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Xu J, Morten KJ. Raman micro-spectroscopy as a tool to study immunometabolism. Biochem Soc Trans 2024; 52:733-745. [PMID: 38477393 DOI: 10.1042/bst20230794] [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: 12/05/2023] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
Abstract
In the past two decades, immunometabolism has emerged as a crucial field, unraveling the intricate molecular connections between cellular metabolism and immune function across various cell types, tissues, and diseases. This review explores the insights gained from studies using the emerging technology, Raman micro-spectroscopy, to investigate immunometabolism. Raman micro-spectroscopy provides an exciting opportunity to directly study metabolism at the single cell level where it can be combined with other Raman-based technologies and platforms such as single cell RNA sequencing. The review showcases applications of Raman micro-spectroscopy to study the immune system including cell identification, activation, and autoimmune disease diagnosis, offering a rapid, label-free, and minimally invasive analytical approach. The review spotlights three promising Raman technologies, Raman-activated cell sorting, Raman stable isotope probing, and Raman imaging. The synergy of Raman technologies with machine learning is poised to enhance the understanding of complex Raman phenotypes, enabling biomarker discovery and comprehensive investigations in immunometabolism. The review encourages further exploration of these evolving technologies in the rapidly advancing field of immunometabolism.
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Affiliation(s)
- Jiabao Xu
- Division of Biomedical Engineering, James Watt School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| | - Karl J Morten
- Nuffield Department of Women's and Reproductive Health, University of Oxford, The Women Centre, John Radcliffe Hospital, Headley Way, Headington, Oxford OX3 9DU, U.K
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2
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Xu J, Chen H, Wang C, Ma Y, Song Y. Raman Flow Cytometry and Its Biomedical Applications. Biosensors (Basel) 2024; 14:171. [PMID: 38667164 PMCID: PMC11048678 DOI: 10.3390/bios14040171] [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] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024]
Abstract
Raman flow cytometry (RFC) uniquely integrates the "label-free" capability of Raman spectroscopy with the "high-throughput" attribute of traditional flow cytometry (FCM), offering exceptional performance in cell characterization and sorting. Unlike conventional FCM, RFC stands out for its elimination of the dependency on fluorescent labels, thereby reducing interference with the natural state of cells. Furthermore, it significantly enhances the detection information, providing a more comprehensive chemical fingerprint of cells. This review thoroughly discusses the fundamental principles and technological advantages of RFC and elaborates on its various applications in the biomedical field, from identifying and characterizing cancer cells for in vivo cancer detection and surveillance to sorting stem cells, paving the way for cell therapy, and identifying metabolic products of microbial cells, enabling the differentiation of microbial subgroups. Moreover, we delve into the current challenges and future directions regarding the improvement in sensitivity and throughput. This holds significant implications for the field of cell analysis, especially for the advancement of metabolomics.
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Affiliation(s)
- Jiayang Xu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Hangzhou 310058, China;
- Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Hongyi Chen
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, China
| | - Ce Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yuting Ma
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, China
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Spiteri AG, Pilkington KR, Wishart CL, Macia L, King NJC. High-Dimensional Methods of Single-Cell Microglial Profiling to Enhance Understanding of Neuropathological Disease. Curr Protoc 2024; 4:e985. [PMID: 38439574 DOI: 10.1002/cpz1.985] [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] [Indexed: 03/06/2024]
Abstract
Microglia are the innate myeloid cells of the central nervous system (CNS) parenchyma, functionally implicated in almost every defined neuroinflammatory and neurodegenerative disorder. Current understanding of disease pathogenesis for many neuropathologies is limited and/or lacks reliable diagnostic markers, vaccines, and treatments. With the increasing aging of society and rise in neurogenerative diseases, improving our understanding of their pathogenesis is essential. Analysis of microglia from murine disease models provides an investigative tool to unravel disease processes. In many neuropathologies, bone-marrow-derived monocytes are recruited to the CNS, adopting a phenotype similar to that of microglia. This significantly confounds the accurate identification of cell-type-specific functions and downstream therapeutic targeting. The increased capacity to analyze more phenotypic markers using spectral-cytometry-based technologies allows improved separation of microglia from monocyte-derived cells. Full-spectrum profiling enables enhanced marker resolution, time-efficient analysis of >40 fluorescence parameters, and extraction of cellular autofluorescence parameters. Coupling this system with additional cytometric technologies, including cell sorting and high-parameter imaging, can improve the understanding of microglial phenotypes in disease. To this end, we provide detailed, step-by-step protocols for the analysis of murine brain tissue by high-parameter ex vivo cytometric analysis using the Aurora spectral cytometer (Cytek), including best practices for unmixing and autofluorescence extraction, cell sorting for single-cell RNA analysis, and imaging mass cytometry. Together, this provides a toolkit for researchers to comprehensively investigate microglial disease processes at protein, RNA, and spatial levels for the identification of therapeutic targets in neuropathology. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Processing the mouse brain into a single-cell suspension for microglia isolation Basic Protocol 2: Staining single-cell mouse brain suspensions for microglial phenotyping by spectral cytometry Basic Protocol 3: Flow cytometric sorting of mouse microglia for ex vivo analysis Basic Protocol 4: Processing the mouse brain for imaging mass cytometry for spatial microglia analysis.
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Affiliation(s)
- Alanna G Spiteri
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | | | - Claire L Wishart
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Laurence Macia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- Sydney Cytometry, The University of Sydney and Centenary Institute, Sydney, Australia
| | - Nicholas J C King
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- Sydney Cytometry, The University of Sydney and Centenary Institute, Sydney, Australia
- The University of Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, Australia
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Robinson M, Zhou K, Kung SHY, Karaoğlanoğlu F, Golin A, Safa A, Cai C, Witherspoon L, Hach F, Flannigan R. A novel sorting method for the enrichment of early human spermatocytes from clinical biopsies. F S Sci 2024:S2666-335X(24)00015-6. [PMID: 38369016 DOI: 10.1016/j.xfss.2024.02.002] [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] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
OBJECTIVE To determine if early spermatocytes can be enriched from a human testis biopsy using fluorescence-activated cell sorting (FACS). DESIGN Potential surface markers for early spermatocytes were identified using bioinformatics analysis of single-cell RNA-sequenced human testis tissue. Testicular sperm extraction samples from three participants with normal spermatogenesis were digested into single-cell suspensions and cryopreserved. Two to four million cells were obtained from each and sorted by FACS as separate biologic replicates using antibodies for the identified surface markers. A portion from each biopsy remained unsorted to serve as controls. The sorted cells were then characterized for enrichment of early spermatocytes. SETTING A laboratory study. PATIENTS Three men with a diagnosis of obstructive azoospermia (age range, 30-40 years). INTERVENTION None. MAIN OUTCOME MEASURES Sorted cells were characterized for RNA expression of markers encompassing the stages of spermatogenesis. Sorting markers were validated by their reactivity on human testis formalin-fixed paraffin-embedded tissue. RESULTS Serine protease 50 (TSP50) and SWI5-dependent homologous recombination repair protein 1 were identified as potential surface proteins specific for early spermatocytes. After FACS sorting, the TSP50-sorted populations accounted for 1.6%-8.9% of total populations and exhibited the greatest average-fold increases in RNA expression for the premeiotic marker stimulated by retinoic acid (STRA8), by 23-fold. Immunohistochemistry showed the staining pattern for TSP50 to be strong in premeiotic undifferentiated embryonic cell transcription factor 1-/doublesex and Mab-3 related transcription factor 1-/STRA8+ spermatogonia as well as SYCP3+/protamine 2- spermatocytes. CONCLUSION This work shows that TSP50 can be used to enrich early STRA8-expressing spermatocytes from human testicular biopsies, providing a means for targeted single-cell RNA sequencing analysis and in vitro functional interrogation of germ cells during the onset of meiosis. This could enable investigation into details of the regulatory pathways underlying this critical stage of spermatogenesis, previously difficult to enrich from whole tissue samples.
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Affiliation(s)
- Meghan Robinson
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Kevin Zhou
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sonia H Y Kung
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Fatih Karaoğlanoğlu
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; School of Computing Science, Department of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Andrew Golin
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Armita Safa
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charley Cai
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Luke Witherspoon
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada; Department of Urology, the Ottawa Hospital, Ottawa, Ontario, Canada
| | - Faraz Hach
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan Flannigan
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada; Department of Urology, Weill Cornell Medicine, New York, New York.
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Fux AC, Casonato Melo C, Schlahsa L, Burzan NB, Felsberger A, Gessner I, Fauerbach JA, Horejs-Hoeck J, Droste M, Siewert C. Generation of Endotoxin-Specific Monoclonal Antibodies by Phage and Yeast Display for Capturing Endotoxin. Int J Mol Sci 2024; 25:2297. [PMID: 38396974 PMCID: PMC10889169 DOI: 10.3390/ijms25042297] [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: 12/21/2023] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Endotoxin, a synonym for lipopolysaccharide (LPS), is anchored in the outer membranes of Gram-negative bacteria. Even minute amounts of LPS entering the circulatory system can have a lethal immunoactivating effect. Since LPS is omnipresent in the environment, it poses a great risk of contaminating any surface or solution, including research products and pharmaceuticals. Therefore, monitoring LPS contamination and taking preventive or decontamination measures to ensure human safety is of the utmost importance. Nevertheless, molecules used for endotoxin detection or inhibition often suffer from interferences, low specificity, and low affinity. For this reason, the selection of new binders that are biocompatible, easy to produce, and that can be used for biopharmaceutical applications, such as endotoxin removal, is of high interest. Powerful techniques for selecting LPS-binding molecules in vitro are display technologies. In this study, we established and compared the selection and production of LPS-specific, monoclonal, human single-chain variable fragments (scFvs) through two display methods: yeast and phage display. After selection, scFvs were fused to a human constant fragment crystallizable (Fc). To evaluate the applicability of the constructs, they were conjugated to polystyrene microbeads. Here, we focused on comparing the functionalized beads and their LPS removal capacity to a polyclonal anti-lipid A bead. Summarized, five different scFvs were selected through phage and yeast display, with binding properties comparable to a commercial polyclonal antibody. Two of the conjugated scFv-Fcs outperformed the polyclonal antibody in terms of the removal of LPS in aqueous solution, resulting in 265 times less residual LPS in solution, demonstrating the potential of display methods to generate LPS-specific binding molecules.
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Affiliation(s)
- Alexandra C. Fux
- Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, 5020 Salzburg, Austria
- Research and Development Department, Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany
| | - Cristiane Casonato Melo
- Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, 5020 Salzburg, Austria
- Research and Development Department, Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany
| | - Laura Schlahsa
- Research and Development Department, Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany
| | - Nico B. Burzan
- Research and Development Department, Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany
| | - André Felsberger
- Research and Development Department, Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany
| | - Isabel Gessner
- Research and Development Department, Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany
| | - Jonathan A. Fauerbach
- Research and Development Department, Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany
| | - Jutta Horejs-Hoeck
- Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, 5020 Salzburg, Austria
| | - Miriam Droste
- Research and Development Department, Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany
| | - Christiane Siewert
- Research and Development Department, Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany
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Perez-Gonzalez A, Lopes T, Martinez L, Bispo C, Gardner R, Riddell A. Evaluation of Sort Recovery via Rmax. Curr Protoc 2024; 4:e986. [PMID: 38363042 DOI: 10.1002/cpz1.986] [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] [Indexed: 02/17/2024]
Abstract
Cell sorting performance can be evaluated in regard to the purity and recovery of the sorted fractions. The purity provides checks on sample quality, acquisition settings, gating strategy, and the sort decisions made by the instrument, but alone it is not sufficient to evaluate sorting performance. Recovery, defined here as the number of target particles sorted relative to the number of original target particles to be sorted, is a key metric of sort fitness and performance but is often neglected due to difficulties in its measurement. Both purity and recovery require re-sampling of the sorted fraction, but unlike determining purity, calculating recovery calls for the absolute counting of particles in the sorted fraction that comes with large errors, and may not be feasible for rare populations or precious samples. Here, we describe a recently developed metric and method for calculating sort recovery called Rmax, representing the maximum expected recovery for a particular set of instrument settings. Rmax calculation avoids re-sampling of the total sorted fraction and absolute counting, being instead based on the ratios of target and non-target populations in the original pre-sort sample and in the waste stream or center stream catch. The Rmax method is ideal to evaluate and troubleshoot the optimum drop-charge delay of the sorter or any instrument-related failures that will affect sort performance. It can be used as a daily quality control check but can be particularly useful to assess instrument fitness before single-cell or rare population sorts. Because the sorted fraction is not perturbed, we can calculate Rmax during the sort run. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Evaluating sorter setup with Rmax Basic Protocol 2: Finding the maximum Rmax: scanning over the drop charge delay Alternate Protocol: Finding the maximum Rmax for cells: scanning over the drop charge delay Basic Protocol 3: Estimating sorted cell number with Rmax.
