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Daunke T, Beckinger S, Rahn S, Krüger S, Heckl S, Schäfer H, Wesch D, Pilarsky C, Eckstein M, Hartmann A, Röcken C, Wandmacher AM, Sebens S. Expression and role of the immune checkpoint regulator PD-L1 in the tumor-stroma interplay of pancreatic ductal adenocarcinoma. Front Immunol 2023; 14:1157397. [PMID: 37449210 PMCID: PMC10337136 DOI: 10.3389/fimmu.2023.1157397] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Immune checkpoint inhibitors (ICI), e.g., targeting programmed cell death protein 1-ligand 1 (PD-L1) or its receptor PD-1, have markedly improved the therapy of many cancers but so far failed in pancreatic ductal adenocarcinoma (PDAC). Macrophages represent one of the most abundant immune cell populations within the tumor microenvironment (TME) of PDAC being able to either support or restrain tumor progression depending on their phenotype. To better understand treatment failure of PD-L1/PD-1 inhibitors in PDAC, this study examined PD-L1 expression in the context of a dynamic TME in PDAC with a particular focus on the impact of macrophages. Methods Formalin-fixed and paraffin embedded tissue samples of primary PDAC tissues and corresponding liver metastases were used for immunohistochemical analyses. Serial sections were stained with antibodies detecting Pan-Cytokeratin, CD68, CD163, CD8, and PD-L1.To investigate whether the PD-1/PD-L1 axis and macrophages contribute to immune escape of PDAC cells, a stroma enriched 3D spheroid coculture model was established in vitro, using different PDAC cell lines and macrophages subtypes as well as CD8+ T cells. Functional and flow cytometry analyses were conducted to characterize cell populations. Results Immunohistochemical analyses revealed that PD-L1 is mainly expressed by stroma cells, including macrophages and not PDAC cells in primary PDAC tissues and corresponding liver metastases. Notably, high local abundance of macrophages and strong PD-L1 staining were commonly found at invasion fronts of tumoral lesions between CD8+ T cells and tumor cells. In order to investigate whether PD-L1 expressing macrophages impact the response of PDAC cells to treatment with PD-L1/PD-1 inhibitors, we developed a spheroid model comprising two different PDAC cell lines and different ratios of in vitro differentiated primary M1- or M2-like polarized macrophages. In line with our in situ findings, high PD-L1 expression was observed in macrophages rather than PDAC cells, which was further increased by the presence of PDAC cells. The effector phenotype of co-cultured CD8+ T cells exemplified by expression of activation markers and release of effector molecules was rather enhanced by PDAC macrophage spheroids, particularly with M1-like macrophages compared to mono-culture spheroids. However, this was not associated with enhanced PDAC cell death. ICI treatment with either Durvalumab or Pembrolizumab alone or in combination with Gemcitabine hardly affected the effector phenotype of CD8+ T cells along with PDAC cell death. Thus, despite strong PD-L1 expression in macrophages, ICI treatment did not result in an enhanced activation and cytotoxic phenotype of CD8+ T cells. Conclusion Overall, our study revealed novel insights into the interplay of PDAC cells and macrophages in the presence of ICI.
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Affiliation(s)
- Tina Daunke
- Institute for Experimental Cancer Research, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Silje Beckinger
- Institute for Experimental Cancer Research, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sascha Rahn
- Biochemical Institute, Kiel University, Kiel, Germany
| | - Sandra Krüger
- Institute of Pathology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Steffen Heckl
- Institute of Pathology, University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine II, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Heiner Schäfer
- Institute for Experimental Cancer Research, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Daniela Wesch
- Institute of Immunology, Kiel University and University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Christian Pilarsky
- Translational Research Center, University Hospital Erlangen, Erlangen, Germany
| | - Markus Eckstein
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christoph Röcken
- Institute of Pathology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Anna Maxi Wandmacher
- Institute for Experimental Cancer Research, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine II, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Susanne Sebens
- Institute for Experimental Cancer Research, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
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Liu Z, Jiang X, Li S, Chen J, Jiang C, Wang K, Zhang C, Wang B. A disposable impedance-based sensor for in-line cell growth monitoring in CAR-T cell manufacturing. Bioelectrochemistry 2023; 152:108416. [PMID: 37023618 DOI: 10.1016/j.bioelechem.2023.108416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 04/08/2023]
Abstract
This paper presents the development of low-cost, disposable impedance-based sensors for real-time, in-line monitoring of suspension cell culture. The sensors consist of electrical discharge machining (EDM) cut aluminum electrodes and polydimethylsiloxane (PDMS) spacers, both of which are low-cost materials that can be safely disposed of. Our research demonstrates the capability of these low-cost sensors for in-line, non-invasive monitoring of suspension cell growth in cell manufacturing. We use a hybrid equivalent circuit model to extract key features/parameters from intertwined impedance signals, which are then fed to a novel physics-inspired (gray-box) model designed for α-relaxation. This model determines viable cell count (VCC), a critical quality attribute (CQA) in cell manufacturing. Predicted VCC trends are then compared with image-based cell count data to verify their accuracy.
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Affiliation(s)
- Zhaonan Liu
- Georgia Tech Manufacturing Institute, Georgia Institute of Technology, Atlanta 30332, United States; School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta 30332, United States
| | - Xuzhou Jiang
- Georgia Tech Manufacturing Institute, Georgia Institute of Technology, Atlanta 30332, United States
| | - Shuai Li
- Georgia Tech Manufacturing Institute, Georgia Institute of Technology, Atlanta 30332, United States
| | - Jialei Chen
- Georgia Tech Manufacturing Institute, Georgia Institute of Technology, Atlanta 30332, United States; H. Milton Stewart School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta 30332, United States
| | - Chen Jiang
- Georgia Tech Manufacturing Institute, Georgia Institute of Technology, Atlanta 30332, United States; School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta 30332, United States
| | - Kan Wang
- Georgia Tech Manufacturing Institute, Georgia Institute of Technology, Atlanta 30332, United States
| | - Chuck Zhang
- Georgia Tech Manufacturing Institute, Georgia Institute of Technology, Atlanta 30332, United States; H. Milton Stewart School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta 30332, United States.
| | - Ben Wang
- Georgia Tech Manufacturing Institute, Georgia Institute of Technology, Atlanta 30332, United States; School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta 30332, United States; H. Milton Stewart School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta 30332, United States
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3
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Xu ST, Yang C, Yan XP. Organic Mass Cytometry Discriminating Cycle Stages of Single Cells with Small Molecular Indicators. Anal Chem 2023; 95:2312-2320. [PMID: 36651064 DOI: 10.1021/acs.analchem.2c04165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cell cycle is a significant factor toward cellular heterogeneity, so cell cycle discrimination is a precise measurement on the top of single-cell analysis. Single-cell analysis based on organic mass spectrometry has received great attention for its unique ability to profile single-cell metabolome, but the influence of cell cycle on cellular metabolome heterogeneity has been overlooked until now due to the lack of a compatible cell cycle discrimination method. Here, we report a robust protocol based on the combination of three small molecular indicators, consisting of two small molecular labels (Hoechst and docetaxel) and one cellular endogenous compound [phosphocholine (34:1)], to discriminate single cells at different cycle stages in real time by organic mass cytometry. More than 6000 HeLa cells were acquired by an improved organic mass cytometry system to build a cell cycle differentiation model. The model successfully discriminated single HeLa cells, SCC7, and Hep G2 cells, at G0/G1, S, and G2/M stages with larger than 85% sensitivity and larger than 89% specificity. Along with cell cycle discrimination, obvious heterogeneity of amino acids, nucleotides, energy metabolic intermediates, and phospholipids was observed among single cells at different cycle stages by this protocol, further demonstrating the necessity of cell cycle discrimination for cellular metabolome heterogeneity research and the potential of more endogenous small molecular compounds for cell cycle discrimination.
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Affiliation(s)
- Shu-Ting Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Cheng Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiu-Ping Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China
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4
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Cao Y, Meng L, Cheng Y, Azhar M, Jiang X, Xing X, Bao J. Optimized protocol for isolation of germ cells from mouse testis by centrifugal elutriation. STAR Protoc 2022; 3:101540. [PMID: 35834386 PMCID: PMC9293666 DOI: 10.1016/j.xpro.2022.101540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/26/2022] [Accepted: 06/15/2022] [Indexed: 11/19/2022] Open
Abstract
Germline development is challenging to study due to the diversity of cell types in mammalian testis. Here, we present an optimized protocol, namely centrifugal elutriation, that allows the simultaneous isolation of mouse germ cells at different stages with high purity within ∼2 h. This approach exploits the JE-5.0 centrifugal elutriation system that fractionates cells based on differential sedimentation gravity. We herein provide the optimized parameters and procedures for isolation of elongating spermatids, round spermatids, and pachytene spermatocytes from adult mouse testes. For complete details on the use and execution of this protocol, please refer to Bao et al. (2018). Optimized protocol for efficient preparation of testicular single-cell suspension Rapid purification of three germ cell populations with high viability from mouse testes Easily scaled up and down depending on downstream applications
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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Affiliation(s)
- Yuzhu Cao
- The First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui 230001, China.
| | - Lan Meng
- The First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui 230001, China
| | - Yu Cheng
- The First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui 230001, China
| | - Muhammad Azhar
- The First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui 230001, China
| | - Xue Jiang
- The First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui 230001, China
| | - Xuemei Xing
- The First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui 230001, China
| | - Jianqiang Bao
- The First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui 230001, China.
