101
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Mourikis TP, Benedetti L, Foxall E, Temelkovski D, Nulsen J, Perner J, Cereda M, Lagergren J, Howell M, Yau C, Fitzgerald RC, Scaffidi P, Ciccarelli FD. Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma. Nat Commun 2019; 10:3101. [PMID: 31308377 PMCID: PMC6629660 DOI: 10.1038/s41467-019-10898-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 06/04/2019] [Indexed: 12/25/2022] Open
Abstract
The identification of cancer-promoting genetic alterations is challenging particularly in highly unstable and heterogeneous cancers, such as esophageal adenocarcinoma (EAC). Here we describe a machine learning algorithm to identify cancer genes in individual patients considering all types of damaging alterations simultaneously. Analysing 261 EACs from the OCCAMS Consortium, we discover helper genes that, alongside well-known drivers, promote cancer. We confirm the robustness of our approach in 107 additional EACs. Unlike recurrent alterations of known drivers, these cancer helper genes are rare or patient-specific. However, they converge towards perturbations of well-known cancer processes. Recurrence of the same process perturbations, rather than individual genes, divides EACs into six clusters differing in their molecular and clinical features. Experimentally mimicking the alterations of predicted helper genes in cancer and pre-cancer cells validates their contribution to disease progression, while reverting their alterations reveals EAC acquired dependencies that can be exploited in therapy.
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Affiliation(s)
- Thanos P Mourikis
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Lorena Benedetti
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Elizabeth Foxall
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Damjan Temelkovski
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Joel Nulsen
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Juliane Perner
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Matteo Cereda
- Italian Institute for Genomic Medicine (IIGM), Turin, 10126, Italy
| | - Jesper Lagergren
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | | | - Rebecca C Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Paola Scaffidi
- Cancer Epigenetics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK.
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102
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Bykov YS, Cohen N, Gabrielli N, Manenschijn H, Welsch S, Chlanda P, Kukulski W, Patil KR, Schuldiner M, Briggs JAG. High-throughput ultrastructure screening using electron microscopy and fluorescent barcoding. J Cell Biol 2019; 218:2797-2811. [PMID: 31289126 PMCID: PMC6683748 DOI: 10.1083/jcb.201812081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/28/2019] [Accepted: 06/11/2019] [Indexed: 01/24/2023] Open
Abstract
Genetic screens using high-throughput fluorescent microscopes have generated large datasets, contributing many cell biological insights. Such approaches cannot tackle questions requiring knowledge of ultrastructure below the resolution limit of fluorescent microscopy. Electron microscopy (EM) reveals detailed cellular ultrastructure but requires time-consuming sample preparation, limiting throughput. Here we describe a robust method for screening by high-throughput EM. Our approach uses combinations of fluorophores as barcodes to uniquely mark each cell type in mixed populations and correlative light and EM (CLEM) to read the barcode of each cell before it is imaged by EM. Coupled with an easy-to-use software workflow for correlation, segmentation, and computer image analysis, our method, called "MultiCLEM," allows us to extract and analyze multiple cell populations from each EM sample preparation. We demonstrate several uses for MultiCLEM with 15 different yeast variants. The methodology is not restricted to yeast, can be scaled to higher throughput, and can be used in multiple ways to enable EM to become a powerful screening technique.
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Affiliation(s)
- Yury S Bykov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Nir Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Natalia Gabrielli
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hetty Manenschijn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sonja Welsch
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Petr Chlanda
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Wanda Kukulski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kiran R Patil
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany .,Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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103
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Intracellular Signaling in Key Pathways Is Induced by Treatment with Ultrasound and Microbubbles in a Leukemia Cell Line, but Not in Healthy Peripheral Blood Mononuclear Cells. Pharmaceutics 2019; 11:pharmaceutics11070319. [PMID: 31284599 PMCID: PMC6680714 DOI: 10.3390/pharmaceutics11070319] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/03/2019] [Accepted: 07/04/2019] [Indexed: 12/21/2022] Open
Abstract
Treatment with ultrasound and microbubbles (sonoporation) to enhance therapeutic efficacy in cancer therapy is rapidly expanding, but there is still very little consensus as to why it works. Despite the original assumption that pore formation in the cell membrane is responsible for increased uptake of drugs, the molecular mechanisms behind this phenomenon are largely unknown. We treated cancer cells (MOLM-13) and healthy peripheral blood mononuclear cells (PBMCs) with ultrasound at three acoustic intensities (74, 501, 2079 mW/cm2) ± microbubbles. We subsequently monitored the intracellular response of a number of key signaling pathways using flow cytometry or western blotting 5 min, 30 min and 2 h post-treatment. This was complemented by studies on uptake of a cell impermeable dye (calcein) and investigations of cell viability (cell count, Hoechst staining and colony forming assay). Ultrasound + microbubbles resulted in both early changes (p38 (Arcsinh ratio at high ultrasound + microbubbles: +0.5), ERK1/2 (+0.7), CREB (+1.3), STAT3 (+0.7) and AKT (+0.5)) and late changes (ribosomal protein S6 (Arcsinh ratio at low ultrasound: +0.6) and eIF2α in protein phosphorylation). Observed changes in protein phosphorylation corresponded to changes in sonoporation efficiency and in viability, predominantly in cancer cells. Sonoporation induced protein phosphorylation in healthy cells was pronounced (p38 (+0.03), ERK1/2 (−0.03), CREB (+0.0), STAT3 (−0.1) and AKT (+0.04) and S6 (+0.2)). This supports the hypothesis that sonoporation may enhance therapeutic efficacy of cancer treatment, without causing damage to healthy cells.
