1
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Dreo B, Muralikrishnan AS, Husic R, Lackner A, Brügmann T, Haudum P, Bosch P, Thiel J, Fessler J, Stradner M. JAK/STAT signaling in rheumatoid arthritis leukocytes is uncoupled from serum cytokines in a subset of patients. Clin Immunol 2024; 264:110238. [PMID: 38729230 DOI: 10.1016/j.clim.2024.110238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
OBJECTIVE Rheumatoid Arthritis (RA) is a systemic autoimmune disease involving pro-inflammatory cytokines that can be therapeutically targeted by antibodies or kinase inhibitors. Nevertheless, these drugs fail in a subset of patients independent of the abundance of the targeted cytokines. We aim to explore the cellular basis of this phenomenon by analyzing the relation of cytokine abundance and activation of downstream signaling pathways in RA. METHODS The study included 62 RA patients and 9 healthy controls (HC). Phosphorylation of STAT 1-6 in various immune cell subsets was determined ex vivo using a novel robust flow cytometry-based protocol. Serum concentrations of IL-6, IL-10, IL-12p70, IL-17 A, interferon gamma, and TNFα in the same samples were measured using highly sensitive single molecule array (SIMOA). RESULTS We found an increase in circulating cytokines in RA patients, while STAT activity was lower in RA patients compared to HC. Based on STAT activity we determined three endotypes in active RA patients (cDAI>10, n = 28): 1) those with active STAT5a/b signaling in T cells (n = 7/28), 2) those with a low STAT activity in all assessed cell types (n = 14/28), and 3) those with active STAT1 and STAT3 signaling mainly in myeloid cells (n = 7/28). Integrating intracellular STAT activation and cytokine analysis revealed diminished JAK/STAT signaling in a subset of patients (n = 8/20) despite elevated serum cytokine concentrations. CONCLUSION Diminished JAK/STAT signaling in active RA may partly explain unresponsiveness to therapy targeting cytokine signaling. Analysis of JAK/STAT phosphorylation may identify patients at risk for non-response to these therapies.
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Affiliation(s)
- Barbara Dreo
- Division of Rheumatology and Immunology, Medical University of Graz, Austria
| | | | - Rusmir Husic
- Division of Rheumatology and Immunology, Medical University of Graz, Austria
| | - Angelika Lackner
- Division of Rheumatology and Immunology, Medical University of Graz, Austria
| | - Theresa Brügmann
- Division of Rheumatology and Immunology, Medical University of Graz, Austria
| | - Patrizia Haudum
- Division of Rheumatology and Immunology, Medical University of Graz, Austria
| | - Philipp Bosch
- Division of Rheumatology and Immunology, Medical University of Graz, Austria
| | - Jens Thiel
- Division of Rheumatology and Immunology, Medical University of Graz, Austria
| | - Johannes Fessler
- Division of Immunology, Otto Loewi Research Center, Medical University of Graz, Austria.
| | - Martin Stradner
- Division of Rheumatology and Immunology, Medical University of Graz, Austria
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2
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Manohar SM. Shedding Light on Intracellular Proteins using Flow Cytometry. Cell Biochem Biophys 2024:10.1007/s12013-024-01338-1. [PMID: 38831173 DOI: 10.1007/s12013-024-01338-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2024] [Indexed: 06/05/2024]
Abstract
Intracellular protein abundance is routinely measured in mammalian cells using population-based techniques such as western blotting which fail to capture single cell protein levels or using fluorescence microscopy which is although suitable for single cell protein detection but not for rapid analysis of large no. of cells. Flow cytometry offers rapid, high-throughput, multiparameter-based analysis of intracellular protein expression in statistically significant no. of cells at single cell resolution. In past few decades, customized assays have been developed for flow cytometric detection of specific intracellular proteins. This review discusses the scope of flow cytometry for intracellular protein detection in mammalian cells along with specific applications. Technological advancements to overcome the limitations of traditional flow cytometry for the same are also discussed.
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Affiliation(s)
- Sonal M Manohar
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be) University, Vile Parle (West), Mumbai, 400056, India.
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3
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Verbist W, Breukers J, Sharma S, Rutten I, Gerstmans H, Coelmont L, Dal Dosso F, Dallmeier K, Lammertyn J. SeParate: multiway fluorescence-activated droplet sorting based on integration of serial and parallel triaging concepts. LAB ON A CHIP 2024; 24:2107-2121. [PMID: 38450543 DOI: 10.1039/d3lc01075a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a versatile high-throughput sorting tool that is, unlike most fluorescence-activated cell sorting (FACS) platforms, capable of sorting droplet-compartmentalized cells, cell secretions, entire enzymatic reactions and more. Recently, multiplex FADS platforms have been developed for the sorting of multi-fluorophore populations towards different outlets in addition to the standard, more commonly used, 2-way FADS platform. These multiplex FADS platforms consist of either multiple 2-way junctions one after the other (i.e. serial sorters) or of one junction sorting droplets in more than 2 outlets (i.e. parallel sorters). In this work, we present SeParate, a novel platform based on integrating s̲e̲rial and p̲a̲r̲allel sorting principles for accura̲t̲e̲ multiplex droplet sorting that is able to mitigate limitations of current multiplex sorters. We show the SeParate platform and its capability in highly accurate 4-way sorting of a multi-fluorophore population into four subpopulations with the potential to expand to more. More specifically, the SeParate platform was thoroughly validated using mixed populations of fluorescent beads and picoinjected droplets, yielding sorting accuracies up to 100% and 99.9%, respectively. Finally, transfected HEK-293T cells were sorted employing two different optical setups, resulting in an accuracy up to 99.5%. SeParate's high accuracy for a diverse set of samples, including highly variable biological specimens, together with its scalability beyond the demonstrated 4-way sorting, warrants a broad applicability for multi-fluorophore studies in life sciences, environmental sciences and others.
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Affiliation(s)
- Wannes Verbist
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Jolien Breukers
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Sapna Sharma
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, KU Leuven, 3000 Leuven, Belgium
| | - Iene Rutten
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Lotte Coelmont
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, KU Leuven, 3000 Leuven, Belgium
| | - Francesco Dal Dosso
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Kai Dallmeier
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, KU Leuven, 3000 Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
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4
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De Biasi S, Gigan JP, Borella R, Santacroce E, Lo Tartaro D, Neroni A, Paschalidis N, Piwocka K, Argüello RJ, Gibellini L, Cossarizza A. Cell metabolism: Functional and phenotypic single cell approaches. Methods Cell Biol 2024; 186:151-187. [PMID: 38705598 DOI: 10.1016/bs.mcb.2024.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Several metabolic pathways are essential for the physiological regulation of immune cells, but their dysregulation can cause immune dysfunction. Hypermetabolic and hypometabolic states represent deviations in the magnitude and flexibility of effector cells in different contexts, for example in autoimmunity, infections or cancer. To study immunometabolism, most methods focus on bulk populations and rely on in vitro activation assays. Nowadays, thanks to the development of single-cell technologies, including multiparameter flow cytometry, mass cytometry, RNA cytometry, among others, the metabolic state of individual immune cells can be measured in a variety of samples obtained in basic, translational and clinical studies. Here, we provide an overview of different single-cell approaches that are employed to investigate both mitochondrial functions and cell dependence from mitochondria metabolism. Moreover, besides the description of the appropriate experimental settings, we discuss the strengths and weaknesses of different approaches with the aim to suggest how to study cell metabolism in the settings of interest.
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Affiliation(s)
- Sara De Biasi
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy.
| | - Julien Paul Gigan
- Aix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Rebecca Borella
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Elena Santacroce
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Domenico Lo Tartaro
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Anita Neroni
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Katarzyna Piwocka
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Rafael José Argüello
- Aix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Lara Gibellini
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
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5
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Kwok SJJ, Forward S, Fahlberg MD, Assita ER, Cosgriff S, Lee SH, Abbott GR, Zhu H, Minasian NH, Vote AS, Martino N, Yun SH. High-dimensional multi-pass flow cytometry via spectrally encoded cellular barcoding. Nat Biomed Eng 2024; 8:310-324. [PMID: 38036616 DOI: 10.1038/s41551-023-01144-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/21/2023] [Indexed: 12/02/2023]
Abstract
Advances in immunology, immuno-oncology, drug discovery and vaccine development demand improvements in the capabilities of flow cytometry to allow it to measure more protein markers per cell at multiple timepoints. However, the size of panels of fluorophore markers is limited by overlaps in fluorescence-emission spectra, and flow cytometers typically perform cell measurements at one timepoint. Here we describe multi-pass high-dimensional flow cytometry, a method leveraging cellular barcoding via microparticles emitting near-infrared laser light to track and repeatedly measure each cell using more markers and fewer colours. By using live human peripheral blood mononuclear cells, we show that the method enables the time-resolved characterization of the same cells before and after stimulation, their analysis via a 10-marker panel with minimal compensation for spectral spillover and their deep immunophenotyping via a 32-marker panel, where the same cells are analysed in 3 back-to-back cycles with 10-13 markers per cycle, reducing overall spillover and simplifying marker-panel design. Cellular barcoding in flow cytometry extends the utility of the technique for high-dimensional multi-pass single-cell analyses.
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Affiliation(s)
| | | | | | | | | | | | | | - Han Zhu
- LASE Innovation Inc., Woburn, MA, USA
| | | | | | - Nicola Martino
- Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, Cambridge, MA, USA
| | - Seok-Hyun Yun
- Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, Cambridge, MA, USA.
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6
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Lazarski CA, Hanley PJ. Review of flow cytometry as a tool for cell and gene therapy. Cytotherapy 2024; 26:103-112. [PMID: 37943204 PMCID: PMC10872958 DOI: 10.1016/j.jcyt.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Quality control testing and analytics are critical for the development and manufacture of cell and gene therapies, and flow cytometry is a key quality control and analytical assay that is used extensively. However, the technical scope of characterization assays and safety assays must keep apace as the breadth of cell therapy products continues to expand beyond hematopoietic stem cell products into producing novel adoptive immune therapies and gene therapy products. Flow cytometry services are uniquely positioned to support the evolving needs of cell therapy facilities, as access to flow cytometers, new antibody clones and improved fluorochrome reagents becomes more egalitarian. This report will outline the features, logistics, limitations and the current state of flow cytometry within the context of cellular therapy.
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Affiliation(s)
- Christopher A Lazarski
- Program for Cell Enhancement and Technology for Immunotherapy, Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA; The George Washington University, Washington, DC, USA.
| | - Patrick J Hanley
- Program for Cell Enhancement and Technology for Immunotherapy, Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA; The George Washington University, Washington, DC, USA.