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5
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Improving cell viability using counterflow centrifugal elutriation. Cytotherapy 2022; 24:650-658. [DOI: 10.1016/j.jcyt.2022.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/15/2022] [Accepted: 01/24/2022] [Indexed: 11/19/2022]
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Bordhan P, Razavi Bazaz S, Jin D, Ebrahimi Warkiani M. Advances and enabling technologies for phase-specific cell cycle synchronisation. LAB ON A CHIP 2022; 22:445-462. [PMID: 35076046 DOI: 10.1039/d1lc00724f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell cycle synchronisation is the process of isolating cell populations at specific phases of the cell cycle from heterogeneous, asynchronous cell cultures. The process has important implications in targeted gene-editing and drug efficacy of cells and in studying cell cycle events and regulatory mechanisms involved in the cell cycle progression of multiple cell species. Ideally, cell cycle synchrony techniques should be applicable for all cell types, maintain synchrony across multiple cell cycle events, maintain cell viability and be robust against metabolic and physiological perturbations. In this review, we categorize cell cycle synchronisation approaches and discuss their operational principles and performance efficiencies. We highlight the advances and technological development trends from conventional methods to the more recent microfluidics-based systems. Furthermore, we discuss the opportunities and challenges for implementing high throughput cell synchronisation and provide future perspectives on synchronisation platforms, specifically hybrid cell synchrony modalities, to allow the highest level of phase-specific synchrony possible with minimal alterations in diverse types of cell cultures.
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Affiliation(s)
- Pritam Bordhan
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Institute for Biomedical Materials & Devices, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Institute for Biomedical Materials & Devices, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
| | - Dayong Jin
- Institute for Biomedical Materials & Devices, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Institute for Biomedical Materials & Devices, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
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7
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Abstract
The cell cycle is the series of events that take place in a cell that drives it to divide and produce two new daughter cells. Through more than 100 years of efforts by scientists, we now have a much clearer picture of cell cycle progression and its regulation. The typical cell cycle in eukaryotes is composed of the G1, S, G2, and M phases. The M phase is further divided into prophase, prometaphase, metaphase, anaphase, telophase, and cytokinesis. Cell cycle progression is mediated by cyclin-dependent kinases (Cdks) and their regulatory cyclin subunits. However, the driving force of cell cycle progression is growth factor-initiated signaling pathways that controls the activity of various Cdk-cyclin complexes. Most cellular events, including DNA duplication, gene transcription, protein translation, and post-translational modification of proteins, occur in a cell-cycle-dependent manner. To understand these cellular events and their underlying molecular mechanisms, it is desirable to have a population of cells that are traversing the cell cycle synchronously. This can be achieved through a process called cell synchronization. Many methods have been developed to synchronize cells to the various phases of the cell cycle. These methods could be classified into two groups: synchronization methods using chemical inhibitors and synchronization methods without using chemical inhibitors. All these methods have their own merits and shortcomings.
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Affiliation(s)
- Zhixiang Wang
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada.
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8
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Tsubouchi T, Pereira CF. Reprogramming Stars #1: Genome Programming Through the Cell Cycle-An Interview with Dr. Tomomi Tsubouchi. Cell Reprogram 2021; 23:153-157. [PMID: 34165359 DOI: 10.1089/cell.2021.29039.tt] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Tomomi Tsubouchi
- Laboratory of Stem Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Carlos-Filipe Pereira
- Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
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9
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Otto L, Rahn S, Daunke T, Walter F, Winter E, Möller JL, Rose-John S, Wesch D, Schäfer H, Sebens S. Initiation of Pancreatic Cancer: The Interplay of Hyperglycemia and Macrophages Promotes the Acquisition of Malignancy-Associated Properties in Pancreatic Ductal Epithelial Cells. Int J Mol Sci 2021; 22:ijms22105086. [PMID: 34064969 PMCID: PMC8151031 DOI: 10.3390/ijms22105086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/26/2021] [Accepted: 05/08/2021] [Indexed: 01/02/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is still one of the most aggressive solid malignancies with a poor prognosis. Obesity and type 2 diabetes mellitus (T2DM) are two major risk factors linked to the development and progression of PDAC, both often characterized by high blood glucose levels. Macrophages represent the main immune cell population in PDAC contributing to PDAC development. It has already been shown that pancreatic ductal epithelial cells (PDEC) undergo epithelial–mesenchymal transition (EMT) when exposed to hyperglycemia or macrophages. Thus, this study aimed to investigate whether concomitant exposure to hyperglycemia and macrophages aggravates EMT-associated alterations in PDEC. Exposure to macrophages and elevated glucose levels (25 mM glucose) impacted gene expression of EMT inducers such as IL-6 and TNF-α as well as EMT transcription factors in benign (H6c7-pBp) and premalignant (H6c7-kras) PDEC. Most strikingly, exposure to hyperglycemic coculture with macrophages promoted downregulation of the epithelial marker E-cadherin, which was associated with an elevated migratory potential of PDEC. While blocking IL-6 activity by tocilizumab only partially reverted the EMT phenotype in H6c7-kras cells, neutralization of TNF-α by etanercept was able to clearly impair EMT-associated properties in premalignant PDEC. Altogether, the current study attributes a role to a T2DM-related hyperglycemic, inflammatory micromilieu in the acquisition of malignancy-associated alterations in premalignant PDEC, thus providing new insights on how metabolic diseases might promote PDAC initiation.
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Affiliation(s)
- Lilli Otto
- Institute for Experimental Cancer Research, Kiel University (CAU) and University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, 24105 Kiel, Germany; (L.O.); (T.D.); (F.W.); (E.W.); (H.S.)
| | - Sascha Rahn
- Institute of Biochemistry, Kiel University, 24118 Kiel, Germany; (S.R.); (S.R.-J.)
| | - Tina Daunke
- Institute for Experimental Cancer Research, Kiel University (CAU) and University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, 24105 Kiel, Germany; (L.O.); (T.D.); (F.W.); (E.W.); (H.S.)
| | - Frederik Walter
- Institute for Experimental Cancer Research, Kiel University (CAU) and University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, 24105 Kiel, Germany; (L.O.); (T.D.); (F.W.); (E.W.); (H.S.)
| | - Elsa Winter
- Institute for Experimental Cancer Research, Kiel University (CAU) and University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, 24105 Kiel, Germany; (L.O.); (T.D.); (F.W.); (E.W.); (H.S.)
| | - Julia Luisa Möller
- Department of Hematology and Oncology, University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, 24105 Kiel, Germany;
| | - Stefan Rose-John
- Institute of Biochemistry, Kiel University, 24118 Kiel, Germany; (S.R.); (S.R.-J.)
| | - Daniela Wesch
- Institute of Immunology, Kiel University and University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, 24105 Kiel, Germany;
| | - Heiner Schäfer
- Institute for Experimental Cancer Research, Kiel University (CAU) and University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, 24105 Kiel, Germany; (L.O.); (T.D.); (F.W.); (E.W.); (H.S.)
| | - Susanne Sebens
- Institute for Experimental Cancer Research, Kiel University (CAU) and University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, 24105 Kiel, Germany; (L.O.); (T.D.); (F.W.); (E.W.); (H.S.)
- Correspondence: ; Tel.: +49-431-500-30501
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Liu Y, Nan B, Niu J, Kapler GM, Gao S. An Optimized and Versatile Counter-Flow Centrifugal Elutriation Workflow to Obtain Synchronized Eukaryotic Cells. Front Cell Dev Biol 2021; 9:664418. [PMID: 33959616 PMCID: PMC8093812 DOI: 10.3389/fcell.2021.664418] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/23/2021] [Indexed: 11/21/2022] Open
Abstract
Cell synchronization is a powerful tool to understand cell cycle events and its regulatory mechanisms. Counter-flow centrifugal elutriation (CCE) is a more generally desirable method to synchronize cells because it does not significantly alter cell behavior and/or cell cycle progression, however, adjusting specific parameters in a cell type/equipment-dependent manner can be challenging. In this paper, we used the unicellular eukaryotic model organism, Tetrahymena thermophila as a testing system for optimizing CCE workflow. Firstly, flow cytometry conditions were identified that reduced nuclei adhesion and improved the assessment of cell cycle stage. We then systematically examined how to achieve the optimal conditions for three critical factors affecting the outcome of CCE, including loading flow rate, collection flow rate and collection volume. Using our optimized workflow, we obtained a large population of highly synchronous G1-phase Tetrahymena as measured by 5-ethynyl-2'-deoxyuridine (EdU) incorporation into nascent DNA strands, bulk DNA content changes by flow cytometry, and cell cycle progression by light microscopy. This detailed protocol can be easily adapted to synchronize other eukaryotic cells.
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Affiliation(s)
- Yongqiang Liu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Bei Nan
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Junhua Niu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Geoffrey M. Kapler
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, United States
| | - Shan Gao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
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Halsall JA, Andrews S, Krueger F, Rutledge CE, Ficz G, Reik W, Turner BM. Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle. Sci Rep 2021; 11:3009. [PMID: 33542322 PMCID: PMC7862352 DOI: 10.1038/s41598-021-82539-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023] Open
Abstract
Chromatin configuration influences gene expression in eukaryotes at multiple levels, from individual nucleosomes to chromatin domains several Mb long. Post-translational modifications (PTM) of core histones seem to be involved in chromatin structural transitions, but how remains unclear. To explore this, we used ChIP-seq and two cell types, HeLa and lymphoblastoid (LCL), to define how changes in chromatin packaging through the cell cycle influence the distributions of three transcription-associated histone modifications, H3K9ac, H3K4me3 and H3K27me3. We show that chromosome regions (bands) of 10-50 Mb, detectable by immunofluorescence microscopy of metaphase (M) chromosomes, are also present in G1 and G2. They comprise 1-5 Mb sub-bands that differ between HeLa and LCL but remain consistent through the cell cycle. The same sub-bands are defined by H3K9ac and H3K4me3, while H3K27me3 spreads more widely. We found little change between cell cycle phases, whether compared by 5 Kb rolling windows or when analysis was restricted to functional elements such as transcription start sites and topologically associating domains. Only a small number of genes showed cell-cycle related changes: at genes encoding proteins involved in mitosis, H3K9 became highly acetylated in G2M, possibly because of ongoing transcription. In conclusion, modified histone isoforms H3K9ac, H3K4me3 and H3K27me3 exhibit a characteristic genomic distribution at resolutions of 1 Mb and below that differs between HeLa and lymphoblastoid cells but remains remarkably consistent through the cell cycle. We suggest that this cell-type-specific chromosomal bar-code is part of a homeostatic mechanism by which cells retain their characteristic gene expression patterns, and hence their identity, through multiple mitoses.