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Affiliation(s)
- Alexis Perez-Gonzalez
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Melbourne Cytometry Platform, The University of Melbourne, Parkville, Victoria, Australia
| | - Telma Lopes
- Roche Pharma Research and Early Development (pRED), Basel, Switzerland
| | - Lola Martinez
- Flow Cytometry Core Unit. Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Claudia Bispo
- Flow Cytometry Core Facility, AbbVie Biotherapeutics Inc., South San Francisco, California
| | - Rui Gardner
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andy Riddell
- Flow Cytometry Science and Technology Platform, The Francis Crick Institute, London, United Kingdom
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Macaraniag C, Zhou J, Li J, Putzbach W, Hay N, Papautsky I. Microfluidic isolation of breast cancer circulating tumor cells from microvolumes of mouse blood. Electrophoresis 2023; 44:1859-1867. [PMID: 37528726 DOI: 10.1002/elps.202300108] [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: 05/16/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 08/03/2023]
Abstract
Liquid biopsy has shown significant research and clinical implications in cancer. Particularly, the isolation of circulating tumor cells (CTCs) in preclinical studies can provide crucial information about disease progression and therefore may guide treatment decisions. Microfluidic isolation systems have played a considerable role in CTC isolation for cancer studies, disease diagnosis, and prognosis. CTCs are often studied using preclinical animal models such as xenografts or syngeneic models. However, most isolation systems are tested on human cell lines and human blood, whereas less validation studies are done on preclinical samples such as CTCs from mouse models. Here, we demonstrate and evaluate a complete workflow of a sized-based inertial microfluidic device to isolate CTCs from blood using exclusively mouse blood and mouse cancer cell lines. We then incorporate the cytospin, a commonly used method for enumeration of small number of cells in a glass slide to quantify the total cell yield of our workflow.
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Affiliation(s)
- Celine Macaraniag
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois, USA
| | - Jian Zhou
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois, USA
- University of Illinois Cancer Center, Chicago, Illinois, USA
| | - Jing Li
- Department of Biochemistry and Molecular Genetics, University of Illinois Chicago, Chicago, Illinois, USA
| | - William Putzbach
- Department of Biochemistry and Molecular Genetics, University of Illinois Chicago, Chicago, Illinois, USA
| | - Nissim Hay
- University of Illinois Cancer Center, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois Chicago, Chicago, Illinois, USA
| | - Ian Papautsky
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois, USA
- University of Illinois Cancer Center, Chicago, Illinois, USA
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Zhang W, Wei P, Liu L, Ding T, Yang Y, Jin P, Zhang L, Zhao Z, Wang M, Hu B, Jin X, Xu Z, Zhang H, Song Y, Wang L, Zhong S, Chen J, Yang Z, Chen Z, Wu Y, Ye Z, Xu Y, Zhang Y, Wen LP. AIE-enabled transfection-free identification and isolation of viable cell subpopulations differing in the level of autophagy. Autophagy 2023; 19:3062-3078. [PMID: 37533292 PMCID: PMC10621245 DOI: 10.1080/15548627.2023.2235197] [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: 05/16/2022] [Revised: 07/02/2023] [Accepted: 07/06/2023] [Indexed: 08/04/2023] Open
Abstract
ABBREVIATIONS 3-MA, 3-methyladenine; AIE, aggregation-induced emission; AIEgens, aggregation-induced emission luminogens; ATG5, autophagy related 5; BMDM, bone marrow-derived macrophage; CQ, chloroquine; DiD, 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbocyanine perchlorate; DiO, 3,3'-dioctadecyloxacarbocyanine perchlorate; DMSO, dimethyl sulfoxide; d-THP-1, differentiated THP-1; FACS, fluorescence activated cell sorting; FBS, fetal bovine serum; FCCP, carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone; GABARAP, GABA type A receptor-associated protein; GFP, green fluorescent protein; HBSS, Hanks' balanced salt solution; HPLC, high-performance liquid chromatography; HRP, horseradish peroxidase; IL1B, interleukin 1 beta; KT, an AIE probe composed of a cell-penetrating peptide and an AIEgen tetraphenyl ethylene; LC3-II, lipidated LC3; LDH, lactate dehydrogenase; LIR, LC3-interacting region; LKR, engineered molecular probe composed of an LC3-interacting peptide, a cell-penetrating peptide and a non-AIE fluorescent molecule rhodamine; LKT, engineered molecular probe composed of an LC3-interacting peptide, a cell-penetrating peptide and an AIEgen tetraphenyl ethylene; LPS, lipopolysaccharide; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MEF, mouse embryonic fibroblast; mRFP, monomeric red fluorescent protein; NHS, N-hydroxysuccinimide; NLRP3, NLR family pyrin domain containing 3; PBS, phosphate-buffered saline; PCC, pearson's correlation coefficient; PL, photoluminescence; PMA, phorbol 12-myristate 13-acetate; RAP, rapamycin; RIM, restriction of intramolecular motions; s.e.m., standard error of the mean; SPR, surface plasmon resonance; SQSTM1/p62, sequestosome 1; TAX1BP1, Tax1 binding protein 1; TPE, tetraphenylethylene; TPE-yne, 1-(4-ethynylphenyl)-1,2,2-triphenylethene; Tre, trehalose; u-THP-1: undifferentiated THP-1; UV-Vis, ultraviolet visible.
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Affiliation(s)
- Wenbin Zhang
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Pengfei Wei
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong, China
| | - Liu Liu
- Department of Clinical Laboratory, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Tao Ding
- School of Medicine, School of Biomedical Sciences and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction and Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, China
| | - Yinyin Yang
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Peipei Jin
- School of Medicine, School of Biomedical Sciences and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction and Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, China
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zhibin Zhao
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Meimei Wang
- School of Medicine, School of Biomedical Sciences and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction and Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, China
| | - Bochuan Hu
- School of Medicine, School of Biomedical Sciences and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction and Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, China
| | - Xin Jin
- School of Medicine, School of Biomedical Sciences and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction and Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, China
| | - Zeng Xu
- Center for Aggregation-Induced Emission, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou, Guangdong, China
| | - Han Zhang
- Center for Aggregation-Induced Emission, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou, Guangdong, China
| | - Yang Song
- School of Medicine, School of Biomedical Sciences and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction and Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, China
| | - Liansheng Wang
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Suqin Zhong
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Jing Chen
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zhenyu Yang
- China-Singapore International Joint Research Institute, Guangzhou, Guangdong, China
| | - Ziying Chen
- School of Medicine, School of Biomedical Sciences and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction and Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, China
| | - Yu Wu
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Zhiming Ye
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Youcui Xu
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Yunjiao Zhang
- School of Medicine, School of Biomedical Sciences and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction and Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, China
| | - Long-Ping Wen
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
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Chu PY, Nguyen TNA, Wu AY, Huang PS, Huang KL, Liao CJ, Hsieh CH, Wu MH. The Utilization of Optically Induced Dielectrophoresis (ODEP)-Based Cell Manipulation in a Microfluidic System for the Purification and Sorting of Circulating Tumor Cells (CTCs) with Different Sizes. Micromachines (Basel) 2023; 14:2170. [PMID: 38138338 PMCID: PMC10745986 DOI: 10.3390/mi14122170] [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] [Received: 11/09/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]
Abstract
The analysis of circulating tumor cells (CTCs) at the molecular level holds great promise for several clinical applications. For this goal, the harvest of high-purity, size-sorted CTCs with different subtypes from a blood sample are important. For this purpose, a two-step CTC isolation protocol was proposed, by which the immunomagnetic beads-based cell separation was first utilized to remove the majority of blood cells. After that, an optically induced dielectrophoresis (ODEP) microfluidic system was developed to (1) purify the CTCs from the remaining magnetic microbeads-bound blood cells and to (2) sort and separate the CTCs with different sizes. In this study, the ODEP microfluidic system was designed and fabricated. Moreover, its optimum operation conditions and performance were explored. The results exhibited that the presented technique was able to purify and sort the cancer cells with two different sizes from a tested cell suspension in a high-purity (93.5% and 90.1% for the OECM 1 and HA22T cancer cells, respectively) manner. Overall, this study presented a technique for the purification and sorting of cancer cells with different sizes. Apart from this application, the technique is also useful for other applications in which the high-purity and label-free purification and sorting of cells with different sizes is required.
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Affiliation(s)
- Po-Yu Chu
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (T.N.A.N.); (A.-Y.W.); (P.-S.H.); (K.-L.H.)
| | - Thi Ngoc Anh Nguyen
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (T.N.A.N.); (A.-Y.W.); (P.-S.H.); (K.-L.H.)
| | - Ai-Yun Wu
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (T.N.A.N.); (A.-Y.W.); (P.-S.H.); (K.-L.H.)
| | - Po-Shuan Huang
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (T.N.A.N.); (A.-Y.W.); (P.-S.H.); (K.-L.H.)
| | - Kai-Lin Huang
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (T.N.A.N.); (A.-Y.W.); (P.-S.H.); (K.-L.H.)
| | - Chia-Jung Liao
- Department of Biomedical Sciences, College of Medicine, Chang-Gung University, Taoyuan 333, Taiwan;
| | - Chia-Hsun Hsieh
- Division of Hematology-Oncology, Department of Internal Medicine, New Taipei City Municipal Tucheng Hospital, New Taipei City 23652, Taiwan;
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City 33302, Taiwan
| | - Min-Hsien Wu
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (T.N.A.N.); (A.-Y.W.); (P.-S.H.); (K.-L.H.)
- Division of Hematology-Oncology, Department of Internal Medicine, New Taipei City Municipal Tucheng Hospital, New Taipei City 23652, Taiwan;
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City 33302, Taiwan
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10
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Schraivogel D, Steinmetz LM, Parts L. Pooled Genome-Scale CRISPR Screens in Single Cells. Annu Rev Genet 2023; 57:223-244. [PMID: 37562410 DOI: 10.1146/annurev-genet-072920-013842] [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] [Indexed: 08/12/2023]
Abstract
Assigning functions to genes and learning how to control their expression are part of the foundation of cell biology and therapeutic development. An efficient and unbiased method to accomplish this is genetic screening, which historically required laborious clone generation and phenotyping and is still limited by scale today. The rapid technological progress on modulating gene function with CRISPR-Cas and measuring it in individual cells has now relaxed the major experimental constraints and enabled pooled screening with complex readouts from single cells. Here, we review the principles and practical considerations for pooled single-cell CRISPR screening. We discuss perturbation strategies, experimental model systems, matching the perturbation to the individual cells, reading out cell phenotypes, and data analysis. Our focus is on single-cell RNA sequencing and cell sorting-based readouts, including image-enabled cell sorting. We expect this transformative approach to fuel biomedical research for the next several decades.
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Affiliation(s)
- Daniel Schraivogel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany;
| | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany;
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA;
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, California, USA
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11
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Kare AJ, Nichols L, Zermeno R, Raie MN, Tumbale SK, Ferrara KW. OMIP-095: 40-Color spectral flow cytometry delineates all major leukocyte populations in murine lymphoid tissues. Cytometry A 2023; 103:839-850. [PMID: 37768325 PMCID: PMC10843696 DOI: 10.1002/cyto.a.24788] [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: 02/24/2023] [Revised: 07/26/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023]
Abstract
High-dimensional immunoprofiling is essential for studying host response to immunotherapy, infection, and disease in murine model systems. However, the difficulty of multiparameter panel design combined with a lack of existing murine tools has prevented the comprehensive study of all major leukocyte phenotypes in a single assay. Herein, we present a 40-color flow cytometry panel for deep immunophenotyping of murine lymphoid tissues, including the spleen, blood, Peyer's patches, inguinal lymph nodes, bone marrow, and thymus. This panel uses a robust set of surface markers capable of differentiating leukocyte subsets without the use of intracellular staining, thus allowing for the use of cells in downstream functional experiments or multiomic analyses. Our panel classifies T cells, B cells, natural killer cells, innate lymphoid cells, monocytes, macrophages, dendritic cells, basophils, neutrophils, eosinophils, progenitors, and their functional subsets by using a series of co-stimulatory, checkpoint, activation, migration, and maturation markers. This tool has a multitude of systems immunology applications ranging from serial monitoring of circulating blood signatures to complex endpoint analysis, especially in pre-clinical settings where treatments can modulate leukocyte abundance and/or function. Ultimately, this 40-color panel resolves a diverse array of immune cells on the axes of time, tissue, and treatment, filling the niche for a modern tool dedicated to murine immunophenotyping.