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104
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Roy AL. Transcriptional Regulation in the Immune System: One Cell at a Time. Front Immunol 2019; 10:1355. [PMID: 31258532 PMCID: PMC6587892 DOI: 10.3389/fimmu.2019.01355] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/29/2019] [Indexed: 12/27/2022] Open
Abstract
Transcriptional regulation of cells in the immune system must be strictly controlled at multiple levels to ensure that a proper immune response is elicited only when required. Analysis in bulk, or ensemble of cells, provides a wealth of important information leading to a better understanding of the various molecular steps and mechanisms involved in regulating gene expression in immune cells. However, given the substantial heterogeneity of these cells, it is imperative now to decipher these mechanisms at a single cell level. Here I bring together several recent examples to review our understanding of transcriptional regulation of the immune system via single cell analysis and to further illustrate the immense power of such analyses to interrogate immune cell heterogeneity.
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Affiliation(s)
- Ananda L Roy
- National Institutes of Health, Laboratory of Molecular Biology and Immunology, Biomedical Research Center, National Institute on Aging (NIH), Baltimore, MD, United States
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105
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Critical Analysis of Particle Detection Artifacts in Synaptosome Flow Cytometry. eNeuro 2019; 6:ENEURO.0009-19.2019. [PMID: 31118205 PMCID: PMC6565374 DOI: 10.1523/eneuro.0009-19.2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/01/2019] [Accepted: 04/27/2019] [Indexed: 11/21/2022] Open
Abstract
Flow cytometry and fluorescence-activated sorting are powerful techniques that hold great promise for studying heterogeneous populations of submicron particles such as synaptosomes, but many technical challenges arise in these experiments. To date, most flow cytometry studies of synaptosomes have relied on particle detection using forward scatter (FSC) measurements and size estimation with polystyrene (PS) bead standards. However, these practices have serious limitations, and special care must be taken to overcome the poor sensitivity of conventional flow cytometers in the analysis of submicron particles. Technical artifacts can confound these experiments, especially the detection of multiple particles as a single event. Here, we compared analysis of P2 crude synaptosomal preparations from murine forebrain on multiple flow cytometers using both FSC-triggered and fluorescence-triggered detection. We implemented multicolor fluorescent dye-based assays to quantify coincident particle detection and aggregation, and we assessed the false colocalization of antigens in immunostaining analyses. Our results demonstrate that fluorescence triggering and proper dilution can control for coincident particle detection, but not particle aggregation. We confirmed previous studies showing that FSC-based size estimation with PS beads underestimates biological particle size, and we identified pervasive aggregation in the FSC range analyzed in most synaptosome flow cytometry studies. We found that analyzing P2 samples in sucrose/EDTA/tris (SET) buffer reduces aggregation compared to PBS, but does not completely eliminate the presence of aggregates, especially in immunostaining experiments. Our study highlights challenges and pitfalls in synaptosome flow cytometry and provides a methodological framework for future studies.
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106
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Heterogeneity Studies of Mammalian Cells for Bioproduction: From Tools to Application. Trends Biotechnol 2019; 37:645-660. [DOI: 10.1016/j.tibtech.2018.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/22/2022]
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107
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Gao D, Jin F, Zhou M, Jiang Y. Recent advances in single cell manipulation and biochemical analysis on microfluidics. Analyst 2019; 144:766-781. [PMID: 30298867 DOI: 10.1039/c8an01186a] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single cell analysis has become of great interest with unprecedented capabilities for the systematic investigation of cell-to-cell variation in large populations. Rapid and multi-parametric analysis of intercellular biomolecules at the single-cell level is imperative for the improvement of early disease diagnosis and personalized medicine. However, the small size of cells and the low concentration levels of target biomolecules are critical challenges for single cell analysis. In recent years, microfluidic platforms capable of handling small-volume fluid have been demonstrated to be powerful tools for single cell analysis. In addition, microfluidic techniques allow for precise control of the localized microenvironment, which yield more accurate outcomes. Many different microfluidic techniques have been greatly improved for highly efficient single-cell manipulation and highly sensitive detection over the past few decades. To date, microfluidics-based single cell analysis has become the hot research topic in this field. In this review, we particularly highlight the advances in this field during the past three years in the following three aspects: (1) microfluidic single cell manipulation based on microwells, micropatterns, droplets, traps and flow cytometric methods; (2) detection methods based on fluorescence, mass spectrometry, electrochemical, and polymerase chain reaction-based analysis; (3) applications in the fields of small molecule detection, protein analysis, multidrug resistance analysis, and single cell sequencing with droplet microfluidics. We also discuss future research opportunities by focusing on key performances of throughput, multiparametric target detection and data processing.
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Affiliation(s)
- Dan Gao
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China.
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108
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Modulation of phospho-proteins by interferon-alpha and valproic acid in acute myeloid leukemia. J Cancer Res Clin Oncol 2019; 145:1729-1749. [PMID: 31111215 PMCID: PMC6571093 DOI: 10.1007/s00432-019-02931-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 05/07/2019] [Indexed: 02/06/2023]
Abstract
PURPOSE Valproic acid (VPA) is suggested to be therapeutically beneficial in combination with interferon-alpha (IFNα) in various cancers. Therefore, we examined IFNα and VPA alone and in combinations in selected AML models, examining immune regulators and intracellular signaling mechanisms involved in phospho-proteomics. METHODS The anti-leukemic effects of IFNα and VPA were examined in vitro and in vivo. We mapped the in vitro phosphoprotein modulation by IFNα-2b and human IFNα-Le in MOLM-13 cells by IMAC/2D DIGE/MS analysis and phospho-flow cytometry, and in primary healthy and AML patient-derived PBMCs by CyTOF. In vivo, IFNα-Le and VPA efficacy were investigated in the immunodeficient NOD/Scid IL2γ-/- MOLM-13Luc+ mouse model and the syngeneic immunocompetent BNML rat model. RESULTS IFNα-2b and IFNα-Le differed in the modulation of phospho-proteins involved in protein folding, cell stress, cell death and p-STAT6 Y641, whereas VPA and IFNα-Le shared signaling pathways involving phosphorylation of Akt (T308), ERK1/2 (T202/T204), p38 (T180/Y182), and p53 (S15). Both IFNα compounds induced apoptosis synergistically with VPA in vitro. However, in vivo, VPA monotherapy increased survival, but no benefit was observed by IFNα-Le treatment. CyTOF analysis of primary human PBMCs indicated that lack of immune-cell activation could be a reason for the absence of response to IFNα in the animal models investigated. CONCLUSIONS IFNα-2b and IFNα-Le showed potent and synergistic anti-leukemic effects with VPA in vitro but not in leukemic mouse and rat models in vivo. The absence of IFNα immune activation in lymphocyte subsets may potentially explain the limited in vivo anti-leukemic effect of IFNα-monotherapy in AML.
