1
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Tan J, Virtue S, Norris DM, Conway OJ, Yang M, Bidault G, Gribben C, Lugtu F, Kamzolas I, Krycer JR, Mills RJ, Liang L, Pereira C, Dale M, Shun-Shion AS, Baird HJ, Horscroft JA, Sowton AP, Ma M, Carobbio S, Petsalaki E, Murray AJ, Gershlick DC, Nathan JA, Hudson JE, Vallier L, Fisher-Wellman KH, Frezza C, Vidal-Puig A, Fazakerley DJ. Limited oxygen in standard cell culture alters metabolism and function of differentiated cells. EMBO J 2024:10.1038/s44318-024-00084-7. [PMID: 38580776 DOI: 10.1038/s44318-024-00084-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 04/07/2024] Open
Abstract
The in vitro oxygen microenvironment profoundly affects the capacity of cell cultures to model physiological and pathophysiological states. Cell culture is often considered to be hyperoxic, but pericellular oxygen levels, which are affected by oxygen diffusivity and consumption, are rarely reported. Here, we provide evidence that several cell types in culture actually experience local hypoxia, with important implications for cell metabolism and function. We focused initially on adipocytes, as adipose tissue hypoxia is frequently observed in obesity and precedes diminished adipocyte function. Under standard conditions, cultured adipocytes are highly glycolytic and exhibit a transcriptional profile indicative of physiological hypoxia. Increasing pericellular oxygen diverted glucose flux toward mitochondria, lowered HIF1α activity, and resulted in widespread transcriptional rewiring. Functionally, adipocytes increased adipokine secretion and sensitivity to insulin and lipolytic stimuli, recapitulating a healthier adipocyte model. The functional benefits of increasing pericellular oxygen were also observed in macrophages, hPSC-derived hepatocytes and cardiac organoids. Our findings demonstrate that oxygen is limiting in many terminally-differentiated cell types, and that considering pericellular oxygen improves the quality, reproducibility and translatability of culture models.
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Affiliation(s)
- Joycelyn Tan
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Sam Virtue
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - Dougall M Norris
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Olivia J Conway
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ming Yang
- MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Cologne, 50931, Germany
| | - Guillaume Bidault
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Christopher Gribben
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Fatima Lugtu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Ioannis Kamzolas
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - James R Krycer
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - Richard J Mills
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - Lu Liang
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Conceição Pereira
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Martin Dale
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Amber S Shun-Shion
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Harry Jm Baird
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - James A Horscroft
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Alice P Sowton
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Marcella Ma
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Stefania Carobbio
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
- Centro de Investigacion Principe Felipe, Valencia, 46012, Spain
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Andrew J Murray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - David C Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - James A Nathan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
| | - James E Hudson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Kelsey H Fisher-Wellman
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, 27834, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC, 27834, USA
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Cologne, 50931, Germany
| | - Antonio Vidal-Puig
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
- Centro de Investigacion Principe Felipe, Valencia, 46012, Spain.
| | - Daniel J Fazakerley
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
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Zhang Y, Ding X, Guo L, Zhong Y, Xie J, Xu Y, Li H, Zheng D. Protocol for induction of human kidney cell fibrosis. STAR Protoc 2024; 5:102881. [PMID: 38386546 PMCID: PMC10901133 DOI: 10.1016/j.xpro.2024.102881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/03/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Here, we present a protocol for inducing fibrosis in human kidney-2 (HK2) cells followed by quantitative real-time PCR analysis of fibrosis-related genes. We describe steps for growing and expanding cells, inducing HK2 fibrosis, and collecting cells for downstream applications. Given the limited cell quantity in culture flasks and the challenges of cell collection, we utilized 10-cm Petri dishes for cell harvesting, with each experimental group comprising five replicate samples. For complete details on the use and execution of this protocol, please refer to Zhang et al.1.
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Affiliation(s)
- Yiyuan Zhang
- Department of Nephrology, The Affiliated Huai'an Hospital of Xuzhou Medical University and Huai'an Second People's Hospital, Huai'an, Jiangsu Province, China
| | - Xiaobao Ding
- Department of Nephrology, The Affiliated Huai'an Hospital of Xuzhou Medical University and Huai'an Second People's Hospital, Huai'an, Jiangsu Province, China; Department of Pharmacology, Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Lihao Guo
- Department of Nephrology, The Affiliated Huai'an Hospital of Xuzhou Medical University and Huai'an Second People's Hospital, Huai'an, Jiangsu Province, China
| | - Yanan Zhong
- Department of Nephrology, The Affiliated Huai'an Hospital of Xuzhou Medical University and Huai'an Second People's Hospital, Huai'an, Jiangsu Province, China
| | - Juan Xie
- Department of Nephrology, The Affiliated Huai'an Hospital of Xuzhou Medical University and Huai'an Second People's Hospital, Huai'an, Jiangsu Province, China
| | - Yong Xu
- Department of Nephrology, The Affiliated Huai'an Hospital of Xuzhou Medical University and Huai'an Second People's Hospital, Huai'an, Jiangsu Province, China.
| | - Hailun Li
- Department of Nephrology, The Affiliated Huai'an Hospital of Xuzhou Medical University and Huai'an Second People's Hospital, Huai'an, Jiangsu Province, China.
| | - Donghui Zheng
- Department of Nephrology, The Affiliated Huai'an Hospital of Xuzhou Medical University and Huai'an Second People's Hospital, Huai'an, Jiangsu Province, China.
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Martinez-Uribe O, Becker TC, Garman KS. Promises and Limitations of Current Models for Understanding Barrett's Esophagus and Esophageal Adenocarcinoma. Cell Mol Gastroenterol Hepatol 2024; 17:1025-1038. [PMID: 38325549 PMCID: PMC11041847 DOI: 10.1016/j.jcmgh.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND & AIMS This review was developed to provide a thorough and effective update on models relevant to esophageal metaplasia, dysplasia, and carcinogenesis, focusing on the advantages and limitations of different models of Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC). METHODS This expert review was written on the basis of a thorough review of the literature combined with expert interpretation of the state of the field. We emphasized advances over the years 2012-2023 and provided detailed information related to the characterization of established human esophageal cell lines. RESULTS New insights have been gained into the pathogenesis of BE and EAC using patient-derived samples and single-cell approaches. Relevant animal models include genetic as well as surgical mouse models and emphasize the development of lesions at the squamocolumnar junction in the mouse stomach. Rat models are generated using surgical approaches that directly connect the small intestine and esophagus. Large animal models have the advantage of including features in human esophagus such as esophageal submucosal glands. Alternatively, cell culture approaches remain important in the field and allow for personalized approaches, and scientific rigor can be ensured by authentication of cell lines. CONCLUSIONS Research in BE and EAC remains highly relevant given the morbidity and mortality associated with cancers of the tubular esophagus and gastroesophageal junction. Careful selection of models and inclusion of human samples whenever possible will ensure relevance to human health and disease.
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Affiliation(s)
- Omar Martinez-Uribe
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Thomas C Becker
- Division of Endocrinology, Department of Medicine, Duke University, Durham, North Carolina
| | - Katherine S Garman
- Division of Endocrinology, Department of Medicine, Duke University, Durham, North Carolina.
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4
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Wang J, Gleeson PA, Fourriere L. Long-term live cell imaging during differentiation of human iPSC-derived neurons. STAR Protoc 2023; 4:102699. [PMID: 37938977 PMCID: PMC10665918 DOI: 10.1016/j.xpro.2023.102699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/15/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023] Open
Abstract
Live-cell imaging is crucial to appreciate the dynamics and the complexity of cellular interaction processes. However, live-cell imaging of human neurons is challenging due to neuronal sensitivity. Here, we describe a long-term live-cell imaging protocol for neurons derived from human induced pluripotent stem cells. By using an IncuCyte live-cell imaging system, we have obtained information on neuronal dynamics during the different stages of neurogenesis. The protocol has also been developed to monitor the dynamics of the neuronal intracellular organelles. For complete details on the use and execution of this protocol, please refer to Wang et al.1.
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Affiliation(s)
- Jingqi Wang
- The Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul A Gleeson
- The Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Lou Fourriere
- The Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
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5
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Park S, Patel SA, Torr EE, Dureke AGN, McIntyre AM, Skop AR. A protocol for isolating and imaging large extracellular vesicles or midbody remnants from mammalian cell culture. STAR Protoc 2023; 4:102562. [PMID: 37690025 PMCID: PMC10500451 DOI: 10.1016/j.xpro.2023.102562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/14/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
Traditionally, midbody remnants (MBRs) are isolated from cell culture medium using ultracentrifugation, which is expensive and time consuming. Here, we present a protocol for isolating MBRs or large extracellular vesicles (EVs) from mammalian cell culture using either 1.5% polyethylene glycol 6000 (PEG6000) or PEG5000-coated gold nanoparticles. We describe steps for growing cells, collecting media, and precipitating MBRs and EVs from cell culture medium. We then detail characterization of MBRs through immunofluorescent antibody staining and immunofluorescent imaging.