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Affiliation(s)
- John A Halsall
- Chromatin and Gene Regulation Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Simon Andrews
- Bioinformatics, The Babraham Institute, Cambridge, UK
| | - Felix Krueger
- Bioinformatics, The Babraham Institute, Cambridge, UK
| | - Charlotte E Rutledge
- Chromatin and Gene Regulation Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Gabriella Ficz
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Bryan M Turner
- Chromatin and Gene Regulation Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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12
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Surani AA, Colombo SL, Barlow G, Foulds GA, Montiel-Duarte C. Optimizing Cell Synchronization Using Nocodazole or Double Thymidine Block. Methods Mol Biol 2021; 2329:111-121. [PMID: 34085219 DOI: 10.1007/978-1-0716-1538-6_9] [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] [Indexed: 12/15/2022]
Abstract
Cell synchronization is crucial when studying events that take place at specific points of the cell cycle. Several chemical agents can be used to achieve the cell culture synchronization but not all type of cells respond equally to a given concentration of these drugs. Here we describe a simple optimization method to select concentrations and timings for nocodazole or thymidine treatments using fluorescence staining. In addition, we provide detailed protocols to arrest an asynchronous culture of either suspension or adherent cells in G1/S or in G2/M.
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Affiliation(s)
- Arif A Surani
- The John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Sergio L Colombo
- Centre for Diabetes, Chronic Diseases and Ageing, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - George Barlow
- The John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Gemma A Foulds
- The John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Cristina Montiel-Duarte
- The John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK.
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Walter F, Winter E, Rahn S, Heidland J, Meier S, Struzek AM, Lettau M, Philipp LM, Beckinger S, Otto L, Möller JL, Helm O, Wesch D, Scherließ R, Sebens S. Chitosan nanoparticles as antigen vehicles to induce effective tumor specific T cell responses. PLoS One 2020; 15:e0239369. [PMID: 32997691 PMCID: PMC7526875 DOI: 10.1371/journal.pone.0239369] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/07/2020] [Indexed: 12/27/2022] Open
Abstract
Cancer vaccinations sensitize the immune system to recognize tumor-specific antigens de novo or boosting preexisting immune responses. Dendritic cells (DCs) are regarded as the most potent antigen presenting cells (APCs) for induction of (cancer) antigen-specific CD8+ T cell responses. Chitosan nanoparticles (CNPs) used as delivery vehicle have been shown to improve anti-tumor responses. This study aimed at exploring the potential of CNPs as antigen delivery system by assessing activation and expansion of antigen-specific CD8+ T cells by DCs and subsequent T cell-mediated lysis of pancreatic ductal adenocarcinoma (PDAC) cells. As model antigen the ovalbumin-derived peptide SIINFEKL was chosen. Using imaging cytometry, intracellular uptake of FITC-labelled CNPs of three different sizes and qualities (90/10, 90/20 and 90/50) was demonstrated in DCs and in pro- and anti-inflammatory macrophages to different extents. While larger particles (90/50) impaired survival of all APCs, small CNPs (90/10) were not toxic for DCs. Internalization of SIINFEKL-loaded but not empty 90/10-CNPs promoted a pro-inflammatory phenotype of DCs indicated by elevated expression of pro-inflammatory cytokines. Treatment of murine DC2.4 cells with SIINFEKL-loaded 90/10-CNPs led to a marked MHC-related presentation of SIINFEKL and enabled DC2.4 cells to potently activate SIINFEKL-specific CD8+ OT-1 T cells finally leading to effective lysis of the PDAC cell line Panc-OVA. Overall, our study supports the suitability of CNPs as antigen vehicle to induce potent anti-tumor immune responses by activation and expansion of tumor antigen-specific CD8+ T cells.
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Affiliation(s)
- Frederik Walter
- Institute for Experimental Cancer Research, Kiel University and University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
| | - Elsa Winter
- Institute for Experimental Cancer Research, Kiel University and University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
| | - Sascha Rahn
- Institute of Biochemistry, Kiel University, Kiel, Germany
| | - Judith Heidland
- Department of Pharmaceutics and Biopharmaceutics, Kiel University, Kiel, Germany
| | - Saskia Meier
- Department of Pharmaceutics and Biopharmaceutics, Kiel University, Kiel, Germany
| | - Anna-Maria Struzek
- Department of Pharmaceutics and Biopharmaceutics, Kiel University, Kiel, Germany
| | - Marcus Lettau
- Institute of Immunology, Kiel University and UKSH Campus Kiel, Kiel, Germany
| | - Lisa-Marie Philipp
- Institute for Experimental Cancer Research, Kiel University and University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
| | - Silje Beckinger
- Institute for Experimental Cancer Research, Kiel University and University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
| | - Lilli Otto
- Institute for Experimental Cancer Research, Kiel University and University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
| | - Julia Luisa Möller
- Department of Hematology and Oncology, University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
| | - Ole Helm
- Institute for Experimental Cancer Research, Kiel University and University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
| | - Daniela Wesch
- Institute of Immunology, Kiel University and UKSH Campus Kiel, Kiel, Germany
| | - Regina Scherließ
- Department of Pharmaceutics and Biopharmaceutics, Kiel University, Kiel, Germany
| | - Susanne Sebens
- Institute for Experimental Cancer Research, Kiel University and University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
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14
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Goepp M, Le Guennec D, Rossary A, Vasson MP. Cell Cycle Synchronization of the Murine EO771 Cell Line Using Double Thymidine Block Treatment. Bioessays 2020; 42:e1900116. [PMID: 32643186 DOI: 10.1002/bies.201900116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 05/14/2020] [Indexed: 12/16/2022]
Abstract
This study shows that double thymidine block treatment efficiently arrests the EO771 cells in the S-phase without altering cell growth or survival. A long-term analysis of cell behavior, using 5(6)-carboxyfluorescein diacetate N-succinimidyl ester (CFSE) staining, show synchronization to be stable and consistent over time. The EO771 cell line is a medullary breast-adenocarcinoma cell line isolated from a spontaneous murine mammary tumor, and can be used to generate murine tumor implantation models. Different biological (serum or amino acid deprivation), physical (elutriation, mitotic shake-off), or chemical (colchicine, nocodazole, thymidine) treatments are widely used for cell synchronization. Of the different methods tested, the double thymidine block is the most efficient for synchronization of murine EO771 cells if a large quantity of highly synchronized cells is recommended to study functional and biochemical events occurring in specific points of cell cycle progression.
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Affiliation(s)
- Marie Goepp
- Université Clermont Auvergne, UMR 1019 INRAE-UCA, UNH (Human Nutrition Unity), ECREIN Team, Clermont-Ferrand, F-63000, France
| | - Delphine Le Guennec
- Université Clermont Auvergne, UMR 1019 INRAE-UCA, UNH (Human Nutrition Unity), ECREIN Team, Clermont-Ferrand, F-63000, France
| | - Adrien Rossary
- Université Clermont Auvergne, UMR 1019 INRAE-UCA, UNH (Human Nutrition Unity), ECREIN Team, Clermont-Ferrand, F-63000, France
| | - Marie-Paule Vasson
- Université Clermont Auvergne, UMR 1019 INRAE-UCA, UNH (Human Nutrition Unity), ECREIN Team, Clermont-Ferrand, F-63000, France.,Unité de Nutrition, CHU, Centre Jean Perrin, CLARA, Clermont-Ferrand, F-63000, France
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15
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Blank HM, Papoulas O, Maitra N, Garge R, Kennedy BK, Schilling B, Marcotte EM, Polymenis M. Abundances of transcripts, proteins, and metabolites in the cell cycle of budding yeast reveal coordinate control of lipid metabolism. Mol Biol Cell 2020; 31:1069-1084. [PMID: 32129706 PMCID: PMC7346729 DOI: 10.1091/mbc.e19-12-0708] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Establishing the pattern of abundance of molecules of interest during cell division has been a long-standing goal of cell cycle studies. Here, for the first time in any system, we present experiment-matched datasets of the levels of RNAs, proteins, metabolites, and lipids from unarrested, growing, and synchronously dividing yeast cells. Overall, transcript and protein levels were correlated, but specific processes that appeared to change at the RNA level (e.g., ribosome biogenesis) did not do so at the protein level, and vice versa. We also found no significant changes in codon usage or the ribosome content during the cell cycle. We describe an unexpected mitotic peak in the abundance of ergosterol and thiamine biosynthesis enzymes. Although the levels of several metabolites changed in the cell cycle, by far the most significant changes were in the lipid repertoire, with phospholipids and triglycerides peaking strongly late in the cell cycle. Our findings provide an integrated view of the abundance of biomolecules in the eukaryotic cell cycle and point to a coordinate mitotic control of lipid metabolism.