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109
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Lago SG, Tomasik J, van Rees GF, Steeb H, Cox DA, Rustogi N, Ramsey JM, Bishop JA, Petryshen T, Haggarty SJ, Vázquez-Bourgon J, Papiol S, Suarez-Pinilla P, Crespo-Facorro B, van Beveren NJ, Bahn S. Drug discovery for psychiatric disorders using high-content single-cell screening of signaling network responses ex vivo. SCIENCE ADVANCES 2019; 5:eaau9093. [PMID: 31086815 PMCID: PMC6506238 DOI: 10.1126/sciadv.aau9093] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 04/01/2019] [Indexed: 05/07/2023]
Abstract
There is a paucity of efficacious new compounds to treat neuropsychiatric disorders. We present a novel approach to neuropsychiatric drug discovery based on high-content characterization of druggable signaling network responses at the single-cell level in patient-derived lymphocytes ex vivo. Primary T lymphocytes showed functional responses encompassing neuropsychiatric medications and central nervous system ligands at established (e.g., GSK-3β) and emerging (e.g., CrkL) drug targets. Clinical application of the platform to schizophrenia patients over the course of antipsychotic treatment revealed therapeutic targets within the phospholipase Cγ1-calcium signaling pathway. Compound library screening against the target phenotype identified subsets of L-type calcium channel blockers and corticosteroids as novel therapeutically relevant drug classes with corresponding activity in neuronal cells. The screening results were validated by predicting in vivo efficacy in an independent schizophrenia cohort. The approach has the potential to discern new drug targets and accelerate drug discovery and personalized medicine for neuropsychiatric conditions.
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Affiliation(s)
- Santiago G. Lago
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Jakub Tomasik
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Geertje F. van Rees
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Hannah Steeb
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - David A. Cox
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Nitin Rustogi
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Jordan M. Ramsey
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Joshua A. Bishop
- Chemical Neurobiology Laboratory, Departments of Neurology and Psychiatry, Massachusetts General Hospital, Center for Genomic Medicine, Harvard Medical School, Boston, MA, USA
| | - Tracey Petryshen
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Stephen J. Haggarty
- Chemical Neurobiology Laboratory, Departments of Neurology and Psychiatry, Massachusetts General Hospital, Center for Genomic Medicine, Harvard Medical School, Boston, MA, USA
| | - Javier Vázquez-Bourgon
- Department of Psychiatry, Marqués de Valdecilla University Hospital, IDIVAL, School of Medicine, University of Cantabria, Santander, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Santander, Spain
- IDIVAL, Valdecilla Biomedical Research Institute, Santander, Spain
| | - Sergi Papiol
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Barcelona, Spain
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, Ludwig Maximilian University, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig Maximilian University, Munich, Germany
| | - Paula Suarez-Pinilla
- Department of Psychiatry, Marqués de Valdecilla University Hospital, IDIVAL, School of Medicine, University of Cantabria, Santander, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Santander, Spain
| | - Benedicto Crespo-Facorro
- Department of Psychiatry, Marqués de Valdecilla University Hospital, IDIVAL, School of Medicine, University of Cantabria, Santander, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Santander, Spain
- IDIVAL, Valdecilla Biomedical Research Institute, Santander, Spain
| | - Nico J. van Beveren
- Department of Neuroscience, Erasmus Medical Centre, Rotterdam, Netherlands
- Department of Psychiatry, Erasmus Medical Centre, Rotterdam, Netherlands
- Department “Nieuwe Kennis,” Delta Centre for Mental Health Care, Rotterdam, Netherlands
| | - Sabine Bahn
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Corresponding author.
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110
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Shah S, Dubey AK, Reif J. Programming Temporal DNA Barcodes for Single-Molecule Fingerprinting. NANO LETTERS 2019; 19:2668-2673. [PMID: 30896178 DOI: 10.1021/acs.nanolett.9b00590] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fluorescence microscopy enables simultaneous observation of the dynamics of single molecules in a large region of interest. Most traditional techniques employ either the geometry or the color of single molecules to uniquely identify (or barcode) different species of interest. However, these techniques require complex sample preparation and multicolor hardware setup. In this work, we introduce a time-based amplification-free single-molecule barcoding technique using easy-to-design nucleic acid strands. A dye-labeled complementary reporter strand transiently binds to the programmed nucleic acid strands to emit temporal intensity signals. We program the DNA strands to emit uniquely identifiable temporal signals for molecular-scale fingerprinting. Since the reporters bind transiently to DNA devices, our method offers relative immunity to photobleaching. We use a single universal reporter strand for all DNA devices making our design extremely cost-effective. We show DNA strands can be programmed for generating a multitude of uniquely identifiable molecular barcodes. Our technique can be easily incorporated with the existing orthogonal methods that use wavelength or geometry to generate a large pool of distinguishable molecular barcodes thereby enhancing the overall multiplexing capabilities of single-molecule imaging.