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7
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Kudláčová J, Kužílková D, Bárta F, Brdičková N, Vávrová A, Kostka L, Hovorka O, Kalina T, Etrych T. Hybrid Macromolecular Constructs as a Platform for Spectral Nanoprobes for Advanced Cellular Barcoding in Flow Cytometry. Macromol Biosci 2024; 24:e2300306. [PMID: 37691533 DOI: 10.1002/mabi.202300306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/17/2023] [Indexed: 09/12/2023]
Abstract
Herein, an advanced bioconjugation technique to synthesize hybrid polymer-antibody nanoprobes tailored for fluorescent cell barcoding in flow cytometry-based immunophenotyping of leukocytes is applied. A novel approach of attachment combining two fluorescent dyes on the copolymer precursor and its conjugation to antibody is employed to synthesize barcoded nanoprobes of antibody polymer dyes allowing up to six nanoprobes to be resolved in two-dimensional cytometry analysis. The major advantage of these nanoprobes is the construct design in which the selected antibody is labeled with an advanced copolymer bearing two types of fluorophores in different molar ratios. The cells after antibody recognition and binding to the target antigen have a characteristic double fluorescence signal for each nanoprobe providing a unique position on the dot plot, thus allowing antibody-based barcoding of cellular samples in flow cytometry assays. This technique is valuable for cellular assays that require low intersample variability and is demonstrated by the live cell barcoding of clinical samples with B cell abnormalities. In total, the samples from six various donors were successfully barcoded using only two detection channels. This barcoding of clinical samples enables sample preparation and measurement in a single tube.
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Affiliation(s)
- Júlia Kudláčová
- Department of Biomedical Polymers, Institute of Macromolecular Chemistry CAS, Heyrovského nám. 2, Prague, 162 00, Czech Republic
| | - Daniela Kužílková
- CLIP (Childhood Leukemia Investigation Prague), Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, V Úvalu 84, Prague, 150 06, Czech Republic
| | - František Bárta
- R&D division, I.T.A.-Intertact s.r.o, Černokostelecká 143, Prague, 108 00, Czech Republic
| | - Naděžda Brdičková
- CLIP (Childhood Leukemia Investigation Prague), Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, V Úvalu 84, Prague, 150 06, Czech Republic
| | - Adéla Vávrová
- CLIP (Childhood Leukemia Investigation Prague), Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, V Úvalu 84, Prague, 150 06, Czech Republic
| | - Libor Kostka
- Department of Biomedical Polymers, Institute of Macromolecular Chemistry CAS, Heyrovského nám. 2, Prague, 162 00, Czech Republic
| | - Ondřej Hovorka
- R&D division, I.T.A.-Intertact s.r.o, Černokostelecká 143, Prague, 108 00, Czech Republic
| | - Tomáš Kalina
- CLIP (Childhood Leukemia Investigation Prague), Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, V Úvalu 84, Prague, 150 06, Czech Republic
| | - Tomáš Etrych
- Department of Biomedical Polymers, Institute of Macromolecular Chemistry CAS, Heyrovského nám. 2, Prague, 162 00, Czech Republic
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8
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Jiang M, Wang Y, Yu X, He Y, Zheng X, Qin J, Gu Y, Li X, Shi Y, Ma X, Li J, Pu K. An image-based Abplex method for high-throughput GPCRs antibody discovery. Biotechnol J 2024; 19:e2300336. [PMID: 37941478 DOI: 10.1002/biot.202300336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
As the field of antibody therapeutics advances rapidly, membrane proteins, particularly G protein-coupled receptors (GPCRs), have emerged as highly sought-after drug targets. However, the challenges associated with extracting membrane proteins have created a demand for effective antibody screening systems targeting these proteins. In this study, we propose developing an innovative antibody screening strategy (Abplex) based on high-content imaging. This approach leverages intact cells that express target membrane proteins, facilitating the presentation of proteins in their native conformation. Furthermore, it acquires both specific and non-specific binding signals in a single well, thereby bolstering the robustness of the outcomes. The technique involves just one step and can be completed within 50 min, enabling the analysis of a single sample in just one second. The amalgamation of dependable experimental findings, a simplified workflow, reduced hands-on time, and a swift analytical pace positions our method for superior throughput and precision when juxtaposed with traditional techniques such as CbELISA and FACS. Moreover, we introduce the concept of cell barcoding, wherein cells are labeled with different fluorescence spatial patterns. This feature allows for multiplexed detection to meet the needs of various experiments. The characteristics of Abplex promise to expedite GPCR-targeting antibody discovery, advance therapeutics and enable new disease treatments.
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Affiliation(s)
- Min Jiang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Yuanyuan Wang
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Xinke Yu
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) & Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Yiran He
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Xuewen Zheng
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Jingyi Qin
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Yayun Gu
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Xin Li
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Ying Shi
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Xiaochuan Ma
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) & Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Jiong Li
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
| | - Kefeng Pu
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, China
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9
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Connors J, Cusimano G, Mege N, Woloszczuk K, Konopka E, Bell M, Joyner D, Marcy J, Tardif V, Kutzler MA, Muir R, Haddad EK. Using the power of innate immunoprofiling to understand vaccine design, infection, and immunity. Hum Vaccin Immunother 2023; 19:2267295. [PMID: 37885158 PMCID: PMC10760375 DOI: 10.1080/21645515.2023.2267295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023] Open
Abstract
In the field of immunology, a systems biology approach is crucial to understanding the immune response to infection and vaccination considering the complex interplay between genetic, epigenetic, and environmental factors. Significant progress has been made in understanding the innate immune response, including cell players and critical signaling pathways, but many questions remain unanswered, including how the innate immune response dictates host/pathogen responses and responses to vaccines. To complicate things further, it is becoming increasingly clear that the innate immune response is not a linear pathway but is formed from complex networks and interactions. To further our understanding of the crosstalk and complexities, systems-level analyses and expanded experimental technologies are now needed. In this review, we discuss the most recent immunoprofiling techniques and discuss systems approaches to studying the global innate immune landscape which will inform on the development of personalized medicine and innovative vaccine strategies.
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Affiliation(s)
- Jennifer Connors
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Gina Cusimano
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Nathan Mege
- Tower Health, Reading Hospital, West Reading, PA, USA
| | - Kyra Woloszczuk
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Emily Konopka
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Matthew Bell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - David Joyner
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Molecular and Cellular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Jennifer Marcy
- Department of Molecular and Cellular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Virginie Tardif
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Michele A. Kutzler
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Roshell Muir
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Family, Community, and Preventative Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Elias K. Haddad
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
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10
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Koladiya A, Davis KL. Advances in Clinical Mass Cytometry. Clin Lab Med 2023; 43:507-519. [PMID: 37481326 DOI: 10.1016/j.cll.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
The advent of high-dimensional single-cell technologies has enabled detection of cellular heterogeneity and functional diversity of immune cells during health and disease conditions. Because of its multiplexing capabilities and limited compensation requirements, mass cytometry or cytometry by time of flight (CyTOF) has played a superior role in immune monitoring compared with flow cytometry. Further, it has higher throughput and lower cost compared with other single-cell techniques. Several published articles have utilized CyTOF to identify cellular phenotypes and features associated with disease outcomes. This article introduces CyTOF-based assays to profile immune cell-types, cell-states, and their applications in clinical research.
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Affiliation(s)
- Abhishek Koladiya
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kara L Davis
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Center for Cancer Cell Therapy, Stanford University, Stanford, CA, USA.
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11
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Simon Davis DA, Ritchie M, Hammill D, Garrett J, Slater RO, Otoo N, Orlov A, Gosling K, Price J, Yip D, Jung K, Syed FM, Atmosukarto II, Quah BJC. Identifying cancer-associated leukocyte profiles using high-resolution flow cytometry screening and machine learning. Front Immunol 2023; 14:1211064. [PMID: 37600768 PMCID: PMC10435879 DOI: 10.3389/fimmu.2023.1211064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/26/2023] [Indexed: 08/22/2023] Open
Abstract
Background Machine learning (ML) is a valuable tool with the potential to aid clinical decision making. Adoption of ML to this end requires data that reliably correlates with the clinical outcome of interest; the advantage of ML is that it can model these correlations from complex multiparameter data sets that can be difficult to interpret conventionally. While currently available clinical data can be used in ML for this purpose, there exists the potential to discover new "biomarkers" that will enhance the effectiveness of ML in clinical decision making. Since the interaction of the immune system and cancer is a hallmark of tumor establishment and progression, one potential area for cancer biomarker discovery is through the investigation of cancer-related immune cell signatures. Hence, we hypothesize that blood immune cell signatures can act as a biomarker for cancer progression. Methods To probe this, we have developed and tested a multiparameter cell-surface marker screening pipeline, using flow cytometry to obtain high-resolution systemic leukocyte population profiles that correlate with detection and characterization of several cancers in murine syngeneic tumor models. Results We discovered a signature of several blood leukocyte subsets, the most notable of which were monocyte subsets, that could be used to train CATboost ML models to predict the presence and type of cancer present in the animals. Conclusions Our findings highlight the potential utility of a screening approach to identify robust leukocyte biomarkers for cancer detection and characterization. This pipeline can easily be adapted to screen for cancer specific leukocyte markers from the blood of cancer patient.
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Affiliation(s)
- David A. Simon Davis
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
| | - Melissa Ritchie
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
| | - Dillon Hammill
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Jessica Garrett
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Robert O. Slater
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Naomi Otoo
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Anna Orlov
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Katharine Gosling
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
| | - Jason Price
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Desmond Yip
- Australian National University, Canberra, ACT, Australia
- Department of Medical Oncology, Canberra Hospital & Health Services, Canberra, ACT, Australia
| | - Kylie Jung
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
- Radiation Oncology Department, Canberra Hospital & Health Services, Canberra, ACT, Australia
| | - Farhan M. Syed
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
- Radiation Oncology Department, Canberra Hospital & Health Services, Canberra, ACT, Australia
| | - Ines I. Atmosukarto
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Ben J. C. Quah
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
- Radiation Oncology Department, Canberra Hospital & Health Services, Canberra, ACT, Australia
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12
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Xie B, Gao D, Zhou B, Chen S, Wang L. New discoveries in the field of metabolism by applying single-cell and spatial omics. J Pharm Anal 2023; 13:711-725. [PMID: 37577385 PMCID: PMC10422156 DOI: 10.1016/j.jpha.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 08/15/2023] Open
Abstract
Single-cell multi-Omics (SCM-Omics) and spatial multi-Omics (SM-Omics) technologies provide state-of-the-art methods for exploring the composition and function of cell types in tissues/organs. Since its emergence in 2009, single-cell RNA sequencing (scRNA-seq) has yielded many groundbreaking new discoveries. The combination of this method with the emergence and development of SM-Omics techniques has been a pioneering strategy in neuroscience, developmental biology, and cancer research, especially for assessing tumor heterogeneity and T-cell infiltration. In recent years, the application of these methods in the study of metabolic diseases has also increased. The emerging SCM-Omics and SM-Omics approaches allow the molecular and spatial analysis of cells to explore regulatory states and determine cell fate, and thus provide promising tools for unraveling heterogeneous metabolic processes and making them amenable to intervention. Here, we review the evolution of SCM-Omics and SM-Omics technologies, and describe the progress in the application of SCM-Omics and SM-Omics in metabolism-related diseases, including obesity, diabetes, nonalcoholic fatty liver disease (NAFLD) and cardiovascular disease (CVD). We also conclude that the application of SCM-Omics and SM-Omics approaches can help resolve the molecular mechanisms underlying the pathogenesis of metabolic diseases in the body and facilitate therapeutic measures for metabolism-related diseases. This review concludes with an overview of the current status of this emerging field and the outlook for its future.