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Affiliation(s)
- Aris J. Kare
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Lisa Nichols
- Stanford Shared FACS Facility, Stanford University, Stanford, CA 94305, USA
| | - Ricardo Zermeno
- Stanford Shared FACS Facility, Stanford University, Stanford, CA 94305, USA
| | - Marina N. Raie
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
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12
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Fardoos R, Christensen C, Øbro NF, Overgaard UM, Als-Nielsen B, Madsen HO, Marquart HV. Flow Sorting, Whole Genome Amplification and Next-Generation Sequencing as Combined Tools to Study Heterogeneous Acute Lymphoblastic Leukemia. Diagnostics (Basel) 2023; 13:3306. [PMID: 37958202 PMCID: PMC10650172 DOI: 10.3390/diagnostics13213306] [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: 09/26/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
Next-generation sequencing (NGS) methods have been introduced for immunoglobulin (IG)/T-cell receptor (TR) gene rearrangement analysis in acute lymphoblastic leukemia (ALL) and lymphoma (LBL). These methods likely constitute faster and more sensitive approaches to analyze heterogenous cases of ALL/LBL, yet it is not known whether gene rearrangements constituting low percentages of the total sequence reads represent minor subpopulations of malignant cells or background IG/TR gene rearrangements in normal B-and T-cells. In a comparison of eight cases of B-cell precursor ALL (BCP-ALL) using both the EuroClonality NGS method and the IdentiClone multiplex-PCR/gene-scanning method, the NGS method identified between 29% and 139% more markers than the gene-scanning method, depending on whether the NGS data analysis used a threshold of 5% or 1%, respectively. As an alternative to using low thresholds, we show that IG/TR gene rearrangements in subpopulations of cancer cells can be discriminated from background IG/TR gene rearrangements in normal B-and T-cells through a combination of flow cytometry cell sorting and multiple displacement amplification (MDA)-based whole genome amplification (WGA) prior to the NGS. Using this approach to investigate the clonal evolution in a BCP-ALL patient with double relapse, clonal TR rearrangements were found in sorted leukemic cells at the time of second relapse that could be identified at the time of diagnosis, below 1% of the total sequence reads. These data emphasize that caution should be exerted when interpreting rare sequences in NGS experiments and show the advantage of employing the flow sorting of malignant cell populations in NGS clonality assessments.
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Affiliation(s)
- Rabiah Fardoos
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Claus Christensen
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Nina Friesgaard Øbro
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Ulrik Malthe Overgaard
- Department of Hematology, The University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Bodil Als-Nielsen
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Hans Ole Madsen
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Hanne Vibeke Marquart
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark
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13
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Zhang J, Lin H, Xu J, Zhang M, Ge X, Zhang C, Huang WE, Cheng JX. High-throughput single- cell sorting by stimulated Raman-activated cell ejection. bioRxiv 2023:2023.10.16.562526. [PMID: 37904930 PMCID: PMC10614813 DOI: 10.1101/2023.10.16.562526] [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: 11/01/2023]
Abstract
Single-cell sorting is essential to explore cellular heterogeneity in biology and medicine. Recently developed Raman-activated cell sorting (RACS) circumvents the limitations of fluorescence-activated cell sorting, such as the cytotoxicity of labels. However, the sorting throughputs of all forms of RACS are limited by the intrinsically small cross-section of spontaneous Raman scattering. Here, we report a stimulated Raman-activated cell ejection (S-RACE) platform that enables high-throughput single-cell sorting based on high-resolution multi-channel stimulated Raman chemical imaging, in situ image decomposition, and laser-induced cell ejection. The performance of this platform was illustrated by sorting a mixture of 1 μm polymer beads, where 95% yield, 98% purity, and 14 events per second throughput were achieved. Notably, our platform allows live cell ejection, allowing for the growth of single colonies of bacteria and fungi after sorting. To further illustrate the chemical selectivity, lipid-rich Rhodotorula glutinis cells were successfully sorted from a mixture with Saccharomyces cerevisiae, confirmed by downstream quantitative PCR. Furthermore, by integrating a closed-loop feedback control circuit into the system, we realized real-time single-cell imaging and sorting, and applied this method to precisely eject regions of interest from a rat brain tissue section. The reported S-RACE platform opens exciting opportunities for a wide range of single-cell applications in biology and medicine.
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Affiliation(s)
- Jing Zhang
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
| | - Haonan Lin
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
| | - Jiabao Xu
- Division of Biomedical Engineering, James Watt School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
| | - Meng Zhang
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Xiaowei Ge
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Chi Zhang
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
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14
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Ogut MG, Ma P, Gupta R, Hoerner CR, Fan AC, El-Kaffas AN, Durmus NG. Automated Image Analysis for Characterization of Circulating Tumor Cells and Clusters Sorted by Magnetic Levitation. Adv Biol (Weinh) 2023; 7:e2300109. [PMID: 37462226 DOI: 10.1002/adbi.202300109] [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: 03/13/2023] [Revised: 05/05/2023] [Indexed: 10/24/2023]
Abstract
Magnetic levitation-based sorting technologies have revolutionized the detection and isolation of rare cells, including circulating tumor cells (CTCs) and circulating tumor cell clusters (CTCCs). Manual counting and quantification of these cells are prone to time-consuming processes, human error, and inter-observer variability, particularly challenging when heterogeneous cell types in 3D clusters are present. To overcome these challenges, we developed "Fastcount," an in-house MATLAB-based algorithm for precise, automated quantification and phenotypic characterization of CTCs and CTCCs, in both 2D and 3D. Fastcount is 120 times faster than manual counting and produces reliable results with a ±7.3% deviation compared to a trained laboratory technician. By analyzing 400 GB of fluorescence imaging data, we showed that Fastcount outperforms manual counting and commercial software when cells are aggregated in 3D or staining artifacts are present, delivering more accurate results. We further employed Fastcount for automated analysis of 3D image stacks obtained from CTCCs isolated from colorectal adenocarcinoma and renal cell carcinoma blood samples. Interestingly, we observed a highly heterogeneous spatial cellular composition within CTCCs, even among clusters from the same patient. Overall, Fastcount can be employed for various applications with lab-chip devices, such as CTC detection, CTCC analysis in 3D and cell detection in biosensors.
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Affiliation(s)
- Mehmet Giray Ogut
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
- School of Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Peng Ma
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Rakhi Gupta
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Christian R Hoerner
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alice C Fan
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ahmed Nagy El-Kaffas
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology, Stanford University, Palo Alto, CA, 94305, USA
| | - Naside Gozde Durmus
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology, Stanford University, Palo Alto, CA, 94305, USA
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15
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Wang H, Zhang Y, Dai L, Bo X, Liu X, Zhao X, Yu J, Kwok LY, Bao Q. Metabolomic Differences between Viable but Nonculturable and Recovered Lacticaseibacillus paracasei Zhang. Foods 2023; 12:3472. [PMID: 37761181 PMCID: PMC10527867 DOI: 10.3390/foods12183472] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
The fermentation process can be affected when the starter culture enters the viable but nonculturable (VBNC) state. Therefore, it is of interest to investigate how VBNC cells change physiologically. Lacticaseibacillus (L.) paracasei Zhang is both a probiotic and a starter strain. This study aimed to investigate the metabolomic differences between VBNC and recovered L. paracasei Zhang cells. First, L. paracasei Zhang was induced to enter the VBNC state by keeping the cells in a liquid de Man-Rogosa-Sharpe (MRS) medium at 4 °C for 220 days. Flow cytometry was used to sort the induced VBNC cells, and three different types of culture media (MRS medium, skim milk with 1% yeast extract, and skim milk) were used for cell resuscitation. Cell growth responses in the three types of recovery media suggested that the liquid MRS medium was the most effective in reversing the VBNC state in L. paracasei Zhang. Metabolomics analysis revealed 25 differential metabolites from five main metabolite classes (amino acid, carbohydrate, lipid, vitamin, and purine and pyrimidine). The levels of L-cysteine, L-alanine, L-lysine, and L-arginine notably increased in the revived cells, while cellulose, alginose, and guanine significantly decreased. This study confirmed that VBNC cells had an altered physiology.
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Affiliation(s)
- Huiying Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yuhong Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lixia Dai
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xiaoyu Bo
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xiangyun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xin Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Qiuhua Bao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
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16
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Matsumoto M, Tashiro S, Ito T, Takahashi K, Hashimoto G, Kajihara J, Miyahara Y, Shiku H, Katsumoto Y. Fully closed cell sorter for immune cell therapy manufacturing. Mol Ther Methods Clin Dev 2023; 30:367-376. [PMID: 37637381 PMCID: PMC10457513 DOI: 10.1016/j.omtm.2023.07.012] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023]
Abstract
By analyzing patients treated with adoptive immune cell therapies, various immune cell phenotypes have been found in the starting and infused materials as determinants of sustained remission. The isolation of these specific phenotypes for clinical use requires current Good Manufacturing Practice (cGMP)-compliant cell-sorting technologies with multiparameter selection capabilities. Here, we developed a cGMP-requirement-applicable fully closed cell sorter that has a suction mechanism and multiparameter detection using two laser optical settings. Negative pressure generated by a change in the chamber volume at a sorting point allows the isolation of cells of interest with high viability and purity. Our study demonstrated that this microfluidic sorter enables the isolation of cells of interest at an effective rate of 7,000 sorts per second on average. A purity of 85.5% and 77.1% effective yield with 93.7% viability was obtained when applying a target population of 35.9% in total (lymphocyte+CD8+) at 15,000 events per second (2 × 107 cells/mL). The sorted gene-modified T cells maintain largely unaltered proliferation, antigen recognition, cytokine release, and cytotoxicity functionalities.
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Affiliation(s)
| | - Shinji Tashiro
- Tokyo Laboratory 11, R&D Center, Sony Group Corporation, Tokyo, Japan
| | - Tatsumi Ito
- Tokyo Laboratory 11, R&D Center, Sony Group Corporation, Tokyo, Japan
| | - Kazuya Takahashi
- Tokyo Laboratory 11, R&D Center, Sony Group Corporation, Tokyo, Japan
| | - Gakuji Hashimoto
- Tokyo Laboratory 11, R&D Center, Sony Group Corporation, Tokyo, Japan
| | - Junji Kajihara
- Tokyo Laboratory 11, R&D Center, Sony Group Corporation, Tokyo, Japan
| | - Yoshihiro Miyahara
- Department of Personalized Cancer Immunotherapy, Mie University Graduate School of Medicine, Mie, Japan
- Center for Comprehensive Cancer Immunotherapy, Mie University, Mie, Japan
- Department of Cellular and Molecular Immunology, Mie University Graduate School of Medicine, Mie, Japan
| | - Hiroshi Shiku
- Department of Personalized Cancer Immunotherapy, Mie University Graduate School of Medicine, Mie, Japan
- Center for Comprehensive Cancer Immunotherapy, Mie University, Mie, Japan
- Department of Cellular and Molecular Immunology, Mie University Graduate School of Medicine, Mie, Japan
| | - Yoichi Katsumoto
- Tokyo Laboratory 11, R&D Center, Sony Group Corporation, Tokyo, Japan
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17
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Giordani S, Marassi V, Placci A, Zattoni A, Roda B, Reschiglian P. Field-Flow Fractionation in Molecular Biology and Biotechnology. Molecules 2023; 28:6201. [PMID: 37687030 PMCID: PMC10488451 DOI: 10.3390/molecules28176201] [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: 07/17/2023] [Revised: 08/08/2023] [Accepted: 08/15/2023] [Indexed: 09/10/2023] Open
Abstract
Field-flow fractionation (FFF) is a family of single-phase separative techniques exploited to gently separate and characterize nano- and microsystems in suspension. These techniques cover an extremely wide dynamic range and are able to separate analytes in an interval between a few nm to 100 µm size-wise (over 15 orders of magnitude mass-wise). They are flexible in terms of mobile phase and can separate the analytes in native conditions, preserving their original structures/properties as much as possible. Molecular biology is the branch of biology that studies the molecular basis of biological activity, while biotechnology deals with the technological applications of biology. The areas where biotechnologies are required include industrial, agri-food, environmental, and pharmaceutical. Many species of biological interest belong to the operational range of FFF techniques, and their application to the analysis of such samples has steadily grown in the last 30 years. This work aims to summarize the main features, milestones, and results provided by the application of FFF in the field of molecular biology and biotechnology, with a focus on the years from 2000 to 2022. After a theoretical background overview of FFF and its methodologies, the results are reported based on the nature of the samples analyzed.
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Affiliation(s)
- Stefano Giordani
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy (V.M.)
| | - Valentina Marassi
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy (V.M.)
- byFlow srl, 40129 Bologna, Italy
| | - Anna Placci
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy (V.M.)
| | - Andrea Zattoni
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy (V.M.)
- byFlow srl, 40129 Bologna, Italy
| | - Barbara Roda
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy (V.M.)
- byFlow srl, 40129 Bologna, Italy
| | - Pierluigi Reschiglian
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy (V.M.)
- byFlow srl, 40129 Bologna, Italy
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18
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Nan X, Zhang J, Wang X, Kang T, Cao X, Hao J, Jia Q, Qin B, Mei S, Xu Z. Design of a Low-Frequency Dielectrophoresis-Based Arc Microfluidic Chip for Multigroup Cell Sorting. Micromachines (Basel) 2023; 14:1561. [PMID: 37630097 PMCID: PMC10456708 DOI: 10.3390/mi14081561] [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] [Received: 07/13/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023]
Abstract
Dielectrophoresis technology is applied to microfluidic chips to achieve microscopic control of cells. Currently, microfluidic chips based on dielectrophoresis have certain limitations in terms of cell sorting species, in order to explore a microfluidic chip with excellent performance and high versatility. In this paper, we designed a microfluidic chip that can be used for continuous cell sorting, with the structural design of a curved channel and curved double side electrodes. CM factors were calculated for eight human healthy blood cells and cancerous cells using the software MyDEP, the simulation of various blood cells sorting and the simulation of the joule heat effect of the microfluidic chip were completed using the software COMSOL Multiphysics. The effect of voltage and inlet flow velocity on the simulation results was discussed using the control variables method. We found feasible parameters from simulation results under different voltages and inlet flow velocities, and the feasibility of the design was verified from multiple perspectives by measuring cell movement trajectories, cell recovery rate and separation purity. This paper provides a universal method for cell, particle and even protein sorting.