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Affiliation(s)
| | - Abhishek K Dubey
- Computational Sciences and Engineering Division, Health Data Sciences Institute , Oak Ridge National Lab , Oak Ridge , Tennessee 37831 , United States
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111
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de la Higuera L, López-García M, Castro M, Abourashchi N, Lythe G, Molina-París C. Fate of a Naive T Cell: A Stochastic Journey. Front Immunol 2019; 10:194. [PMID: 30894850 PMCID: PMC6415700 DOI: 10.3389/fimmu.2019.00194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/23/2019] [Indexed: 01/11/2023] Open
Abstract
The homeostasis of T cell populations depends on migration, division and death of individual cells (1). T cells migrate between spatial compartments (spleen, lymph nodes, lung, liver, etc.), where they may divide or differentiate, and eventually die (2). The kinetics of recirculation influences the speed at which local infections are detected and controlled (3). New experimental techniques have been developed to measure the lifespan of cells, and their migration dynamics; for example, fluorescence-activated cell sorting (4), in vitro time-lapse microscopy (5), or in vivo stable isotope labeling (e.g., deuterium) (6). When combined with mathematical and computational models, they allow estimation of rates of migration, division, differentiation and death (6, 7). In this work, we develop a stochastic model of a single cell migrating between spatial compartments, dividing and eventually dying. We calculate the number of division events during a T cell's journey, its lifespan, the probability of dying in each compartment and the number of progeny cells. A fast-migration approximation allows us to compute these quantities when migration rates are larger than division and death rates. Making use of published rates: (i) we analyse how perturbations in a given spatial compartment impact the dynamics of a T cell, (ii) we study the accuracy of the fast-migration approximation, and (iii) we quantify the role played by direct migration (not via the blood) between some compartments.
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Affiliation(s)
- Luis de la Higuera
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Martín López-García
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Mario Castro
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
- Grupo Interdisciplinar de Sistemas Complejos and DNL, Universidad Pontificia Comillas, Madrid, Spain
| | - Niloufar Abourashchi
- Department of Statistical Science, University College London, London, United Kingdom
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
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112
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Lago SG, Bahn S. Clinical Trials and Therapeutic Rationale for Drug Repurposing in Schizophrenia. ACS Chem Neurosci 2019; 10:58-78. [PMID: 29944339 DOI: 10.1021/acschemneuro.8b00205] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
There is a paucity of efficacious novel drugs to address high rates of treatment resistance and refractory symptoms in schizophrenia. The identification of novel therapeutic indications for approved drugs-drug repurposing-has the potential to expedite clinical trials and reduce the costly risk of failure which currently limits central nervous system drug discovery efforts. In the present Review we discuss the historical role of drug repurposing in schizophrenia drug discovery and review the main classes of repurposing candidates currently in clinical trials for schizophrenia in terms of their therapeutic rationale, mechanisms of action, and preliminary results from clinical trials. Subsequently we outline the challenges and limitations which face the clinical repurposing pipeline and how novel technologies might serve to address these.
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Affiliation(s)
- Santiago G. Lago
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, U.K
| | - Sabine Bahn
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, U.K
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113
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Abstract
Immunophenotyping using flow cytometry highly benefits from multiplexing samples for generation of more robust data, because of reduction of antibody consumption, batch effect and technical variations. One way to multiplex is via fluorescent cell barcoding (FCB) prior to staining procedure.FCB is a high-throughput multiplexed assay using various concentrations of different fluorescent dyes. Individual samples are uniquely labeled, then mixed together, stained and analyzed as a single sample, decreasing technical variations and increasing throughput and speed of acquisition. In addition, FCB simplifies implementation of normalization using a bridge control sample.In this chapter, we illustrate the protocol for FCB and recommendations for choosing barcoding dyes and concentrations among other technical considerations.
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Affiliation(s)
- Valentina Giudice
- Department of Medicine, Surgery, and Dentistry, Scuola Medica Salernitana, University of Salerno, Baronissi, Italy
| | | | - Angélique Biancotto
- Precision Immunology, Immunology and Inflammation Research Therapeutic Area, Cambridge, MA, USA.
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114
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Abstract
Barcoded bioassays are ready to promote bioanalysis and biomedicine toward the point of care.
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Affiliation(s)
- Mingzhu Yang
- Beijing Engineering Research Center for BioNanotechnology
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- National Center for NanoScience and Technology
- Beijing
| | - Yong Liu
- Beijing Engineering Research Center for BioNanotechnology
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- National Center for NanoScience and Technology
- Beijing
| | - Xingyu Jiang
- Beijing Engineering Research Center for BioNanotechnology
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- National Center for NanoScience and Technology
- Beijing
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115
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Abstract
Sample barcoding is a powerful method for harmonizing mass cytometry data. By assigning a unique combination of barcode labels to each cell sample, a set of individual samples can be pooled and further processed and acquired as a large, single sample. For assays that require uncompromised profiling of cell-surface markers on live cells, barcoding by metal-labeled antibodies targeting cell-surface epitopes is the barcoding approach of choice. Here we provide an optimized and validated protocol for cell-surface barcoding of ten PBMC samples with palladium-labeled β2-microglobulin (B2M) antibodies used in a 5-choose-2 barcoding scheme, for subsequent immune phenotyping by mass cytometry. We further provide details on the generation of palladium-labeled antibodies utilizing amine-reactive isothiocyanobenzyl-EDTA (ITCB-EDTA) that permits the implementation of antibody-based barcoding not interfering with lanthanide channels typically used for analyte detection in mass cytometry assays.
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Affiliation(s)
- Axel Ronald Schulz
- Mass Cytometry Lab, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
| | - Henrik E Mei
- Mass Cytometry Lab, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Berlin, Germany.
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116
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Stoeckius M, Zheng S, Houck-Loomis B, Hao S, Yeung BZ, Mauck WM, Smibert P, Satija R. Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. Genome Biol 2018; 19:224. [PMID: 30567574 PMCID: PMC6300015 DOI: 10.1186/s13059-018-1603-1] [Citation(s) in RCA: 531] [Impact Index Per Article: 88.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 12/04/2018] [Indexed: 12/11/2022] Open
Abstract
Despite rapid developments in single cell sequencing, sample-specific batch effects, detection of cell multiplets, and experimental costs remain outstanding challenges. Here, we introduce Cell Hashing, where oligo-tagged antibodies against ubiquitously expressed surface proteins uniquely label cells from distinct samples, which can be subsequently pooled. By sequencing these tags alongside the cellular transcriptome, we can assign each cell to its original sample, robustly identify cross-sample multiplets, and "super-load" commercial droplet-based systems for significant cost reduction. We validate our approach using a complementary genetic approach and demonstrate how hashing can generalize the benefits of single cell multiplexing to diverse samples and experimental designs.