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Affiliation(s)
- Baocai Xie
- Department of Critical Care Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, 518060, China
- Department of Respiratory Diseases, The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450014, China
| | - Dengfeng Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Biqiang Zhou
- Department of Geriatric & Spinal Pain Multi-Department Treatment, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen, Guangdong, 518035, China
| | - Shi Chen
- Department of Critical Care Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, 518060, China
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Lianrong Wang
- Department of Respiratory Diseases, The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450014, China
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
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13
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Mukherjee S, Kim B, Cheng LY, Doerfert MD, Li J, Hernandez A, Liang L, Jarvis MI, Rios PD, Ghani S, Joshi I, Isa D, Ray T, Terlier T, Fell C, Song P, Miranda RN, Oberholzer J, Zhang DY, Veiseh O. Screening hydrogels for antifibrotic properties by implanting cellularly barcoded alginates in mice and a non-human primate. Nat Biomed Eng 2023; 7:867-886. [PMID: 37106151 PMCID: PMC10593184 DOI: 10.1038/s41551-023-01016-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 02/27/2023] [Indexed: 04/29/2023]
Abstract
Screening implantable biomaterials for antifibrotic properties is constrained by the need for in vivo testing. Here we show that the throughput of in vivo screening can be increased by cellularly barcoding a chemically modified combinatorial library of hydrogel formulations. The method involves the implantation of a mixture of alginate formulations, each barcoded with human umbilical vein endothelial cells from different donors, and the association of the identity and performance of each formulation by genotyping single nucleotide polymorphisms of the cells via next-generation sequencing. We used the method to screen 20 alginate formulations in a single mouse and 100 alginate formulations in a single non-human primate, and identified three lead hydrogel formulations with antifibrotic properties. Encapsulating human islets with one of the formulations led to long-term glycaemic control in a mouse model of diabetes, and coating medical-grade catheters with the other two formulations prevented fibrotic overgrowth. High-throughput screening of barcoded biomaterials in vivo may help identify formulations that enhance the long-term performance of medical devices and of biomaterial-encapsulated therapeutic cells.
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Affiliation(s)
- Sudip Mukherjee
- Department of Bioengineering, Rice University, Houston, TX, USA
- School of Biomedical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Boram Kim
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Lauren Y Cheng
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Jiaming Li
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Lily Liang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Maria I Jarvis
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | | | | | | | - Trisha Ray
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Tanguy Terlier
- SIMS Laboratory, Shared Equipment Authority, Rice University, Houston, TX, USA
| | - Cody Fell
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Ping Song
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Roberto N Miranda
- Department of Hematopathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jose Oberholzer
- Division of Transplant Surgery, University of Virginia, Charlottesville, VA, USA
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, TX, USA.
- NuProbe USA, Houston, TX, USA.
| | - Omid Veiseh
- Department of Bioengineering, Rice University, Houston, TX, USA.
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14
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Garcia C, Dejean S, Savy N, Bordet JC, Series J, Cadot S, Ribes A, Voisin S, Rugeri L, Payrastre B, Sié P. Multicolor flow cytometry in clinical samples for platelet signaling assessment. Res Pract Thromb Haemost 2023; 7:100180. [PMID: 37538502 PMCID: PMC10394564 DOI: 10.1016/j.rpth.2023.100180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 08/05/2023] Open
Abstract
Background Availability of multichannel cytometers and specific commercial antibodies makes flow cytometry a new option to simultaneously assess multiple intracellular platelet signaling pathways for clinical purposes, in small volume of blood or low platelet count. Objectives To describe a multicolor flow cytometry with fluorescent barcoding technique for screening signaling pathways downstream membrane receptors of major platelet agonists (adenosine diphosphate, thrombin, thromboxane, and collagen). Methods By comparison with immunoblotting, we first selected the target phosphoproteins, AKT, P38MAPK, LIMK, and SPL76; the times of stimulation; and phosphoflow barcoding conditions. We then performed a clinical study on whole blood of patients without evidence of blood platelet disorder on standard biological screening, consulting for trivial or occasionally provoked bleeds without familial antecedent (bleeding of unknown origin, n = 23) or type-1 von Willebrand disease (n = 9). In addition, we included a small group of patients with definite platelet disorders (Glanzmann thrombasthenia, δ-storage pool deficiency, and immune glycoprotein VI-related disease with granule secretion defect). Results The range, kinetics, and distribution of fluorescence intensity were established for each agonist-target protein combination. Principal component analysis indicates a correlation in response to a target phosphoprotein (AKT and P38MAPK) to different agonists but no correlation in the response of different target phosphoproteins to the same agonist. The heterogeneity of individual responses in the whole population displayed was analyzed using clustering algorithm. Patients with platelet storage pool deficiency were positioned as lowest responders on the heatmap. Conclusion In complement of functional tests, this study introduces a new approach for rapid platelet signaling profiling in clinical practice.
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Affiliation(s)
- Cedric Garcia
- CHU de Toulouse, Laboratoire d’Hématologie, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires INSERM U1048, Université de Toulouse, Toulouse, France
| | - Sebastien Dejean
- Université Paul Sabatier Toulouse III, Institut de Mathématiques, CNRS UMR 5219, Toulouse, France
| | - Nicolas Savy
- Université Paul Sabatier Toulouse III, Institut de Mathématiques, CNRS UMR 5219, Toulouse, France
| | - Jean-Claude Bordet
- Laboratoire d’Hématologie, Hospices Civiles de Lyon, Lyon, France
- EA 4609-Hémostase et Cancer, Université Claude Bernard Lyon 1, Lyon, France
| | - Jennifer Series
- Institut des Maladies Métaboliques et Cardiovasculaires INSERM U1048, Université de Toulouse, Toulouse, France
| | - Sarah Cadot
- Institut des Maladies Métaboliques et Cardiovasculaires INSERM U1048, Université de Toulouse, Toulouse, France
| | - Agnès Ribes
- CHU de Toulouse, Laboratoire d’Hématologie, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires INSERM U1048, Université de Toulouse, Toulouse, France
- Faculté de Médecine, Université Paul Sabatier Toulouse III, Toulouse, France
| | - Sophie Voisin
- CHU de Toulouse, Laboratoire d’Hématologie, Toulouse, France
| | - Lucia Rugeri
- Laboratoire d’Hématologie, Hospices Civiles de Lyon, Lyon, France
- Hospices Civils de Lyon, Unité d’Hémostase clinique, Bron, France
| | - Bernard Payrastre
- CHU de Toulouse, Laboratoire d’Hématologie, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires INSERM U1048, Université de Toulouse, Toulouse, France
- Faculté de Médecine, Université Paul Sabatier Toulouse III, Toulouse, France
| | - Pierre Sié
- CHU de Toulouse, Laboratoire d’Hématologie, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires INSERM U1048, Université de Toulouse, Toulouse, France
- Université Paul Sabatier Toulouse III, Faculté de Pharmacie, Toulouse, France
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15
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Wu J, Bahri R, Tsoumani M, Semic‐Jusufagic A, Murray C, Custovic A, Guibas GV, Bennett M, Wang R, Gauvreau G, Cusack R, Mills C, Bulfone‐Paus S, Simpson A. Progenitor cell-derived basophils: A novel barcoded passive degranulation assay in allergic diseases. Clin Exp Allergy 2023; 53:405-416. [PMID: 36385515 PMCID: PMC10946533 DOI: 10.1111/cea.14251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 10/19/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND Effector cells assays provide an overall measure of responsiveness to allergen, but the lack of reliable and high-throughput assays limits the clinical utility. We aimed to develop a high-throughput basophil activation test based on human progenitor cell-derived basophils (PCB) and investigate the role of PCB activation test (PCBAT) in allergic diseases. METHODS Progenitor cell-derived basophils were differentiated from CD34+ progenitor cells and sensitized with sera from subjects sensitized to cat, peanut or atopic controls. Sensitized PCBs were stimulated with increasing concentrations of the corresponding allergens in vitro. Degranulation was assessed by measuring CD63 expression using flow cytometry. The correlations between PCBAT and clinical allergy were assessed. RESULTS Following passive sensitization of the mature PCBs with serum and allergen stimulation, an allergen specific dose-dependent increase in CD63 expression was observed. Sera from subjects sensitized to cat (n = 35, of which 17 subjects had clinical reactivity quantified using inhaled allergen challenge), peanut allergic (n = 30, of which 15 subjects had clinical reactivity validated using double blind, placebo controlled food challenges [DBPCFC]), peanut-sensitized but tolerant subjects (n = 5) were used to sensitize PCBs. PCBAT area under the curve (AUC) correlated with sIgE (r2 = .49, p = .001) in subjects sensitized to cat (sIgE ≥ 0.35KU/L). The provocation concentration of inhaled cat allergen (PC20 ) correlated with PCBAT AUC (r2 = .33, p = .016). In subjects sensitized to peanut, PCBAT AUC was highly correlated with sIgE to Ara h 2 (r2 = .59, p < .0001). Peanut threshold cumulative dose during DBPCFC was negatively correlated with PCBAT AUC (r2 = .57, p = .001) and IgE to Ara h1 (r2 = .55, p = .007), but not with sIgE to whole peanut or Ara h2. All peanut-sensitized but tolerant subjects showed no reaction to peanut on PCBAT. CONCLUSION Progenitor cell-derived basophils activation test is a high-throughput assay, which correlates with clinical allergy and may confer a powerful alternative tool in allergy testing.
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Affiliation(s)
- Jiakai Wu
- Division of Infection, Immunity and Respiratory Medicine, School of Biological SciencesUniversity of ManchesterManchesterUK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation TrustManchester Academic Health Science CentreManchesterUK
| | - Rajia Bahri
- Centre for Dermatological Research & Manchester Collaborative Centre for Inflammation Research (MCCIR), School of Biological SciencesUniversity of ManchesterManchesterUK
| | - Marina Tsoumani
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation TrustManchester Academic Health Science CentreManchesterUK
| | - Aida Semic‐Jusufagic
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation TrustManchester Academic Health Science CentreManchesterUK
| | - Clare S. Murray
- Division of Infection, Immunity and Respiratory Medicine, School of Biological SciencesUniversity of ManchesterManchesterUK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation TrustManchester Academic Health Science CentreManchesterUK
| | - Adnan Custovic
- National Heart and Lung InstituteImperial College LondonLondonUK
| | - George V. Guibas
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation TrustManchester Academic Health Science CentreManchesterUK
| | - Miriam Bennett
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation TrustManchester Academic Health Science CentreManchesterUK
| | - Ran Wang
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation TrustManchester Academic Health Science CentreManchesterUK
| | - Gail Gauvreau
- Division of Respirology, Department of MedicineMcMaster UniversityHamiltonOntarioCanada
| | - Ruth Cusack
- Division of Respirology, Department of MedicineMcMaster UniversityHamiltonOntarioCanada
| | - Clare Mills
- Division of Infection, Immunity and Respiratory Medicine, School of Biological SciencesUniversity of ManchesterManchesterUK
| | - Silvia Bulfone‐Paus
- Centre for Dermatological Research & Manchester Collaborative Centre for Inflammation Research (MCCIR), School of Biological SciencesUniversity of ManchesterManchesterUK
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological SciencesUniversity of ManchesterManchesterUK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation TrustManchester Academic Health Science CentreManchesterUK
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16
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Alonso-Gil D, Cuadrado A, Giménez-Llorente D, Rodríguez-Corsino M, Losada A. Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2. Nat Commun 2023; 14:1326. [PMID: 36898992 PMCID: PMC10006224 DOI: 10.1038/s41467-023-36900-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Cohesin organizes the genome through the formation of chromatin loops. NIPBL activates cohesin's ATPase and is essential for loop extrusion, but its requirement for cohesin loading is unclear. Here we have examined the effect of reducing NIPBL levels on the behavior of the two cohesin variants carrying STAG1 or STAG2 by combining a flow cytometry assay to measure chromatin-bound cohesin with analyses of its genome-wide distribution and genome contacts. We show that NIPBL depletion results in increased cohesin-STAG1 on chromatin that further accumulates at CTCF positions while cohesin-STAG2 diminishes genome-wide. Our data are consistent with a model in which NIPBL may not be required for chromatin association of cohesin but it is for loop extrusion, which in turn facilitates stabilization of cohesin-STAG2 at CTCF positions after being loaded elsewhere. In contrast, cohesin-STAG1 binds chromatin and becomes stabilized at CTCF sites even under low NIPBL levels, but genome folding is severely impaired.