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Affiliation(s)
- Sungjin Park
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Smit A Patel
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Elizabeth E Torr
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | | | - Alina M McIntyre
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Ahna R Skop
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA.
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6
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Cao K, Hajy Heydary Y, Tong G, Martinez TF. Integrated workflow for discovery of microprotein-coding small open reading frames. STAR Protoc 2023; 4:102649. [PMID: 37874679 PMCID: PMC10618807 DOI: 10.1016/j.xpro.2023.102649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
Small open reading frame (smORF)-encoded microproteins, proteins containing less than 100-150 amino acids, are an emerging class of functional biomolecules. Here, we present a protocol for identifying translated smORFs in mammalian systems genome wide. We describe steps for generation of ribosome profiling (Ribo-seq) data, in silico translation of a transcriptome assembly to create an ORF database, and computational analysis of Ribo-seq to score individual smORFs for translation. Identification of translated smORFs is the first step to studying the functions of microproteins. For complete details on the use and execution of this protocol, please refer to Martinez et al.1.
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Affiliation(s)
- Kevin Cao
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, USA
| | - Yasamin Hajy Heydary
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, USA
| | - Gregory Tong
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, USA
| | - Thomas Farid Martinez
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92617, USA.
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7
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Villanueva-Carmona T, Cedó L, Núñez-Roa C, Maymó-Masip E, Vendrell J, Fernández-Veledo S. Protocol for the in vitro isolation and culture of mature adipocytes and white adipose tissue explants from humans and mice. STAR Protoc 2023; 4:102693. [PMID: 37924518 PMCID: PMC10656257 DOI: 10.1016/j.xpro.2023.102693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/10/2023] [Accepted: 10/12/2023] [Indexed: 11/06/2023] Open
Abstract
White adipose tissue (WAT) explants culture allows the study of this tissue ex vivo, maintaining its structure and properties. Concurrently, isolating mature adipocytes facilitates research into fat cell metabolism and hormonal regulation. Here, we present a protocol for obtaining, isolating, and processing mature adipocytes, alongside the cultivation of WAT explants from humans and mice. We describe steps for WAT retrieval, culturing of WAT explants, WAT digestion, and adipocytes separation. We then detail procedures for culturing isolated mature adipocytes. For complete details on the use and execution of this protocol, please refer to Villanueva-Carmona et al. (2023).1.
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Affiliation(s)
- Teresa Villanueva-Carmona
- Department of Endocrinology and Nutrition, Research Unit, Institut d'Investigació Sanitària Pere Virgili (IISPV), Hospital Universitari de Tarragona Joan XXIII, 43005 Tarragona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain; Department of Medicine and Surgery, Universitat Rovira i Virgili (URV), 43201 Reus, Spain
| | - Lídia Cedó
- Department of Endocrinology and Nutrition, Research Unit, Institut d'Investigació Sanitària Pere Virgili (IISPV), Hospital Universitari de Tarragona Joan XXIII, 43005 Tarragona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Catalina Núñez-Roa
- Department of Endocrinology and Nutrition, Research Unit, Institut d'Investigació Sanitària Pere Virgili (IISPV), Hospital Universitari de Tarragona Joan XXIII, 43005 Tarragona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Elsa Maymó-Masip
- Department of Endocrinology and Nutrition, Research Unit, Institut d'Investigació Sanitària Pere Virgili (IISPV), Hospital Universitari de Tarragona Joan XXIII, 43005 Tarragona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Joan Vendrell
- Department of Endocrinology and Nutrition, Research Unit, Institut d'Investigació Sanitària Pere Virgili (IISPV), Hospital Universitari de Tarragona Joan XXIII, 43005 Tarragona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain; Department of Medicine and Surgery, Universitat Rovira i Virgili (URV), 43201 Reus, Spain
| | - Sonia Fernández-Veledo
- Department of Endocrinology and Nutrition, Research Unit, Institut d'Investigació Sanitària Pere Virgili (IISPV), Hospital Universitari de Tarragona Joan XXIII, 43005 Tarragona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain.
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8
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Pollock SD, Galicia-Silva IM, Liu M, Gruskin ZL, Alvarez-Dominguez JR. Scalable generation of 3D pancreatic islet organoids from human pluripotent stem cells in suspension bioreactors. STAR Protoc 2023; 4:102580. [PMID: 37738117 PMCID: PMC10519857 DOI: 10.1016/j.xpro.2023.102580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/24/2023] [Accepted: 08/28/2023] [Indexed: 09/24/2023] Open
Abstract
Here, we present a protocol for producing 3D pancreatic-like organoids from human pluripotent stem cells in suspension bioreactors. We describe scalable techniques for generating 10,000-100,000 organoids that further mature in 4-5 weeks into α- and β-like cells with glucose-responsive insulin and glucagon release. We detail procedures for culturing, passaging, and cryopreserving stem cells as suspended clusters and specify growth media and differentiation factors for differentiation. Finally, we discuss functional assays for research applications. For complete details on the use and execution of this protocol, please refer to Alvarez-Dominguez et al.1.
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Affiliation(s)
- Samuel D Pollock
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Israeli M Galicia-Silva
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mai Liu
- Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zoe L Gruskin
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Juan R Alvarez-Dominguez
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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9
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Lu P, Wu B, Wang Y, Zhang J, Zhou B. A sandwiched ventricular explant assay to model mouse coronary angiogenesis ex vivo. STAR Protoc 2023; 4:102619. [PMID: 37897735 PMCID: PMC10751554 DOI: 10.1016/j.xpro.2023.102619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/27/2023] [Accepted: 09/13/2023] [Indexed: 10/30/2023] Open
Abstract
Developing an ex vivo system that mimics in vivo developmental coronary angiogenesis provides an improved understanding of its underlying molecular and cellular mechanisms. Here, we present a sandwiched embryonic ventricular explant assay to model mouse coronary angiogenesis ex vivo. We describe steps for breeding mice, labeling endocardial cells, isolating murine hearts, dissecting left ventricles, and making sandwiched explants in Matrigel. We then detail procedures for modeling coronary angiogenesis and taking images. For complete details on the use and execution of this protocol, please refer to Lu et al. (2023)1.
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Affiliation(s)
- Pengfei Lu
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Bingruo Wu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Yidong Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Cardiovascular Research Center, School of Basic Medical Sciences, Jiaotong University, Xi'an 710061, China
| | - Jingran Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Bin Zhou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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10
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Li Z, Reint G, Haapaniemi EM. Protocol for editing fibroblasts with in vitro transcribed Cas9 mRNA and profile off-target editing by optimized GUIDE-seq. STAR Protoc 2023; 4:102662. [PMID: 37889758 PMCID: PMC10641304 DOI: 10.1016/j.xpro.2023.102662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/04/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
CRISPR-Cas9 gene editing is an efficient technique to modify specific sites/regions of DNA. Delivery of the Cas9 by mRNA is particularly promising in pre-clinical genome editing applications for its transient, nonintegrating feature. However, the off-target of Cas9-gRNA still remains a concern and needs a specific monitor. Here, we present a revised protocol to edit fibroblasts by in vitro transcribed Cas9 mRNA and profile its off-target effect by the optimized GUIDE-seq method. This protocol can also be applied to other cell lines. For complete details on the use and execution of this protocol, please refer to Ganna Reint et al. (2021).1.
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Affiliation(s)
- Zhuokun Li
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway.
| | - Ganna Reint
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
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11
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Kainov Y, Zhuravskaya A, Makeyev EV. Protocol for auxin-inducible depletion of the RNA-binding protein PTBP1 in mouse embryonic stem cells. STAR Protoc 2023; 4:102644. [PMID: 37862173 PMCID: PMC10594634 DOI: 10.1016/j.xpro.2023.102644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/28/2023] [Accepted: 09/25/2023] [Indexed: 10/22/2023] Open
Abstract
Inducible degradation of proteins of interest provides a powerful approach for functional studies. Here, we present a protocol for tightly controlled depletion of the RNA-binding protein PTBP1 in mouse embryonic stem cells (ESCs). We describe steps for establishing an ESC line expressing doxycycline-inducible auxin receptor protein OsTIR1 and tagging endogenous Ptbp1 alleles using CRISPR-Cas9 and homology-directed repair reagents. We then detail procedures for assaying the efficiency of inducible PTBP1 knockdown by immunoblotting. This protocol is adaptable for other protein targets. For complete details on the use and execution of this protocol, please refer to Iannone et al.1.
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Affiliation(s)
- Yaroslav Kainov
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK.