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Affiliation(s)
- Marlon Stoeckius
- Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Shiwei Zheng
- NYU Center for Genomics and Systems Biology, New York Genome Center, New York, NY, USA
| | | | - Stephanie Hao
- Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | | | - William M Mauck
- NYU Center for Genomics and Systems Biology, New York Genome Center, New York, NY, USA
| | - Peter Smibert
- Technology Innovation Lab, New York Genome Center, New York, NY, USA.
| | - Rahul Satija
- NYU Center for Genomics and Systems Biology, New York Genome Center, New York, NY, USA.
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117
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Fluorescent genetic barcoding for cellular multiplex analyses. Exp Hematol 2018; 67:10-17. [DOI: 10.1016/j.exphem.2018.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022]
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118
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Doxie DB, Greenplate AR, Gandelman JS, Diggins KE, Roe CE, Dahlman KB, Sosman JA, Kelley MC, Irish JM. BRAF and MEK inhibitor therapy eliminates Nestin-expressing melanoma cells in human tumors. Pigment Cell Melanoma Res 2018; 31:708-719. [PMID: 29778085 PMCID: PMC6188784 DOI: 10.1111/pcmr.12712] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/18/2018] [Accepted: 05/14/2018] [Indexed: 02/06/2023]
Abstract
Little is known about the in vivo impacts of targeted therapy on melanoma cell abundance and protein expression. Here, 21 antibodies were added to an established melanoma mass cytometry panel to measure 32 cellular features, distinguish malignant cells, and characterize dabrafenib and trametinib responses in BRAFV600mut melanoma. Tumor cells were biopsied before neoadjuvant therapy and compared to cells surgically resected from the same site after 4 weeks of therapy. Approximately 50,000 cells per tumor were characterized by mass cytometry and computational tools t-SNE/viSNE, FlowSOM, and MEM. The resulting single-cell view of melanoma treatment response revealed initially heterogeneous melanoma tumors were consistently cleared of Nestin-expressing melanoma cells. Melanoma cell subsets that persisted to week 4 were heterogeneous but expressed SOX2 or SOX10 proteins and specifically lacked surface expression of MHC I proteins by MEM analysis. Traditional histology imaging of tissue microarrays from the same tumors confirmed mass cytometry results, including persistence of NES- SOX10+ S100β+ melanoma cells. This quantitative single-cell view of melanoma treatment response revealed protein features of malignant cells that are not eliminated by targeted therapy.
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Affiliation(s)
- Deon B. Doxie
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Allison R. Greenplate
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jocelyn S. Gandelman
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Division of Hematology-Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kirsten E. Diggins
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caroline E. Roe
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kimberly B. Dahlman
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey A. Sosman
- Department of Medicine, Division of Hematology-Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mark C. Kelley
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Division of Hematology-Oncology, Northwestern University, Feinberg School of Medicine, Evanston, IL, USA
| | - Jonathan M. Irish
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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119
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Sinha N, Subedi N, Tel J. Integrating Immunology and Microfluidics for Single Immune Cell Analysis. Front Immunol 2018; 9:2373. [PMID: 30459757 PMCID: PMC6232771 DOI: 10.3389/fimmu.2018.02373] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/24/2018] [Indexed: 12/16/2022] Open
Abstract
The field of immunoengineering aims to develop novel therapies and modern vaccines to manipulate and modulate the immune system and applies innovative technologies toward improved understanding of the immune system in health and disease. Microfluidics has proven to be an excellent technology for analytics in biology and chemistry. From simple microsystem chips to complex microfluidic designs, these platforms have witnessed an immense growth over the last decades with frequent emergence of new designs. Microfluidics provides a highly robust and precise tool which led to its widespread application in single-cell analysis of immune cells. Single-cell analysis allows scientists to account for the heterogeneous behavior of immune cells which often gets overshadowed when conventional bulk study methods are used. Application of single-cell analysis using microfluidics has facilitated the identification of several novel functional immune cell subsets, quantification of signaling molecules, and understanding of cellular communication and signaling pathways. Single-cell analysis research in combination with microfluidics has paved the way for the development of novel therapies, point-of-care diagnostics, and even more complex microfluidic platforms that aid in creating in vitro cellular microenvironments for applications in drug and toxicity screening. In this review, we provide a comprehensive overview on the integration of microsystems and microfluidics with immunology and focus on different designs developed to decode single immune cell behavior and cellular communication. We have categorized the microfluidic designs in three specific categories: microfluidic chips with cell traps, valve-based microfluidics, and droplet microfluidics that have facilitated the ongoing research in the field of immunology at single-cell level.
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Affiliation(s)
- Nidhi Sinha
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Nikita Subedi
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
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120
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Skånland SS. Phospho Flow Cytometry with Fluorescent Cell Barcoding for Single Cell Signaling Analysis and Biomarker Discovery. J Vis Exp 2018. [PMID: 30346411 DOI: 10.3791/58386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Aberrant cell signaling plays a central role in cancer development and progression. Most novel targeted therapies are indeed directed at proteins and protein functions, and cell signaling aberrations may therefore serve as biomarkers to indicate personalized treatment options. As opposed to DNA and RNA analyses, changes in protein activity can more efficiently evaluate the mechanisms underlying drug sensitivity and resistance. Phospho flow cytometry is a powerful technique that measures protein phosphorylation events at the cellular level, an important feature that distinguishes this method from other antibody-based approaches. The method allows for simultaneous analysis of multiple signaling proteins. In combination with fluorescent cell barcoding, larger medium- to high-throughput data-sets can be acquired by standard cytometer hardware in short time. Phospho flow cytometry has applications both in studies of basic biology and in clinical research, including signaling analysis, biomarker discovery and assessment of pharmacodynamics. Here, a detailed experimental protocol is provided for phospho flow analysis of purified peripheral blood mononuclear cells, using chronic lymphocytic leukemia cells as an example.