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Affiliation(s)
- Dácil Alonso-Gil
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Cuadrado
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Daniel Giménez-Llorente
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Miriam Rodríguez-Corsino
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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17
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Gong J, Jin Z, Chen H, He J, Zhang Y, Yang X. Super-resolution fluorescence microscopic imaging in pathogenesis and drug treatment of neurological disease. Adv Drug Deliv Rev 2023; 196:114791. [PMID: 37004939 DOI: 10.1016/j.addr.2023.114791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/16/2023] [Accepted: 03/19/2023] [Indexed: 04/03/2023]
Abstract
Since super-resolution fluorescence microscopic technology breaks the diffraction limit that has existed for a long time in optical imaging, it can observe the process of synapses formed between nerve cells and the protein aggregation related to neurological disease. Thus, super-resolution fluorescence microscopic imaging has significantly impacted several industries, including drug development and pathogenesis research, and it is anticipated that it will significantly alter the future of life science research. Here, we focus on several typical super-resolution fluorescence microscopic technologies, introducing their benefits and drawbacks, as well as applications in several common neurological diseases, in the hope that their services will be expanded and improved in the pathogenesis and drug treatment of neurological diseases.
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18
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Shi D, Wang Y, Yang N, Li F, Li X, Ye J, Zhou X, Li B. Synthesis of a CaAl 2O 4:Eu 2+, Dy 3+ Phosphor by the Polymer Slurry Method and Its Application in Anticounterfeiting. Ind Eng Chem Res 2023. [DOI: 10.1021/acs.iecr.2c03708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- Dongxin Shi
- Hebei Key Laboratory of Inorganic Nonmetallic Materials, School of Materials Science and Engineering, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Yue Wang
- Hebei Key Laboratory of Inorganic Nonmetallic Materials, School of Materials Science and Engineering, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Nan Yang
- Hebei Key Laboratory of Inorganic Nonmetallic Materials, School of Materials Science and Engineering, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Fengfeng Li
- Hebei Key Laboratory of Inorganic Nonmetallic Materials, School of Materials Science and Engineering, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Xiaohui Li
- Hebei Key Laboratory of Inorganic Nonmetallic Materials, School of Materials Science and Engineering, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Jiahao Ye
- Hebei Key Laboratory of Inorganic Nonmetallic Materials, School of Materials Science and Engineering, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Xiaona Zhou
- Hebei Key Laboratory of Inorganic Nonmetallic Materials, School of Materials Science and Engineering, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Baozhong Li
- Center for High Pressure Science (CHiPS), State Key Laboratory of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, China
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19
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Malihi G, Nikoui V, Elson EL. A review on qualifications and cost effectiveness of induced pluripotent stem cells (IPSCs)-induced cardiomyocytes in drug screening tests. Arch Physiol Biochem 2023; 129:131-142. [PMID: 32783745 DOI: 10.1080/13813455.2020.1802600] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human induced pluripotent stem cells (hIPSCs) have initiated a higher degree of successes in disease modelling, preclinical evaluation of drug therapy and pharmaco-toxicological testing. Since the discovery of iPSCs in 2006, many advanced techniques have been introduced to differentiate iPSCs to cardiomyocytes, which have been progressively improved. The disease models from iPSC-induced cardiomyocytes (iPSC-CM) have been successfully helping to study a variety of cardiac diseases such as long QT syndrome, drug-induced long QT, different cardiomyopathies related to mutations in mitochondria or desmosomal proteins and other rare genetic diseases. IPSC-CMs have also been used to screen the role of chemicals in cardiovascular drug discovery and individualisation of drug dosages. In this review, the quality of current procedures for characterisation and maturation of iPSC-CM lines will be discussed. Also, we will focus on time efficiency and cost of standard differentiation methods after reprogramming.
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Affiliation(s)
| | - Vahid Nikoui
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Elliot L Elson
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
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20
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Luque GM, Schiavi-Ehrenhaus LJ, Jabloñski M, Balestrini PA, Novero AG, Torres NI, Osycka-Salut CE, Darszon A, Krapf D, Buffone MG. High-throughput screening method for discovering CatSper inhibitors using membrane depolarization caused by external calcium chelation and fluorescent cell barcoding. Front Cell Dev Biol 2023; 11:1010306. [PMID: 36743410 PMCID: PMC9892719 DOI: 10.3389/fcell.2023.1010306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
The exclusive expression of CatSper in sperm and its critical role in sperm function makes this channel an attractive target for contraception. The strategy of blocking CatSper as a male, non-hormonal contraceptive has not been fully explored due to the lack of robust screening methods to discover novel and specific inhibitors. The reason for this lack of appropriate methodology is the structural and functional complexity of this channel. We have developed a high-throughput method to screen drugs with the capacity to block CatSper in mammalian sperm. The assay is based on removing external free divalent cations by chelation, inducing CatSper to efficiently conduct monovalent cations. Since Na+ is highly concentrated in the extracellular milieu, a sudden influx depolarizes the cell. Using CatSper1 KO sperm we demonstrated that this depolarization depends on CatSper function. A membrane potential (Em) assay was combined with fluorescent cell barcoding (FCB), enabling higher throughput flow cytometry based on unique fluorescent signatures of different sperm samples. These differentially labeled samples incubated in distinct experimental conditions can be combined into one tube for simultaneous acquisition. In this way, acquisition times are highly reduced, which is essential to perform larger screening experiments for drug discovery using live cells. Altogether, a simple strategy for assessing CatSper was validated, and this assay was used to develop a high-throughput drug screening for new CatSper blockers.
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Affiliation(s)
- Guillermina M. Luque
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina,*Correspondence: Guillermina M. Luque, ; Mariano G. Buffone,
| | | | - Martina Jabloñski
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina
| | - Paula A. Balestrini
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina
| | - Analia G. Novero
- Instituto de Biología Molecular y Celular de Rosario (CONICET-UNR), Rosario, Santa Fe, Argentina
| | - Nicolás I. Torres
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina
| | - Claudia E. Osycka-Salut
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM-CONICET), Buenos Aires, Argentina
| | | | - Dario Krapf
- Instituto de Biología Molecular y Celular de Rosario (CONICET-UNR), Rosario, Santa Fe, Argentina
| | - Mariano G. Buffone
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina,*Correspondence: Guillermina M. Luque, ; Mariano G. Buffone,
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21
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Hudson WH, Wieland A. Technology meets TILs: Deciphering T cell function in the -omics era. Cancer Cell 2023; 41:41-57. [PMID: 36206755 PMCID: PMC9839604 DOI: 10.1016/j.ccell.2022.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/15/2022] [Accepted: 09/15/2022] [Indexed: 01/17/2023]
Abstract
T cells are at the center of cancer immunology because of their ability to recognize mutations in tumor cells and directly mediate cancer cell killing. Immunotherapies to rejuvenate exhausted T cell responses have transformed the clinical management of several malignancies. In parallel, the development of novel multidimensional analysis platforms, such as single-cell RNA sequencing and high-dimensional flow cytometry, has yielded unprecedented insights into immune cell biology. This convergence has revealed substantial heterogeneity of tumor-infiltrating immune cells in single tumors, across tumor types, and among individuals with cancer. Here we discuss the opportunities and challenges of studying the complex tumor microenvironment with -omics technologies that generate vast amounts of data, highlighting the opportunities and limitations of these technologies with a particular focus on interpreting high-dimensional studies of CD8+ T cells in the tumor microenvironment.
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Affiliation(s)
- William H Hudson
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Andreas Wieland
- Department of Otolaryngology, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH 43210, USA.
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22
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Hines WC, Hines WC. Lost in transduction: Critical considerations when using viral vectors. Front Cell Dev Biol 2023; 10:1080265. [PMID: 36684429 PMCID: PMC9849944 DOI: 10.3389/fcell.2022.1080265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023] Open
Abstract
The application of retroviral vectors in the laboratory requires considerations that often go overlooked but are often easy to circumvent. Here, we discuss the relationship between the observed transduction efficiency of a cell population and per-cell viral insertions-and describe how differential cell-type susceptibilities can confound results. We consider the math underlying this problem and review an alternative approach to the commonly used "multiplicity of infection" (MOI) method of titering and using viral vectors in the biomedical research laboratory.
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Affiliation(s)
| | - William C. Hines
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, University of NM, Albuquerque, NM, United States,*Correspondence: William C. Hines III,
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23
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Giudice V, Fonseca V, Selleri C, Gadina M. Cell Viability Multiplexing: Quantification of Cellular Viability by Barcode Flow Cytometry and Computational Analysis. Methods Mol Biol 2023; 2644:99-121. [PMID: 37142918 DOI: 10.1007/978-1-0716-3052-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Fluorescent cell barcoding (FCB) is a useful flow cytometric technique for high-throughput multiplexed analyses and can minimize technical variations after preliminary optimization and validation of protocols. To date, FCB is widely used for measurement of phosphorylation status of certain proteins, while it can be also employed for cellular viability assessment. In this chapter, we describe the protocol to perform FCB combined with viability assessment on lymphocytes and monocytes using manual and computational analysis. We also provide recommendations for FCB protocol optimization and validation for clinical sample analysis.
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Affiliation(s)
- Valentina Giudice
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, Salerno, Italy.
- Cell Biology Section, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Victoria Fonseca
- Translational Immunology Section, Office of Science Technology (OST), National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD, USA
| | - Carmine Selleri
- Cell Biology Section, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Massimo Gadina
- Translational Immunology Section, Office of Science Technology (OST), National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD, USA.