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12
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Ram BM, Dai C. Detection of the DNA binding of transcription factors in situ at the single-cell resolution in cultured cells by proximity ligation assay. STAR Protoc 2023; 4:102692. [PMID: 37917578 PMCID: PMC10651771 DOI: 10.1016/j.xpro.2023.102692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023] Open
Abstract
Transcription factors (TFs) play a pivotal role in gene expression, and their DNA binding is the prerequisite to instigating gene transcription. Here, we present a protocol that exploits the proximity ligation assay technique to measure the DNA-binding activities of TFs in situ at the single-cell resolution. We describe steps for immunostaining with specific antibodies against double-stranded DNA and the TFs of interest, probe incubation, proximity ligation, and signal amplification. We then detail procedures for imaging and image analysis. For complete details on the use and execution of this protocol, please refer to Dai et al. (2015)1 and Xu et al. (2023).2.
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Affiliation(s)
- Babul Moni Ram
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA.
| | - Chengkai Dai
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA.
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13
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Ravi NS, George A, Mohankumar KM. Protocol for arrayed gRNA screening by base editors in mammalian cell lines using lentiviral system. STAR Protoc 2023; 4:102668. [PMID: 37922314 PMCID: PMC10656259 DOI: 10.1016/j.xpro.2023.102668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/25/2023] [Accepted: 10/04/2023] [Indexed: 11/05/2023] Open
Abstract
Base editing, a CRISPR-based genome engineering technique, enables precise single-nucleotide modifications while minimizing double-strand breaks. Here, we present a protocol for arrayed mutagenesis using base editors to identify regulatory elements within the gamma-globin locus. We describe steps for guide RNA (gRNA) cloning into lentiviral vectors, establishing stable cell lines with base editor expression, transducing gRNAs, and assessing editing efficiency. This protocol can be applied to diverse genomic regions and cell lines for arrayed screening, facilitating genetic research, and target discovery. For complete details on the use and execution of this protocol, please refer to Ravi et al. (2022)1.
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Affiliation(s)
- Nithin Sam Ravi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India.
| | - Anila George
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Kumarasamypet M Mohankumar
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India.
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14
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Rawat A, Jha MK, Morrison BM. Adoptive cell transfer of macrophages following peripheral nerve injury in mice. STAR Protoc 2023; 4:102624. [PMID: 37995193 PMCID: PMC10687290 DOI: 10.1016/j.xpro.2023.102624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/29/2023] [Accepted: 09/15/2023] [Indexed: 11/25/2023] Open
Abstract
Macrophages are key innate immune cells involved in multiple biological processes, including peripheral nerve regeneration. Here, we describe a protocol for the adoptive cell transfer of bone-marrow-derived macrophages (BMDMs) following sciatic nerve crush injury (SNCI). This procedure involves isolating BMDMs from a donor mouse, potentially manipulating them ex vivo, and reintroducing them into an animal following SNCI. Preclinical studies show that BMDMs can infiltrate injured nerves and impact functional recovery, potentially providing a novel therapy for nerve injuries. For complete details on the use and execution of this protocol, please refer to Jha et al.1.
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Affiliation(s)
- Atul Rawat
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mithilesh Kumar Jha
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Brett Michael Morrison
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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15
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Guo J, Ying F, Cai J, Wang Z. A protocol for selection in mice of highly metastatic ovarian cancer cell with omental tropism. STAR Protoc 2023; 4:102642. [PMID: 37924519 PMCID: PMC10656258 DOI: 10.1016/j.xpro.2023.102642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/23/2023] [Accepted: 09/25/2023] [Indexed: 11/06/2023] Open
Abstract
Preclinical models mimicking spontaneous omental metastasis from ovarian cancer (OC) can benefit the study of anti-metastatic therapies for OC patients. Here, we present a protocol to establish a highly metastatic (HM) mouse model with omental tropism by in vivo selection. We describe the processes of implanting OC cells in the ovaries of mice and obtaining HM sublines from their omental metastases. HM cells can metastasize from the ovary to the omentum within 2 weeks. For complete details on the use and execution of this protocol, please refer to Ying et al.1.
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Affiliation(s)
- Jing Guo
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Feiquan Ying
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jing Cai
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Zehua Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, Wuhan 430022, China.
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16
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Li L, Gunewardena AM, Nyima T, Feldman BJ. Quantification of cell energetics in human subcutaneous adipose progenitor cells after target gene knockdown. STAR Protoc 2023; 4:102607. [PMID: 37742183 PMCID: PMC10751552 DOI: 10.1016/j.xpro.2023.102607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/17/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
Pro-preadipocytes are adipocyte progenitor cells within subcutaneous adipose tissue that are conserved in human adipose tissue with distinct cellular energetics. Here, we detail a protocol to quantify cellular oxygen consumption rates of primary human cells harvested from adipose tissue. We describe steps for primary cell expansion, cell seeding, transfection, differentiation, and respirometry followed by Agilent Seahorse Analytics. The measurement of bioenergetic profiles and resulting data further expand our knowledge of the functional properties of primary cells isolated from adipose tissue. For complete details on the use and execution of this protocol, please refer to Chen et al. (2023).1.
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Affiliation(s)
- Liang Li
- University of California San Francisco, San Francisco, CA 94158, USA.
| | | | - Tenzin Nyima
- University of California San Francisco, San Francisco, CA 94158, USA
| | - Brian J Feldman
- University of California San Francisco, San Francisco, CA 94158, USA.
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17
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Stephens DC, Mungai M, Crabtree A, Beasley HK, Garza-Lopez E, Vang L, Neikirk K, Vue Z, Vue N, Marshall AG, Turner K, Shao JQ, Sarker B, Murray S, Gaddy JA, Davis J, Damo SM, Hinton AO. Protocol for isolating mice skeletal muscle myoblasts and myotubes via differential antibody validation. STAR Protoc 2023; 4:102591. [PMID: 37938976 PMCID: PMC10663959 DOI: 10.1016/j.xpro.2023.102591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/06/2023] [Accepted: 09/01/2023] [Indexed: 11/10/2023] Open
Abstract
Isolation of skeletal muscles allows for the exploration of many complex diseases. Here, we present a protocol for isolating mice skeletal muscle myoblasts and myotubes that have been differentiated through antibody validation. We describe steps for collecting and preparing murine skeletal tissue, myoblast cell maintenance, plating, and cell differentiation. We then detail procedures for cell incubation, immunostaining, slide preparation and storage, and imaging for immunofluorescence validation.
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Affiliation(s)
- Dominique C Stephens
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; Department of Life and Physical Sciences, Fisk University, Nashville, TN 37232, USA
| | - Margaret Mungai
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Amber Crabtree
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Heather K Beasley
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Edgar Garza-Lopez
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Larry Vang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Kit Neikirk
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Zer Vue
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Neng Vue
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Andrea G Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Kyrin Turner
- Department of Life and Physical Sciences, Fisk University, Nashville, TN 37232, USA
| | - Jian-Qiang Shao
- Central Microscopy Research Facility, University of Iowa, Iowa City, IA 52242, USA
| | - Bishnu Sarker
- School of Applied Computational Sciences, Meharry Medical College, Nashville, TN 37232, USA
| | - Sandra Murray
- Department of Cell Biology, College of Medicine, University of Pittsburgh, Pittsburgh, TN 15260, USA
| | - Jennifer A Gaddy
- Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville, TN, USA; Tennessee Valley Healthcare Systems, U.S. Department of Veterans Affairs, Nashville, TN, USA
| | - Jamaine Davis
- Department of Biochemistry and Cancer Biology. Meharry Medical College, Nashville, TN, USA
| | - Steven M Damo
- Department of Life and Physical Sciences, Fisk University, Nashville, TN 37232, USA.
| | - Antentor O Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA.
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18
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McLaurin KA, Li H, Khalili K, Mactutus CF, Booze RM. HIV-1 mRNA Knockdown with CRISPR/Cas9 Enhances Neurocognitive Function. Res Sq 2023:rs.3.rs-3266933. [PMID: 37886577 PMCID: PMC10602171 DOI: 10.21203/rs.3.rs-3266933/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Mixed glia are infiltrated with HIV-1 virus early in the course of infection leading to the development of a persistent viral reservoir in the central nervous system. Modification of the HIV-1 genome using gene editing techniques, including CRISPR/Cas9, has shown great promise towards eliminating HIV-1 viral reservoirs; whether these techniques are capable of removing HIV-1 viral proteins from mixed glia, however, has not been systematically evaluated. Herein, the efficacy of adeno-associated virus 9 (AAV9)-CRISPR/Cas9 gene editing for eliminating HIV-1 mRNA from cortical mixed glia was evaluated in vitro and in vivo. In vitro, a within-subjects experimental design was utilized to treat mixed glia isolated from neonatal HIV-1 transgenic (Tg) rats with varying doses (0, 0.9, 1.8, 2.7, 3.6, 4.5, or 5.4 μL) of CRISPR/Cas9 for 72 hours. Dose-dependent decreases in the number of HIV-1 mRNA, quantified using an innovative in situ hybridization technique, were observed in a subset (i.e., n=5 out of 8) of primary mixed glia. In vivo, HIV-1 Tg rats were retro-orbitally inoculated with CRISPR/Cas9 for two weeks, whereby treatment resulted in profound excision (i.e., approximately 53.2%) of HIV-1 mRNA from the mPFC. Given incomplete excision of the HIV-1 viral genome, the clinical relevance of HIV-1 mRNA knockdown for eliminating neurocognitive impairments was evaluated via examination of temporal processing, a putative neurobehavioral mechanism underlying HIV-1 associated neurocognitive disorders (HAND). Indeed, treatment with CRISPR/Cas9 partially restored the developmental trajectory of temporal processing. Proof-of-concept studies, therefore, support the susceptibility of mixed glia to gene editing and the potential of CRISPR/Cas9 to serve as a novel therapeutic strategy for HAND, even in the absence of full viral eradication.