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Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Ophelia Papoulas
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Nairita Maitra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Riddhiman Garge
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Brian K Kennedy
- Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596.,Centre for Healthy Ageing, National University of Singapore, National University Health System, Singapore 117609.,Buck Institute for Research on Aging, Novato, CA 94945
| | | | - Edward M Marcotte
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
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16
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Möller J, Korte K, Pörtner R, Zeng AP, Jandt U. Model-based identification of cell-cycle-dependent metabolism and putative autocrine effects in antibody producing CHO cell culture. Biotechnol Bioeng 2018; 115:2996-3008. [DOI: 10.1002/bit.26828] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/20/2018] [Accepted: 08/30/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Johannes Möller
- Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering; Hamburg Germany
| | - Katrin Korte
- Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering; Hamburg Germany
| | - Ralf Pörtner
- Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering; Hamburg Germany
| | - An-Ping Zeng
- Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering; Hamburg Germany
| | - Uwe Jandt
- Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering; Hamburg Germany
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17
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Dai L, Zhao T, Bisteau X, Sun W, Prabhu N, Lim YT, Sobota RM, Kaldis P, Nordlund P. Modulation of Protein-Interaction States through the Cell Cycle. Cell 2018; 173:1481-1494.e13. [PMID: 29706543 DOI: 10.1016/j.cell.2018.03.065] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/25/2018] [Accepted: 03/26/2018] [Indexed: 11/25/2022]
Abstract
Global profiling of protein expression through the cell cycle has revealed subsets of periodically expressed proteins. However, expression levels alone only give a partial view of the biochemical processes determining cellular events. Using a proteome-wide implementation of the cellular thermal shift assay (CETSA) to study specific cell-cycle phases, we uncover changes of interaction states for more than 750 proteins during the cell cycle. Notably, many protein complexes are modulated in specific cell-cycle phases, reflecting their roles in processes such as DNA replication, chromatin remodeling, transcription, translation, and disintegration of the nuclear envelope. Surprisingly, only small differences in the interaction states were seen between the G1 and the G2 phase, suggesting similar hardwiring of biochemical processes in these two phases. The present work reveals novel molecular details of the cell cycle and establishes proteome-wide CETSA as a new strategy to study modulation of protein-interaction states in intact cells.
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Affiliation(s)
- Lingyun Dai
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Tianyun Zhao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Xavier Bisteau
- Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Wendi Sun
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yan Ting Lim
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Institute of Medical Biology, A(∗)STAR, Singapore 138648, Singapore
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Biochemistry, National University of Singapore, Singapore 117597, Singapore
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, 17177 Stockholm, Sweden.
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18
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Abstract
In early S phase the newly replicated DNA is folded back to increasingly compact structures. The process of chromatin condensation inside the nucleus starts with the formation of a micronucleus observed in five established cell lines (K562, CHO, Indian muntjac, murine preB and SCC). Supercoiling of chromatin generates a polarized end-plate region extruded from the nucleus. The extruded chromatin is turned around itself forming the head portion (micronucleus) visible by fluorescence microscopy until the middle of S phase when chromatin structures are succeeded by distinguishable early forms of chromosomes. The generation of micronuclei upon apoptotic treatment was achieved by the methotrexate (MTX) treatment of cells. A close correlation was found between the frequency of micronucleus and MTX concentration, with low frequency at low (0.1 µM) and increasingly higher frequency between 1 and 100 µM concentrations. Characteristic deformation and shrinkage of nuclei indicated apoptosis. High MTX concentration (100 µM) caused the enlargement and necrotic disruption of nuclei. Inhibition of DNA synthesis during replicative DNA synthesis by biotinylated nucleotide prevented the formation of metaphase chromosomes and elevated the frequency of early intermediates of chromosome condensation including micronucleus formation. Based on these observations the micronucleus is regarded as: (a) a regularly occuring element of early chromatin condensation and (b) a typical sign of nuclear membrane damage under toxic conditions. Explanation is given why the micronucleus is hidden in nuclei under normal chromatin condensation and why chromatin motifs including micronuclei become visible upon cellular damage.
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19
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Abstract
When removed from the follicles, during the 44 h process of in vitro maturation (IVM) fully grown porcine oocytes resume meiosis spontaneously from the late diplotene stage of the first meiotic prophase and proceed to the metaphase-II (MII) stage at which they remain arrested until fertilization. However, the spontaneous resumption may start at various times causing heterogeneity in the nuclear stage and also in cytoplasmic characteristics within a population. Those oocytes that reach the MII stage earlier than others undergo an aging process which is detrimental for further embryo development. The synchronization of nuclear progression of porcine oocytes can be achieved by a transient inhibition of meiotic resumption during the first 20-22 h of IVM by the elevation of intracellular levels of cyclic adenosine monophosphate (cAMP) using the cellular membrane-permeable analog of cAMP, dibutyryl cyclic AMP. A simple and efficient protocol for such treatment is described below.
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Affiliation(s)
- Tamás Somfai
- National Agriculture and Food Research Organization (NARO), Institute of Livestock and Grassland Science, 2 Ikenodai, Tsukuba, Ibaraki, 305-0901, Japan.
| | - Yuji Hirao
- National Agriculture and Food Research Organization (NARO), Institute of Livestock and Grassland Science, 2 Ikenodai, Tsukuba, Ibaraki, 305-0901, Japan
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20
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Abstract
The widespread interest in cell synchronization is maintained by the studies of control mechanism involved in cell cycle regulation. During the synchronization distinct subpopulations of cells are obtained representing different stages of the cell cycle. These subpopulations are then used to study regulatory mechanisms of the cycle at the level of macromolecular biosynthesis (DNA synthesis, gene expression, protein synthesis), protein phosphorylation, development of new drugs, etc. Although several synchronization methods have been described, it is of general interest that scientists get a compilation and an updated view of these synchronization techniques. This introductory chapter summarizes: (1) the basic concepts and principal criteria of cell cycle synchronizations, (2) the most frequently used synchronization methods, such as physical fractionation (flow cytometry, dielectrophoresis, cytofluorometric purification), chemical blockade, (3) synchronization of embryonic cells, (4) synchronization at low temperature, (5) comparison of cell synchrony techniques, (6) synchronization of unicellular organisms, and (7) the effect of synchronization on transfection.
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21
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Aeby E, Ahmed W, Redon S, Simanis V, Lingner J. Peroxiredoxin 1 Protects Telomeres from Oxidative Damage and Preserves Telomeric DNA for Extension by Telomerase. Cell Rep 2017; 17:3107-3114. [PMID: 28009281 DOI: 10.1016/j.celrep.2016.11.071] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/04/2016] [Accepted: 11/22/2016] [Indexed: 01/19/2023] Open
Abstract
Oxidative damage of telomeres can promote cancer, cardiac failure, and muscular dystrophy. Specific mechanisms protecting telomeres from oxidative damage have not been described. We analyzed telomeric chromatin composition during the cell cycle and show that the antioxidant enzyme peroxiredoxin 1 (PRDX1) is enriched at telomeres during S phase. Deletion of the PRDX1 gene leads to damage of telomeric DNA upon oxidative stress, revealing a protective function of PRDX1 against oxidative damage at telomeres. We also show that the oxidized nucleotide 8-oxo-2'deoxyguanosine-5'-triphosphate (8oxodGTP) causes premature chain termination when incorporated by telomerase and that some DNA substrates terminating in 8oxoG prevent extension by telomerase. Thus, PRDX1 safeguards telomeres from oxygen radicals to counteract telomere damage and preserve telomeric DNA for elongation by telomerase.
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Affiliation(s)
- Eric Aeby
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Wareed Ahmed
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sophie Redon
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Viesturs Simanis
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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22
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Delgado M, Kothari A, Hittelman WN, Chambers TC. Preparation of Primary Acute Lymphoblastic Leukemia Cells in Different Cell Cycle Phases by Centrifugal Elutriation. J Vis Exp 2017. [PMID: 29155772 DOI: 10.3791/56418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The ability to synchronize cells has been central to advancing our understanding of cell cycle regulation. Common techniques employed include serum deprivation; chemicals which arrest cells at different cell cycle phases; or the use of mitotic shake-off which exploits their reduced adherence. However, all of these have disadvantages. For example, serum starvation works well for normal cells but less well for tumor cells with compromised cell cycle checkpoints due to oncogene activation or tumor suppressor loss. Similarly, chemically-treated cell populations can harbor drug-induced damage and show stress-related alterations. A technique which circumvents these problems is counterflow centrifugal elutriation (CCE), where cells are subjected to two opposing forces, centrifugal force and fluid velocity, which results in the separation of cells on the basis of size and density. Since cells advancing through the cycle typically enlarge, CCE can be used to separate cells into different cell cycle phases. Here we apply this technique to primary acute lymphoblastic leukemia cells. Under optimal conditions, an essentially pure population of cells in G1 phase and a highly enriched population of cells in G2/M phases can be obtained in excellent yield. These cell populations are ideally suited for studying cell cycle-dependent mechanisms of action of anticancer drugs and for other applications. We also show how modifications to the standard procedure can result in suboptimal performance and discuss the limitations of the technique. The detailed methodology presented should facilitate application and exploration of the technique to other types of cells.