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24
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Gaggero S, Martinez-Fabregas J, Cozzani A, Fyfe PK, Leprohon M, Yang J, Thomasen FE, Winkelmann H, Magnez R, Conti AG, Wilmes S, Pohler E, van Gijsel Bonnello M, Thuru X, Quesnel B, Soncin F, Piehler J, Lindorff-Larsen K, Roychoudhuri R, Moraga I, Mitra S. IL-2 is inactivated by the acidic pH environment of tumors enabling engineering of a pH-selective mutein. Sci Immunol 2022; 7:eade5686. [PMID: 36459543 DOI: 10.1126/sciimmunol.ade5686] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Cytokines interact with their receptors in the extracellular space to control immune responses. How the physicochemical properties of the extracellular space influence cytokine signaling is incompletely elucidated. Here, we show that the activity of interleukin-2 (IL-2), a cytokine critical to T cell immunity, is profoundly affected by pH, limiting IL-2 signaling within the acidic environment of tumors. Generation of lactic acid by tumors limits STAT5 activation, effector differentiation, and antitumor immunity by CD8+ T cells and renders high-dose IL-2 therapy poorly effective. Directed evolution enabled selection of a pH-selective IL-2 mutein (Switch-2). Switch-2 binds the IL-2 receptor subunit IL-2Rα with higher affinity, triggers STAT5 activation, and drives CD8+ T cell effector function more potently at acidic pH than at neutral pH. Consequently, high-dose Switch-2 therapy induces potent immune activation and tumor rejection with reduced on-target toxicity in normal tissues. Last, we show that sensitivity to pH is a generalizable property of a diverse range of cytokines with broad relevance to immunity and immunotherapy in healthy and diseased tissues.
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Affiliation(s)
- Silvia Gaggero
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
| | | | - Adeline Cozzani
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
| | - Paul K Fyfe
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Malo Leprohon
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Jie Yang
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - F Emil Thomasen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Hauke Winkelmann
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Barbarastr. 11, 49076 Osnabrück, Germany
| | - Romain Magnez
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
| | - Alberto G Conti
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Stephan Wilmes
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Elizabeth Pohler
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Xavier Thuru
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
| | - Bruno Quesnel
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
| | - Fabrice Soncin
- CNRS/IIS/Centre Oscar Lambret/Lille University SMMiL-E Project, CNRS Délégation Hauts-de-France, Lille, France
- CNRS IRL 2820; Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Jacob Piehler
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Barbarastr. 11, 49076 Osnabrück, Germany
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Rahul Roychoudhuri
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Ignacio Moraga
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Suman Mitra
- Inserm UMR1277, CNRS UMR9020-CANTHER, Université de Lille, Lille University Hospital, Lille, France
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25
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Junker F, Camillo Teixeira P. Barcoding of live peripheral blood mononuclear cells to assess immune cell phenotypes using full spectrum flow cytometry. Cytometry A 2022; 101:909-921. [PMID: 35150047 DOI: 10.1002/cyto.a.24543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/11/2022] [Accepted: 02/07/2022] [Indexed: 01/27/2023]
Abstract
Barcoded flow cytometry is a multiplexing technique allowing for the simultaneous acquisition of cells from different donors or experimental conditions in a high-throughput manner. This approach allows to synchronize acquisition of samples and reduce variance introduced through the operator or technical platform. However, to date, only very few flow cytometry barcoding protocols have been developed, which often suffer from technical limitations. Here, we developed a novel barcoding protocol for a full-spectrum flow cytometry platform. We developed a 21-color immunophenotyping assay for up to 20 different samples analyzed simultaneously with comparable variance between repeated single-tube acquisition and postde-multiplexing. Barcoding offers great potential in parallelizing the analysis of complex cell populations such as peripheral blood mononuclear cells (PBMCs). Consequently, we assessed the performance of our method in situations where PBMCs were challenged with phytohaemagglutinin (PHA), a strong mitogen and broad activator of B cells and T cells, and superantigen Staphylococcus enterotoxin B (SEB) that has been reported to induce polyclonal T cell activation. PBMCs were either barcoded before pooled challenge or challenged individually pre-barcoding. Our final workflow included pooled immunophenotyping followed by machine learning aided single-cell data analysis and enabled us to identify robust PHA and SEB mode of action related phenotypic changes in PBMC immune cell lineages. Conclusively, we present a novel technique allowing the barcoded acquisition and analysis of PBMCs from up to 20 different donors and present a valid basis for the future development of complex immunophenotyping protocols.
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Affiliation(s)
- Fabian Junker
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Priscila Camillo Teixeira
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
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26
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Biswas S, Tikader B, Kar S, Viswanathan GA. Modulation of signaling cross-talk between pJNK and pAKT generates optimal apoptotic response. PLoS Comput Biol 2022; 18:e1010626. [PMID: 36240239 PMCID: PMC9604984 DOI: 10.1371/journal.pcbi.1010626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/26/2022] [Accepted: 10/03/2022] [Indexed: 01/25/2023] Open
Abstract
Tumor necrosis factor alpha (TNFα) is a well-known modulator of apoptosis by maintaining a balance between proliferation and cell-death in normal cells. Cancer cells often evade apoptotic response following TNFα stimulation by altering signaling cross-talks. Thus, varying the extent of signaling cross-talk could enable optimal TNFα mediated apoptotic dynamics. Herein, we use an experimental data-driven mathematical modeling to quantitate the extent of synergistic signaling cross-talk between the intracellular entities phosphorylated JNK (pJNK) and phosphorylated AKT (pAKT) that orchestrate the phenotypic apoptosis level by modulating the activated Caspase3 dynamics. Our study reveals that this modulation is orchestrated by the distinct dynamic nature of the synergism at early and late phases. We show that this synergism in signal flow is governed by branches originating from either TNFα receptor and NFκB, which facilitates signaling through survival pathways. We demonstrate that the experimentally quantified apoptosis levels semi-quantitatively correlates with the model simulated Caspase3 transients. Interestingly, perturbing pJNK and pAKT transient dynamics fine-tunes this accumulated Caspase3 guided apoptotic response. Thus, our study offers useful insights for identifying potential targeted therapies for optimal apoptotic response.
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Affiliation(s)
- Sharmila Biswas
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Baishakhi Tikader
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Sandip Kar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
- * E-mail: (SK); (GAV)
| | - Ganesh A. Viswanathan
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
- * E-mail: (SK); (GAV)
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27
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Lannigan J. Flow cytometry has seen the light: All of it. Cytometry A 2022; 101:809-811. [PMID: 36203398 DOI: 10.1002/cyto.a.24694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2022] [Indexed: 01/27/2023]
Affiliation(s)
- Joanne Lannigan
- Flow Cytometry Support Services, LLC, Alexandria, Virginia, USA
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28
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Martinelli AL, Wagner J, Bodenmiller B, Rapsomaniki MA. scQUEST: Quantifying tumor ecosystem heterogeneity from mass or flow cytometry data. STAR Protoc 2022; 3:101578. [PMID: 35880127 PMCID: PMC9307583 DOI: 10.1016/j.xpro.2022.101578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
| | - Johanna Wagner
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
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29
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Jin Y, Fyfe PK, Gardner S, Wilmes S, Bubeck D, Moraga I. Structural insights into the assembly and activation of the
IL
‐27 signaling complex. EMBO Rep 2022; 23:e55450. [PMID: 35920255 PMCID: PMC9535766 DOI: 10.15252/embr.202255450] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 12/14/2022] Open
Abstract
Interleukin 27 (IL‐27) is a heterodimeric cytokine that elicits potent immunosuppressive responses. Comprised of EBI3 and p28 subunits, IL‐27 binds GP130 and IL‐27Rα receptor chains to activate the JAK/STAT signaling cascade. However, how these receptors recognize IL‐27 and form a complex capable of phosphorylating JAK proteins remains unclear. Here, we used cryo electron microscopy (cryoEM) and AlphaFold modeling to solve the structure of the IL‐27 receptor recognition complex. Our data show how IL‐27 serves as a bridge connecting IL‐27Rα (domains 1–2) with GP130 (domains 1–3) to initiate signaling. While both receptors contact the p28 component of the heterodimeric cytokine, EBI3 stabilizes the complex by binding a positively charged surface of IL‐27Rα and Domain 1 of GP130. We find that assembly of the IL‐27 receptor recognition complex is distinct from both IL‐12 and IL‐6 cytokine families and provides a mechanistic blueprint for tuning IL‐27 pleiotropic actions.
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Affiliation(s)
- Yibo Jin
- Department of Life Sciences, Sir Ernst Chain Building Imperial College London London UK
| | - Paul K Fyfe
- Division of Cell Signaling and Immunology, School of Life Sciences University of Dundee Dundee UK
| | - Scott Gardner
- Department of Life Sciences, Sir Ernst Chain Building Imperial College London London UK
| | - Stephan Wilmes
- Division of Cell Signaling and Immunology, School of Life Sciences University of Dundee Dundee UK
| | - Doryen Bubeck
- Department of Life Sciences, Sir Ernst Chain Building Imperial College London London UK
| | - Ignacio Moraga
- Division of Cell Signaling and Immunology, School of Life Sciences University of Dundee Dundee UK
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30
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Balsamo JA, Penton KE, Zhao Z, Hayes MJ, Lima SM, Irish JM, Bachmann BO. An immunogenic cell injury module for the single-cell multiplexed activity metabolomics platform to identify promising anti-cancer natural products. J Biol Chem 2022; 298:102300. [PMID: 35931117 PMCID: PMC9424577 DOI: 10.1016/j.jbc.2022.102300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/05/2022] Open
Abstract
Natural products constitute and significantly impact many current anti-cancer medical interventions. A subset of natural products induces injury processes in malignant cells that recruit and activate host immune cells to produce an adaptive anti-cancer immune response, a process known as immunogenic cell death. However, a challenge in the field is to delineate forms of cell death and injury that best promote durable antitumor immunity. Addressing this with a single-cell chemical biology natural product discovery platform, like multiplex activity metabolomics, would be especially valuable in human leukemia, where cancer cells are heterogeneous and may react differently to the same compounds. Herein, a new ten-color, fluorescent cell barcoding-compatible module measuring six immunogenic cell injury signaling readouts are as follows: DNA damage response (γH2AX), apoptosis (cCAS3), necroptosis (p-MLKL), mitosis (p-Histone H3), autophagy (LC3), and the unfolded protein response (p-EIF2α). A proof-of-concept screen was performed to validate functional changes in single cells induced by secondary metabolites with known mechanisms within bacterial extracts. This assay was then applied in multiplexed activity metabolomics to reveal an unexpected mammalian cell injury profile induced by the natural product narbomycin. Finally, the functional consequences of injury pathways on immunogenicity were compared with three canonical assays for immunogenic hallmarks, ATP, HMGB1, and calreticulin, to correlate secondary metabolite-induced cell injury profiles with canonical markers of immunogenic cell death. In total, this work demonstrated a new phenotypic screen for discovery of natural products that modulate injury response pathways that can contribute to cancer immunogenicity.
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Affiliation(s)
- Joseph A Balsamo
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, US
| | - Kathryn E Penton
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Zhihan Zhao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Madeline J Hayes
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sierra M Lima
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brian O Bachmann
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, US; Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN, USA.