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Affiliation(s)
- Sigrid S Skånland
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo; K. G. Jebsen Centre for B cell malignancies and K. G. Jebsen Centre for Cancer Immunotherapy, University of Oslo;
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121
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Manohar S, Shah P, Biswas S, Mukadam A, Joshi M, Viswanathan G. Combining fluorescent cell barcoding and flow cytometry‐based phospho‐ERK1/2 detection at short time scales in adherent cells. Cytometry A 2018; 95:192-200. [DOI: 10.1002/cyto.a.23602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/09/2018] [Accepted: 08/20/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Sonal Manohar
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Prachi Shah
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Sharmila Biswas
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Anam Mukadam
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Madhura Joshi
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Ganesh Viswanathan
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
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122
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Wu X, DeGottardi Q, Wu IC, Wu L, Yu J, Kwok WW, Chiu DT. Ratiometric Barcoding for Mass Cytometry. Anal Chem 2018; 90:10688-10694. [PMID: 30139253 DOI: 10.1021/acs.analchem.8b03201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Barcoding is of importance for high-throughput cellular and molecular analysis. A ratiometric barcoding strategy using lanthanide-coordinated polymer dots (Ln-Pdots) was developed for mass cytometric analysis. By using 3 metal isotopes and 4 ratio intensity levels, 16 barcodes were generated to code, and later decode, cell samples in mass cytometry. The ratiometric Ln-Pdot barcodes not only provided high-mass-signal intensities but also eliminated the bias caused by different concentrations of the labeling reagents/barcodes and run-to-run differences in cell labeling efficiency. The ability to distinguish clearly the 16 sets of labeled MCF-7 cells with mass cytometry demonstrated the excellent resolving power of the ratiometric Ln-Pdot barcodes. Furthermore, the results from barcoding PBMC samples via CD45-specific cellular targeting indicated that the ratiometric Ln-Pdot barcodes could facilitate mass cytometry in high-throughput and multiplexed analysis, especially with precious human samples.
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Affiliation(s)
- Xu Wu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital , Central South University , Changsha , Hunan 410078 , China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute , Central South University , Changsha , Hunan 410078 , China
| | - Quinn DeGottardi
- Benaroya Research Institute at Virginia Mason , Seattle , Washington 98101 , United States
| | - I-Che Wu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Li Wu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Jiangbo Yu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason , Seattle , Washington 98101 , United States
| | - Daniel T Chiu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
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123
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Stonyte V, Boye E, Grallert B. Regulation of global translation during the cell cycle. J Cell Sci 2018; 131:jcs.220327. [PMID: 30072440 DOI: 10.1242/jcs.220327] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/20/2018] [Indexed: 01/10/2023] Open
Abstract
It is generally accepted that global translation varies during the cell cycle and is low during mitosis. However, addressing this issue is challenging because it involves cell synchronization, which evokes stress responses that, in turn, affect translation rates. Here, we have used two approaches to measure global translation rates in different cell-cycle phases. First, synchrony in different cell-cycle phases was obtained involving the same stress, by using temperature-sensitive mutants. Second, translation and DNA content were measured by flow cytometry in exponentially growing, single cells. We found no major variation in global translation rates through the cell cycle in either fission yeast or mammalian cells. We also measured phosphorylation of eukaryotic initiation factor-2α, an event that is thought to downregulate global translation in mitosis. In contrast with the prevailing view, eIF2α phosphorylation correlated poorly with downregulation of global translation and ectopically induced eIF2α phosphorylation inhibited global translation only at high levels.
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Affiliation(s)
- Vilte Stonyte
- Department of Radiation Biology, Institute for Cancer Research, Montebello, 0379 Oslo University Hospital, Oslo, Norway
| | - Erik Boye
- Department of Radiation Biology, Institute for Cancer Research, Montebello, 0379 Oslo University Hospital, Oslo, Norway
| | - Beáta Grallert
- Department of Radiation Biology, Institute for Cancer Research, Montebello, 0379 Oslo University Hospital, Oslo, Norway
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124
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Wang Y, Du R, Qiao L, Liu B. Ultrasensitive profiling of multiple biomarkers from single cells by signal amplification mass spectrometry. Chem Commun (Camb) 2018; 54:9659-9662. [PMID: 30101261 DOI: 10.1039/c8cc05308a] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A signal amplification protocol based on mass spectrometry (MS) was developed to profile simultaneously multiple biomarkers from a single cell using various mass label (ML)-modified Au nanoparticles (AuNPs). The strategy with ultrahigh sensitivity and specificity has potential prospects in the deep exploration of molecular and cellular characterization.
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Affiliation(s)
- Yuning Wang
- Department of Chemistry, Shanghai Stomatological Hospital, and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China.
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125
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Roy AL, Conroy RS. Toward mapping the human body at a cellular resolution. Mol Biol Cell 2018; 29:1779-1785. [PMID: 30058989 PMCID: PMC6085824 DOI: 10.1091/mbc.e18-04-0260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/01/2018] [Accepted: 06/07/2018] [Indexed: 12/21/2022] Open
Abstract
The adult human body is composed of nearly 37 trillion cells, each with potentially unique molecular characteristics. This Perspective describes some of the challenges and opportunities faced in mapping the molecular characteristics of these cells in specific regions of the body and highlights areas for international collaboration toward the broader goal of comprehensively mapping the human body with cellular resolution.
