon carcinoma multicellular spheroids. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:654-658. [PMID: 26212283 PMCID: PMC4763982 DOI: 10.1002/rcm.7150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 06/17/2023]
Abstract
RATIONALE Proteomic analysis of single multicellular spheroids has not been previously reported. As three-dimensional cell cultures are an increasingly popular model system for biological research, there is interest in obtaining proteomic profiles of these samples. We investigated the proteome of single HCT 116 multicellular spheroids using protocols optimized for small sample sizes. METHODS Six biological replicates were analyzed via microscopy for size. Total protein content was assessed via the bicinchoninic acid assay (BCA assay). Five separate biological replicate spheroids were analyzed via mass spectrometry in technical duplicate. An ultra-performance liquid chromatography (UPLC) system coupled with an LTQ Orbitrap Velos was used for peptide separation, analysis, and identification. RESULTS The average diameter of six replicate HCT 116 spheroids was 940 ± 30 µm and the average total protein amount was determined to be 39 ± 4 µg. At least 1300 protein groups were identified in each single LC/MS/MS run with 10% of the material from each single spheroid loaded. Database search results showed variation between spheroid protein group identifications. Pearson correlations show that the disparity in identifications is due to random variations in spectra and protocol. CONCLUSIONS We detected more than 1350 protein groups in each replicate HCT 116 spheroid. While some variation was detected between replicates, differences in the number of protein groups identified were determined to be the result of random variations in mass spectra acquisition.
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Daniëls VW, Smans K, Royaux I, Chypre M, Swinnen JV, Zaidi N. Cancer cells differentially activate and thrive on de novo lipid synthesis pathways in a low-lipid environment. PLoS One 2014; 9:e106913. [PMID: 25215509 PMCID: PMC4162556 DOI: 10.1371/journal.pone.0106913] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 08/03/2014] [Indexed: 01/22/2023] Open
Abstract
Increased lipogenesis is a hallmark of a wide variety of cancers and is under intense investigation as potential antineoplastic target. Although brisk lipogenesis is observed in the presence of exogenous lipids, evidence is mounting that these lipids may adversely affect the efficacy of inhibitors of lipogenic pathways. Therefore, to fully exploit the therapeutic potential of lipid synthesis inhibitors, a better understanding of the interrelationship between de novo lipid synthesis and exogenous lipids and their respective role in cancer cell proliferation and therapeutic response to lipogenesis inhibitors is of critical importance. Here, we show that the proliferation of various cancer cell lines (PC3M, HepG2, HOP62 and T24) is attenuated when cultured in lipid-reduced conditions in a cell line-dependent manner, with PC3M being the least affected. Interestingly, all cell lines - lipogenic (PC3M, HepG2, HOP62) as well as non-lipogenic (T24) - raised their lipogenic activity in these conditions, albeit to a different degree. Cells that attained the highest lipogenic activity under these conditions were best able to cope with lipid reduction in term of proliferative capacity. Supplementation of the medium with very low density lipoproteins, free fatty acids and cholesterol reversed this activation, indicating that the mere lack of lipids is sufficient to activate de novo lipogenesis in cancer cells. Consequently, cancer cells grown in lipid-reduced conditions became more dependent on de novo lipid synthesis pathways and were more sensitive to inhibitors of lipogenic pathways, like Soraphen A and Simvastatin. Collectively, these data indicate that limitation of access to exogenous lipids, as may occur in intact tumors, activates de novo lipogenesis is cancer cells, helps them to thrive under these conditions and makes them more vulnerable to lipogenesis inhibitors. These observations have important implications for the design of new antineoplastic strategies targeting the cancer cell's lipid metabolism.