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Affiliation(s)
- Xueli Nan
- School of Automation and Software Engineering, Shanxi University, Taiyuan 030006, China; (J.Z.); (X.W.); (T.K.); (X.C.); (J.H.); (Q.J.); (B.Q.); (S.M.); (Z.X.)
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jiale Zhang
- School of Automation and Software Engineering, Shanxi University, Taiyuan 030006, China; (J.Z.); (X.W.); (T.K.); (X.C.); (J.H.); (Q.J.); (B.Q.); (S.M.); (Z.X.)
| | - Xin Wang
- School of Automation and Software Engineering, Shanxi University, Taiyuan 030006, China; (J.Z.); (X.W.); (T.K.); (X.C.); (J.H.); (Q.J.); (B.Q.); (S.M.); (Z.X.)
| | - Tongtong Kang
- School of Automation and Software Engineering, Shanxi University, Taiyuan 030006, China; (J.Z.); (X.W.); (T.K.); (X.C.); (J.H.); (Q.J.); (B.Q.); (S.M.); (Z.X.)
| | - Xinxin Cao
- School of Automation and Software Engineering, Shanxi University, Taiyuan 030006, China; (J.Z.); (X.W.); (T.K.); (X.C.); (J.H.); (Q.J.); (B.Q.); (S.M.); (Z.X.)
| | - Jinjin Hao
- School of Automation and Software Engineering, Shanxi University, Taiyuan 030006, China; (J.Z.); (X.W.); (T.K.); (X.C.); (J.H.); (Q.J.); (B.Q.); (S.M.); (Z.X.)
| | - Qikun Jia
- School of Automation and Software Engineering, Shanxi University, Taiyuan 030006, China; (J.Z.); (X.W.); (T.K.); (X.C.); (J.H.); (Q.J.); (B.Q.); (S.M.); (Z.X.)
| | - Bolin Qin
- School of Automation and Software Engineering, Shanxi University, Taiyuan 030006, China; (J.Z.); (X.W.); (T.K.); (X.C.); (J.H.); (Q.J.); (B.Q.); (S.M.); (Z.X.)
| | - Shixuan Mei
- School of Automation and Software Engineering, Shanxi University, Taiyuan 030006, China; (J.Z.); (X.W.); (T.K.); (X.C.); (J.H.); (Q.J.); (B.Q.); (S.M.); (Z.X.)
| | - Zhikuan Xu
- School of Automation and Software Engineering, Shanxi University, Taiyuan 030006, China; (J.Z.); (X.W.); (T.K.); (X.C.); (J.H.); (Q.J.); (B.Q.); (S.M.); (Z.X.)
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19
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Faber GP, Hauschner H, Atrash MK, Bilinsky L, Shav-Tal Y. Utilizing flow cytometry sorting signal width to enrich for cells positive to endogenous gene integration of fluorescent proteins. Cytometry A 2023; 103:664-669. [PMID: 37158244 DOI: 10.1002/cyto.a.24735] [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: 01/06/2023] [Revised: 04/03/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Endogenous gene knock-in using CRIPSR is becoming the standard for fluorescent tagging of endogenous proteins. Some protocols, particularly those that utilize insert cassettes that carry a fluorescent protein tag, can yield many types of cells with off-target insertions that have diffuse fluorescent signal throughout the whole cell in addition to scarce cells with on-target gene insertions that show the correct sub-cellular localization of the tagged protein. As such, when searching for cells with on-target integration using flow cytometry, the off-target fluorescent cells yield a high percentage of false positives. Here, we show that by changing the gating used to select for fluorescence during flow cytometry sorting, namely utilizing the width of the signal as opposed to the area, we can highly enrich for positively integrated cells. Reproducible gates were created to select even minuscule percentages of correct subcellular signal, and these parameters were validated by fluorescence microscopy. This method is a powerful tool to rapidly enhance the generation of cell lines with correctly integrated gene knock-ins encoding endogenous fluorescent proteins.
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Affiliation(s)
- Gabriel P Faber
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Hagit Hauschner
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Mohammad K Atrash
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | | | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
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20
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Hanin G, Ferguson-Smith AC. Mammary adipocyte flow cytometry as a tool to study mammary gland biology. FEBS Open Bio 2023; 13:1218-1227. [PMID: 37394996 DOI: 10.1002/2211-5463.13620] [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: 12/12/2022] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 07/04/2023] Open
Abstract
The mammary gland is a vital exocrine organ that has evolved in mammals to secrete milk and provide nutrition to ensure the growth and survival of the neonate The mouse mammary gland displays extraordinary plasticity each time the female undergoes pregnancy and lactation, including a sophisticated process of tertiary branching and alveologenesis to form a branched epithelial tree and subsequently milk-producing alveoli. Upon the cessation of lactation, the gland remodels back to a simple ductal architecture via highly regulated involution processes. At the cellular level, the plasticity is characterised by proliferation of mammary cell populations, differentiation and apoptosis, accompanied by major changes in cell function and morphology. The mammary epithelium requires a specific stromal environment to grow, known as the mammary fat pad. Mammary adipocytes are one of the most prominent cell types in the fat pad, but despite their vast proportion in the tissue and their crucial interaction with epithelial cells, their physiology remains largely unknown. Over the past decade, the need to understand the properties and contribution of mammary adipocytes has become more recognised. However, the development of adequate methods and protocols to study this cellular niche is still lagging, partially due to their fragile nature, the difficulty of isolating them, the lack of reliable cell surface markers and the heterogenous environment in this tissue, which differs from other adipocyte depots. Here, we describe a new rapid and simple flow cytometry protocol specifically designed for the analysis and isolation of mouse mammary adipocytes across mammary gland developmental stages.
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Affiliation(s)
- Geula Hanin
- Department of Genetics, University of Cambridge, UK
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21
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Radoua A, Pernon B, Pernet N, Jean C, Elmallah M, Guerrache A, Constantinescu AA, Hadj Hamou S, Devy J, Micheau O. ptARgenOM-A Flexible Vector For CRISPR/CAS9 Nonviral Delivery. Small Methods 2023:e2300069. [PMID: 37156748 DOI: 10.1002/smtd.202300069] [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] [Received: 01/17/2023] [Revised: 04/11/2023] [Indexed: 05/10/2023]
Abstract
Viral-mediated delivery of the CRISPR-Cas9 system is one the most commonly used techniques to modify the genome of a cell, with the aim of analyzing the function of the targeted gene product. While these approaches are rather straightforward for membrane-bound proteins, they can be laborious for intracellular proteins, given that selection of full knockout (KO) cells often requires the amplification of single-cell clones. Moreover, viral-mediated delivery systems, besides the Cas9 and gRNA, lead to the integration of unwanted genetic material, such as antibiotic resistance genes, introducing experimental biases. Here, an alternative non-viral delivery approach is presented for CRISPR/Cas9, allowing efficient and flexible selection of KO polyclonal cells. This all-in-one mammalian CRISPR-Cas9 expression vector, ptARgenOM, encodes the gRNA and the Cas9 linked to a ribosomal skipping peptide sequence followed by the enhanced green fluorescent protein and the puromycin N-acetyltransferase, allowing for transient, expression-dependent selection and enrichment of isogenic KO cells. After evaluation using more than 12 distinct targets in 6 cell lines, ptARgenOM is found to be efficient in producing KO cells, reducing the time required to obtain a polyclonal isogenic cell line by 4-6 folds. Altogether ptARgenOM provides a simple, fast, and cost-effective delivery tool for genome editing.
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Affiliation(s)
- Abdelmnim Radoua
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- INSERM, Université de Bourgogne Franche-Comté (UBFC), UMR1231, LNC, Dijon, 21000, France
| | - Baptiste Pernon
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
| | - Nicolas Pernet
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- INSERM, Université de Bourgogne Franche-Comté (UBFC), UMR1231, LNC, Dijon, 21000, France
| | - Chloé Jean
- UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne (URCA), Reims, Cedex, 51687, France
- Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, UMR 7369 CNRS, Reims, 51687, France
| | - Mohammed Elmallah
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- Chemistry Department, Faculty of Science, Helwan University, Ain Helwan, Cairo, 11795, Egypt
| | - Abderrahmane Guerrache
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- INSERM, Université de Bourgogne Franche-Comté (UBFC), UMR1231, LNC, Dijon, 21000, France
| | | | - Sofiane Hadj Hamou
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
| | - Jérôme Devy
- UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne (URCA), Reims, Cedex, 51687, France
- Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, UMR 7369 CNRS, Reims, 51687, France
| | - Olivier Micheau
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- INSERM, Université de Bourgogne Franche-Comté (UBFC), UMR1231, LNC, Dijon, 21000, France
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22
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Szydlak R, Øvreeide IH, Luty M, Zieliński T, Prot VE, Zemła J, Stokke BT, Lekka M. Bladder Cancer Cells Interaction with Lectin-Coated Surfaces under Static and Flow Conditions. Int J Mol Sci 2023; 24:ijms24098213. [PMID: 37175920 PMCID: PMC10179195 DOI: 10.3390/ijms24098213] [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: 03/30/2023] [Revised: 04/21/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
Aberrant expression of glycans, i.e., oligosaccharide moiety covalently attached to proteins or lipids, is characteristic of various cancers, including urothelial ones. The binding of lectins to glycans is classified as molecular recognition, which makes lectins a strong tool for understanding their role in developing diseases. Here, we present a quantitative approach to tracing glycan-lectin interactions in cells, from the initial to the steady phase of adhesion. The cell adhesion was measured between urothelial cell lines (non-malignant HCV29 and carcinoma HT1376 and T24 cells) and lectin-coated surfaces. Depending on the timescale, single-cell force spectroscopy, and adhesion assays conducted in static and flow conditions were applied. The obtained results reveal that the adhesion of urothelial cells to two specific lectins, i.e., phytohemagglutinin-L and wheat germ agglutinin, was specific and selective. Thus, these lectins can be applied to selectively capture, identify, and differentiate between cancer types in a label-free manner. These results open up the possibility of designing lectin-based biosensors for diagnostic or prognostic purposes and developing strategies for drug delivery that could target cancer-associated glycans.
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Affiliation(s)
- Renata Szydlak
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
| | - Ingrid H Øvreeide
- Biophysics and Medical Technology, Department of Physics, The Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Marcin Luty
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
| | - Tomasz Zieliński
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
| | - Victorien E Prot
- Biomechanics, Department of Structural Engineering, The Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Joanna Zemła
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
| | - Bjørn T Stokke
- Biophysics and Medical Technology, Department of Physics, The Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Małgorzata Lekka
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
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23
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Tian Y, Hu R, Du G, Xu N. Microfluidic Chips: Emerging Technologies for Adoptive Cell Immunotherapy. Micromachines (Basel) 2023; 14:877. [PMID: 37421109 DOI: 10.3390/mi14040877] [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] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 07/09/2023]
Abstract
Adoptive cell therapy (ACT) is a personalized therapy that has shown great success in treating hematologic malignancies in clinic, and has also demonstrated potential applications for solid tumors. The process of ACT involves multiple steps, including the separation of desired cells from patient tissues, cell engineering by virus vector systems, and infusion back into patients after strict tests to guarantee the quality and safety of the products. ACT is an innovative medicine in development; however, the multi-step method is time-consuming and costly, and the preparation of the targeted adoptive cells remains a challenge. Microfluidic chips are a novel platform with the advantages of manipulating fluid in micro/nano scales, and have been developed for various biological research applications as well as ACT. The use of microfluidics to isolate, screen, and incubate cells in vitro has the advantages of high throughput, low cell damage, and fast amplification rates, which can greatly simplify ACT preparation steps and reduce costs. Moreover, the customizable microfluidic chips fit the personalized demands of ACT. In this mini-review, we describe the advantages and applications of microfluidic chips for cell sorting, cell screening, and cell culture in ACT compared to other existing methods. Finally, we discuss the challenges and potential outcomes of future microfluidics-related work in ACT.