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Affiliation(s)
- Magdalena Delgado
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences
| | - Anisha Kothari
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences
| | - Walter N Hittelman
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center
| | - Timothy C Chambers
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences;
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Piao L, Park H, Jo CH. Theoretical prediction and validation of cell recovery rates in preparing platelet-rich plasma through a centrifugation. PLoS One 2017; 12:e0187509. [PMID: 29095890 PMCID: PMC5667898 DOI: 10.1371/journal.pone.0187509] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 10/22/2017] [Indexed: 12/20/2022] Open
Abstract
In the present study, we propose a theoretical framework to predict the recovery rates of platelets and white blood cells in the process of centrifugal separation of whole blood contained in a tube for the preparation of platelet-rich plasma. Compared to previous efforts to optimize or standardize the protocols of centrifugation, we try to further the physical background (i.e., based on the multiphase flow phenomena) of analysis to develop a universal approach that can be applied to widely different conditions. That is, one-dimensional quasi-linear partial differential equation to describe the centrifugal sedimentation of dispersed phase (red and white blood cells) in continuous phase (plasma) is derived based on the kinematic-wave theory. With the information of whole blood volume and tube geometry considered, it is possible to determine the positions of interfaces between supernatant/suspension and suspension/sediment, i.e., the particle concentration gradient in a tube, for a wide range of centrifugation parameters (time and acceleration). While establishing a theory to predict the recovery rates of the platelet and white blood cell from the pre-determined interface positions, we also propose a new correlation model between the recovery rates of plasma and platelets, which is found to be a function of the whole blood volume, centrifugal time and acceleration, and tube geometry. The present predictions for optimal condition show good agreements with available human clinical data, obtained from different conditions, indicating the universal applicability of our method. Furthermore, the dependence of recovery rates on centrifugal conditions reveals that there exist a different critical acceleration and time for the maximum recovery rate of platelets and white blood cells, respectively. The other parameters such as hematocrit, whole blood volume and tube geometry are also found to strongly affect the maximum recovery rates of blood cells, and finally, as a strategy for increasing the efficiency, we suggest to dilute the whole blood, increase the whole blood volume with a tube geometry fixed.
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Affiliation(s)
- Linfeng Piao
- Department of Mechanical & Aerospace Enginnering, Seoul National University, Seoul, Korea
| | - Hyungmin Park
- Department of Mechanical & Aerospace Enginnering, Seoul National University, Seoul, Korea
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea
| | - Chris Hyunchul Jo
- Department of Orthopedic Surgery, Seoul Metropolitan Government–Seoul National University Boramae Medical Center, Seoul National University College of Medicine, Seoul, Korea
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The macrophage marker translocator protein (TSPO) is down-regulated on pro-inflammatory 'M1' human macrophages. PLoS One 2017; 12:e0185767. [PMID: 28968465 PMCID: PMC5624624 DOI: 10.1371/journal.pone.0185767] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/19/2017] [Indexed: 12/14/2022] Open
Abstract
The translocator protein (TSPO) is a mitochondrial membrane protein, of as yet uncertain function. Its purported high expression on activated macrophages, has lent utility to TSPO targeted molecular imaging in the form of positron emission tomography (PET), as a means to detect and quantify inflammation in vivo. However, existing literature regarding TSPO expression on human activated macrophages is lacking, mostly deriving from brain tissue studies, including studies of brain malignancy, and inflammatory diseases such as multiple sclerosis. Here, we utilized three human sources of monocyte derived macrophages (MDM), from THP-1 monocytes, healthy peripheral blood monocytes and synovial fluid monocytes from patients with rheumatoid arthritis, to undertake a detailed investigation of TSPO expression in activated macrophages. In this work, we demonstrate a consistent down-regulation of TSPO mRNA and protein in macrophages activated to a pro-inflammatory, or ‘M1’ phenotype. Conversely, stimulation of macrophages to an M2 phenotype with IL-4, dexamethasone or TGF-β1 did not alter TSPO expression, regardless of MDM source. The reasons for this are uncertain, but our study findings add some supporting evidence for recent investigations concluding that TSPO may be involved in negative regulation of inflammatory responses in macrophages.
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25
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Drug-Free Approach To Study the Unusual Cell Cycle of Giardia intestinalis. mSphere 2017; 2:mSphere00384-16. [PMID: 28959734 PMCID: PMC5607323 DOI: 10.1128/msphere.00384-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 08/21/2017] [Indexed: 11/20/2022] Open
Abstract
Giardia intestinalis is a protozoan parasite that causes giardiasis, a form of severe and infectious diarrhea. Despite the importance of the cell cycle in the control of proliferation and differentiation during a giardia infection, it has been difficult to study this process due to the absence of a synchronization procedure that would not induce cellular damage resulting in artifacts. We utilized counterflow centrifugal elutriation (CCE), a size-based separation technique, to successfully obtain fractions of giardia cultures enriched in G1, S, and G2. Unlike drug-induced synchronization of giardia cultures, CCE did not induce double-stranded DNA damage or endoreplication. We observed increases in the appearance and size of the median body in the cells from elutriation fractions corresponding to the progression of the cell cycle from early G1 to late G2. Consequently, CCE could be used to examine the dynamics of the median body and other structures and organelles in the giardia cell cycle. For the cell cycle gene expression studies, the actin-related gene was identified by the program geNorm as the most suitable normalizer for reverse transcription-quantitative PCR (RT-qPCR) analysis of the CCE samples. Ten of 11 suspected cell cycle-regulated genes in the CCE fractions have expression profiles in giardia that resemble those of higher eukaryotes. However, the RNA levels of these genes during the cell cycle differ less than 4-fold to 5-fold, which might indicate that large changes in gene expression are not required by giardia to regulate the cell cycle. IMPORTANCE Giardias are among the most commonly reported intestinal protozoa in the world, with infections seen in humans and over 40 species of animals. The life cycle of giardia alternates between the motile trophozoite and the infectious cyst. The regulation of the cell cycle controls the proliferation of giardia trophozoites during an active infection and contains the restriction point for the differentiation of trophozoite to cyst. Here, we developed counterflow centrifugal elutriation as a drug-free method to obtain fractions of giardia cultures enriched in cells from the G1, S, and G2 stages of the cell cycle. Analysis of these fractions showed that the cells do not show side effects associated with the drugs used for synchronization of giardia cultures. Therefore, counterflow centrifugal elutriation would advance studies on key regulatory events during the giardia cell cycle and identify potential drug targets to block giardia proliferation and transmission.
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26
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Owen DR, Narayan N, Wells L, Healy L, Smyth E, Rabiner EA, Galloway D, Williams JB, Lehr J, Mandhair H, Peferoen LA, Taylor PC, Amor S, Antel JP, Matthews PM, Moore CS. Pro-inflammatory activation of primary microglia and macrophages increases 18 kDa translocator protein expression in rodents but not humans. J Cereb Blood Flow Metab 2017; 37:2679-2690. [PMID: 28530125 PMCID: PMC5536262 DOI: 10.1177/0271678x17710182] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The 18kDa Translocator Protein (TSPO) is the most commonly used tissue-specific marker of inflammation in positron emission tomography (PET) studies. It is expressed in myeloid cells such as microglia and macrophages, and in rodent myeloid cells expression increases with cellular activation. We assessed the effect of myeloid cell activation on TSPO gene expression in both primary human and rodent microglia and macrophages in vitro, and also measured TSPO radioligand binding with 3H-PBR28 in primary human macrophages. As observed previously, we found that TSPO expression increases (∼9-fold) in rodent-derived macrophages and microglia upon pro-inflammatory stimulation. However, TSPO expression does not increase with classical pro-inflammatory activation in primary human microglia (fold change 0.85 [95% CI 0.58-1.12], p = 0.47). In contrast, pro-inflammatory activation of human monocyte-derived macrophages is associated with a reduction of both TSPO gene expression (fold change 0.60 [95% CI 0.45-0.74], p = 0.02) and TSPO binding site abundance (fold change 0.61 [95% CI 0.49-0.73], p < 0.0001). These findings have important implications for understanding the biology of TSPO in activated macrophages and microglia in humans. They are also clinically relevant for the interpretation of PET studies using TSPO targeting radioligands, as they suggest changes in TSPO expression may reflect microglial and macrophage density rather than activation phenotype.
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Affiliation(s)
- David R Owen
- 1 Division of Brain Sciences, Department of Medicine Hammersmith Hospital, Imperial College London, London, UK
| | - Nehal Narayan
- 2 Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Lisa Wells
- 3 Imanova Centre for Imaging Science, Hammersmith Hospital, London, UK
| | - Luke Healy
- 4 Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Erica Smyth
- 3 Imanova Centre for Imaging Science, Hammersmith Hospital, London, UK
| | - Eugenii A Rabiner
- 3 Imanova Centre for Imaging Science, Hammersmith Hospital, London, UK.,5 Centre for Neuroimaging Sciences, King's College, London, UK
| | - Dylan Galloway
- 6 Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland
| | - John B Williams
- 6 Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland
| | - Joshua Lehr
- 6 Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland
| | - Harpreet Mandhair
- 2 Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Laura An Peferoen
- 7 Pathology Department, VU Medical Centre, VU University of Amsterdam, The Netherlands
| | - Peter C Taylor
- 2 Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Sandra Amor
- 7 Pathology Department, VU Medical Centre, VU University of Amsterdam, The Netherlands.,8 Neuroimmunology Unit, Blizard Institute, Barts and the London School of medicine & Dentistry Queen Mary University of London, UK
| | - Jack P Antel
- 4 Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Paul M Matthews
- 1 Division of Brain Sciences, Department of Medicine Hammersmith Hospital, Imperial College London, London, UK.,9 UK Dementia Research Institute, Imperial College London, London, UK
| | - Craig S Moore
- 6 Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland
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Ribosome profiling the cell cycle: lessons and challenges. Curr Genet 2017; 63:959-964. [PMID: 28451847 DOI: 10.1007/s00294-017-0698-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 04/14/2017] [Accepted: 04/20/2017] [Indexed: 12/31/2022]
Abstract
Understanding the causes and consequences of dynamic changes in the abundance and activity of cellular components during cell division is what most cell cycle studies are about. Here we focus on control of gene expression in the cell cycle at the level of translation. The advent of deep sequencing methodologies led to technologies that quantify the levels of all mRNAs that are bound by ribosomes and engaged in translation in the cell (Ingolia et al. Science 324:218-223, 2009). This approach has been applied recently to synchronous cell populations to find transcripts under translational control at different cell cycle phases (Blank et al. EMBO J 36:487-502, 2017; Stumpf et al. Mol Cell 52:574-582, 2013; Tanenbaum et al. Elife 4:e07957, 2015). These studies revealed new biology, but they also have limitations, pointing to challenges that need to be addressed in the future.