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31
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Richter S, Böttcher M, Völkl S, Mackensen A, Ullrich E, Jacobs B, Mougiakakos D. The metabolic profile of reconstituting T-cells, NK-cells, and monocytes following autologous stem cell transplantation and its impact on outcome. Sci Rep 2022; 12:11406. [PMID: 35794135 PMCID: PMC9259617 DOI: 10.1038/s41598-022-15136-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/20/2022] [Indexed: 12/20/2022] Open
Abstract
Previous studies indicated a role of the reconstituting immune system for disease outcome upon high-dose chemotherapy (HDCT) and autologous stem cell transplantation (auto-SCT) in multiple myeloma (MM) and lymphoma patients. Since immune cell metabolism and function are closely interconnected, we used flow-cytometry techniques to analyze key components and functions of the metabolic machinery in reconstituting immune cells upon HDCT/auto-SCT. We observed increased proliferative activity and an upregulation of the glycolytic and fatty acid oxidation (FAO) machinery in immune cells during engraftment. Metabolic activation was more pronounced in T-cells of advanced differentiation stages, in CD56bright NK-cells, and CD14++CD16+ intermediate monocytes. Next, we investigated a potential correlation between the immune cells’ metabolic profile and early progression or relapse in lymphoma patients within the first twelve months following auto-SCT. Here, persistently increased metabolic parameters correlated with a rather poor disease course. Taken together, reconstituting immune cells display an upregulated bioenergetic machinery following auto-SCT. Interestingly, a persistently enhanced metabolic immune cell phenotype correlated with reduced PFS. However, it remains to be elucidated, if the clinical data can be confirmed within a larger set of patients and if residual malignant cells not detected by conventional means possibly caused the metabolic activation.
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32
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Dannenberg PH, Kang J, Martino N, Kashiparekh A, Forward S, Wu J, Liapis AC, Wang J, Yun SH. Laser particle activated cell sorting in microfluidics. LAB ON A CHIP 2022; 22:2343-2351. [PMID: 35621381 PMCID: PMC9195882 DOI: 10.1039/d2lc00235c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/22/2022] [Indexed: 05/30/2023]
Abstract
Laser particles providing bright, spectrally narrowband emission renders them suitable for use as cellular barcodes. Here, we demonstrate a microfluidic platform integrated with a high-speed spectrometer, capable of reading the emission from laser particles in fluidic channels and routing cells based on their optical barcodes. The sub-nanometer spectral emission of each laser particle enables us to distinguish individual cells labeled with hundreds of different laser colors in the near infrared. Furthermore, cells tagged with laser particles are sorted based on their spectral barcodes at a kilohertz rate by using a real-time field programmable gate array and 2-way electric field switch. We demonstrate several different flavors of sorting, including isolation of barcoded cells, and cells tagged with a specific laser color. We term this novel sorting technique laser particle activated cell sorting (LACS). This flow reading and sorting technology adds to the arsenal of single-cell analysis tools using laser particles.
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Affiliation(s)
- Paul H Dannenberg
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA.
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jisoo Kang
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicola Martino
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA.
| | - Anokhi Kashiparekh
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sarah Forward
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jiamin Wu
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Automation, Tsinghua University, Beijing, China
| | - Andreas C Liapis
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA.
| | - Jie Wang
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, Jiangsu 210031, China
| | - Seok-Hyun Yun
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA.
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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33
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Molvi Z, O'Reilly RJ. Allogeneic Tumor Antigen-Specific T Cells for Broadly Applicable Adoptive Cell Therapy of Cancer. Cancer Treat Res 2022; 183:131-159. [PMID: 35551658 DOI: 10.1007/978-3-030-96376-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
T cells specific for major histocompatibility complex (MHC)-presented tumor antigens are capable of inducing durable remissions when adoptively transferred to patients with refractory cancers presenting such antigens. When such T cells are derived from healthy donors, they can be banked for off-the-shelf administration in appropriately tissue matched patients. Therefore, tumor antigen-specific, donor-derived T cells are expected to be a mainstay in the cancer immunotherapy armamentarium. In this chapter, we analyze clinical evidence that tumor antigen-specific donor-derived T cells can induce tumor regressions when administered to appropriately matched patients whose tumors are refractory to standard therapy. We also delineate the landscape of MHC-presented and unconventional tumor antigens recognized by T cells in healthy individuals that have been targeted for adoptive T cell therapy, as well as emerging antigens for which mounting evidence suggests their utility as targets for adoptive T cell therapy. We discuss the growing technological advancements that have facilitated sequence identification of such antigens and their cognate T cells, and applicability of such technologies in the pre-clinical and clinical settings.
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Affiliation(s)
- Zaki Molvi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Richard J O'Reilly
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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34
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Wolf C, Maus C, Persicke MRO, Filarsky K, Tausch E, Schneider C, Döhner H, Stilgenbauer S, Lichter P, Höfer T, Mertens D. Modeling the B‐cell receptor signaling on single cell level reveals a stable network circuit topology between non‐malignant B cells and chronic lymphocytic leukemia cells and between untreated cells and cells treated with kinase inhibitors. Int J Cancer 2022; 151:783-796. [DOI: 10.1002/ijc.34112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Christine Wolf
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Carsten Maus
- Division of Theoretical Systems Biology German Cancer Research Center (DXDKFZ) Heidelberg Germany
- Bioquant Heidelberg University Heidelberg Germany
| | - Michael RO Persicke
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ) Heidelberg Germany
- Department of Internal Medicine III University Hospital Ulm Ulm Germany
- Faculty of Biosciences Heidelberg University Heidelberg Germany
| | - Katharina Filarsky
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Eugen Tausch
- Department of Internal Medicine III University Hospital Ulm Ulm Germany
| | | | - Hartmut Döhner
- Department of Internal Medicine III University Hospital Ulm Ulm Germany
| | | | - Peter Lichter
- Division of Molecular Genetics German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology German Cancer Research Center (DXDKFZ) Heidelberg Germany
- Bioquant Heidelberg University Heidelberg Germany
| | - Daniel Mertens
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ) Heidelberg Germany
- Department of Internal Medicine III University Hospital Ulm Ulm Germany
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35
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes NM, Guirao-Ortiz M, Narducci A, Smit JH, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling. Angew Chem Int Ed Engl 2022; 61:e202112959. [PMID: 35146855 PMCID: PMC9305292 DOI: 10.1002/anie.202112959] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Indexed: 12/27/2022]
Abstract
Many life‐science techniques and assays rely on selective labeling of biological target structures with commercial fluorophores that have specific yet invariant properties. Consequently, a fluorophore (or dye) is only useful for a limited range of applications, e.g., as a label for cellular compartments, super‐resolution imaging, DNA sequencing or for a specific biomedical assay. Modifications of fluorophores with the goal to alter their bioconjugation chemistry, photophysical or functional properties typically require complex synthesis schemes. We here introduce a general strategy that allows to customize these properties during biolabelling with the goal to introduce the fluorophore in the last step of biolabelling. For this, we present the design and synthesis of ‘linker’ compounds, that bridge biotarget, fluorophore and a functional moiety via well‐established labeling protocols. Linker molecules were synthesized via the Ugi four‐component reaction (Ugi‐4CR) which facilitates a modular design of linkers with diverse functional properties and bioconjugation‐ and fluorophore attachment moieties. To demonstrate the possibilities of different linkers experimentally, we characterized the ability of commercial fluorophores from the classes of cyanines, rhodamines, carbopyronines and silicon‐rhodamines to become functional labels on different biological targets in vitro and in vivo via thiol‐maleimide chemistry. With our strategy, we showed that the same commercial dye can become a photostable self‐healing dye or a sensor for bivalent ions subject to the linker used. Finally, we quantified the photophysical performance of different self‐healing linker–fluorophore conjugates and demonstrated their applications in super‐resolution imaging and single‐molecule spectroscopy.
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Affiliation(s)
- Lei Zhang
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Michael Isselstein
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Köhler
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Nikolaos Eleftheriadis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nadia M Huisjes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Miguel Guirao-Ortiz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jochem H Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Janko Stoffels
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Hartmann Harz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Andreas Herrmann
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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36
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Qian N, Min W. Super-multiplexed vibrational probes: Being colorful makes a difference. Curr Opin Chem Biol 2022; 67:102115. [PMID: 35077919 PMCID: PMC8940683 DOI: 10.1016/j.cbpa.2021.102115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/03/2022]
Abstract
Biological systems with intrinsic complexity require multiplexing techniques to comprehensively describe the phenotype, interaction, and heterogeneity. Recent years have witnessed the development of super-multiplexed vibrational microscopy, overcoming the 'color barrier' of fluorescence-based optical techniques. Here, we will review the recent progress in the design and applications of super-multiplexed vibrational probes. We hope to illustrate how rainbow-like vibrational colors can be generated from systematic studies on structure-spectroscopy relationships and how being colorful makes a difference to various biomedical applications.
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37
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Xie H, Ding X. The Intriguing Landscape of Single-Cell Protein Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105932. [PMID: 35199955 PMCID: PMC9036017 DOI: 10.1002/advs.202105932] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Indexed: 05/15/2023]
Abstract
Profiling protein expression at single-cell resolution is essential for fundamental biological research (such as cell differentiation and tumor microenvironmental examination) and clinical precision medicine where only a limited number of primary cells are permitted. With the recent advances in engineering, chemistry, and biology, single-cell protein analysis methods are developed rapidly, which enable high-throughput and multiplexed protein measurements in thousands of individual cells. In combination with single cell RNA sequencing and mass spectrometry, single-cell multi-omics analysis can simultaneously measure multiple modalities including mRNAs, proteins, and metabolites in single cells, and obtain a more comprehensive exploration of cellular signaling processes, such as DNA modifications, chromatin accessibility, protein abundance, and gene perturbation. Here, the recent progress and applications of single-cell protein analysis technologies in the last decade are summarized. Current limitations, challenges, and possible future directions in this field are also discussed.
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Affiliation(s)
- Haiyang Xie
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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38
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes N, Guirao M, Narducci A, Smit J, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Bio‐labeling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lei Zhang
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jens Köhler
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemie GERMANY
| | | | - Nadia Huisjes
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Miguel Guirao
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jochem Smit
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Janko Stoffels
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Hartmann Harz
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Andreas Herrmann
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Thorben Cordes
- Ludwig-Maximilians-Universitat Munchen Faculty of Biology Großhadernerstr. 2-4 82152 Planegg-Martiensried GERMANY
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Samson LD, Engelfriet P, Verschuren WMM, Picavet HSJ, Ferreira JA, de Zeeuw-Brouwer ML, Buisman AM, Boots AMH. Impaired JAK-STAT pathway signaling in leukocytes of the frail elderly. Immun Ageing 2022; 19:5. [PMID: 35039055 PMCID: PMC8762193 DOI: 10.1186/s12979-021-00261-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/23/2021] [Indexed: 12/30/2022]
Abstract
Background Elderly often show reduced immune functioning and can develop chronic low-grade inflammation. Why some elderly are more prone to become frail is unknown. We investigated whether frailty is associated with altered cytokine signaling through the JAK-STAT pathway in leukocytes of 34 individuals aged 65–74 years. In addition, we investigated how this relation is affected by chronic low-grade inflammation during the previous 20 years. Cytokine signaling was quantified by measuring intracellular STAT1, STAT3, and STAT5 phosphorylation in monocytes, B cells, CD4+ T cells and CD8+ T cells upon stimulation with IL-2, IL-6, IL-10, IFNα and IFNγ, using phospho-flow cytometry. Presence of chronic low-grade inflammation was investigated by evaluating 18 different plasma inflammatory markers that had been measured repeatedly in the same individuals over the previous 20 years. Frailty was assessed as a score on a frailty index. Results We found that lower cytokine-induced pSTAT responsiveness in the various cell subsets was seen with higher frailty scores in both men and women, indicative of dysfunctional pSTAT responses in frailer individuals. Associations differed between men and women, with frailer women showing lower pSTAT1 responses in monocytes and frailer men showing lower pSTAT5 responses in CD4+ and CD8+ T cells. Notably, lower IL-10-induced pSTAT3 responses in men were related to both higher frailty scores and higher CRP levels over the past 20 years. This might indicate poor resolution of low-grade inflammation due to defective regulatory pSTAT signaling in older men. Conclusions Our results emphasize the importance of preserved JAK-STAT pathway signaling in healthy aging and reveal cellular pSTAT levels as a candidate biomarker of frailty. Supplementary Information The online version contains supplementary material available at 10.1186/s12979-021-00261-w.