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Affiliation(s)
- Yishen Tian
- Translational Medicine Research Center, Guizhou Medical University, Guiyang 550025, China
| | - Rong Hu
- Translational Medicine Research Center, Guizhou Medical University, Guiyang 550025, China
| | - Guangshi Du
- Translational Medicine Research Center, Guizhou Medical University, Guiyang 550025, China
| | - Na Xu
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan 430065, China
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24
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Skamrahl M, Schünemann J, Mukenhirn M, Pang H, Gottwald J, Jipp M, Ferle M, Rübeling A, Oswald T, Honigmann A, Janshoff A. Cellular segregation in cocultures is driven by differential adhesion and contractility on distinct timescales. Proc Natl Acad Sci U S A 2023; 120:e2213186120. [PMID: 37011207 PMCID: PMC10104523 DOI: 10.1073/pnas.2213186120] [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: 08/03/2022] [Accepted: 03/02/2023] [Indexed: 04/05/2023] Open
Abstract
Cellular sorting and pattern formation are crucial for many biological processes such as development, tissue regeneration, and cancer progression. Prominent physical driving forces for cellular sorting are differential adhesion and contractility. Here, we studied the segregation of epithelial cocultures containing highly contractile, ZO1/2-depleted MDCKII cells (dKD) and their wild-type (WT) counterparts using multiple quantitative, high-throughput methods to monitor their dynamical and mechanical properties. We observe a time-dependent segregation process governed mainly by differential contractility on short (<5 h) and differential adhesion on long (>5 h) timescales. The overly contractile dKD cells exert strong lateral forces on their WT neighbors, thereby apically depleting their surface area. Concomitantly, the tight junction-depleted, contractile cells exhibit weaker cell-cell adhesion and lower traction force. Drug-induced contractility reduction and partial calcium depletion delay the initial segregation but cease to change the final demixed state, rendering differential adhesion the dominant segregation force at longer timescales. This well-controlled model system shows how cell sorting is accomplished through a complex interplay between differential adhesion and contractility and can be explained largely by generic physical driving forces.
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Affiliation(s)
- Mark Skamrahl
- University of Göttingen, Institute of Physical Chemistry,37077Göttingen, Germany
| | - Justus Schünemann
- University of Göttingen, Institute of Physical Chemistry,37077Göttingen, Germany
| | - Markus Mukenhirn
- Max Planck Institute of Molecular Cell Biology and Genetics,01307Dresden, Germany
| | - Hongtao Pang
- University of Göttingen, Institute of Physical Chemistry,37077Göttingen, Germany
| | - Jannis Gottwald
- University of Göttingen, Institute of Physical Chemistry,37077Göttingen, Germany
| | - Marcel Jipp
- University of Göttingen, Institute of Physical Chemistry,37077Göttingen, Germany
| | - Maximilian Ferle
- University of Göttingen, Institute of Physical Chemistry,37077Göttingen, Germany
| | - Angela Rübeling
- University of Göttingen, Institute of Organic and Biomolecular Chemistry, Göttingen37077, Germany
| | - Tabea A. Oswald
- University of Göttingen, Institute of Organic and Biomolecular Chemistry, Göttingen37077, Germany
| | - Alf Honigmann
- Max Planck Institute of Molecular Cell Biology and Genetics,01307Dresden, Germany
| | - Andreas Janshoff
- University of Göttingen, Institute of Physical Chemistry,37077Göttingen, Germany
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25
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Salomon R, Razavi Bazaz S, Li W, Gallego-Ortega D, Jin D, Warkiani ME. A Method for Rapid, Quantitative Evaluation of Particle Sorting in Microfluidics Using Basic Cytometry Equipment. Micromachines (Basel) 2023; 14:751. [PMID: 37420984 DOI: 10.3390/mi14040751] [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] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 07/09/2023]
Abstract
This paper describes, in detail, a method that uses flow cytometry to quantitatively characterise the performance of continuous-flow microfluidic devices designed to separate particles. Whilst simple, this approach overcomes many of the issues with the current commonly utilised methods (high-speed fluorescent imaging, or cell counting via either a hemocytometer or a cell counter), as it can accurately assess device performance even in complex, high concentration mixtures in a way that was previously not possible. Uniquely, this approach takes advantage of pulse processing in flow cytometry to allow quantitation of cell separation efficiencies and resulting sample purities on both single cells as well as cell clusters (such as circulating tumour cell (CTC) clusters). Furthermore, it can readily be combined with cell surface phenotyping to measure separation efficiencies and purities in complex cell mixtures. This method will facilitate the rapid development of a raft of continuous flow microfluidic devices, will be helpful in testing novel separation devices for biologically relevant clusters of cells such as CTC clusters, and will provide a quantitative assessment of device performance in complex samples, which was previously impossible.
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Affiliation(s)
- Robert Salomon
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Sajad Razavi Bazaz
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW 2052, Australia
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Wenyan Li
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW 2052, Australia
| | - David Gallego-Ortega
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Dayong Jin
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Majid Ebrahimi Warkiani
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
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26
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Semchenkova A, Zhogov V, Zakharova E, Mikhailova E, Illarionova O, Larin S, Novichkova G, Karachunskiy A, Maschan M, Popov A. Flow cell sorting followed by PCR-based clonality testing may assist in questionable diagnosis and monitoring of acute lymphoblastic leukemia. Int J Lab Hematol 2023. [PMID: 36871952 DOI: 10.1111/ijlh.14053] [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: 07/26/2022] [Accepted: 02/21/2023] [Indexed: 03/07/2023]
Abstract
INTRODUCTION Multicolor flow cytometry (MFC) has highly reliable and flexible algorithms for diagnosis and monitoring of acute lymphoblastic leukemia (ALL). However, MFC analysis can be affected by poor sample quality or novel therapeutic options (e.g., targeted therapies and immunotherapy). Therefore, an additional confirmation of MFC data may be needed. We propose a simple approach for validation of MFC findings in ALL by sorting questionable cells and analyzing immunoglobulin/T-cell receptor (IG/TR) gene rearrangements via EuroClonality-based multiplex PCR. PATIENTS AND METHODS We obtained questionable MFC results for 38 biological samples from 37 patients. In total, 42 cell populations were isolated by flow cell sorting for downstream multiplex PCR. Most of the patients (n = 29) had B-cell precursor ALL and were investigated for measurable residual disease (MRD); 79% of them received CD19-directed therapy (blinatumomab or CAR-T). RESULTS We established the clonal nature of 40 cell populations (95.2%). By using this technique, we confirmed very low MRD levels (<0.01% MFC-MRD). We also applied it to several ambiguous findings for diagnostic samples, including those with mixed-phenotype acute leukemia, and the results obtained impacted the final diagnosis. CONCLUSION We have demonstrated possibilities of a combined approach (cell sorting and PCR-based clonality assessment) to validate MFC findings in ALL. The technique is easy to implement in diagnostic and monitoring workflows, as it does not require isolation of a large number of cells and knowledge of individual clonal rearrangements. We believe it provides important information for further treatment.
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Affiliation(s)
- Alexandra Semchenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Vladimir Zhogov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Elena Zakharova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Ekaterina Mikhailova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Olga Illarionova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Sergey Larin
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Galina Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alexander Karachunskiy
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Michael Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alexander Popov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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27
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Sobol MS, Kaster AK. Back to Basics: A Simplified Improvement to Multiple Displacement Amplification for Microbial Single-Cell Genomics. Int J Mol Sci 2023; 24. [PMID: 36901710 DOI: 10.3390/ijms24054270] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/23/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Microbial single-cell genomics (SCG) provides access to the genomes of rare and uncultured microorganisms and is a complementary method to metagenomics. Due to the femtogram-levels of DNA in a single microbial cell, sequencing the genome requires whole genome amplification (WGA) as a preliminary step. However, the most common WGA method, multiple displacement amplification (MDA), is known to be costly and biased against specific genomic regions, preventing high-throughput applications and resulting in uneven genome coverage. Thus, obtaining high-quality genomes from many taxa, especially minority members of microbial communities, becomes difficult. Here, we present a volume reduction approach that significantly reduces costs while improving genome coverage and uniformity of DNA amplification products in standard 384-well plates. Our results demonstrate that further volume reduction in specialized and complex setups (e.g., microfluidic chips) is likely unnecessary to obtain higher-quality microbial genomes. This volume reduction method makes SCG more feasible for future studies, thus helping to broaden our knowledge on the diversity and function of understudied and uncharacterized microorganisms in the environment.
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Petrogiannis-Haliotis T, Pehr K, Roberge D, Rys RN, Monczak Y, Popradi G, Ajjamada L, Benlimame N, Querfeld C, Johnson N, Knecht H. Primary Cutaneous Multifocal Indolent CD8+ T-Cell Lymphoma: A Novel Primary Cutaneous CD8+ T-Cell Lymphoma. Biomedicines 2023; 11. [PMID: 36831170 DOI: 10.3390/biomedicines11020634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/03/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
We report the case of a patient who was referred to our institution with a diagnosis of CD4+ small/medium-sized pleomorphic lymphoma. At the time, the patient showed a plethora of lesions mainly localizing to the legs; thus, we undertook studies to investigate the lineage and immunophenotype of the neoplastic clone. Immunohistochemistry (IHC) showed marked CD4 and CD8 positivity. Flow cytometry (FCM) showed two distinct T-cell populations, CD4+ and CD8+ (+/- PD1), with no CD4/CD8 co-expression and no loss of panT-cell markers in either T-cell subset. FCM, accompanied by cell-sorting (CS), permitted the physical separation of four populations, as follows: CD4+/PD1-, CD4+/PD1+, CD8+/PD1- and CD8+/PD1+. TCR gene rearrangement studies on each of the four populations (by next generation sequencing, NGS) showed that the neoplastic population was of T-cytotoxic cell lineage. IHC showed the CD8+ population to be TIA-1+, but perforin- and granzyme-negative. Moreover, histiocytic markers did not render the peculiar staining pattern, which is characteristic of acral CD8+ T-cell lymphoma (PCACD8). Compared to the entities described in the 2018 update of the WHO-EORTC classification for primary cutaneous lymphomas, we found that the indolent lymphoma described herein differed from all of them. We submit that this case represents a hitherto-undescribed type of CTCL.
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29
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Tian D, Wang C, Liu Y, Zhang Y, Caliari A, Lu H, Xia Y, Xu B, Xu J, Yomo T. Cell Sorting-Directed Selection of Bacterial Cells in Bigger Sizes Analyzed by Imaging Flow Cytometry during Experimental Evolution. Int J Mol Sci 2023; 24:ijms24043243. [PMID: 36834655 PMCID: PMC9966196 DOI: 10.3390/ijms24043243] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Cell morphology is an essential and phenotypic trait that can be easily tracked during adaptation and evolution to environmental changes. Thanks to the rapid development of quantitative analytical techniques for large populations of cells based on their optical properties, morphology can be easily determined and tracked during experimental evolution. Furthermore, the directed evolution of new culturable morphological phenotypes can find use in synthetic biology to refine fermentation processes. It remains unknown whether and how fast we can obtain a stable mutant with distinct morphologies using fluorescence-activated cell sorting (FACS)-directed experimental evolution. Taking advantage of FACS and imaging flow cytometry (IFC), we direct the experimental evolution of the E. coli population undergoing continuous passage of sorted cells with specific optical properties. After ten rounds of sorting and culturing, a lineage with large cells resulting from incomplete closure of the division ring was obtained. Genome sequencing highlighted a stop-gain mutation in amiC, leading to a dysfunctional AmiC division protein. The combination of FACS-based selection with IFC analysis to track the evolution of the bacteria population in real-time holds promise to rapidly select and culture new morphologies and association tendencies with many potential applications.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jian Xu
- Correspondence: (J.X.); (T.Y.); Tel.: +86-(21)-62233727 (J.X. & T.Y.)
| | - Tetsuya Yomo
- Correspondence: (J.X.); (T.Y.); Tel.: +86-(21)-62233727 (J.X. & T.Y.)
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30
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Abdulkadir N, Saraiva JP, Schattenberg F, Toscan RB, Borim Correa F, Harms H, Müller S, da Rocha UN. Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge. Microorganisms 2023; 11. [PMID: 36677467 DOI: 10.3390/microorganisms11010175] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
The recovery of metagenome-assembled genomes is biased towards the most abundant species in a given community. To improve the identification of species, even if only dominant species are recovered, we investigated the integration of flow cytometry cell sorting with bioinformatics tools to recover metagenome-assembled genomes. We used a cell culture of a wastewater microbial community as our model system. Cells were separated based on fluorescence signals via flow cytometry cell sorting into sub-communities: dominant gates, low abundant gates, and outer gates into subsets of the original community. Metagenome sequencing was performed for all groups. The unsorted community was used as control. We recovered a total of 24 metagenome-assembled genomes (MAGs) representing 11 species-level genome operational taxonomic units (gOTUs). In addition, 57 ribosomal operational taxonomic units (rOTUs) affiliated with 29 taxa at species level were reconstructed from metagenomic libraries. Our approach suggests a two-fold increase in the resolution when comparing sorted and unsorted communities. Our results also indicate that species abundance is one determinant of genome recovery from metagenomes as we can recover taxa in the sorted libraries that are not present in the unsorted community. In conclusion, a combination of cell sorting and metagenomics allows the recovery of MAGs undetected without cell sorting.