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19
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Wallisch S, Neef SK, Denzinger L, Mönch D, Koch J, Marzi J, Mürdter T, Janssen N. Protocol for establishing a coculture with fibroblasts and colorectal cancer organoids. STAR Protoc 2023; 4:102481. [PMID: 37542715 PMCID: PMC10430577 DOI: 10.1016/j.xpro.2023.102481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 08/07/2023] Open
Abstract
The tumor microenvironment is essential for mediating drug resistance and tumor progression. Here, we present a coculture system, which enables drug testing of colorectal cancer organoids and fibroblasts without additional matrix components such as Matrigel or basement membrane extracts. First, we describe steps to use a readout for high-throughput drug testing using a luminescence-based viability assay. Second, we detail a readout that uses flow cytometry to distinguish toxic effects on either colorectal cancer organoids or fibroblasts.
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Affiliation(s)
- Svenja Wallisch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; University of Tübingen, 72076 Tübingen, Germany
| | - Sylvia Karin Neef
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; University of Tübingen, 72076 Tübingen, Germany
| | - Lukas Denzinger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; University of Tübingen, 72076 Tübingen, Germany
| | - Dina Mönch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; University of Tübingen, 72076 Tübingen, Germany
| | - Jana Koch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; University of Tübingen, 72076 Tübingen, Germany
| | - Julia Marzi
- Department for Medical Technologies and Regenerative Medicine, Institute of Biomedical Engineering, University of Tübingen, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Thomas Mürdter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; University of Tübingen, 72076 Tübingen, Germany
| | - Nicole Janssen
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; University of Tübingen, 72076 Tübingen, Germany.
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20
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Karaca M, Fritsche K, Lichtenstein D, Vural Ö, Kreuzer K, Alarcan J, Braeuning A, Marx-Stoelting P, Tralau T. Adverse outcome pathway-based analysis of liver steatosis in vitro using human liver cell lines. STAR Protoc 2023; 4:102500. [PMID: 37616165 PMCID: PMC10463250 DOI: 10.1016/j.xpro.2023.102500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/21/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023] Open
Abstract
Here, we present an in vitro test battery to analyze chemicals for their potential to induce liver triglyceride accumulation, a hallmark of liver steatosis. We describe steps for using HepG2 and HepaRG human hepatoma cells in conjunction with a combination of several in vitro assays covering the different molecular initiating events and key events of the respective adverse outcome pathway. This protocol is suitable for assessing single substance effects as well as mixtures allowing their classification as steatotic or non-steatotic. For complete details on the use and execution of this protocol, please refer to Luckert et al. (2018),1 Lichtenstein et al. (2020),2 and Knebel et al. (2019).3.
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Affiliation(s)
- Mawien Karaca
- German Federal Institute for Risk Assessment, Department of Pesticides Safety, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Kristin Fritsche
- German Federal Institute for Risk Assessment, Department Food Safety, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Dajana Lichtenstein
- German Federal Institute for Risk Assessment, Department Food Safety, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Özlem Vural
- German Federal Institute for Risk Assessment, Department Food Safety, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Katrin Kreuzer
- German Federal Institute for Risk Assessment, Department Food Safety, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Jimmy Alarcan
- German Federal Institute for Risk Assessment, Department Food Safety, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Albert Braeuning
- German Federal Institute for Risk Assessment, Department Food Safety, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Philip Marx-Stoelting
- German Federal Institute for Risk Assessment, Department of Pesticides Safety, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; Technical University of Berlin, Institute for Chemistry, Straße des 17. Juni 115, 10623 Berlin, Germany.
| | - Tewes Tralau
- German Federal Institute for Risk Assessment, Department of Pesticides Safety, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
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21
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Korsgen ME, Sun C, Seranova E, Zatyka M, Astuti D, Kataura T, Barrett T, Korolchuk VI, Sarkar S. Analysis of autophagy deficiency and cytotoxicity in autophagy-deficient human embryonic stem cell-derived neurons. STAR Protoc 2023; 4:102529. [PMID: 37624702 PMCID: PMC10474488 DOI: 10.1016/j.xpro.2023.102529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/28/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Autophagy, a catabolic process governing cellular and energy homeostasis, is essential for cell survival and human health. Here, we present a protocol for generating autophagy-deficient (ATG5-/-) human neurons from human embryonic stem cell (hESC)-derived neural precursors. We describe steps for analyzing loss of autophagy by immunoblotting. We then detail analysis of cell death by luminescence-based cytotoxicity assay and fluorescence-based TUNEL staining. This hESC-based experimental platform provides a genetic knockout model for undertaking autophagy studies relevant to human biology. For complete details on the use and execution of this protocol, please refer to Sun et al. (2023).1.
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Affiliation(s)
- Miriam E Korsgen
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Congxin Sun
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Elena Seranova
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Malgorzata Zatyka
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Dewi Astuti
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Tetsushi Kataura
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK
| | - Timothy Barrett
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; Department of Endocrinology, Birmingham Women's and Children's Hospital, Steelhouse Lane, Birmingham B4 6NH, UK
| | - Viktor I Korolchuk
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK.
| | - Sovan Sarkar
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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22
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Wang Y, Yan J. Intracellular ATP delivery to in vitro expanded mouse CD27 - γδ T cells. STAR Protoc 2023; 4:102532. [PMID: 37632744 PMCID: PMC10477735 DOI: 10.1016/j.xpro.2023.102532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/12/2023] [Accepted: 08/01/2023] [Indexed: 08/28/2023] Open
Abstract
Intracellular ATP supports the function of γδT17 cells in mice. Here, we present a protocol for intracellular ATP delivery to in vitro expanded mouse CD27- γδ T cells. We describe steps for pre-coating well plates, preparing lymphocytes, culturing CD27- γδ T cells, and ATP delivery. We then detail functional evaluation of γδ T cells by flow cytometry. Appropriate concentrations of control and ATP vesicles are detailed for intracellular ATP delivery, which can also be applied to other immune cells. For complete details on the use and execution of this protocol, please refer to Wang et al. (2023).1.
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Affiliation(s)
- Yunke Wang
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40202, USA; Department of Head and Neck Radiotherapy, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Zhejiang 310022, China
| | - Jun Yan
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40202, USA.
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23
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Jimenez-Rojo L, Mitsiadis TA. Kidney capsule transplantation of chemically treated embryonic murine tooth germs. STAR Protoc 2023; 4:102377. [PMID: 37379218 PMCID: PMC10320379 DOI: 10.1016/j.xpro.2023.102377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/25/2023] [Accepted: 05/23/2023] [Indexed: 06/30/2023] Open
Abstract
Subcapsular transplantation of developing tissues and organs into the richly vascularized murine kidney provides the necessary trophic support, thus ensuring proper completion of their growth.1,2,3 Here, we provide a protocol for kidney capsule transplantation that allows the full differentiation of embryonic teeth previously exposed to chemicals. We describe steps for dissection and in vitro culture of embryonic teeth, followed by transplantation of tooth germs. We then detail harvesting of kidneys for further analysis. For complete details on the use and execution of this protocol, please refer to Mitsiadis et al.4.
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Affiliation(s)
- Lucia Jimenez-Rojo
- Orofacial Development and Regeneration, Institute of Oral Biology, Centre for Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland.
| | - Thimios A Mitsiadis
- Orofacial Development and Regeneration, Institute of Oral Biology, Centre for Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland.
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24
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Carlisle AK, Götz J, Bodea LG. Three methods for examining the de novo proteome of microglia using BONCAT bioorthogonal labeling and FUNCAT click chemistry. STAR Protoc 2023; 4:102418. [PMID: 37432857 PMCID: PMC10511912 DOI: 10.1016/j.xpro.2023.102418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/04/2023] [Accepted: 06/08/2023] [Indexed: 07/13/2023] Open
Abstract
Bioorthogonal labeling and click chemistry techniques allow the detailed examination of cellular physiology through tagging and visualizing newly synthesized proteins. Here, we describe three methods applying bioorthogonal non-canonical amino acid tagging and fluorescent non-canonical amino acid tagging to quantify protein synthesis in microglia. We describe steps for cell seeding and labeling. We then detail microscopy, flow cytometry, and Western blotting techniques. These methods can be easily adapted for other cell types to explore cellular physiology in health and disease. For complete details on the use and execution of this protocol, please refer to Evans et al. (2021).1.