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Affiliation(s)
- Veerle W. Daniëls
- KU Leuven – University of Leuven, Faculty of Medicine, Department of Oncology, Laboratory of Lipid Metabolism and Cancer, Leuven, Belgium
| | - Karine Smans
- Department of Oncology, Janssen Research and Development, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Ines Royaux
- Department of Oncology, Janssen Research and Development, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Melanie Chypre
- Department of Oncology, Janssen Research and Development, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Johannes V. Swinnen
- KU Leuven – University of Leuven, Faculty of Medicine, Department of Oncology, Laboratory of Lipid Metabolism and Cancer, Leuven, Belgium
| | - Nousheen Zaidi
- KU Leuven – University of Leuven, Faculty of Medicine, Department of Oncology, Laboratory of Lipid Metabolism and Cancer, Leuven, Belgium
- Department of Oncology, Janssen Research and Development, a division of Janssen Pharmaceutica NV, Beerse, Belgium
- Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
- * E-mail:
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Tit-Oon P, Chokchaichamnankit D, Khongmanee A, Sawangareetrakul P, Svasti J, Srisomsap C. Comparative secretome analysis of cholangiocarcinoma cell line in three-dimensional culture. Int J Oncol 2014; 45:2108-16. [PMID: 25189380 DOI: 10.3892/ijo.2014.2636] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/13/2014] [Indexed: 11/06/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a lethal malignancy which occurs with relatively high incidence in Thailand. This cancer is often difficult to diagnose and associated with high mortality. The secretome, containing the secreted proteins from cells, are potentially useful as biomarkers of cancers. Since three-dimensional (3D) cell culture may mimic growth characteristics and microenvironment of solid tumors in vivo better than monolayer culture, we have developed culture of CCA in natural collagen-based scaffold, to enable analysis of the secretome by 2DE. Our results indicated that CCA growth in 3D environment alters cell shape significantly and enhances extracellular matrix deposition. Interestingly, more secreted proteins were detected from 3D culture compared to monolayer culture. Secretome analysis using 2DE coupled with LC-MS/MS demonstrated 10 secreted proteins uniquely found in 3D culture. Moreover, 25 proteins were enriched in 3D culture compared to monolayer culture, including 14-3-3 σ, triosephosphate isomerase, phosphoglycerate mutase 1, α-enolase, and L-plastin. Immunoblotting was used to confirm the presence of L-plastin in conditioned media of CCA and of hepatocellular carcinoma (HCC) cell lines. The results revealed that L-plastin, an actin bundling protein, was uniquely expressed only in the CCA cell line and could be a promising biomarker for differential diagnosis of CCA compared to HCC.
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Affiliation(s)
- Phanthakarn Tit-Oon
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Bangkok 10210, Thailand
| | | | - Amnart Khongmanee
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Bangkok 10210, Thailand
| | | | - Jisnuson Svasti
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Bangkok 10210, Thailand
| | - Chantragan Srisomsap
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok 10210, Thailand
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Champattanachai V, Netsirisawan P, Chaiyawat P, Phueaouan T, Charoenwattanasatien R, Chokchaichamnankit D, Punyarit P, Srisomsap C, Svasti J. Proteomic analysis and abrogated expression of O-GlcNAcylated proteins associated with primary breast cancer. Proteomics 2013; 13:2088-99. [PMID: 23576270 DOI: 10.1002/pmic.201200126] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 02/20/2013] [Accepted: 03/26/2013] [Indexed: 02/06/2023]
Abstract
O-GlcNAcylation is a dynamic PTM of nuclear and cytoplasmic proteins, regulated by O-GlcNAc transferase (OGT) and O-GlcNAcase, which catalyze the addition and removal of O-GlcNAc, respectively. This modification is associated with glucose metabolism, which plays important roles in many diseases including cancer. Although emerging evidence reveals that some tumor-associated proteins are O-GlcNAc modified, the total O-GlcNAcylation in cancer is still largely unexplored. Here, we demonstrate that O-GlcNAcylation was increased in primary breast malignant tumors, not in benign tumors and that this augmentation was associated with increased expression of OGT level. Using 2D O-GlcNAc immnoblotting and LC-MS/MS analysis, we successfully identified 29 proteins, with seven being uniquely O-GlcNAcylated or associated with O-GlcNAcylation in cancer. Of these identified proteins, some were related to the Warburg effect, including metabolic enzymes, proteins involved in stress responses and biosynthesis. In addition, proteins associated with RNA metabolism, gene expression, and cytoskeleton were highly O-GlcNAcylated or associated with O-GlcNAcylation. Moreover, OGT knockdown showed that decreasing O-GlcNAcylation was related to inhibition of the anchorage-independent growth in vitro. These data indicate that aberrant protein O-GlcNAcylation is associated with breast cancer. Abnormal modification of these O-GlcNAc-modified proteins might be one of the vital malignant characteristics of cancer.