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31
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Beauchemin ET, Hunter C, Maurice CF. Actively replicating gut bacteria identified by 5-ethynyl-2'-deoxyuridine (EdU) click chemistry and cell sorting. Gut Microbes 2023; 15:2180317. [PMID: 36823031 PMCID: PMC9980609 DOI: 10.1080/19490976.2023.2180317] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The composition of the intestinal bacterial community is well described, but recent research suggests that the metabolism of these bacteria plays a larger role in health than which species are present. One fundamental aspect of gut bacterial metabolism that remains understudied is bacterial replication. Indeed, there exist few techniques which can identify actively replicating gut bacteria. In this study, we aimed to address this gap by adapting 5-ethynyl-2'-deoxyuridine (EdU) click chemistry (EdU-click), a metabolic labeling method, coupled with fluorescence-activated cell sorting and sequencing (FACS-Seq) to characterize replicating gut bacteria. We first used EdU-click with human gut bacterial isolates and show that many of them are amenable to this technique. We then optimized EdU-click and FACS-Seq for murine fecal bacteria and reveal that Prevotella UCG-001 and Ileibacterium are enriched in the replicating fraction. Finally, we labeled the actively replicating murine gut bacteria during exposure to cell wall-specific antibiotics in vitro. We show that regardless of the antibiotic used, the actively replicating bacteria largely consist of Ileibacterium, suggesting the resistance of this taxon to perturbations. Overall, we demonstrate how combining EdU-click and FACSeq can identify the actively replicating gut bacteria and their link with the composition of the whole community in both homeostatic and perturbed conditions. This technique will be instrumental in elucidating in situ bacterial replication dynamics in a variety of other ecological states, including colonization and species invasion, as well as for investigating the relationship between the replication and abundance of bacteria in complex communities.
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Affiliation(s)
- Eve T. Beauchemin
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Claire Hunter
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Corinne F. Maurice
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada,McGill Centre for Microbiome Research, McGill University, Montreal, Quebec, Canada,CONTACT Corinne F. Maurice Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
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32
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Zhao Y, Isozaki A, Herbig M, Hayashi M, Hiramatsu K, Yamazaki S, Kondo N, Ohnuki S, Ohya Y, Nitta N, Goda K. Intelligent sort-timing prediction for image-activated cell sorting. Cytometry A 2023; 103:88-97. [PMID: 35766305 DOI: 10.1002/cyto.a.24664] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/20/2022] [Accepted: 06/11/2022] [Indexed: 02/07/2023]
Abstract
Intelligent image-activated cell sorting (iIACS) has enabled high-throughput image-based sorting of single cells with artificial intelligence (AI) algorithms. This AI-on-a-chip technology combines fluorescence microscopy, AI-based image processing, sort-timing prediction, and cell sorting. Sort-timing prediction is particularly essential due to the latency on the order of milliseconds between image acquisition and sort actuation, during which image processing is performed. The long latency amplifies the effects of the fluctuations in the flow speed of cells, leading to fluctuation and uncertainty in the arrival time of cells at the sort point on the microfluidic chip. To compensate for this fluctuation, iIACS measures the flow speed of each cell upstream, predicts the arrival timing of the cell at the sort point, and activates the actuation of the cell sorter appropriately. Here, we propose and demonstrate a machine learning technique to increase the accuracy of the sort-timing prediction that would allow for the improvement of sort event rate, yield, and purity. Specifically, we trained an algorithm to predict the sort timing for morphologically heterogeneous budding yeast cells. The algorithm we developed used cell morphology, position, and flow speed as inputs for prediction and achieved 41.5% lower prediction error compared to the previously employed method based solely on flow speed. As a result, our technique would allow for an increase in the sort event rate of iIACS by a factor of ~2.
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Affiliation(s)
- Yaqi Zhao
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Akihiro Isozaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Maik Herbig
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mika Hayashi
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kotaro Hiramatsu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Sota Yamazaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | | | - Keisuke Goda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,CYBO, Tokyo, Japan.,Department of Bioengineering, University of California, California, Los Angeles, USA.,Institute of Technological Sciences, Wuhan University, Hubei, China
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33
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Soe MTM, Spiller KL, Noh M. Dielectrophoretic characterization of macrophage phenotypes. Electrophoresis 2022; 43:2440-2452. [PMID: 36050869 DOI: 10.1002/elps.202200046] [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: 02/22/2022] [Revised: 05/31/2022] [Accepted: 08/10/2022] [Indexed: 12/14/2022]
Abstract
Different macrophage phenotypes play important roles in diverse biological processes and diseases. In this study, we have characterized the dielectrophoretic responses of human monocytes and macrophage phenotypes: nonactivated (M0), pro-inflammatory (M1), and pro-healing (M2a). Dielectrophoretic responses of cells change as a function of frequency of the applied electric field. We measured the crossover frequency at which cells transition from negative to positive dielectrophoresis (DEP) or vice versa using interdigitated electrodes. For these characterization experiments, we also developed a new low-conductivity media formulation that retained 100% of the initial viability for 1 h. Human THP1 monocytes showed a distinguishable DEP response from mature macrophages. M1 macrophages also showed a distinct DEP response compared to M0 and M2a macrophages. No clear distinction could be drawn between M0 and M2a. The median values of the crossover frequencies of monocytes, M0, M1, and M2a were 38, 21, 11, and 23 kHz, respectively. Membrane capacitances of these cells were calculated consequently, and the values were 0.0111, 0.0128, 0.0244, and 0.0117 F/m2 for monocytes, M0, M1, and M2a, respectively. These results show how bioelectric properties are influenced by changes in macrophage phenotype.
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Affiliation(s)
- Mi Thant Mon Soe
- Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania, USA
| | - Kara L Spiller
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania, USA
| | - Moses Noh
- Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania, USA
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Harmon J, Findinier J, Ishii NT, Herbig M, Isozaki A, Grossman A, Goda K. Intelligent image-activated sorting of Chlamydomonas reinhardtii by mitochondrial localization. Cytometry A 2022; 101:1027-1034. [PMID: 35643943 DOI: 10.1002/cyto.a.24661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 03/29/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 01/27/2023]
Abstract
Organelle positioning in cells is associated with various metabolic functions and signaling in unicellular organisms. Specifically, the microalga Chlamydomonas reinhardtii repositions its mitochondria, depending on the levels of inorganic carbon. Mitochondria are typically randomly distributed in the Chlamydomonas cytoplasm, but relocate toward the cell periphery at low inorganic carbon levels. This mitochondrial relocation is linked with the carbon-concentrating mechanism, but its significance is not yet thoroughly understood. A genotypic understanding of this relocation would require a high-throughput method to isolate rare mutant cells not exhibiting this relocation. However, this task is technically challenging due to the complex intracellular morphological difference between mutant and wild-type cells, rendering conventional non-image-based high-event-rate methods unsuitable. Here, we report our demonstration of intelligent image-activated cell sorting by mitochondrial localization. Specifically, we applied an intelligent image-activated cell sorting system to sort for C. reinhardtii cells displaying no mitochondrial relocation. We trained a convolutional neural network (CNN) to distinguish the cell types based on the complex morphology of their mitochondria. The CNN was employed to perform image-activated sorting for the mutant cell type at 180 events per second, which is 1-2 orders of magnitude faster than automated microscopy with robotic pipetting, resulting in an enhancement of the concentration from 5% to 56.5% corresponding to an enrichment factor of 11.3. These results show the potential of image-activated cell sorting for connecting genotype-phenotype relations for rare-cell populations, which require a high throughput and could lead to a better understanding of metabolic functions in cells.
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Affiliation(s)
- Jeffrey Harmon
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Justin Findinier
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | | | - Maik Herbig
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Akihiro Isozaki
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Arthur Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA.,Department of Biology, Stanford University, Stanford, California, USA
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Department of Bioengineering, University of California, California, Los Angeles, USA.,Institute of Technological Sciences, Wuhan University, Hubei, China
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35
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Gharib G, Bütün İ, Muganlı Z, Kozalak G, Namlı İ, Sarraf SS, Ahmadi VE, Toyran E, van Wijnen AJ, Koşar A. Biomedical Applications of Microfluidic Devices: A Review. Biosensors (Basel) 2022; 12:bios12111023. [PMID: 36421141 PMCID: PMC9688231 DOI: 10.3390/bios12111023] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/30/2022] [Accepted: 11/08/2022] [Indexed: 05/26/2023]
Abstract
Both passive and active microfluidic chips are used in many biomedical and chemical applications to support fluid mixing, particle manipulations, and signal detection. Passive microfluidic devices are geometry-dependent, and their uses are rather limited. Active microfluidic devices include sensors or detectors that transduce chemical, biological, and physical changes into electrical or optical signals. Also, they are transduction devices that detect biological and chemical changes in biomedical applications, and they are highly versatile microfluidic tools for disease diagnosis and organ modeling. This review provides a comprehensive overview of the significant advances that have been made in the development of microfluidics devices. We will discuss the function of microfluidic devices as micromixers or as sorters of cells and substances (e.g., microfiltration, flow or displacement, and trapping). Microfluidic devices are fabricated using a range of techniques, including molding, etching, three-dimensional printing, and nanofabrication. Their broad utility lies in the detection of diagnostic biomarkers and organ-on-chip approaches that permit disease modeling in cancer, as well as uses in neurological, cardiovascular, hepatic, and pulmonary diseases. Biosensor applications allow for point-of-care testing, using assays based on enzymes, nanozymes, antibodies, or nucleic acids (DNA or RNA). An anticipated development in the field includes the optimization of techniques for the fabrication of microfluidic devices using biocompatible materials. These developments will increase biomedical versatility, reduce diagnostic costs, and accelerate diagnosis time of microfluidics technology.
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Affiliation(s)
- Ghazaleh Gharib
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - İsmail Bütün
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
| | - Zülâl Muganlı
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
| | - Gül Kozalak
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - İlayda Namlı
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
| | | | | | - Erçil Toyran
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
| | - Andre J. van Wijnen
- Department of Biochemistry, University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Ali Koşar
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
- Turkish Academy of Sciences (TÜBA), Çankaya, Ankara 06700, Turkey
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36
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Mukherjee P, Park SH, Pathak N, Patino CA, Bao G, Espinosa HD. Integrating Micro and Nano Technologies for Cell Engineering and Analysis: Toward the Next Generation of Cell Therapy Workflows. ACS Nano 2022; 16:15653-15680. [PMID: 36154011 DOI: 10.1021/acsnano.2c05494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The emerging field of cell therapy offers the potential to treat and even cure a diverse array of diseases for which existing interventions are inadequate. Recent advances in micro and nanotechnology have added a multitude of single cell analysis methods to our research repertoire. At the same time, techniques have been developed for the precise engineering and manipulation of cells. Together, these methods have aided the understanding of disease pathophysiology, helped formulate corrective interventions at the cellular level, and expanded the spectrum of available cell therapeutic options. This review discusses how micro and nanotechnology have catalyzed the development of cell sorting, cellular engineering, and single cell analysis technologies, which have become essential workflow components in developing cell-based therapeutics. The review focuses on the technologies adopted in research studies and explores the opportunities and challenges in combining the various elements of cell engineering and single cell analysis into the next generation of integrated and automated platforms that can accelerate preclinical studies and translational research.
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Affiliation(s)
- Prithvijit Mukherjee
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
| | - So Hyun Park
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, Texas 77030, United States
| | - Nibir Pathak
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Cesar A Patino
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Gang Bao
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, Texas 77030, United States
| | - Horacio D Espinosa
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
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37
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Abstract
Since the proposal of the differential adhesion hypothesis, scientists have been fascinated by how cell adhesion mediates cellular self-organization to form spatial patterns during development. The search for molecular tool kits with homophilic binding specificity resulted in a diverse repertoire of adhesion molecules. Recent understanding of the dominant role of cortical tension over adhesion binding redirects the focus of differential adhesion studies to the signaling function of adhesion proteins to regulate actomyosin contractility. The broader framework of differential interfacial tension encompasses both adhesion and nonadhesion molecules, sharing the common function of modulating interfacial tension during cell sorting to generate diverse tissue patterns. Robust adhesion-based patterning requires close coordination between morphogen signaling, cell fate decisions, and changes in adhesion. Current advances in bridging theoretical and experimental approaches present exciting opportunities to understand molecular, cellular, and tissue dynamics during adhesion-based tissue patterning across multiple time and length scales.
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Affiliation(s)
- Tony Y-C Tsai
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA;
| | - Rikki M Garner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA;
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA;
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38
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Bartos LM, Kunte ST, Beumers P, Xiang X, Wind K, Ziegler S, Bartenstein P, Choi H, Lee DS, Haass C, von Baumgarten L, Tahirovic S, Albert NL, Lindner S, Brendel M. Single-Cell Radiotracer Allocation via Immunomagnetic Sorting to Disentangle PET Signals at Cellular Resolution. J Nucl Med 2022; 63:1459-1462. [PMID: 35589403 PMCID: PMC9536696 DOI: 10.2967/jnumed.122.264171] [Citation(s) in RCA: 2] [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: 03/22/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
With great interest, our independent groups of scientists located in Korea and Germany recognized the use of a very similar methodologic approach to quantify the uptake of radioactive glucose (18F-FDG) at the cellular level. The focus of our investigations was to disentangle microglial 18F-FDG uptake. To do so, CD11b immunomagnetic cell sorting was applied to isolate microglia cells after in vivo 18F-FDG injection, to allow simple quantification via a γ-counter. Importantly, this technique reveals a snapshot of cellular glucose uptake in living mice at the time of injection since 18F-FDG is trapped by hexokinase phosphorylation without a further opportunity to be metabolized. Both studies indicated high 18F-FDG uptake of single CD11b-positive microglia cells and a significant increase in microglial 18F-FDG uptake when this cell type is activated in the presence of amyloid pathology. Furthermore, another study noticed that immunomagnetic cell sorting after tracer injection facilitated determination of high 18F-FDG uptake in myeloid cells in a range of tumor models. Here, we aim to discuss the rationale for single-cell radiotracer allocation via immunomagnetic cell sorting (scRadiotracing) by providing examples of promising applications of this innovative technology in neuroscience, oncology, and radiochemistry.