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Affiliation(s)
- Alison Keolani Carlisle
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Jürgen Götz
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Liviu-Gabriel Bodea
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, St Lucia, QLD 4072, Australia.
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25
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Chadarevian JP, Davtyan H, Lombroso SI, Bennett FC, Blurton-Jones M. CRISPR generation of CSF1R-G795A human microglia for robust microglia replacement in a chimeric mouse model. STAR Protoc 2023; 4:102490. [PMID: 37516973 PMCID: PMC10407259 DOI: 10.1016/j.xpro.2023.102490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
Chimeric mouse models have recently been developed to study human microglia in vivo. However, widespread engraftment of donor microglia within the adult brain has been challenging. Here, we present a protocol to introduce the G795A point mutation using CRISPR-Cas9 into the CSF1R locus of human pluripotent stem cells. We also describe an optimized microglial differentiation technique for transplantation into newborn or adult recipients. We then detail pharmacological paradigms to achieve widespread and near-complete engraftment of human microglia. For complete details on the use and execution of this protocol, please refer to Chadarevian et al. (2023).1.
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Affiliation(s)
- Jean Paul Chadarevian
- Department of Neurobiology & Behavior, University of California Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA.
| | - Hayk Davtyan
- Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
| | - Sonia I Lombroso
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - F Chris Bennett
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology & Behavior, University of California Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA.
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26
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Ladaigue S, Paget V, Lefranc AC, Quitoco M, Bacquer E, Milliat F, Guipaud O. Protocol for in vitro assessment of human monocyte transendothelial migration using a high-throughput live cell imaging system. STAR Protoc 2023; 4:102388. [PMID: 37379221 PMCID: PMC10331580 DOI: 10.1016/j.xpro.2023.102388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/08/2023] [Accepted: 05/25/2023] [Indexed: 06/30/2023] Open
Abstract
In vitro modeling of the different steps of immune cell recruitment is essential to decipher the role of endothelial cells in this process. Here, we present a protocol for the assessment of human monocyte transendothelial migration using a live cell imaging system. We describe steps for culture of fluorescent monocytic THP-1 cells and chemotaxis plate preparation with HUVEC monolayers. We then detail real-time analysis using the IncuCyte® S3 live-cell imaging system, image analysis, and assessment of transendothelial migration rates. For complete details on the use and execution of this protocol, please refer to Ladaigue et al.1.
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Affiliation(s)
- Ségolène Ladaigue
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRMed, 92260 Fontenay-aux-Roses, France; Sorbonne University, Doctoral College, 75005 Paris, France
| | - Vincent Paget
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRMed, 92260 Fontenay-aux-Roses, France
| | - Anne-Charlotte Lefranc
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRMed, 92260 Fontenay-aux-Roses, France
| | - Monica Quitoco
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRMed, 92260 Fontenay-aux-Roses, France
| | - Emilie Bacquer
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRMed, 92260 Fontenay-aux-Roses, France
| | - Fabien Milliat
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRMed, 92260 Fontenay-aux-Roses, France
| | - Olivier Guipaud
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRMed, 92260 Fontenay-aux-Roses, France.
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27
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Guyon J, Daubon T. Histological analysis of invasive glioblastoma organoids embedded in a 3D collagen matrix. STAR Protoc 2023; 4:102521. [PMID: 37597188 PMCID: PMC10462880 DOI: 10.1016/j.xpro.2023.102521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/30/2023] [Accepted: 07/27/2023] [Indexed: 08/21/2023] Open
Abstract
Organoids are unique tools to mimic how tumors evolve in a 3D environment. Here, we present a protocol to embed spheroids invading a 3D matrix into a paraffin mold. We describe steps for preparing spheroids, collagen and agarose inclusion, and paraffinization. We then detail procedures for sectioning, staining, and visualization. This protocol allows histological identification of markers expressed in cells escaping the tumor. For complete details on the use and execution of this protocol, please refer to Guyon et al. (2022).1.
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Affiliation(s)
- Joris Guyon
- CHU de Bordeaux, Service de Pharmacologie Médicale, 33000 Bordeaux, France; University Bordeaux, INSERM, BPH, U1219, 33000 Bordeaux, France
| | - Thomas Daubon
- University Bordeaux, CNRS, IBGC, UMR 5095, 33000 Bordeaux, France.
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28
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Liufu Z, Liu Y, He J. Protocol for siRNA-mediated TET1 knockdown during differentiation of human embryonic stem cells into definitive endoderm cells. STAR Protoc 2023; 4:102455. [PMID: 37467109 PMCID: PMC10371804 DOI: 10.1016/j.xpro.2023.102455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/31/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
TET1-mediated active DNA demethylation is required for endogenous retrovirus (ERV) enhancer activation during human ES differentiation into definitive endoderm (DE) cells. Here we present a protocol for siRNA-mediated TET1 knockdown during this process to decipher TET1's role in ERV activation and DE differentiation. We describe steps for inducing ES into DE cells. We then detail steps for knocking down TET1 during differentiation and for examining the effects of TET1 knockdown on LTR6B methylation, cell morphology, and gene expression. For complete details on the use and execution of this protocol, please refer to Wu et al. (2022).1.
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Affiliation(s)
- Zhongqi Liufu
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510799, China.
| | - Yujian Liu
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiangping He
- Guangzhou Laboratory, Bio-island, Guangzhou 510320, China.
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29
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Dutta Gupta S, Sen A, Priyadarshi P, Ta M. Enzyme-free isolation of mesenchymal stem cells from decidua basalis of the human placenta. STAR Protoc 2023; 4:102498. [PMID: 37573500 PMCID: PMC10448424 DOI: 10.1016/j.xpro.2023.102498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 08/15/2023] Open
Abstract
Mesenchymal stem cells (MSCs), also referred to as "medicinal signaling cells," have gained prominence as candidates for cell-based therapy and in clinical trials owing to their regenerative and therapeutic properties. Here, we present a protocol for isolating MSCs from the decidua basalis layer of human placenta using an explant culture approach. We describe steps for collecting, disinfecting, and plating placental tissue. We then detail procedures for characterizing the isolated MSCs through flow cytometry and in vitro differentiation.
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Affiliation(s)
- Srishti Dutta Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata (IISER Kolkata), Nadia, West Bengal 741246, India
| | - Ankita Sen
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata (IISER Kolkata), Nadia, West Bengal 741246, India
| | - Priyanshu Priyadarshi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata (IISER Kolkata), Nadia, West Bengal 741246, India
| | - Malancha Ta
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata (IISER Kolkata), Nadia, West Bengal 741246, India.
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30
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van Stalborch AMD, Clark AG, Sonnenberg A, Margadant C. Imaging and quantitative analysis of integrin-dependent cell-matrix adhesions. STAR Protoc 2023; 4:102473. [PMID: 37616164 PMCID: PMC10469561 DOI: 10.1016/j.xpro.2023.102473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 05/21/2023] [Accepted: 06/30/2023] [Indexed: 08/25/2023] Open
Abstract
Integrin-dependent cell-extracellular matrix adhesion is essential for wound healing, embryonic development, immunity, and tissue organization. Here, we present a protocol for the imaging and quantitative analysis of integrin-dependent cell-matrix adhesions. We describe steps for cell culture; virus preparation; lentiviral transduction; imaging with widefield, confocal, and total internal reflection fluorescence microscopy; and using a script for their quantitative analysis. We then detail procedures for analyzing adhesion dynamics by live-cell imaging and fluorescence recovery after photobleaching (FRAP). For complete details on the use and execution of this protocol, please refer to Margadant et al. (2012),1 van der Bijl et al. (2020),2 Amado-Azevedo et al. (2021).3.
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Affiliation(s)
| | - Andrew G Clark
- Institute of Cell Biology and Immunology, Stuttgart Research Center Systems Biology, University of Stuttgart, 70569 Stuttgart, Germany; Center for Personalized Medicine, University of Tübingen, Tübingen, Germany
| | - Arnoud Sonnenberg
- The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
| | - Coert Margadant
- Institute of Biology, Leiden University, 2333 BE Leiden, the Netherlands.
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31
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Chew N, Habarakada D, Firestein R, Daniel P. A protocol to establish cell line models from rare pediatric solid tumors. STAR Protoc 2023; 4:102537. [PMID: 37656627 PMCID: PMC10495629 DOI: 10.1016/j.xpro.2023.102537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/14/2023] [Accepted: 08/02/2023] [Indexed: 09/03/2023] Open
Abstract
Pediatric cell line models are important for basic and translational research. However, their establishment has been hampered by low success rates and the lack of a unified approach. Here, we present a protocol to establish pediatric cancer cell lines from rare childhood tumors. We describe the requirements for successful establishment, including an optimized dissociation technique, and the appropriate media conditions necessary for several types of rare but lethal forms of childhood cancers. For complete details on the use and execution of this protocol, please refer to Sun et al.1.