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Abstract
Low oxygen tension exerts a significant effect on the replication of several DNA and RNA viruses in cultured cells. In vitro propagation of hepatitis C virus (HCV) has thus far been studied under atmospheric oxygen levels despite the fact that the liver tissue microenvironment is hypoxic. In this study, we investigated the efficiency of HCV production in actively dividing or differentiating human hepatoma cells cultured under low or atmospheric oxygen tensions. By using both HCV replicons and infection-based assays, low oxygen was found to enhance HCV RNA replication whereas virus entry and RNA translation were not affected. Hypoxia signaling pathway-focused DNA microarray and real-time quantitative reverse transcription-PCR (qRT-PCR) analyses revealed an upregulation of genes related to hypoxic stress, glycolytic metabolism, cell growth, and proliferation when cells were kept under low (3% [vol/vol]) oxygen tension, likely reflecting cell adaptation to anaerobic conditions. Interestingly, hypoxia-mediated enhancement of HCV replication correlated directly with the increase in anaerobic glycolysis and creatine kinase B (CKB) activity that leads to elevated ATP production. Surprisingly, activation of hypoxia-inducible factor alpha (HIF-α) was not involved in the elevation of HCV replication. Instead, a number of oncogenes known to be associated with glycolysis were upregulated and evidence that these oncogenes contribute to hypoxia-mediated enhancement of HCV replication was obtained. Finally, in liver biopsy specimens of HCV-infected patients, the levels of hypoxia and anaerobic metabolism markers correlated with HCV RNA levels. These results provide new insights into the impact of oxygen tension on the intricate HCV-host cell interaction.
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Jiroutová A, Peterová E, Bittnerová L, Slavkovský R, Cevelová P, Rezáčová M, Cerman J, Mičuda S, Kanta J. Collagenolytic potential of rat liver myofibroblasts. Physiol Res 2012; 62:15-25. [PMID: 23173684 DOI: 10.33549/physiolres.932399] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Rat liver myofibroblasts (MFB) were isolated by repeated passaging of nonparenchymal liver cell fraction. They were cultured on polystyrene Petri dishes, on fibrin or on type I collagen gels for 5 days. Quantitative RT-PCR, Western blotting, zymography and immunocytochemistry were used to study differences in cell morphology and protein expression. MFB were large and spread on plastic substrate, with prominent alpha-smooth muscle (alpha-SMA) fibres. They turned much smaller and elongated on collagen which was accompanied by the rearrangement of the cytoskeleton and a decrease in alpha-SMA and beta-actin content. Collagen gel induced the expression of a group of metalloproteinases (MMP-2, -3, -9, -13), on mRNA and protein level which resulted in the degradation of the gel. This response was accompanied by changes in the mRNA expression of cytokines of TGF-beta family, CTGF and interleukin-6, as well as of osteopontin and thrombospondin-2 that are involved in metalloproteinases (MMPs) regulation. The expression of MMPs substrates, collagen types I, IV and XII did not change or decreased. The effects of fibrin gels on MFB were milder than those of collagen. MFB assumed to deposit collagen and other ECM components in fibrotic liver, besides hepatic stellate cells, also possess a great collagenolytic potential.
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Affiliation(s)
- A Jiroutová
- Faculty of Medicine in Hradec Králové, Hradec Králové, Czech Republic.
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