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Affiliation(s)
- Laura M Bartos
- Department of Nuclear Medicine, University Hospital of Munich, LMU Munich, Munich, Germany
| | - Sebastian T Kunte
- Department of Nuclear Medicine, University Hospital of Munich, LMU Munich, Munich, Germany
| | - Philipp Beumers
- Department of Nuclear Medicine, University Hospital of Munich, LMU Munich, Munich, Germany
| | - Xianyuan Xiang
- Biomedical Center, Division of Metabolic Biochemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
- CAS Key Laboratory of Brain Connectome and Manipulation, the Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, and Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
| | - Karin Wind
- Department of Nuclear Medicine, University Hospital of Munich, LMU Munich, Munich, Germany
| | - Sibylle Ziegler
- Department of Nuclear Medicine, University Hospital of Munich, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology, Munich, Germany
| | - Peter Bartenstein
- Department of Nuclear Medicine, University Hospital of Munich, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology, Munich, Germany
| | - Hongyoon Choi
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong Soo Lee
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Christian Haass
- Biomedical Center, Division of Metabolic Biochemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
- CAS Key Laboratory of Brain Connectome and Manipulation, the Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, and Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Louisa von Baumgarten
- Department of Neurosurgery, University Hospital of Munich, LMU Munich, Munich, Germany; and
- German Cancer Consortium, Munich, Germany
| | | | - Nathalie L Albert
- Department of Nuclear Medicine, University Hospital of Munich, LMU Munich, Munich, Germany
| | - Simon Lindner
- Department of Nuclear Medicine, University Hospital of Munich, LMU Munich, Munich, Germany
| | - Matthias Brendel
- Department of Nuclear Medicine, University Hospital of Munich, LMU Munich, Munich, Germany;
- Munich Cluster for Systems Neurology, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
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39
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Liu H, Yan N, Wong TY, Lam H, Lam JWY, Kwok RTK, Sun J, Tang BZ. Fluorescent Imaging and Sorting of High-Lipid-Content Strains of Green Algae by Using an Aggregation-Induced Emission Luminogen. ACS Nano 2022; 16:14973-14981. [PMID: 36099405 DOI: 10.1021/acsnano.2c05976] [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] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microalgae-based biofuels are receiving attention at the environmental, economic, and social levels because they are clean, renewable, and quickly produced. The green algae Chlorella vulgaris has been extensively studied in research laboratories and the biofuel industry as a model organism to increase lipid production to be cost-effective in commercial production. In this work, we utilized a lipid-droplet-specific luminogen with aggregation-induced emission (AIE) characteristics to increase the lipid production of C. vulgaris by fluorescent imaging and sorting of those algal cells with large and rich lipid droplets for subculturing. The AIE-active TPA-A enabled real-time monitoring of the size and number of lipid droplets in C. vulgaris during their growth period so that we can identify the best time for harvesting. Furthermore, the algae cells with high lipid content were identified and collected for subculturing by the technique of fluorescence-activated cell sorting (FACS). The lipid production in the generation of two successive selections was almost doubled compared to the generation with natural selection. This work demonstrated that the technologies of AIE and FACS could be applied together to improve the production of a third-generation biofuel.
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Affiliation(s)
- Haixiang Liu
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st Rd, South Area, Hi-tech Park, Nanshan, Shenzhen 518057, China
| | - Neng Yan
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Tin Yan Wong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Jacky W Y Lam
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st Rd, South Area, Hi-tech Park, Nanshan, Shenzhen 518057, China
- The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Ryan T K Kwok
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st Rd, South Area, Hi-tech Park, Nanshan, Shenzhen 518057, China
- The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Jianwei Sun
- The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Ben Zhong Tang
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st Rd, South Area, Hi-tech Park, Nanshan, Shenzhen 518057, China
- The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
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Abstract
Here, we review the use of human pluripotent stem cells for skeletal tissue engineering. A number of approaches have been used for generating cartilage and bone from both human embryonic stem cells and induced pluripotent stem cells. These range from protocols relying on intrinsic cell interactions and signals from co-cultured cells to those attempting to recapitulate the series of steps occurring during mammalian skeletal development. The importance of generating authentic tissues rather than just differentiated cells is emphasized and enabling technologies for doing this are reported. We also review the different methods for characterization of skeletal cells and constructs at the tissue and single-cell level, and indicate newer resources not yet fully utilized in this field. There have been many challenges in this research area but the technologies to overcome these are beginning to appear, often adopted from related fields. This makes it more likely that cost-effective and efficacious human pluripotent stem cell-engineered constructs may become available for skeletal repair in the near future.
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Affiliation(s)
- Miguel J S Ferreira
- Department of Mechanical, Aerospace and Civil Engineering, School of Engineering, Faculty of Science and Engineering & Henry Royce Institute, The University of Manchester, Manchester, UK
| | - Fabrizio E Mancini
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Paul A Humphreys
- Department of Mechanical, Aerospace and Civil Engineering, School of Engineering, Faculty of Science and Engineering & Henry Royce Institute, The University of Manchester, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Leona Ogene
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Michael Buckley
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Marco A N Domingos
- Department of Mechanical, Aerospace and Civil Engineering, School of Engineering, Faculty of Science and Engineering & Henry Royce Institute, The University of Manchester, Manchester, UK
| | - Susan J Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
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Wang Z, Wang H, Lin S, Ahmed S, Angers S, Sargent EH, Kelley SO. Nanoparticle Amplification Labeling for High-Performance Magnetic Cell Sorting. Nano Lett 2022; 22:4774-4783. [PMID: 35639489 DOI: 10.1021/acs.nanolett.2c01018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Magnetic cell sorting is an enabling tool for the isolation of specific cellular subpopulations for downstream applications and requires the cells to be labeled by a sufficient number of magnetic nanoparticles to leverage magnetophoresis for efficient separation. This requirement makes it challenging to target weakly expressed biomarkers. Here, we developed a new approach that selectively and efficiently amplifies the magnetic labeling on cells through sequentially connected antibodies and nanoparticles delivered to the surface or interior of the cell. Using this approach, we achieved amplification up to 100-fold for surface and intracellular markers. We also demonstrated the utility of this assay for enabling high-performance magnetic cell sorting when it is applied to the analysis of rare tumor cells for cancer diagnosis and the purification of transfected CAR T cells for immunotherapy. The data presented demonstrate a useful tool for the stratification of rare cell subpopulations.
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Affiliation(s)
- Zongjie Wang
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto M5S 3G9, Canada
| | - Hansen Wang
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Sichun Lin
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
| | - Sharif Ahmed
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Stephane Angers
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
| | - Edward H Sargent
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada
| | - Shana O Kelley
- Institute of Biomedical Engineering, University of Toronto, Toronto M5S 3G9, Canada
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- Department of Chemistry, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto M5S 1A8, Canada
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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Ocañas SR, Pham KD, Blankenship HE, Machalinski AH, Chucair-Elliott AJ, Freeman WM. Minimizing the Ex Vivo Confounds of Cell-Isolation Techniques on Transcriptomic and Translatomic Profiles of Purified Microglia. eNeuro 2022; 9:ENEURO. [PMID: 35228310 DOI: 10.1523/ENEURO.0348-21.2022] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 12/10/2021] [Accepted: 01/25/2022] [Indexed: 01/21/2023] Open
Abstract
Modern molecular and biochemical neuroscience studies require analysis of specific cellular populations derived from brain tissue samples to disambiguate cell type-specific events. This is particularly true in the analysis of minority glial populations in the brain, such as microglia, which may be obscured in whole tissue analyses. Microglia have central functions in development, aging, and neurodegeneration and are a current focus of neuroscience research. A long-standing concern for glial biologists using in vivo models is whether cell isolation from CNS tissue could introduce ex vivo artifacts in microglia, which respond quickly to changes in the environment. Mouse microglia were purified by magnetic-activated cell sorting (MACS), as well as cytometer-based and cartridge-based fluorescence-activated cell sorting (FACS) approaches to compare and contrast performance. The Cx3cr1-NuTRAP mouse model was used to provide an endogenous fluorescent microglial marker and a microglial-specific translatome profile as a baseline comparison lacking cell isolation artifacts. All sorting methods performed similarly for microglial purity with main differences being in cell yield and time of isolation. Ex vivo activation signatures occurred principally during the initial tissue dissociation and cell preparation and not the cell sorting. The cell preparation-induced activational phenotype could be minimized by inclusion of transcriptional and translational inhibitors or non-enzymatic dissociation conducted entirely at low temperatures. These data demonstrate that a variety of microglial isolation approaches can be used, depending on experimental needs, and that inhibitor cocktails are effective at reducing cell preparation artifacts.
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Lewis AE, Kuwahara A, Franzosi J, Bush JO. Tracheal separation is driven by NKX2-1-mediated repression of Efnb2 and regulation of endodermal cell sorting. Cell Rep 2022; 38:110510. [PMID: 35294885 PMCID: PMC9033272 DOI: 10.1016/j.celrep.2022.110510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 12/29/2021] [Accepted: 02/16/2022] [Indexed: 11/05/2022] Open
Abstract
The mechanisms coupling fate specification of distinct tissues to their physical separation remain to be understood. The trachea and esophagus differentiate from a single tube of definitive endoderm, requiring the transcription factors SOX2 and NKX2-1, but how the dorsoventral site of tissue separation is defined to allocate tracheal and esophageal cell types is unknown. Here, we show that the EPH/EPHRIN signaling gene Efnb2 regulates tracheoesophageal separation by controlling the dorsoventral allocation of tracheal-fated cells. Ventral loss of NKX2-1 results in disruption of separation and expansion of Efnb2 expression in the trachea independent of SOX2. Through chromatin immunoprecipitation and reporter assays, we find that NKX2-1 likely represses Efnb2 directly. Lineage tracing shows that loss of NKX2-1 results in misallocation of ventral foregut cells into the esophagus, while mosaicism for NKX2-1 generates ectopic NKX2-1/EPHRIN-B2 boundaries that organize ectopic tracheal separation. Together, these data demonstrate that NKX2-1 coordinates tracheal specification with tissue separation through the regulation of EPHRIN-B2 and tracheoesophageal cell sorting. Lewis et al. show that, in the development of the mammalian trachea and esophagus, cell fate specification is coupled with morphogenesis by NKX2-1-mediated repression of Efnb2. This establishes an EPH/EPHRIN boundary that drives cell allocation and physical separation of the trachea and esophagus.
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Affiliation(s)
- Ace E Lewis
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Program in Craniofacial Biology, University of California, San Francisco, 513 Parnassus Avenue, Box 0512, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Akela Kuwahara
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Program in Craniofacial Biology, University of California, San Francisco, 513 Parnassus Avenue, Box 0512, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jacqueline Franzosi
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Program in Craniofacial Biology, University of California, San Francisco, 513 Parnassus Avenue, Box 0512, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey O Bush
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Program in Craniofacial Biology, University of California, San Francisco, 513 Parnassus Avenue, Box 0512, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.
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Altay R, Yapici MK, Koşar A. A Hybrid Spiral Microfluidic Platform Coupled with Surface Acoustic Waves for Circulating Tumor Cell Sorting and Separation: A Numerical Study. Biosensors (Basel) 2022; 12:bios12030171. [PMID: 35323441 PMCID: PMC8946654 DOI: 10.3390/bios12030171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/08/2022] [Accepted: 03/08/2022] [Indexed: 05/28/2023]
Abstract
The separation of circulating tumor cells (CTCs) from blood samples is crucial for the early diagnosis of cancer. During recent years, hybrid microfluidics platforms, consisting of both passive and active components, have been an emerging means for the label-free enrichment of circulating tumor cells due to their advantages such as multi-target cell processing with high efficiency and high sensitivity. In this study, spiral microchannels with different dimensions were coupled with surface acoustic waves (SAWs). Numerical simulations were conducted at different Reynolds numbers to analyze the performance of hybrid devices in the sorting and separation of CTCs from red blood cells (RBCs) and white blood cells (WBCs). Overall, in the first stage, the two-loop spiral microchannel structure allowed for the utilization of inertial forces for passive separation. In the second stage, SAWs were introduced to the device. Thus, five nodal pressure lines corresponding to the lateral position of the five outlets were generated. According to their physical properties, the cells were trapped and lined up on the corresponding nodal lines. The results showed that three different cell types (CTCs, RBCs, and WBCs) were successfully focused and collected from the different outlets of the microchannels by implementing the proposed multi-stage hybrid system.
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Affiliation(s)
- Rana Altay
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey; (R.A.); (M.K.Y.)
| | - Murat Kaya Yapici
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey; (R.A.); (M.K.Y.)
- Center of Excellence for Functional Surfaces and Interfaces for Nano-Diagnostics, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Ali Koşar
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey; (R.A.); (M.K.Y.)