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Nagy G, Tanczos B, Fidrus E, Talas L, Banfalvi G. Chemically Induced Cell Cycle Arrest in Perfusion Cell Culture. Methods Mol Biol 2017; 1524:161-176. [PMID: 27815902 DOI: 10.1007/978-1-4939-6603-5_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In contrast to most present methods, continuous imaging of live cells would require full automation in each processing step. As an integrated system that would meet all requirements does not exist, we have established a long-term scanning-perfusion platform that: (a) replaces old medium with fresh one, (b) bypasses physical contact with the cell culture during continuous cell growth, (c) provides uninterrupted photomicrography of single cells, and (d) secures near physiological conditions and sterility up to several weeks. The system was validated by synchronizing cells using serum starvation and butyrate-induced cell cycle arrest of HaCaT cells.
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Affiliation(s)
- Gabor Nagy
- Department of Biotechnology and Microbiology, University of Debrecen, 1 Egyetem Square, Debrecen, 4010, Hungary
| | - Bence Tanczos
- Department of Biotechnology and Microbiology, University of Debrecen, 1 Egyetem Square, Debrecen, 4010, Hungary
| | - Eszter Fidrus
- Department of Biotechnology and Microbiology, University of Debrecen, 1 Egyetem Square, Debrecen, 4010, Hungary
| | - Laszlo Talas
- Department of Biotechnology and Microbiology, University of Debrecen, 1 Egyetem Square, Debrecen, 4010, Hungary
| | - Gaspar Banfalvi
- Department of Biotechnology and Microbiology, University of Debrecen, 1 Egyetem Square, Debrecen, 4010, Hungary.
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Abstract
Synchronized populations of large numbers of cells can be obtained by centrifugal elutriation on the basis of sedimentation properties of small round particles, with minimal perturbation of cellular functions. The physical characteristics of cell size and sedimentation velocity are operative in the technique of centrifugal elutriation also known as counterstreaming centrifugation. The elutriator is an advanced device for increasing the sedimentation rate to yield enhanced resolution of cell separation. A random population of cells is introduced into the elutriation chamber of an elutriator rotor running in a specially designed centrifuge. By increasing step-by-step the flow rate of the elutriation fluid, successive populations of relatively homogeneous cell size can be removed from the elutriation chamber and used as synchronized subpopulations. For cell synchronization by centrifugal elutriation, early log S phase cell populations are most suitable where most of the cells are in G1 and S phase (>80 %). Apoptotic cells can be found in the early elutriation fractions belonging to the sub-Go window. Protocols for the synchronization of nuclei of murine pre-B cells and high-resolution centrifugal elutriation of CHO cells are given. The verification of purity and cell cycle positions of cells in elutriated fractions includes the measurement of DNA synthesis by [3H]-thymidine incorporation and DNA content by propidium iodide flow cytometry.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Biotechnology and Microbiology, University of Debrecen, 1 Egyetem Square, Debrecen, 4010, Hungary.
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Abstract
Understanding cell growth and cell division involves the study of regulatory events that occur in a cell cycle phase-dependent manner. Studies analyzing cell cycle regulatory mechanisms and cell cycle progression invariably require synchronization of cell populations at specific cell cycle stages. Several methods have been established to synchronize cells, including serum deprivation, contact inhibition, centrifugal elutriation, and drug-dependent synchronization. Despite potential adverse cellular consequences of synchronizing cells by pharmacological agents, drug-dependent methods can be advantageous when studying later cell cycle events to ensure specific enrichment at selected mitotic stages. This chapter describes protocols used in our laboratory for isolating mitotic mammalian cells in a large-scale manner. In particular, we discuss the technical aspects of adherent or suspension cell isolation, the methods necessary to enrich cells at different mitotic stages and the optimized culture conditions.
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Affiliation(s)
- Kalyan Dulla
- Department of Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Molecular Diagnostics, Philips Corporate Technologies, AE Eindhoven, The Netherlands
| | - Anna Santamaria Margalef
- Cell Cycle and Cancer, Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR) - UAB, Barcelona, 08035, Spain.
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Abstract
HeLa is one of the oldest and most commonly used cell lines in biomedical research. Owing to the ease of which they can be effectively synchronized by various methods, HeLa cells have been used extensively for studying the cell cycle. Here, we describe several protocols for synchronizing HeLa cells from different phases of the cell cycle, including G1 phase using the HMG-CoA reductase inhibitor lovastatin, S phase with a double thymidine block procedure, and G2 phase with the CDK1 inhibitor RO-3306. Cells can also be enriched in mitosis using nocodazole and mechanical shake-off. Releasing the cells from these blocks enables researchers to follow gene expression and other events through the cell cycle. We also describe several protocols, including flow cytometry, BrdU labeling, immunoblotting, and time-lapse microscopy, for validating the synchrony of the cells and monitoring the progression of the cell cycle.
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Affiliation(s)
- Hoi Tang Ma
- Division of Life Science, Center for Cancer Research and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Randy Y C Poon
- Division of Life Science, Center for Cancer Research and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
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Halicka D, Zhao H, Li J, Garcia J, Podhorecka M, Darzynkiewicz Z. DNA Damage Response Resulting from Replication Stress Induced by Synchronization of Cells by Inhibitors of DNA Replication: Analysis by Flow Cytometry. Methods Mol Biol 2017; 1524:107-119. [PMID: 27815899 DOI: 10.1007/978-1-4939-6603-5_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cell synchronization is often achieved by transient inhibition of DNA replication. When cultured in the presence of such inhibitors as hydroxyurea, aphidicolin or excess of thymidine the cells that become arrested at the entrance to S-phase upon release from the block initiate progression through S then G2 and M. However, exposure to these inhibitors at concentrations commonly used to synchronize cells leads to activation of ATR and ATM protein kinases as well as phosphorylation of Ser139 of histone H2AX. This observation of DNA damage signaling implies that synchronization of cells by these inhibitors is inducing replication stress. Thus, a caution should be exercised while interpreting data obtained with use of cells synchronized this way since they do not represent unperturbed cell populations in a natural metabolic state. This chapter critically outlines virtues and vices of most cell synchronization methods. It also presents the protocol describing an assessment of phosphorylation of Ser139 on H2AX and activation of ATM in cells treated with aphidicolin, as a demonstrative of one of several DNA replication inhibitors that are being used for cell synchronization. Phosphorylation of Ser139H2AX and Ser1981ATM in individual cells is detected immunocytochemically with phospho-specific Abs and intensity of immunofluorescence is measured by flow cytometry. Concurrent measurement of cellular DNA content followed by multiparameter analysis allows one to correlate the extent of phosphorylation of these proteins in response to aphidicolin with the cell cycle phase.
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Affiliation(s)
- Dorota Halicka
- Department of Pathology, Brander Cancer Research Institute, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY, 10595, USA
| | - Hong Zhao
- Department of Pathology, Brander Cancer Research Institute, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY, 10595, USA
| | - Jiangwei Li
- Department of Pathology, Brander Cancer Research Institute, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY, 10595, USA
| | - Jorge Garcia
- Department of Pathology, Brander Cancer Research Institute, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY, 10595, USA
| | - Monika Podhorecka
- Department of Hemato-Oncology and Bone Marrow Transplantation, Medical University, Lublin, Poland
| | - Zbigniew Darzynkiewicz
- Department of Pathology, Brander Cancer Research Institute, New York Medical College, 40 Sunshine Cottage Road, Valhalla, NY, 10595, USA.
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Affiliation(s)
- Ralf Pörtner
- Hamburg University of Technology; Institute of Bioprocess and Biosystems Engineering; Denickestr. 15 D21071 Hamburg Germany
| | - Uwe Jandt
- Hamburg University of Technology; Institute of Bioprocess and Biosystems Engineering; Denickestr. 15 D21071 Hamburg Germany
| | - An-Ping Zeng
- Hamburg University of Technology; Institute of Bioprocess and Biosystems Engineering; Denickestr. 15 D21071 Hamburg Germany
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Natisvili T, Yandim C, Silva R, Emanuelli G, Krueger F, Nageshwaran S, Festenstein R. Transcriptional Activation of Pericentromeric Satellite Repeats and Disruption of Centromeric Clustering upon Proteasome Inhibition. PLoS One 2016; 11:e0165873. [PMID: 27806100 PMCID: PMC5091837 DOI: 10.1371/journal.pone.0165873] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/19/2016] [Indexed: 12/27/2022] Open
Abstract
Heterochromatinisation of pericentromeres, which in mice consist of arrays of major satellite repeats, are important for centromere formation and maintenance of genome stability. The dysregulation of this process has been linked to genomic stress and various cancers. Here we show in mice that the proteasome binds to major satellite repeats and proteasome inhibition by MG132 results in their transcriptional de-repression; this de-repression is independent of cell-cycle perturbation. The transcriptional activation of major satellite repeats upon proteasome inhibition is accompanied by delocalisation of heterochromatin protein 1 alpha (HP1α) from chromocentres, without detectable change in the levels of histone H3K9me3, H3K4me3, H3K36me3 and H3 acetylation on the major satellite repeats. Moreover, inhibition of the proteasome was found to increase the number of chromocentres per cell, reflecting destabilisation of the chromocentre structures. Our findings suggest that the proteasome plays a role in maintaining heterochromatin integrity of pericentromeres.