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Affiliation(s)
- Nicole Chew
- Next-Generation Precision Medicine Program, Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia.
| | - Dilru Habarakada
- Next-Generation Precision Medicine Program, Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Ron Firestein
- Next-Generation Precision Medicine Program, Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia.
| | - Paul Daniel
- Next-Generation Precision Medicine Program, Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
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32
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Backes EH, Zamproni LN, Delgado-Garcia LM, Pinto LA, Lemes RMR, Bartolomeo CS, Porcionatto MA. Protocol for designing and bioprinting multi-layered constructs to reconstruct an endothelial-epithelial 3D model. STAR Protoc 2023; 4:102467. [PMID: 37585294 PMCID: PMC10436237 DOI: 10.1016/j.xpro.2023.102467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/30/2023] [Accepted: 06/28/2023] [Indexed: 08/18/2023] Open
Abstract
3D bioprinting has opened new possibilities and elevated tissue engineering complexity. Here, we present a protocol to design a 3D model with two cell lineage layers (A549 and HUVEC) to recreate multi-cell constructs. We describe the steps for slicing the constructs, handling hydrogels, and detailing the bioprinting setup. These 3D-bioprinted constructs can be adapted to various cell models-from primary cell cultures to commercial cell lines and induced pluripotent stem cells (IPCs)-and applications, including drug screening and disease modeling. For complete details on the use and execution of this protocol, please refer to Cruz et al.1.
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Affiliation(s)
- Eduardo Henrique Backes
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, São Paulo 04044020, Brazil; Laboratory of Molecular Neurobiology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04039002, Brazil; Department of Materials Engineering (DEMa), Universidade Federal de São Carlos, São Carlos 13565905, Brazil; Graduate Program in Materials Science and Engineering, Universidade Federal de São Carlos, São Carlos 13565905, Brazil.
| | - Laura Nicoleti Zamproni
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, São Paulo 04044020, Brazil; Laboratory of Molecular Neurobiology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04039002, Brazil
| | - Lina Maria Delgado-Garcia
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, São Paulo 04044020, Brazil; Laboratory of Molecular Neurobiology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04039002, Brazil
| | - Leonardo Alves Pinto
- Graduate Program in Materials Science and Engineering, Universidade Federal de São Carlos, São Carlos 13565905, Brazil
| | | | - Cynthia Silva Bartolomeo
- Department of Interdisciplinary Health Sciences, Universidade Federal de São Paulo, Baixada Santista 11015020, Brazil
| | - Marimélia Aparecida Porcionatto
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, São Paulo 04044020, Brazil; Laboratory of Molecular Neurobiology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04039002, Brazil.
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33
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Stévenin V, Neefjes J. Soft agar colony formation assay to quantify mouse embryonic fibroblast transformation after Salmonella infection. STAR Protoc 2023; 4:102379. [PMID: 37379220 PMCID: PMC10320382 DOI: 10.1016/j.xpro.2023.102379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/20/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023] Open
Abstract
Links between bacterial infections and cancer are actively investigated. Cost-effective assays to quantify bacterial oncogenic potential can shed new light on these links. Here, we present a soft agar colony formation assay to quantify mouse embryonic fibroblast transformation after Salmonella Typhimurium infection. We describe how to infect and seed cells in soft agar for anchorage-independent growth, a hallmark of cell transformation. We further detail automated cell colony enumeration. This protocol is adaptable to other bacteria or host cells. For complete details on the use and execution of this protocol, please refer to Van Elsland et al.1.
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Affiliation(s)
- Virginie Stévenin
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center (LUMC), Leiden 2333ZC, the Netherlands.
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center (LUMC), Leiden 2333ZC, the Netherlands
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34
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Alfar HR, Pariser DN, Chanzu H, Joshi S, Coenen DM, Lykins J, Prakhya KS, Potash MJ, Chao W, Kelschenbach J, Volsky DJ, Metcalf-Pate K, Whiteheart SW. Protocol for optimizing production and quality control of infective EcoHIV virions. STAR Protoc 2023; 4:102368. [PMID: 37342907 PMCID: PMC10511864 DOI: 10.1016/j.xpro.2023.102368] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/03/2023] [Accepted: 05/18/2023] [Indexed: 06/23/2023] Open
Abstract
EcoHIV is a model of HIV infection that recapitulates aspects of HIV-1 pathology in mice. However, there are limited published protocols to guide EcoHIV virion production. Here, we present a protocol for producing infective EcoHIV virions and essential quality controls. We describe steps for viral purification, titering, and multiple techniques to analyze infection efficacy. This protocol produces high infectivity in C57BL/6 mice which will aid investigators in generating preclinical data.
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Affiliation(s)
- Hammodah R Alfar
- University of Kentucky, College of Medicine, Lexington, KY 40506, USA
| | - Daphne N Pariser
- Massachusetts Institute of Technology, Division of Comparative Medicine, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Harry Chanzu
- University of Kentucky, College of Medicine, Lexington, KY 40506, USA
| | - Smita Joshi
- University of Kentucky, College of Medicine, Lexington, KY 40506, USA
| | - Daniëlle M Coenen
- University of Kentucky, College of Medicine, Lexington, KY 40506, USA
| | - Joshua Lykins
- University of Kentucky, College of Medicine, Lexington, KY 40506, USA
| | | | - Mary Jane Potash
- Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA
| | - Wei Chao
- Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA
| | - Jennifer Kelschenbach
- Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA
| | - David J Volsky
- Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA
| | - Kelly Metcalf-Pate
- Massachusetts Institute of Technology, Division of Comparative Medicine, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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35
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Trillsch F, Czogalla B, Kraus F, Burges A, Mahner S, Kessler M. Protocol to optimize the biobanking of ovarian cancer organoids by accommodating patient-specific differences in stemness potential. STAR Protoc 2023; 4:102484. [PMID: 37585293 PMCID: PMC10436238 DOI: 10.1016/j.xpro.2023.102484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/23/2023] [Accepted: 07/10/2023] [Indexed: 08/18/2023] Open
Abstract
We present a protocol for effective biobanking of epithelial ovarian cancer organoids, considering the heterogeneous clinical presentation and high recurrence rates. Our protocol involves parallel testing of three media to identify patient-specific optimal conditions. We describe steps for tissue dissociation, differential seeding, organoid cultivation, and biobanking. We outline procedures for fixation, embedding, and staining for confocal imaging. Furthermore, we demonstrate that brief cultivation of isolates in 2D on plastic enhances organoid-forming potential in selected lines, expanding their application scope. For complete details on the use and execution of this protocol, please refer to Hoffmann et al.1.
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Affiliation(s)
- Fabian Trillsch
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, 81377 Munich, Germany; German Cancer Consortium (DKTK), Partner site Munich (LMU), 69120 Heidelberg, Germany
| | - Bastian Czogalla
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Fabian Kraus
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Alexander Burges
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Sven Mahner
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, 81377 Munich, Germany; German Cancer Consortium (DKTK), Partner site Munich (LMU), 69120 Heidelberg, Germany
| | - Mirjana Kessler
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, 81377 Munich, Germany; German Cancer Consortium (DKTK), Partner site Munich (LMU), 69120 Heidelberg, Germany.
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36
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Goncheva MI, Heinrichs DE. Protocol for studying co-infection between SARS-CoV-2 and Staphylococcus aureus in vitro. STAR Protoc 2023; 4:102411. [PMID: 37393614 PMCID: PMC10258577 DOI: 10.1016/j.xpro.2023.102411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/20/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Bacterial co-infection is one of the most common complications of SARS CoV-2 infection. Here, we present a protocol for the in vitro study of co-infection between SARS CoV-2 and Staphylococcus aureus. We describe steps for quantifying viral and bacterial replication kinetics in the same sample, with the optional extraction of host RNA and proteins. This protocol is applicable to many viral and bacterial strains and can be performed in different cell types. For complete details on the use and execution of this protocol, please refer to Goncheva et al.1.
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Affiliation(s)
- Mariya I Goncheva
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada.
| | - David E Heinrichs
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1, Canada.
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37
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Loubser C, Nikitina NV. Protocol to establish an oviduct epithelial cell line derived from Gallus gallus using Percoll for in vitro validation of recombinant proteins. STAR Protoc 2023; 4:102495. [PMID: 37542716 PMCID: PMC10432238 DOI: 10.1016/j.xpro.2023.102495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/09/2023] [Accepted: 07/17/2023] [Indexed: 08/07/2023] Open
Abstract
In vitro validation of therapeutic and recombinant proteins expressed from transgenic chickens is limited by the co-culture of fibroblasts. Here, we present a protocol for isolating pure epithelial cells derived from the magnum tubular glands of the chicken oviduct. We describe steps for preparing solutions and buffers, tissue collection, processing, dissociation, and Percoll density centrifugation to separate the epithelial cells from co-isolated fibroblasts. We then detail procedures for expressing a recombinant IgG antibody in the Percoll-derived epithelial cell line.