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Affiliation(s)
- Leonard Daniël Samson
- National Institute of Public Health and the Environment, Bilthoven, The Netherlands. .,Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Peter Engelfriet
- National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - W M Monique Verschuren
- National Institute of Public Health and the Environment, Bilthoven, The Netherlands.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - H Susan J Picavet
- National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - José A Ferreira
- National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Anne-Marie Buisman
- National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - A Mieke H Boots
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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40
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Sigal N, Maecker HT. Mass Cytometry Assessment of Cell Phenotypes and Signaling States in Human Whole Blood. Methods Mol Biol 2022; 2543:113-128. [PMID: 36087263 PMCID: PMC9991871 DOI: 10.1007/978-1-0716-2553-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Phosphoflow is a powerful tool that allows researchers to measure distinct signaling responses to various stimuli in multiple subpopulations of cells. Extension of this technique to mass cytometry (cytometry by time-of-flight or CyTOF) allows many more cell phenotypes and signaling nodes to be interrogated in parallel. The use of fresh whole blood is ideal for capturing the in vivo signaling state of all leukocytes, including granulocytes. In this chapter, we provide a detailed protocol for performing CyTOF phosphoflow in human whole blood, using cytokines and other stimuli. Barcoding and combining of multiple samples and other techniques to reduce batch effects and provide optimal comparability between samples/stimulations are also described.
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Affiliation(s)
- Natalia Sigal
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA.
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41
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Drápela S, Fedr R, Vacek O, Remšík J, Souček K. High-Throughput, Parallel Flow Cytometry Screening of Hundreds of Cell Surface Antigens Using Fluorescent Barcoding. Methods Mol Biol 2022; 2543:99-111. [PMID: 36087262 DOI: 10.1007/978-1-0716-2553-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Multicolor flow cytometry allows for analysis of tens of cellular parameters in millions of cells at a single-cell resolution within minutes. The lack of technologies that would facilitate feasible and relatively cheap profiling of such a number of cells with an antibody-based approach led us to the development of a high-throughput cytometry-based platform for surface profiling. We coupled the fluorescent cell barcoding with preexisting, commercially available screening tools to analyze cell surface fingerprint at a large scale. This powerful approach will help to identify novel biomarkers and druggable targets and facilitate the discovery of new concepts in immunology, oncology, and developmental biology.
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Affiliation(s)
- Stanislav Drápela
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Radek Fedr
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Ondřej Vacek
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ján Remšík
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karel Souček
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic.
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
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42
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A cell-based multiplex immunoassay platform using fluorescent protein-barcoded reporter cell lines. Commun Biol 2021; 4:1338. [PMID: 34824350 PMCID: PMC8617053 DOI: 10.1038/s42003-021-02881-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 11/09/2021] [Indexed: 11/08/2022] Open
Abstract
Multiplex immunoassays with acellular antigens are well-established based on solid-phase platforms such as the Luminex® technology. Cell barcoding by amine-reactive fluorescent dyes enables analogous cell-based multiplex assays, but requires multiple labeling reactions and quality checks prior to every assay. Here we describe generation of stable, fluorescent protein-barcoded reporter cell lines suitable for multiplex screening of antibody to membrane proteins. The utility of this cell-based system, with the potential of a 256-plex cell panel, is demonstrated by flow cytometry deconvolution of barcoded cell panels expressing influenza A hemagglutinin trimers, or native human CCR2 or CCR5 multi-span proteins and their epitope-defining mutants. This platform will prove useful for characterizing immunity and discovering antibodies to membrane-associated proteins.
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43
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Brenes AJ, Vandereyken M, James OJ, Watt H, Hukelmann J, Spinelli L, Dikovskaya D, Lamond AI, Swamy M. Tissue environment, not ontogeny, defines murine intestinal intraepithelial T lymphocytes. eLife 2021; 10:e70055. [PMID: 34473623 PMCID: PMC8463072 DOI: 10.7554/elife.70055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Tissue-resident intestinal intraepithelial T lymphocytes (T-IEL) patrol the gut and have important roles in regulating intestinal homeostasis. T-IEL include both induced T-IEL, derived from systemic antigen-experienced lymphocytes, and natural T-IEL, which are developmentally targeted to the intestine. While the processes driving T-IEL development have been elucidated, the precise roles of the different subsets and the processes driving activation and regulation of these cells remain unclear. To gain functional insights into these enigmatic cells, we used high-resolution, quantitative mass spectrometry to compare the proteomes of induced T-IEL and natural T-IEL subsets, with naive CD8+ T cells from lymph nodes. This data exposes the dominant effect of the gut environment over ontogeny on T-IEL phenotypes. Analyses of protein copy numbers of >7000 proteins in T-IEL reveal skewing of the cell surface repertoire towards epithelial interactions and checkpoint receptors; strong suppression of the metabolic machinery indicating a high energy barrier to functional activation; upregulated cholesterol and lipid metabolic pathways, leading to high cholesterol levels in T-IEL; suppression of T cell antigen receptor signalling and expression of the transcription factor TOX, reminiscent of chronically activated T cells. These novel findings illustrate how T-IEL integrate multiple tissue-specific signals to maintain their homeostasis and potentially function.
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Affiliation(s)
- Alejandro J Brenes
- Centre for Gene Regulation and Expression, University of DundeeDundeeUnited Kingdom
- Division of Cell Signalling and Immunology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Maud Vandereyken
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Olivia J James
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Harriet Watt
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Jens Hukelmann
- Centre for Gene Regulation and Expression, University of DundeeDundeeUnited Kingdom
| | - Laura Spinelli
- Division of Cell Signalling and Immunology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Dina Dikovskaya
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, University of DundeeDundeeUnited Kingdom
| | - Mahima Swamy
- Division of Cell Signalling and Immunology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
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Reisman BJ, Barone SM, Bachmann BO, Irish JM. DebarcodeR increases fluorescent cell barcoding capacity and accuracy. Cytometry A 2021; 99:946-953. [PMID: 33960644 PMCID: PMC8410645 DOI: 10.1002/cyto.a.24363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/09/2021] [Accepted: 04/20/2021] [Indexed: 12/25/2022]
Abstract
Fluorescent cell barcoding (FCB) enables efficient collection of tens to hundreds of flow cytometry samples by covalently marking cells with varying concentration of spectrally distinct dyes. A key consideration in FCB is to balance the density of dye barcodes, the complexity of cells in the sample, and the desired accuracy of the debarcoding. Unfortunately, barcoding bench and computational methods have not benefited from the high dimensional revolution in cytometry due to a lack of automated computational tools that effectively balance these common cytometry needs. DebarcodeR addresses these unmet needs by providing a framework for computational debarcoding augmented by improvements to experimental methods. Adaptive regression modeling accounted for differential dye uptake between different cell types and Gaussian mixture modeling provided a robust method to probabilistically assign cells to samples. Assignment tolerance parameters are available to allow users to balance high cell recovery with accurate assignments. Improvements to experimental methods include: (1) inclusion of an "external standard" control where a pool of all cells was stained a single level of each barcoding dyes and (2) an "internal standard" where each cell is stained with a single level of a separate dye. DebarcodeR significantly improved speed, accuracy, and reproducibility of FCB while avoiding selective loss of unusual cell subsets when debarcoding microtiter plates of cell lines and heterogenous mixtures of primary cells. DebarcodeR is available on Github as an R package that works with flowCore and Cytoverse packages at github.com/cytolab/DebarcodeR.
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Affiliation(s)
| | - Sierra M. Barone
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology & Immunology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Jonathan M. Irish
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology & Immunology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
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45
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Zbären N, Brigger D, Bachmann D, Helbling A, Jörg L, Horn MP, Schmid JM, Hoffmann HJ, Kinet JP, Kaufmann T, Eggel A. A novel functional mast cell assay for the detection of allergies. J Allergy Clin Immunol 2021; 149:1018-1030.e11. [PMID: 34418424 DOI: 10.1016/j.jaci.2021.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Clinical management of allergic diseases has been hampered by the lack of safe and convenient tests to reliably identify culprit allergens and to closely follow changes in disease activity over time. Because allergy diagnosis is a complex and laborious multistep procedure, there is an urgent need for simpler but still functionally accurate ex vivo assays allowing objective diagnosis, substantiating treatment choices, and quantifying therapeutic responses. OBJECTIVE In this study, we sought to develop a novel functional cell-based assay that relies on passive sensitization of allergic effector cells with patient serum, circumventing current limitations in allergy diagnosis. METHODS We genetically engineered a conditional homeobox B8 (Hoxb8)-immortalized progenitor line from the bone marrow of mice that are transgenic for the human high-affinity IgE receptor (FcεRIα). These cells can be reproducibly differentiated into mature Hoxb8 mast cells within 5 days of culture in virtually unlimited numbers. RESULTS We demonstrate that the established Hoxb8 mast cell assay can be used to accurately measure total IgE levels, identify culprit allergens, longitudinally monitor allergen-specific immunotherapy, and potentially determine the time point of tolerance induction upon allergen-specific immunotherapy in patients with allergy. To facilitate the analysis of large testing volumes, we demonstrate a proof-of-concept for a high-throughput screening application based on fluorescent cell barcoding using the engineered Hoxb8 mast cells. CONCLUSIONS Our results indicate that this novel mast cell assay could represent a valuable tool to support clinicians in the identification of IgE-mediated allergies and in the quantification of treatment efficacy as well as duration of therapeutic response.
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Affiliation(s)
- Noemi Zbären
- Department of BioMedical Research, University of Bern, Bern, Switzerland; Department of Rheumatology, Immunology and Allergology, University Hospital Bern, Bern, Switzerland
| | - Daniel Brigger
- Department of BioMedical Research, University of Bern, Bern, Switzerland; Department of Rheumatology, Immunology and Allergology, University Hospital Bern, Bern, Switzerland
| | - Daniel Bachmann
- Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Arthur Helbling
- Division of Allergology and Clinical Immunology, Department of Pneumology, Inselspital, University Hospital Bern, Bern, Switzerland
| | - Lukas Jörg
- Division of Allergology and Clinical Immunology, Department of Pneumology, Inselspital, University Hospital Bern, Bern, Switzerland
| | - Michael P Horn
- Department of Clinical Chemistry, Inselspital University Hospital, Bern, Switzerland
| | - Johannes M Schmid
- Department of Respiratory Diseases and Allergy, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Hans Jürgen Hoffmann
- Department of Respiratory Diseases and Allergy, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jean-Pierre Kinet
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Mass
| | - Thomas Kaufmann
- Institute of Pharmacology, University of Bern, Bern, Switzerland.
| | - Alexander Eggel
- Department of BioMedical Research, University of Bern, Bern, Switzerland; Department of Rheumatology, Immunology and Allergology, University Hospital Bern, Bern, Switzerland.