- Center of Excellence for Functional Surfaces and Interfaces for Nano-Diagnostics, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
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Yanagida A, Corujo-Simon E, Revell CK, Sahu P, Stirparo GG, Aspalter IM, Winkel AK, Peters R, De Belly H, Cassani DAD, Achouri S, Blumenfeld R, Franze K, Hannezo E, Paluch EK, Nichols J, Chalut KJ. Cell surface fluctuations regulate early embryonic lineage sorting. Cell 2022; 185:777-793.e20. [PMID: 35196500 PMCID: PMC8896887 DOI: 10.1016/j.cell.2022.01.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 10/22/2021] [Accepted: 01/26/2022] [Indexed: 01/24/2023]
Abstract
In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive. Here, we investigate the mechanical basis of EPI and PrE sorting. We find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting. These differential surface fluctuations systematically correlate with differential cellular fluidity, which we propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, we identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages.
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Affiliation(s)
- Ayaka Yanagida
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK; Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Elena Corujo-Simon
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Christopher K Revell
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0HE, UK
| | - Preeti Sahu
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Giuliano G Stirparo
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Irene M Aspalter
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Alex K Winkel
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Ruby Peters
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Henry De Belly
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Davide A D Cassani
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Sarra Achouri
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Raphael Blumenfeld
- Gonville & Caius College, University of Cambridge, Trinity St., Cambridge CB2 1TA, UK
| | - Kristian Franze
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Edouard Hannezo
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Ewa K Paluch
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
| | - Jennifer Nichols
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
| | - Kevin J Chalut
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
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Patel C, Shi L, Whitesides JF, Foster BM, Fajardo RJ, Quillen EE, Kerr BA. A New Method of Bone Stromal Cell Characterization by Flow Cytometry. Curr Protoc 2022; 2:e400. [PMID: 35349226 PMCID: PMC8981709 DOI: 10.1002/cpz1.400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The bone microenvironment cellular composition plays an essential role in bone health and is disrupted in bone pathologies, such as osteoporosis, osteoarthritis, and cancer. Flow cytometry protocols for hematopoietic stem cell lineages are well defined and well established. Additionally, a consensus for mesenchymal stem cell flow markers has been developed. However, flow cytometry markers for bone-residing cells-osteoblasts, osteoclasts, and osteocytes-have not been proposed. Here, we describe a novel partial digestion method to separate these cells from the bone matrix and present new markers for enumerating these cells by flow cytometry. We optimized bone digestion and analyzed markers across murine, nonhuman primate, and human bone. The isolation and staining protocols can be used with either cell sorting or flow cytometry. Our method allows for the enumeration and collection of hematopoietic and mesenchymal lineage cells in the bone microenvironment combined with bone-residing stromal cells. Thus, we have established a multi-fluorochrome bone marrow cell-typing methodology. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Partial digestion for murine long bone stromal cell isolation Alternate Protocol 1: Partial digestion for primate vertebrae stromal cell isolation Alternate Protocol 2: Murine vertebrae crushing for bone stromal cell isolation Basic Protocol 2: Staining of bone stromal cells Support Protocol 1: Fluorescence minus one control, isotype control, and antibody titration Basic Protocol 3: Cell sorting of bone stromal cells Alternate Protocol 3: Flow cytometry analysis of bone stromal cells Support Protocol 2: Preparing compensation beads.
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Affiliation(s)
- Chirayu Patel
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Lihong Shi
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - John F. Whitesides
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC 27157,Wake Forest Baptist Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Brittni M. Foster
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Roberto J. Fajardo
- University of the Incarnate Word School of Osteopathic Medicine, San Antonio, TX 78235
| | - Ellen E. Quillen
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Bethany A. Kerr
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157,Wake Forest Baptist Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC 27157,Department of Orthopaedic Surgery, Wake Forest School of Medicine, Winston-Salem, NC 27157,Corresponding Author: Telephone: 336-716-0320; Fax: 336-716-0255; Twitter: @BethanyKerrLab;
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Maslennikova A, Kruglova N, Kalinichenko S, Komkov D, Shepelev M, Golubev D, Siniavin A, Vzorov A, Filatov A, Mazurov D. Engineering T-Cell Resistance to HIV-1 Infection via Knock-In of Peptides from the Heptad Repeat 2 Domain of gp41. mBio 2022; 13:e0358921. [PMID: 35073736 DOI: 10.1128/mbio.03589-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Previous studies suggest that short peptides from the heptad repeat 2 (HR2) domain of gp41 expressed on the cell surface are more potent inhibitors of HIV-1 entry than soluble analogs. However, their therapeutic potential has only been examined using lentiviral vectors. Here, we aimed to develop CRISPR/Cas9-based fusion inhibitory peptide knock-in (KI) technology for the generation and selection of HIV-1-resistant T cells. First, we embedded a series of HIV-1 fusion inhibitory peptides in CD52, the shortest glycosylphosphatidylinositol (GPI)-anchored protein, which efficiently delivers epitope tags to the cell surface and maintains a sufficient level of KI. Among the seven peptides tested, MT-C34, HP-23L, and 2P23 exhibited significant activity against both cell-free and cell-to-cell HIV-1 infection. The shed variant of MT-C34 provided insufficient protection against HIV-1 due to its low concentration in the culture medium. Using Cas9 plasmids or ribonucleoprotein electroporation and peptide-specific antibodies, we sorted CEM/R5 cells with biallelic KI of MT-C34 and 2P23 peptides at the CXCR4 locus. In combination, these peptides provided a higher level of protection than individual KI. By extending homology arms and cloning donor DNA into a plasmid containing signals for nuclear localization, we achieved KI of MT-C34 into the CXCR4 locus and HIV-1 proviral DNA at levels of up to 35% in the T-cell line and up to 4 to 5% in primary CD4 lymphocytes. Compared to lentiviral delivery, KI resulted in the higher MT-C34 surface expression and stronger protection of lymphocytes from HIV-1. Thus, we demonstrate that KI is a viable strategy for peptide-based therapy of HIV infection. IMPORTANCE HIV is a human lentivirus that infects CD4-positive immune cells and, when left untreated, manifests in the fatal disease known as AIDS. Antiretroviral therapy (ART) does not lead to viral clearance, and HIV persists in the organism as a latent provirus. One way to control infection is to increase the population of HIV-resistant CD4 lymphocytes via entry molecule knockout or expression of different antiviral genes. Peptides from the heptad repeat (HR) domain of gp41 are potent inhibitors of HIV-1 fusion, especially when designed to express on the cell surface. Individual gp41 peptides encoded by therapeutic lentiviral vectors have been evaluated and some have entered clinical trials. However, a CRISPR/Cas9-based gp41 peptide delivery platform that operates through concomitant target gene modification has not yet been developed due to low knock-in (KI) rates in primary cells. Here, we systematically evaluated the antiviral activity of different HR2 peptides cloned into the shortest carrier molecule, CD52. The resulting small-size transgene constructs encoding selected peptides, in combination with improvements to enhance donor vector nuclear import, helped to overcome precise editing restrictions in CD4 lymphocytes. Using KI into CXCR4, we demonstrated different options for target gene modification, effectively protecting edited cells against HIV-1.
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Chakrabarti L, Chaerkady R, Wang J, Weng SHS, Wang C, Qian C, Cazares L, Hess S, Amaya P, Zhu J, Hatton D. Mitochondrial membrane potential-enriched CHO host: a novel and powerful tool for improving biomanufacturing capability. MAbs 2022; 14:2020081. [PMID: 35030984 PMCID: PMC8765075 DOI: 10.1080/19420862.2021.2020081] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
With the aim of increasing protein productivity of Chinese hamster ovary (CHO) cells, we sought to generate new CHO hosts with favorable biomanufacturing phenotypes and improved functionality. Here, we present an innovative approach of enriching the CHO host cells with a high mitochondrial membrane potential (MMP). Stable transfectant pools and clonal cell lines expressing difficult-to-express bispecific molecules generated from the MMP-enriched host outperformed the parental host by displaying (1) improved fed-batch productivity; (2) enhanced long-term cell viability of pools; (3) more favorable lactate metabolism; and (4) improved cell cloning efficiency during monoclonal cell line generation. Proteomic analysis together with Western blot validation were used to investigate the underlying mechanisms by which high MMP influenced production performance. The MMP-enriched host exhibited multifaceted protection against mitochondrial dysfunction and endoplasmic reticulum stress. Our findings indicate that the MMP-enriched host achieved an overall “fitter” phenotype that contributes to the significant improvement in biomanufacturing capability.
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Affiliation(s)
- Lina Chakrabarti
- Cell Culture & Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, USA
| | | | - Junmin Wang
- Dynamic Omics, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | | | - Chunlei Wang
- Analytical Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Chen Qian
- Analytical Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Lisa Cazares
- Dynamic Omics, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Sonja Hess
- Dynamic Omics, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Peter Amaya
- Cell Culture & Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Jie Zhu
- Cell Culture & Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Diane Hatton
- Cell Culture & Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Cambridge, UK
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49
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Krutty JD, Sun J, Koesser K, Murphy WL, Gopalan P. Polymer-Coated Magnetic Microspheres Conjugated with Growth Factor Receptor Binding Peptides Enable Cell Sorting. ACS Biomater Sci Eng 2021; 7:5927-5932. [PMID: 34851098 DOI: 10.1021/acsbiomaterials.1c01199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The separation and sorting of human cells is an important step in the bioprocessing of cell-based therapeutics. Heterogeneous mixtures of cells must be sorted to isolate the desired cell type and purify the final product. This process is often achieved by antibody-based sorting techniques. In this work, we demonstrate that magnetic microspheres may be functionalized with peptides that selectively bind to cells on the basis of their relative concentration of specific surface proteins. Five-micrometer-magnetic microspheres were coated with the synthetic copolymer PVG (poly(poly(ethylene glycol)methyl ether methacrylate-ran-vinyl dimethyl azlactone-ran-glycidyl methacrylate) and functionalized with the vascular endothelial growth factor receptor binding peptide (VRBP), which binds to the vascular endothelial growth factor receptor (VEGFR). These microspheres exhibited low cytotoxicity and bind to cells depending on their relative surface protein expression. Finally, coated, magnetic microspheres were used to separate heterogeneous populations of cells dependent on their VEGFR expression through magnetic-assisted cell sorting (MACS), demonstrating that peptide-based cell sorting mechanisms may be useful in the bioprocessing of human-cell-based products.
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Affiliation(s)
- John D Krutty
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jian Sun
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kevin Koesser
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - William L Murphy
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Padma Gopalan
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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50
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Staunstrup NH, Petersen CC, Fuglsang T, Starnawska A, Chernomorchenko A, Qvist P, Schack VR. Comparison of electrostatic and mechanical cell sorting with limited starting material. Cytometry A 2021; 101:298-310. [PMID: 34842347 DOI: 10.1002/cyto.a.24523] [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: 09/01/2021] [Revised: 10/15/2021] [Accepted: 11/17/2021] [Indexed: 11/11/2022]
Abstract
Isolation of multiple cell populations from limited starting material and with minimal influence on cell homeostasis and viability are common requirements in both basic and clinical research. Fluorescence-activated cell sorting (FACS) is the most commonly applied sorting methodology with the majority of instruments being based on high pressure and electrostatic deflection. A more recent technology is based on a mechanical valve, operating at low pressure. In the present work we compared the two technologies by parallel sorting of small amounts of peripheral blood and umbilical cord blood on a BD FACSAria™ III and Miltenyi MACSQuant® Tyto® instrument. Concurrent manually performed magnetic-based cell sorting served as reference. Sorting metrics, including purity and viability, were compared. Expression of the heat-shock protein HSPA1A immediately post sorting and the proliferation potential of sorted T-cells in vitro was assessed. In general, there was little to distinguish the two fluorescence-activated technologies with regard to sorting metrics and HSPA1A expression. Variation, however, with respect to recovery and viability, was much smaller among Tyto sorted samples. The proliferation potential of Tyto-sorted T-cells was significantly higher compared to Aria-sorted T-cells, indicating that T-cells of the Tyto instrument are less perturbed. In summary, cell types of blood origin including CD34+ cells could effectively be isolated from small input amounts with either fluorescence-activated technology with little immediate effect on viability. The mechanical valve-based sorting by the Tyto instrument; however, appeared to perturb the cells to a lesser extent as judged by their proliferation potential.
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Affiliation(s)
- Nicklas H Staunstrup
- Department of Biomedicine, University of Aarhus, Aarhus C, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus V, Denmark.,Center for Genomics and Personalized Medicine, CGPM, and Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
| | | | - Tina Fuglsang
- Department of Biomedicine, University of Aarhus, Aarhus C, Denmark
| | - Anna Starnawska
- Department of Biomedicine, University of Aarhus, Aarhus C, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus V, Denmark.,Center for Genomics and Personalized Medicine, CGPM, and Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
| | | | - Per Qvist
- Department of Biomedicine, University of Aarhus, Aarhus C, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus V, Denmark.,Center for Genomics and Personalized Medicine, CGPM, and Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
| | - Vivien R Schack
- Department of Biomedicine, University of Aarhus, Aarhus C, Denmark
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