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Affiliation(s)
- Theona Natisvili
- Gene Control Mechanisms and Disease Group, Department of Medicine, Division of Brain Sciences and MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Cihangir Yandim
- Gene Control Mechanisms and Disease Group, Department of Medicine, Division of Brain Sciences and MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Raquel Silva
- Gene Control Mechanisms and Disease Group, Department of Medicine, Division of Brain Sciences and MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Giulia Emanuelli
- Gene Control Mechanisms and Disease Group, Department of Medicine, Division of Brain Sciences and MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge, United Kingdom
| | - Sathiji Nageshwaran
- Gene Control Mechanisms and Disease Group, Department of Medicine, Division of Brain Sciences and MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Richard Festenstein
- Gene Control Mechanisms and Disease Group, Department of Medicine, Division of Brain Sciences and MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, London, United Kingdom
- * E-mail:
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Bosshart H. Supra-therapeutic plasma concentrations of haloperidol induce moderate inhibition of lipopolysaccharide-induced interleukin-8 release in human monocytes. ANNALS OF TRANSLATIONAL MEDICINE 2016; 4:396. [PMID: 27867948 DOI: 10.21037/atm.2016.10.56] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND The clinical use of antipsychotics and mood-stabilizing drugs with proven efficacy is largely determined by the occurrence of treatment-emergent adverse events and routine clinical chemistry and haematology data, which together define the safety and tolerability profile of these psychopharmaceuticals. Whereas the effects of mood-stabilizing drugs on functional properties of blood cells have been poorly investigated, the effects of antipsychotics have received more attention. Such studies have yielded conflicting results. This study examined the effects of the mood-stabilizing drugs carbamazepine and valproic acid and of the antipsychotic drugs olanzapine, risperidone and haloperidol on the production of the pro-inflammatory chemokine interleukin-8 (IL-8), which is released from human monocytes when activated by Gram-negative lipopolysaccharide (LPS). METHODS Peripheral human whole blood was diluted with Roswell Park Memorial Institute (RPMI) cell culture medium and stimulated with LPS. Accumulating IL-8 was quantified in the supernatant with an adapted enzyme-linked immunosorbent assay (ELISA) and the results correlated to the number of monocytes at venipuncture. RESULTS At supra-therapeutic concentrations of 100 µM, haloperidol inhibited the LPS-induced release of IL-8 in peripheral human monocytes moderately, whereas olanzapine, risperidone, carbamazepine and valproic acid showed no such effect. CONCLUSIONS The results suggest that these mood-stabilizing drugs and antipsychotics are endowed with clinically favorable inertness rather than pro-inflammatory properties.
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Affiliation(s)
- Herbert Bosshart
- Psychiatric Outpatient Facility, Turnerstrasse 7a, CH-8006 Zurich, Switzerland
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36
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An integrated system for synchronous culture of animal cells under controlled conditions. Biotechniques 2016; 61:129-36. [PMID: 27625207 DOI: 10.2144/000114451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/14/2016] [Indexed: 11/23/2022] Open
Abstract
The cell cycle has fundamental effects on cell cultures and their products. Tools to synchronize cultured cells allow the study of cellular physiology and metabolism at particular cell cycle phases. However, cells are most often arrested by methods that alter their homeostasis and are then cultivated in poorly controlled environments. Cell behavior could then be affected by the synchronization method and culture conditions used, and not just by the particular cell cycle phase under study. Moreover, only a few viable cells are recovered. Here, we designed an integrated system where a large number of cells from a controlled bioreactor culture is separated by centrifugal elutriation at high viabilities. In contrast to current elutriation methods, cells are injected directly from a bioreactor into an injection loop, allowing the introduction of a large number of cells into the separation chamber without stressful centrifugation. A low pulsation peristaltic pump increases the stability of the elutriation chamber. Using this approach, a large number of healthy cells at each cell cycle phase were obtained, allowing their direct inoculation into fully instrumented bioreactors. Hybridoma cells synchronized and cultured in this system behaved as expected for a synchronous culture.
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37
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Warkiani ME, Wu L, Tay AKP, Han J. Large-Volume Microfluidic Cell Sorting for Biomedical Applications. Annu Rev Biomed Eng 2015; 17:1-34. [DOI: 10.1146/annurev-bioeng-071114-040818] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Majid Ebrahimi Warkiani
- BioSystems and Micromechanics IRG, Singapore–MIT Alliance for Research and Technology (SMART) Centre, Singapore 138602;
- School of Mechanical and Manufacturing Engineering, Australian Centre for NanoMedicine, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Lidan Wu
- Department of Biological Engineering and
| | - Andy Kah Ping Tay
- BioSystems and Micromechanics IRG, Singapore–MIT Alliance for Research and Technology (SMART) Centre, Singapore 138602;
| | - Jongyoon Han
- BioSystems and Micromechanics IRG, Singapore–MIT Alliance for Research and Technology (SMART) Centre, Singapore 138602;
- Department of Biological Engineering and
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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Xu C, Wang Y, Wang L, Wang Q, Du LQ, Fan S, Liu Q, Li L. Accumulation and Phosphorylation of RecQ-Mediated Genome Instability Protein 1 (RMI1) at Serine 284 and Serine 292 during Mitosis. Int J Mol Sci 2015; 16:26395-405. [PMID: 26556339 PMCID: PMC4661824 DOI: 10.3390/ijms161125965] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 02/07/2023] Open
Abstract
Chromosome instability usually leads to tumorigenesis. Bloom syndrome (BS) is a genetic disease associated with chromosome instability. The BS gene product, BLM, has been reported to function in the spindle assembly checkpoint (SAC) to prevent chromosome instability. BTR complex, composed of BLM, topoisomerase IIIα (Topo IIIα), RMI1 (RecQ-mediated genome instability protein 1, BLAP75) and RMI2 (RecQ-mediated genome instability protein 2, BLAP18), is crucial for maintaining genome stability. Recent work has demonstrated that RMI2 also plays critical role in SAC. However, little is know about RMI1 regulation during the cell cycle. Here we present that RMI1 protein level does not change through G1, S and G2 phases, but significantly increases in M phase. Moreover, phosphorylation of RMI1 occurs in mitosis. Upon microtubule-disturbing agent, RMI1 is phosphorylated primarily at the sites of Serine 284 and Serine 292, which does not interfere with the formation of BTR complex. Additionally, this phosphorylation is partially reversed by roscovitine treatment, implying cycling-dependent kinase 1 (CDK1) might be one of the upstream kinases.
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Affiliation(s)
- Chang Xu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Yan Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Lu Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Qin Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Li-Qing Du
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Saijun Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Qiang Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Lei Li
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Abstract
A close relationship between proliferation and cell fate specification has been well documented in many developmental systems. In addition to the gradual cell fate changes accompanying normal development and tissue homeostasis, it is now commonly appreciated that cell fate could also undergo drastic changes, as illustrated by the induction of pluripotency from many differentiated somatic cell types during the process of Yamanaka reprogramming. Strikingly, the drastic cell fate change induced by Yamanaka factors (Oct4, Sox2, Klf4, and c-Myc) is preceded by extensive cell cycle acceleration. Prompted by our recent discovery that progression toward pluripotency from rare somatic cells could bypass the stochastic phase of reprogramming and that a key feature of these somatic cells is an ultrafast cell cycle (~8 h/cycle), we assess whether cell cycle dynamics could provide a general framework for controlling cell fate. Several potential mechanisms on how cell cycle dynamics may impact cell fate determination by regulating chromatin, key transcription factor concentration, or their interactions are discussed. Specific challenges and implications for studying and manipulating cell fate are considered.
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40
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Castillo Salvador AE, Fuge G, Jandt U, Zeng AP. Growth kinetics and validation of near-physiologically synchronized HEK293S Cultures. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
| | - Grischa Fuge
- Institute of Bioprocess and Biosystems Engineering; Hamburg University of Technology; Hamburg Germany
| | - Uwe Jandt
- Institute of Bioprocess and Biosystems Engineering; Hamburg University of Technology; Hamburg Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering; Hamburg University of Technology; Hamburg Germany
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41
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Song S, Kim MS, Lee J, Choi S. A continuous-flow microfluidic syringe filter for size-based cell sorting. LAB ON A CHIP 2015; 15:1250-4. [PMID: 25599969 DOI: 10.1039/c4lc01417k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
This communication presents a microfluidic method for size-based cell sorting, which provides a simple and robust approach for cell cycle synchronization by manual and stand-alone operation.
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Affiliation(s)
- Seungjeong Song
- Department of Biomedical Engineering, Kyung Hee University, 1732 Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 446-701, Republic of Korea.