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46
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Marsh‐Wakefield FMD, Mitchell AJ, Norton SE, Ashhurst TM, Leman JKH, Roberts JM, Harte JE, McGuire HM, Kemp RA. Making the most of high-dimensional cytometry data. Immunol Cell Biol 2021; 99:680-696. [PMID: 33797774 PMCID: PMC8453896 DOI: 10.1111/imcb.12456] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 01/03/2023]
Abstract
High-dimensional cytometry represents an exciting new era of immunology research, enabling the discovery of new cells and prediction of patient responses to therapy. A plethora of analysis and visualization tools and programs are now available for both new and experienced users; however, the transition from low- to high-dimensional cytometry requires a change in the way users think about experimental design and data analysis. Data from high-dimensional cytometry experiments are often underutilized, because of both the size of the data and the number of possible combinations of markers, as well as to a lack of understanding of the processes required to generate meaningful data. In this article, we explain the concepts behind designing high-dimensional cytometry experiments and provide considerations for new and experienced users to design and carry out high-dimensional experiments to maximize quality data collection.
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Affiliation(s)
- Felix MD Marsh‐Wakefield
- Vascular Immunology UnitDiscipline of PathologyThe University of SydneySydneyNSWAustralia
- Charles Perkins CentreThe University of SydneySydneyNSWAustralia
- School of Medical SciencesFaculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
| | - Andrew J Mitchell
- Department of Chemical EngineeringMaterials Characterisation and Fabrication PlatformThe University of MelbourneParkvilleVICAustralia
| | - Samuel E Norton
- Nanix LtdDunedinNew Zealand
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Thomas Myles Ashhurst
- Charles Perkins CentreThe University of SydneySydneyNSWAustralia
- Sydney CytometryUniversity of SydneySydneyNSWAustralia
- Ramaciotti Facility for Human Systems BiologyThe University of SydneySydneyNSWAustralia
| | - Julia KH Leman
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | | | - Jessica E Harte
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Helen M McGuire
- Charles Perkins CentreThe University of SydneySydneyNSWAustralia
- Ramaciotti Facility for Human Systems BiologyThe University of SydneySydneyNSWAustralia
- Translational Immunology GroupDiscipline of PathologyThe University of SydneySydneyNSWAustralia
| | - Roslyn A Kemp
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
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47
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Chervoneva I, Peck AR, Yi M, Freydin B, Rui H. Quantification of spatial tumor heterogeneity in immunohistochemistry staining images. Bioinformatics 2021; 37:1452-1460. [PMID: 33275142 DOI: 10.1093/bioinformatics/btaa965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 10/19/2020] [Accepted: 11/04/2020] [Indexed: 01/10/2023] Open
Abstract
MOTIVATION Quantitative immunofluorescence is often used for immunohistochemistry quantification of proteins that serve as cancer biomarkers. Advanced image analysis systems for pathology allow capturing expression levels in each individual cell or subcellular compartment. However, only the mean signal intensity within the cancer tissue region of interest is usually considered as biomarker completely ignoring the issue of tumor heterogeneity. RESULTS We propose using immunohistochemistry image-derived information on the spatial distribution of cellular signal intensity (CSI) of protein expression within the cancer cell population to quantify both mean expression level and tumor heterogeneity of CSI levels. We view CSI levels as marks in a marked point process of cancer cells in the tissue and define spatial indices based on conditional mean and conditional variance of the marked point process. The proposed methodology provides objective metrics of cell-to-cell heterogeneity in protein expressions that allow discriminating between different patterns of heterogeneity. The prognostic utility of new spatial indices is investigated and compared to the standard mean signal intensity biomarkers using the protein expressions in tissue microarrays incorporating tumor tissues from 1000+ breast cancer patients. AVAILABILITY AND IMPLEMENTATION: THE R CODE FOR COMPUTING THE PROPOSED SPATIAL INDICES IS INCLUDED AS SUPPLEMENTARY MATERIAL . SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Inna Chervoneva
- Division of Biostatistics, Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Amy R Peck
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Misung Yi
- Division of Biostatistics, Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Boris Freydin
- Division of Biostatistics, Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Hallgeir Rui
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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48
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Tang Y, Zhuang Y, Zhang S, Smith ZJ, Li Y, Mu X, Li M, He C, Zheng X, Pan F, Gao T, Zhang L. Azo-Enhanced Raman Scattering for Enhancing the Sensitivity and Tuning the Frequency of Molecular Vibrations. ACS CENTRAL SCIENCE 2021; 7:768-780. [PMID: 34079895 PMCID: PMC8161494 DOI: 10.1021/acscentsci.1c00117] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Indexed: 05/14/2023]
Abstract
Raman scattering provides stable narrow-banded signals that potentially allow for multicolor microscopic imaging. The major obstacle for the applications of Raman spectroscopy and microscopy is the small cross section of Raman scattering that results in low sensitivity. Here, we report a new concept of azo-enhanced Raman scattering (AERS) by designing the intrinsic molecular structures using resonance Raman and concomitant fluorescence quenching strategies. Based on the selection of vibrational modes and the enhancing unit of azobenzenes, we obtained a library of AERS molecules with specific Raman signals in the fingerprint and silent frequency regions. The spectral characterization and molecular simulation revealed that the azobenzene unit conjugated to the vibrational modes significantly enhanced Raman signals due to the mechanism of extending the conjugation system, coupling the electronic-vibrational transitions, and improving the symmetry of vibrational modes. The nonradiative decay of azobenzene from the excited state quenched the commitment fluorescence, thus providing a clean background for identifying Raman scattering. The most sensitive AERS molecules produced Raman signals of more than 4 orders of magnitude compared to 5-ethynyl-2'-deoxyuridine (EdU). In addition, a frequency tunability of 10 distinct Raman bands was achieved by selecting different types of vibrational modes. This methodology of AERS allows for designing small-molecule Raman probes to visualize various entities in complex systems by multicolor spontaneous Raman imaging. It will open new prospects to explore innovative applications of AERS in interdisciplinary research fields.
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Affiliation(s)
- Yuchen Tang
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yongpeng Zhuang
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Shaohua Zhang
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Zachary J. Smith
- Department
of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei 230027, China
| | - Yuee Li
- School
of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China
| | - Xijiao Mu
- School
of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China
| | - Mengna Li
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Caili He
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Xingxing Zheng
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Fangfang Pan
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Tingjuan Gao
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Lizhi Zhang
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
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49
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Roca CP, Burton OT, Gergelits V, Prezzemolo T, Whyte CE, Halpert R, Kreft Ł, Collier J, Botzki A, Spidlen J, Humblet-Baron S, Liston A. AutoSpill is a principled framework that simplifies the analysis of multichromatic flow cytometry data. Nat Commun 2021; 12:2890. [PMID: 34001872 PMCID: PMC8129071 DOI: 10.1038/s41467-021-23126-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/16/2021] [Indexed: 12/21/2022] Open
Abstract
Compensating in flow cytometry is an unavoidable challenge in the data analysis of fluorescence-based flow cytometry. Even the advent of spectral cytometry cannot circumvent the spillover problem, with spectral unmixing an intrinsic part of such systems. The calculation of spillover coefficients from single-color controls has remained essentially unchanged since its inception, and is increasingly limited in its ability to deal with high-parameter flow cytometry. Here, we present AutoSpill, an alternative method for calculating spillover coefficients. The approach combines automated gating of cells, calculation of an initial spillover matrix based on robust linear regression, and iterative refinement to reduce error. Moreover, autofluorescence can be compensated out, by processing it as an endogenous dye in an unstained control. AutoSpill uses single-color controls and is compatible with common flow cytometry software. AutoSpill allows simpler and more robust workflows, while reducing the magnitude of compensation errors in high-parameter flow cytometry.
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Affiliation(s)
- Carlos P Roca
- VIB Center for Brain and Disease Research, Leuven, Belgium.
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium.
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK.
| | - Oliver T Burton
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Václav Gergelits
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Teresa Prezzemolo
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Carly E Whyte
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | | | | | | | | | | | - Stéphanie Humblet-Baron
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Adrian Liston
- VIB Center for Brain and Disease Research, Leuven, Belgium.
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium.
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK.
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50
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Wilmes S, Jeffrey PA, Martinez-Fabregas J, Hafer M, Fyfe PK, Pohler E, Gaggero S, López-García M, Lythe G, Taylor C, Guerrier T, Launay D, Mitra S, Piehler J, Molina-París C, Moraga I. Competitive binding of STATs to receptor phospho-Tyr motifs accounts for altered cytokine responses. eLife 2021; 10:66014. [PMID: 33871355 PMCID: PMC8099432 DOI: 10.7554/elife.66014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/18/2021] [Indexed: 12/29/2022] Open
Abstract
Cytokines elicit pleiotropic and non-redundant activities despite strong overlap in their usage of receptors, JAKs and STATs molecules. We use IL-6 and IL-27 to ask how two cytokines activating the same signaling pathway have different biological roles. We found that IL-27 induces more sustained STAT1 phosphorylation than IL-6, with the two cytokines inducing comparable levels of STAT3 phosphorylation. Mathematical and statistical modeling of IL-6 and IL-27 signaling identified STAT3 binding to GP130, and STAT1 binding to IL-27Rα, as the main dynamical processes contributing to sustained pSTAT1 levels by IL-27. Mutation of Tyr613 on IL-27Rα decreased IL-27-induced STAT1 phosphorylation by 80% but had limited effect on STAT3 phosphorgylation. Strong receptor/STAT coupling by IL-27 initiated a unique gene expression program, which required sustained STAT1 phosphorylation and IRF1 expression and was enriched in classical Interferon Stimulated Genes. Interestingly, the STAT/receptor coupling exhibited by IL-6/IL-27 was altered in patients with systemic lupus erythematosus (SLE). IL-6/IL-27 induced a more potent STAT1 activation in SLE patients than in healthy controls, which correlated with higher STAT1 expression in these patients. Partial inhibition of JAK activation by sub-saturating doses of Tofacitinib specifically lowered the levels of STAT1 activation by IL-6. Our data show that receptor and STATs concentrations critically contribute to shape cytokine responses and generate functional pleiotropy in health and disease.
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Affiliation(s)
- Stephan Wilmes
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Polly-Anne Jeffrey
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Jonathan Martinez-Fabregas
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Maximillian Hafer
- Department of Biology and Centre of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Paul K Fyfe
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Elizabeth Pohler
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Silvia Gaggero
- Université de Lille, INSERM UMR1277 CNRS UMR9020-CANTHER and Institut pour la Recherche sur le Cancer de Lille (IRCL), Lille, France
| | - Martín López-García
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Charles Taylor
- Department of Statistics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Thomas Guerrier
- Univ. Lille, Univ. LilleInserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
| | - David Launay
- Univ. Lille, Univ. LilleInserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
| | - Suman Mitra
- Université de Lille, INSERM UMR1277 CNRS UMR9020-CANTHER and Institut pour la Recherche sur le Cancer de Lille (IRCL), Lille, France
| | - Jacob Piehler
- Department of Biology and Centre of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom.,T-6 Theoretical Division, Los Alamos National Laboratory, Los Alamos, United States
| | - Ignacio Moraga
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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