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Affiliation(s)
- Chiron Loubser
- University of the Witwatersrand, School of Molecular and Cell Biology, Johannesburg, Gauteng 2000, South Africa.
| | - Natalya V Nikitina
- University of the Witwatersrand, School of Molecular and Cell Biology, Johannesburg, Gauteng 2000, South Africa.
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38
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Kusakabe M, Sugasawa K. Fluorescence-microscopy-based assay assessing regulatory mechanisms of global genome nucleotide excision repair in cultured cells. STAR Protoc 2023; 4:102378. [PMID: 37352107 PMCID: PMC10320318 DOI: 10.1016/j.xpro.2023.102378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/14/2023] [Accepted: 05/23/2023] [Indexed: 06/25/2023] Open
Abstract
It remains uncertain how global genome nucleotide excision repair (GG-NER) efficiently removes various helix distorting DNA lesions in the cell nucleus. Here, we present a protocol to assess the contribution of factors of interest to GG-NER using two types of fluorescence-microscopy-based techniques. First, we describe steps for analyzing the localization of the factors upon local ultraviolet (UV) irradiation. We then detail the second technique, which quantifies the removal of UV-induced photolesions combined with lesion-specific antibodies and program-based image analysis. For complete details on the use and execution of this protocol, please refer to Kusakabe et al.1.
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Affiliation(s)
- Masayuki Kusakabe
- Biosignal Research Center and Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center and Graduate School of Science, Kobe University, Kobe 657-8501, Japan.
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39
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Scherer SD, Zhao L, Butterfield AJ, Yang CH, Cortes-Sanchez E, Guillen KP, Welm BE, Welm AL. Breast cancer PDxO cultures for drug discovery and functional precision oncology. STAR Protoc 2023; 4:102402. [PMID: 37402170 PMCID: PMC10339058 DOI: 10.1016/j.xpro.2023.102402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/21/2023] [Accepted: 06/01/2023] [Indexed: 07/06/2023] Open
Abstract
Patient-derived xenografts (PDXs) have clinical value but are time-, cost-, and labor-intensive and thus ill-suited for large-scale experiments. Here, we present a protocol to convert PDX tumors into PDxOs for long-term cultures amenable to moderate-throughput drug screens, including in-depth PDxO validation. We describe steps for PDxO preparation and mouse cell removal. We then detail PDxO validation and characterization and drug response assay. Our PDxO drug screening platform can predict therapy response in vivo and inform functional precision oncology for patients. For complete details on the use and execution of this protocol, please refer to Guillen et al.1.
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Affiliation(s)
- Sandra D Scherer
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Ling Zhao
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Andrew J Butterfield
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Chieh-Hsiang Yang
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Emilio Cortes-Sanchez
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Katrin P Guillen
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Bryan E Welm
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA; Department of Surgery, University of Utah, 30 N 1900 E, Salt Lake City, UT 84132, USA.
| | - Alana L Welm
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA.
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40
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Sanchini C, Rosito M, Comincini A, De Panfilis S, Bartolini F, Di Angelantonio S. Protocol for observing microtubules and microtubule ends in both fixed and live primary microglia cells. STAR Protoc 2023; 4:102499. [PMID: 37573502 PMCID: PMC10448205 DOI: 10.1016/j.xpro.2023.102499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/26/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023] Open
Abstract
Microtubule dynamics and orientation have crucial roles in many vital cellular processes. However, functional live imaging of microtubules and/or microtubule ends in primary microglia can be challenging. Here, we present a protocol for observing microtubules and microtubule ends in both fixed and live primary microglia cells. We describe steps for microglia culture and in vitro stimulation, SiR-tubulin labeling, lentivirus preparation, live imaging, immunostaining, and image acquisition. We also provide procedures for SiR-tubulin, EB3-EGFP, and EB1 analyses. For complete details on the use and execution of this protocol, please refer to Rosito et al. (2023).1.
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Affiliation(s)
- Caterina Sanchini
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, 00161 Rome, Italy
| | - Maria Rosito
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, 00161 Rome, Italy; Department of Physiology and Pharmacology, Sapienza University, 00185 Rome, Italy
| | - Alessandro Comincini
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Simone De Panfilis
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, 00161 Rome, Italy
| | - Francesca Bartolini
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA.
| | - Silvia Di Angelantonio
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, 00161 Rome, Italy; Department of Physiology and Pharmacology, Sapienza University, 00185 Rome, Italy; D-Tails s.r.l., 00165 Rome, Italy.
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41
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Cybulski JD, Leung KS, Leung CON, Baker DM, Lee TKW. Protocol to track the biosynthesis of cholesterol in cultured HCC cells using 13C compound-specific stable isotopic tracers. STAR Protoc 2023; 4:102506. [PMID: 37594893 PMCID: PMC10462878 DOI: 10.1016/j.xpro.2023.102506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/21/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023] Open
Abstract
Cholesterol biosynthesis supports proliferation and drives resistance to tyrosine kinase inhibitor (TKI) therapy in hepatocellular carcinoma (HCC). Here, we present a protocol for using stable isotopic tracers to track the biosynthesis of cholesterol in cultured HCC cells. We describe steps for cell preparation, incubation, separation, and homogenization. We then detail lipid extraction and compound-specific isotope analysis for comparing and quantifying cholesterol synthesis between TKI-resistant HCC cells and their mock counterparts. This protocol can be expanded for use with other shorter-chained lipids.
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Affiliation(s)
- Jonathan D Cybulski
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, Hong Kong SAR; Smithsonian Tropical Research Institute, Balboa, Republic of Panama.
| | - Kit Sum Leung
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Carmen Oi Ning Leung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR
| | - David M Baker
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama.
| | - Terence Kin Wah Lee
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR; State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR.
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42
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Coppo R, Kondo J, Onuma K, Inoue M. Tracking the growth fate of single cells and isolating slow-growing cells in human colorectal cancer organoids. STAR Protoc 2023; 4:102395. [PMID: 37384521 PMCID: PMC10511865 DOI: 10.1016/j.xpro.2023.102395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/02/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Patient-derived tumor organoids are three-dimensionally cultured cancer cells that enable a suitable platform for studying heterogeneity and plasticity of cancer. We present a protocol for tracking the growth fate of single cells and isolating slow-growing cells in human colorectal cancer organoids. We describe steps for organoid preparation and culturing using the cancer-tissue-originating spheroid method, maintaining cell-cell contact throughout. We then detail a single-cell-derived spheroid-forming and growth assay, confirming single-cell plating, monitoring growth over time, and isolating slow-growing cells. For complete details on the use and execution of this protocol, please refer to Coppo et al.1.
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Affiliation(s)
- Roberto Coppo
- Department of Clinical Bio-resource Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
| | - Jumpei Kondo
- Department of Clinical Bio-resource Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kunishige Onuma
- Department of Clinical Bio-resource Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Inoue
- Department of Clinical Bio-resource Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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43
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Fukushima Y, Minato N, Hattori M. Protocol for the isolation of mouse senescence-associated CD4 + T cells using flow cytometry and functional assays. STAR Protoc 2023; 4:102472. [PMID: 37515759 PMCID: PMC10400959 DOI: 10.1016/j.xpro.2023.102472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/30/2023] [Accepted: 06/30/2023] [Indexed: 07/31/2023] Open
Abstract
Senescence-associated (SA) CD4+ T cells, which increase with age, may underlie the development of autoimmunity and chronic inflammation, but their pathological function remains understudied. Here, we present a protocol to isolate CD153+ SA-T cells and evaluate their characteristic responses upon T cell receptor stimulation. We describe steps for the isolation of CD153+ SA-T cells using flow cytometry and in vitro culture with stimulatory antibodies against CD3, CD28, and CD153. We then detail the assessment of the proliferation capacity and cytokine production. For complete details on the use and execution of this protocol, please refer to Fukushima et al. (2022).1.
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Affiliation(s)
- Yuji Fukushima
- Department of Regulation of Neurocognitive Disorders (Cyn-K project), Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Department of Immunosenescence, Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
| | - Nagahiro Minato
- Medical Innovation Center, Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Masakazu Hattori
- Department of Immunosenescence, Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Laboratory of Tumor Tissue Response, Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
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44
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Lian E, Pietrobon A, Stanford WL. Differentiation and single-cell RNA-seq analyses of human pluripotent-stem-cell-derived renal organoids. STAR Protoc 2023; 4:102314. [PMID: 37220001 DOI: 10.1016/j.xpro.2023.102314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/24/2023] [Accepted: 04/25/2023] [Indexed: 05/25/2023] Open
Abstract
Here, we present a protocol for the maintenance and differentiation of human pluripotent stem cells into renal organoids. We describe steps for using a series of readily made differentiation media, multiplexed sample single-cell RNA-seq analysis, quality control, and validation of organoids using immunofluorescence. This provides a rapid and reproducible model of human kidney development and renal disease modeling. Finally, we detail genome engineering using CRISPR-Cas9 homology-directed repair for the generation of renal disease models. For complete details on the use and execution of this protocol, please refer to Pietrobon et al.1.