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Affiliation(s)
- Ananda L. Roy
- Office of Strategic Coordination, Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director, National Institutes of Health, Bethesda, MD 20892
| | - Richard S. Conroy
- Office of Strategic Coordination, Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director, National Institutes of Health, Bethesda, MD 20892
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126
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Hartmann FJ, Simonds EF, Bendall SC. A Universal Live Cell Barcoding-Platform for Multiplexed Human Single Cell Analysis. Sci Rep 2018; 8:10770. [PMID: 30018331 PMCID: PMC6050312 DOI: 10.1038/s41598-018-28791-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/22/2018] [Indexed: 02/07/2023] Open
Abstract
Single-cell barcoding enables the combined processing and acquisition of multiple individual samples as one. This maximizes assay efficiency and eliminates technical variability in both sample preparation and analysis. Remaining challenges are the barcoding of live, unprocessed cells to increase downstream assay performance combined with the flexibility of the approach towards a broad range of cell types. To that end, we developed a novel antibody-based platform that allows the robust barcoding of live human cells for mass cytometry (CyTOF). By targeting both the MHC class I complex (beta-2-microglobulin) and a broadly expressed sodium-potassium ATPase-subunit (CD298) with platinum-conjugated antibodies, human immune cells, stem cells as well as tumor cells could be multiplexed in the same single-cell assay. In addition, we present a novel palladium-based covalent viability reagent compatible with this barcoding strategy. Altogether, this platform enables mass cytometry-based, live-cell barcoding across a multitude of human sample types and provides a scheme for multiplexed barcoding of human single-cell assays in general.
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Affiliation(s)
- Felix J Hartmann
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | | | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA.
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127
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Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses. Nat Immunol 2018; 19:742-754. [PMID: 29925993 DOI: 10.1038/s41590-018-0133-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 04/19/2018] [Indexed: 12/20/2022]
Abstract
To tackle the complexity of cross-reactive and pathogen-specific T cell responses against related Salmonella serovars, we used mass cytometry, unbiased single-cell cloning, live fluorescence barcoding, and T cell-receptor sequencing to reconstruct the Salmonella-specific repertoire of circulating effector CD4+ T cells, isolated from volunteers challenged with Salmonella enterica serovar Typhi (S. Typhi) or Salmonella Paratyphi A (S. Paratyphi). We describe the expansion of cross-reactive responses against distantly related Salmonella serovars and of clonotypes recognizing immunodominant antigens uniquely expressed by S. Typhi or S. Paratyphi A. In addition, single-amino acid variations in two immunodominant proteins, CdtB and PhoN, lead to the accumulation of T cells that do not cross-react against the different serovars, thus demonstrating how minor sequence variations in a complex microorganism shape the pathogen-specific T cell repertoire. Our results identify immune-dominant, serovar-specific, and cross-reactive T cell antigens, which should aid in the design of T cell-vaccination strategies against Salmonella.
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128
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Zhao Z, Henowitz L, Zweifach A. A Multiplexed Assay That Monitors Effects of Multiple Compound Treatment Times Reveals Candidate Immune-Enhancing Compounds. SLAS DISCOVERY 2018; 23:646-655. [PMID: 29884089 DOI: 10.1177/2472555218777731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We previously developed a flow cytometry assay that monitored lytic granule exocytosis in cytotoxic T lymphocytes stimulated by contacting beads coated with activating anti-CD3 antibodies. That assay was multiplexed in that responses of cells that did or did not receive the activating stimulus were distinguished via changes in light scatter accompanying binding of cells to beads, allowing us to discriminate compounds that activate responses on their own from compounds that enhance responses in cells that received the activating stimulus, all within a single sample. Here we add a second dimension of multiplexing by developing means to assess in a single sample the effects of treating cells with test compounds for different times. Bar-coding cells before adding them to test wells lets us determine compound treatment time while also monitoring activation status and response amplitude at the point of interrogation. This multiplexed assay is suitable for screening 96-well plates. We used it to screen compounds from the National Cancer Institute, identifying several compounds that enhance anti-LAMP1 responses. Multiple-treatment-time (MTT) screening enabled by bar-coding and read via high-throughput flow cytometry may be a generally useful method for facilitating the discovery of compounds of interest.
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Affiliation(s)
- Ziyan Zhao
- 1 Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Liza Henowitz
- 1 Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Adam Zweifach
- 1 Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
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129
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Aarebrot AK, Solberg SM, Davies R, Bader LI, Holmes TD, Gavasso S, Bryceson YT, Jonsson R, Sandvik LF, Appel S. Phosphorylation of intracellular signalling molecules in peripheral blood cells from patients with psoriasis on originator or biosimilar infliximab. Br J Dermatol 2018; 179:371-380. [PMID: 29274242 DOI: 10.1111/bjd.16269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Psoriasis vulgaris is a chronic, inflammatory skin disease characterized by a dysregulated immune response and it is associated with substantial systemic comorbidities. Biological drugs such as tumour necrosis factor (TNF)-α inhibitors can ameliorate the disease but are expensive. Biosimilar drugs have the same amino-acid sequence as the originator, but differences in manufacturing can affect biological activity, efficacy and tolerability. OBJECTIVES To explore potential differences in intracellular phosphorylation of signalling molecules in peripheral blood cells from patients with psoriasis treated with the TNF-α inhibitor infliximab compared with healthy controls, and to investigate if the phosphorylation pattern was influenced by switching from the originator infliximab to the biosimilar CT-P13. METHODS By flow cytometry, we measured phosphorylation of nuclear factor kappa B, extracellular signal-regulated kinase 1/2, p38 mitogen-activated protein kinase and signal transducer and activator of transcription 3, before and after TNF-α stimulation in monocytes and T, B, natural killer and CD3+ CD56+ cells from 25 patients with psoriasis treated with infliximab and 19 healthy controls. RESULTS At inclusion, phosphorylation levels of peripheral blood mononuclear cells (PBMCs) were increased in patients with psoriasis compared with healthy controls, even though clinical remission had already been achieved. Phosphorylation levels declined in patients on both originator infliximab and biosimilar during continued treatment. No significant differences were detected between the two medications after 12 months. CONCLUSIONS Patients with psoriasis on infliximab have higher activation levels of PBMCs than do healthy controls, possibly reflecting systemic inflammation. Switching from the originator infliximab to biosimilar CT-P13 did not affect phosphorylation levels or clinical parameters, suggesting that CT-P13 is a noninferior treatment alternative to the originator infliximab.