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Barradas OP, Jandt U, Becker M, Bahnemann J, Pörtner R, Zeng AP. Synchronized mammalian cell culture: Part I-A physical strategy for synchronized cultivation under physiological conditions. Biotechnol Prog 2014; 31:165-74. [DOI: 10.1002/btpr.1944] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/10/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Oscar Platas Barradas
- Bioprocess and Biosystems Engineering; Hamburg University of Technology, Denickestr. 15, 21071; Hamburg Germany
| | - Uwe Jandt
- Bioprocess and Biosystems Engineering; Hamburg University of Technology, Denickestr. 15, 21071; Hamburg Germany
| | - Max Becker
- Bioprocess and Biosystems Engineering; Hamburg University of Technology, Denickestr. 15, 21071; Hamburg Germany
| | - Janina Bahnemann
- Bioprocess and Biosystems Engineering; Hamburg University of Technology, Denickestr. 15, 21071; Hamburg Germany
| | - Ralf Pörtner
- Bioprocess and Biosystems Engineering; Hamburg University of Technology, Denickestr. 15, 21071; Hamburg Germany
| | - An-Ping Zeng
- Bioprocess and Biosystems Engineering; Hamburg University of Technology, Denickestr. 15, 21071; Hamburg Germany
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44
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Jandt U, Platas Barradas O, Pörtner R, Zeng AP. Mammalian cell culture synchronization under physiological conditions and population dynamic simulation. Appl Microbiol Biotechnol 2014; 98:4311-9. [DOI: 10.1007/s00253-014-5553-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/14/2014] [Accepted: 01/18/2014] [Indexed: 02/05/2023]
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Menter DG, Tucker SC, Kopetz S, Sood AK, Crissman JD, Honn KV. Platelets and cancer: a casual or causal relationship: revisited. Cancer Metastasis Rev 2014; 33:231-69. [PMID: 24696047 PMCID: PMC4186918 DOI: 10.1007/s10555-014-9498-0] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human platelets arise as subcellular fragments of megakaryocytes in bone marrow. The physiologic demand, presence of disease such as cancer, or drug effects can regulate the production circulating platelets. Platelet biology is essential to hemostasis, vascular integrity, angiogenesis, inflammation, innate immunity, wound healing, and cancer biology. The most critical biological platelet response is serving as "First Responders" during the wounding process. The exposure of extracellular matrix proteins and intracellular components occurs after wounding. Numerous platelet receptors recognize matrix proteins that trigger platelet activation, adhesion, aggregation, and stabilization. Once activated, platelets change shape and degranulate to release growth factors and bioactive lipids into the blood stream. This cyclic process recruits and aggregates platelets along with thrombogenesis. This process facilitates wound closure or can recognize circulating pathologic bodies. Cancer cell entry into the blood stream triggers platelet-mediated recognition and is amplified by cell surface receptors, cellular products, extracellular factors, and immune cells. In some cases, these interactions suppress immune recognition and elimination of cancer cells or promote arrest at the endothelium, or entrapment in the microvasculature, and survival. This supports survival and spread of cancer cells and the establishment of secondary lesions to serve as important targets for prevention and therapy.
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Affiliation(s)
- David G Menter
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
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Sabbattini P, Sjoberg M, Nikic S, Frangini A, Holmqvist PH, Kunowska N, Carroll T, Brookes E, Arthur SJ, Pombo A, Dillon N. An H3K9/S10 methyl-phospho switch modulates Polycomb and Pol II binding at repressed genes during differentiation. Mol Biol Cell 2014; 25:904-15. [PMID: 24430871 PMCID: PMC3952858 DOI: 10.1091/mbc.e13-10-0628] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Polycomb-repressed genes are marked by H3K9me3 and H3K27me3 in pluripotent ES cells, but the effects of this combination are altered by H3S10 phosphorylation in differentiated cells. Acquisition of H3K9me3/S10ph at Polycomb-target genes during differentiation reduces binding of Ezh1 and paused RNA Pol II and affects poising of repressed genes. Methylated histones H3K9 and H3K27 are canonical epigenetic silencing modifications in metazoan organisms, but the relationship between the two modifications has not been well characterized. H3K9me3 coexists with H3K27me3 in pluripotent and differentiated cells. However, we find that the functioning of H3K9me3 is altered by H3S10 phosphorylation in differentiated postmitotic osteoblasts and cycling B cells. Deposition of H3K9me3/S10ph at silent genes is partially mediated by the mitogen- and stress-activated kinases (MSK1/2) and the Aurora B kinase. Acquisition of H3K9me3/S10ph during differentiation correlates with loss of paused S5 phosphorylated RNA polymerase II, which is present on Polycomb-regulated genes in embryonic stem cells. Reduction of the levels of H3K9me3/S10ph by kinase inhibition results in increased binding of RNAPIIS5ph and the H3K27 methyltransferase Ezh1 at silent promoters. Our results provide evidence of a novel developmentally regulated methyl-phospho switch that modulates Polycomb regulation in differentiated cells and stabilizes repressed states.
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Affiliation(s)
- Pierangela Sabbattini
- Gene Regulation and Chromatin Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, London W12 0NN, United Kingdom Genome Function Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, London W12 0NN, United Kingdom MRC Protein Phosphorylation Unit, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
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47
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Burger R, Ducrée J. Handling and analysis of cells and bioparticles on centrifugal microfluidic platforms. Expert Rev Mol Diagn 2014; 12:407-21. [DOI: 10.1586/erm.12.28] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Lee WC, Bhagat AAS, Lim CT. High-throughput synchronization of mammalian cell cultures by spiral microfluidics. Methods Mol Biol 2014; 1104:3-13. [PMID: 24297405 DOI: 10.1007/978-1-62703-733-4_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The development of mammalian cell cycle synchronization techniques has greatly advanced our understanding of many cellular regulatory events and mechanisms specific to different phases of the cell cycle. In this chapter, we describe a high-throughput microfluidic-based approach for cell cycle synchronization. By exploiting the relationship between cell size and its phase in the cell cycle, large numbers of synchronized cells can be obtained by size fractionation in a spiral microfluidic channel. Protocols for the synchronization of primary cells such as mesenchymal stem cells, and immortal cell lines such as Chinese hamster ovarian cells (CHO-CD36) and HeLa cells are provided as examples.
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Affiliation(s)
- Wong Cheng Lee
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
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49
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Ly T, Ahmad Y, Shlien A, Soroka D, Mills A, Emanuele MJ, Stratton MR, Lamond AI. A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells. eLife 2014; 3:e01630. [PMID: 24596151 PMCID: PMC3936288 DOI: 10.7554/elife.01630] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 01/24/2014] [Indexed: 12/22/2022] Open
Abstract
Technological advances have enabled the analysis of cellular protein and RNA levels with unprecedented depth and sensitivity, allowing for an unbiased re-evaluation of gene regulation during fundamental biological processes. Here, we have chronicled the dynamics of protein and mRNA expression levels across a minimally perturbed cell cycle in human myeloid leukemia cells using centrifugal elutriation combined with mass spectrometry-based proteomics and RNA-Seq, avoiding artificial synchronization procedures. We identify myeloid-specific gene expression and variations in protein abundance, isoform expression and phosphorylation at different cell cycle stages. We dissect the relationship between protein and mRNA levels for both bulk gene expression and for over ∼6000 genes individually across the cell cycle, revealing complex, gene-specific patterns. This data set, one of the deepest surveys to date of gene expression in human cells, is presented in an online, searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/). DOI: http://dx.doi.org/10.7554/eLife.01630.001.
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MESH Headings
- Cell Cycle
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Cell Separation/methods
- Cell Size
- Centrifugation
- Chromatography, Liquid
- Databases, Protein
- Gene Expression Profiling/methods
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/metabolism
- Leukemia, Myeloid/pathology
- Phosphorylation
- Proteomics/methods
- RNA Interference
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Analysis, RNA
- Tandem Mass Spectrometry
- Time Factors
- Transfection
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Affiliation(s)
- Tony Ly
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Yasmeen Ahmad
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Adam Shlien
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Dominique Soroka
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Allie Mills
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Michael J Emanuele
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Michael R Stratton
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
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50
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Wada T, Miyashita Y, Sasaki M, Aruga Y, Nakamura Y, Ishii Y, Sasahara M, Kanasaki K, Kitada M, Koya D, Shimano H, Tsuneki H, Sasaoka T. Eplerenone ameliorates the phenotypes of metabolic syndrome with NASH in liver-specific SREBP-1c Tg mice fed high-fat and high-fructose diet. Am J Physiol Endocrinol Metab 2013; 305:E1415-25. [PMID: 24129399 DOI: 10.1152/ajpendo.00419.2013] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Because the renin-angiotensin-aldosterone system has been implicated in the development of insulin resistance and promotion of fibrosis in some tissues, such as the vasculature, we examined the effect of eplerenone, a selective mineralocorticoid receptor (MR) antagonist, on nonalcoholic steatohepatitis (NASH) and metabolic phenotypes in a mouse model reflecting metabolic syndrome in humans. We adopted liver-specific transgenic (Tg) mice overexpressing the active form of sterol response element binding protein-1c (SREBP-1c) fed a high-fat and fructose diet (HFFD) as the animal model in the present study. When wild-type (WT) C57BL/6 and liver-specific SREBP-1c Tg mice grew while being fed HFFD for 12 wk, body weight and epididymal fat weight increased in both groups with an elevation in blood pressure and dyslipidemia. Glucose intolerance and insulin resistance were also observed. Adipose tissue hypertrophy and macrophage infiltration with crown-like structure formation were also noted in mice fed HFFD. Interestingly, the changes noted in both genotypes fed HFFD were significantly ameliorated with eplerenone. HFFD-fed Tg mice exhibited the histological features of NASH in the liver, including macrovesicular steatosis and fibrosis, whereas HFFD-fed WT mice had hepatic steatosis without apparent fibrotic changes. Eplerenone effectively ameliorated these histological abnormalities. Moreover, the direct suppressive effects of eplerenone on lipopolysaccharide-induced TNFα production in the presence and absence of aldosterone were observed in primary-cultured Kupffer cells and bone marrow-derived macrophages. These results indicated that eplerenone prevented the development of NASH and metabolic abnormalities in mice by inhibiting inflammatory responses in both Kupffer cells and macrophages.
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