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Affiliation(s)
- Eric Lian
- The Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Ottawa Institute of Systems Biology, Ottawa, ON K1H 8L1, Canada.
| | - Adam Pietrobon
- The Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Ottawa Institute of Systems Biology, Ottawa, ON K1H 8L1, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - William L Stanford
- The Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Ottawa Institute of Systems Biology, Ottawa, ON K1H 8L1, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8L1, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
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45
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Rimmer N, Liang CY, Coelho R, Lopez MN, Jacob F. Generation of endogenously tagged E-cadherin cells using gene editing via non-homologous end joining. STAR Protoc 2023; 4:102305. [PMID: 37178110 DOI: 10.1016/j.xpro.2023.102305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/31/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
We provide a protocol using non-homologous end joining to integrate an oligonucleotide sequence of a fluorescence protein at the CDH1 locus encoding for the epithelial glycoprotein E-cadherin. We describe steps for implementing the CRISPR-Cas9-mediated knock-in procedure by transfecting a cancer cell line with a pool of plasmids. The EGFP-tagged cells are traced by fluorescence-activated cell sorting and validated on DNA and protein levels. The protocol is flexible and can be applied in principle to any protein expressed in a cell line. For complete details on the use and execution of this protocol, please refer to Cumin et al. (2022).1.
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Affiliation(s)
- Natalie Rimmer
- Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel 4031, Switzerland.
| | - Ching-Yeu Liang
- Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel 4031, Switzerland
| | - Ricardo Coelho
- Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel 4031, Switzerland
| | - Monica Nunez Lopez
- Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel 4031, Switzerland
| | - Francis Jacob
- Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel 4031, Switzerland; Hospital for Women, University Hospital Basel, Basel 4031, Switzerland.
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46
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Roelofsen LM, Voabil P, de Bruijn M, Herzig P, Zippelius A, Schumacher TN, Thommen DS. Protocol for ex vivo culture of patient-derived tumor fragments. STAR Protoc 2023; 4:102282. [PMID: 37149855 DOI: 10.1016/j.xpro.2023.102282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/27/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023] Open
Abstract
The lack of suitable models currently hampers our understanding of how the tumor microenvironment responds to immunotherapy treatment. Here, we present a protocol for ex vivo culture of patient-derived tumor fragments (PDTFs). We describe the steps for tumor collection, generation and cryopreservation of PDTFs, and their subsequent thawing. We detail culture of PDTFs and their preparation for analysis. This protocol preserves the tumor microenvironment's composition, architecture, and cellular interactions, which can be perturbed by ex vivo treatment. For complete details on the use and execution of this protocol, please refer to Voabil et al. (2021).1.
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Affiliation(s)
- Lisanne M Roelofsen
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paula Voabil
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marjolein de Bruijn
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Petra Herzig
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Alfred Zippelius
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Hematology, LUMC, Leiden, the Netherlands
| | - Daniela S Thommen
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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47
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Goto A, Hanada K. Protocol for casein kinase 1γ3 CSNK1G3 gene knockout and recombinant gene expression in cultured HeLa cells. STAR Protoc 2023; 4:102251. [PMID: 37119140 PMCID: PMC10173854 DOI: 10.1016/j.xpro.2023.102251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/23/2023] [Accepted: 03/28/2023] [Indexed: 04/30/2023] Open
Abstract
Casein kinase 1γ is a subfamily of the casein kinase 1 family. Here, we present a protocol for gene knockout of CSNK1G3 in human cells and cloning and/or expression of CSNK1G1-3 cDNAs using a retroviral vector system. We first describe the genome editing procedures, including sgRNA design, introduction into HeLa cells, and verification of genome editing. Next, we describe the procedures for cloning human CSNK1G cDNAs, introduction into HeLa cells, and expression verification by western blot analysis. For complete information on the generation and use of this protocol, please refer to Goto et al.1.
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Affiliation(s)
- Asako Goto
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan; Department of Virology III, National Institute of Infectious Diseases, Musashimurayama City, Tokyo 208-0011, Japan.
| | - Kentaro Hanada
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan; Department of Quality Assurance, Radiation Safety, and Information System, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan
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48
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Guo Y, Miller B, Heim M, Gutierrez-Garcia A, Jaskula-Sztul R, Ren B, Sewell-Loftin MK. Protocol for indirect and direct co-culture between human cancer cells and endothelial cells. STAR Protoc 2023; 4:102177. [PMID: 37086411 PMCID: PMC10160801 DOI: 10.1016/j.xpro.2023.102177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/30/2022] [Accepted: 02/23/2023] [Indexed: 04/23/2023] Open
Abstract
The cross talk between cancer cells and endothelial cells (ECs) within the tumor microenvironment plays a critical role in tumor progression, recurrence, and cancer stemness. Here, we present a protocol containing two in vitro approaches to study such interactions. We first describe an indirect co-culture system to study the regulation of stemness markers in cancer cells by secreted factors from ECs. We then detail a direct co-culture system to study juxtracrine communications between the cell types. For complete details on the use and execution of this protocol, please refer to Sewell-Loftin et al.1 and Guo et al.2.
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Affiliation(s)
- Yichen Guo
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham AL 35294, USA; Department of Surgery, University of Alabama at Birmingham, Birmingham AL 35233, USA
| | - Bronte Miller
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham AL 35294, USA
| | - Michael Heim
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham AL 35294, USA
| | - Ana Gutierrez-Garcia
- Department of Surgery, University of Alabama at Birmingham, Birmingham AL 35233, USA
| | - Renata Jaskula-Sztul
- Department of Surgery, University of Alabama at Birmingham, Birmingham AL 35233, USA; O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham AL 35233, USA
| | - Bin Ren
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham AL 35294, USA; Department of Surgery, University of Alabama at Birmingham, Birmingham AL 35233, USA; O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham AL 35233, USA.
| | - Mary Kathryn Sewell-Loftin
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham AL 35294, USA; O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham AL 35233, USA.
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49
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Martinez-Ordoñez A, Cid-Diaz T, Duran A, Han Q, Moscat J, Diaz-Meco MT. Whole-mount staining of mouse colorectal cancer organoids and fibroblast-organoid co-cultures. STAR Protoc 2023; 4:102243. [PMID: 37083323 PMCID: PMC10323124 DOI: 10.1016/j.xpro.2023.102243] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/27/2023] [Accepted: 03/24/2023] [Indexed: 04/22/2023] Open
Abstract
Imaging organoid culture provides an excellent tool for studying complex diseases such as cancer. However, retaining the morphology of intact organoids for immunolabeling has been challenging. Here, we describe a protocol for immunofluorescence staining in intact colorectal cancer organoids derived from mice. We also describe additional steps for co-culture with mouse fibroblasts to enable the study of interactions with other cellular components of the tissue microenvironment. For complete details on the use and execution of this protocol, please refer to Martinez-Ordoñez et al. (2023).1.
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Affiliation(s)
- Anxo Martinez-Ordoñez
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Tania Cid-Diaz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Angeles Duran
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Qixiu Han
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jorge Moscat
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Maria T Diaz-Meco
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
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50
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Wasserman JS, Feiser F, Palacio S, Patel K, Gonzalez J, Fowle H, Graña X. Protocol to assess substrate dephosphorylation by serine/threonine phosphoprotein phosphatases in vitro. STAR Protoc 2023; 4:102148. [PMID: 37074907 DOI: 10.1016/j.xpro.2023.102148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/18/2023] [Accepted: 02/10/2023] [Indexed: 04/20/2023] Open
Abstract
Serine/threonine protein phosphatase 2 (PP2A) forms heterotrimeric holoenzymes, where a scaffold subunit bridges the PP2A catalytic subunit to a B regulatory subunit, e.g., B55α. The PP2A/B55α holoenzyme plays key roles in signaling and cell-cycle control targeting multiple substrates. Here, we describe semiquantitative approaches to determine PP2A/B55α substrate specificity. Parts I and II detail approaches to assess PP2A/B55α-mediated dephosphorylation of immobilized substrate peptide variants. Parts III and IV detail methods to assess PP2A/B55α-substrate-binding specificity. These approaches are adaptable to other serine/threonine phosphatases. For complete details on the use and execution of this protocol, please refer to Fowle et al..1.
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Affiliation(s)
- Jason S Wasserman
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
| | - Felicity Feiser
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Seren Palacio
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Kishan Patel
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Joy Gonzalez
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Holly Fowle
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Xavier Graña
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
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