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Affiliation(s)
- A K Aarebrot
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - S M Solberg
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Dermatology, Haukeland University Hospital, Bergen, Norway
| | - R Davies
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - L I Bader
- Bergen Group of Epidemiology and Biomarkers in Rheumatic Disease (BEaBiRD), Department of Rheumatology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - T D Holmes
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - S Gavasso
- Neuroimmunology Laboratory, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Y T Bryceson
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway.,Centre for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - R Jonsson
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway.,Bergen Group of Epidemiology and Biomarkers in Rheumatic Disease (BEaBiRD), Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
| | - L F Sandvik
- Department of Dermatology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - S Appel
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
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130
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Ding M, Clark R, Bardelle C, Backmark A, Norris T, Williams W, Wigglesworth M, Howes R. Application of High-Throughput Flow Cytometry in Early Drug Discovery: An AstraZeneca Perspective. SLAS DISCOVERY 2018; 23:719-731. [PMID: 29787326 DOI: 10.1177/2472555218775074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Flow cytometry is a powerful tool providing multiparametric analysis of single cells or particles. The introduction of faster plate-based sampling technologies on flow cytometers has transformed the technology into one that has become attractive for higher throughput drug discovery screening. This article describes AstraZeneca's perspectives on the deployment and application of high-throughput flow cytometry (HTFC) platforms for small-molecule high-throughput screening (HTS), structure-activity relationship (SAR) and phenotypic screening, and antibody screening. We describe the overarching HTFC workflow, including the associated automation and data analysis, along with a high-level overview of our HTFC assay portfolio. We go on to discuss the practical challenges encountered and solutions adopted in the course of our deployment of HTFC, as well as future enhancements and expansion of the technology to new areas of drug discovery.
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Affiliation(s)
- Mei Ding
- 1 Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Roger Clark
- 2 Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | | | - Anna Backmark
- 1 Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Tyrrell Norris
- 1 Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Wendy Williams
- 4 Antibody Discovery and Protein Engineering, MedImmune, Cambridge, UK
| | - Mark Wigglesworth
- 3 Discovery Sciences, IMED Biotech Unit, AstraZeneca, Macclesfield, UK
| | - Rob Howes
- 1 Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
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131
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Chan BM, Badh A, Berry KA, Grauer SA, King CT. Flow Cytometry-Based Epitope Binning Using Competitive Binding Profiles for the Characterization of Monoclonal Antibodies against Cellular and Soluble Protein Targets. SLAS DISCOVERY 2018; 23:613-623. [DOI: 10.1177/2472555218774334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A key step in the therapeutic antibody drug discovery process is early identification of diverse candidate molecules. Information comparing antibody binding epitopes can be used to classify antibodies within a large panel, guiding rational lead molecule selection. We describe a novel epitope binning method utilizing high-throughput flow cytometry (HTFC) that leverages cellular barcoding or spectrally distinct beads to multiplex samples to characterize antibodies raised against cell membrane receptor or soluble protein targets. With no requirement for sample purification or direct labeling, the method is suited for early characterization of antibody candidates. This method generates competitive binding profiles of each antibody against a defined set of known or unknown reference antibodies for binding to epitopes of an antigen. Antibodies with closely related competitive binding profiles indicate similar epitopes and are classified in the same bin. These large, high-throughput, multiplexed experiments can yield epitope bins or clusters for the entire antibody panel, from which a conceptual map of the epitope space for each antibody can be created. Combining this valuable epitope information with other data, such as functional activity, sequence, and selectivity of binding to orthologs and paralogs, enables us to advance the best epitope-diverse candidates for further development.
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Affiliation(s)
| | - Anita Badh
- Amgen Discovery Research, Burnaby, BC, Canada
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132
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Bøe CA, Håland TW, Boye E, Syljuåsen RG, Grallert B. A novel role for ATR/Rad3 in G1 phase. Sci Rep 2018; 8:6880. [PMID: 29720710 PMCID: PMC5931961 DOI: 10.1038/s41598-018-25238-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/12/2018] [Indexed: 12/29/2022] Open
Abstract
Checkpoint kinases are important in cellular surveillance pathways that help cells to cope with DNA damage and protect their genomes. In cycling cells, DNA replication is one of the most sensitive processes and therefore all organisms carefully regulate replication initiation and progression. The checkpoint kinase ATR plays important roles both in response to DNA damage and replication stress, and ATR inhibitors are currently in clinical trials for cancer treatment. Therefore, it is important to understand the roles of ATR in detail. Here we show that the fission yeast homologue Rad3 and the human ATR regulate events also in G1 phase in an unperturbed cell cycle. Rad3Δ mutants or human cells exposed to ATR inhibitor in G1 enter S phase prematurely, which results in increased DNA damage. Furthermore, ATR inhibition in a single G1 reduces clonogenic survival, demonstrating that long-term effects of ATR inhibition during G1 are deleterious for the cell. Interestingly, ATR inhibition through G1 and S phase reduces survival in an additive manner, strongly arguing that different functions of ATR are targeted in the different cell-cycle phases. We propose that potential effects of ATR inhibitors in G1 should be considered when designing future treatment protocols with such inhibitors.
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Affiliation(s)
- Cathrine A Bøe
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Tine W Håland
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Erik Boye
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Randi G Syljuåsen
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Beáta Grallert
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
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133
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Kanner SA, Jain A, Colecraft HM. Development of a High-Throughput Flow Cytometry Assay to Monitor Defective Trafficking and Rescue of Long QT2 Mutant hERG Channels. Front Physiol 2018; 9:397. [PMID: 29725305 PMCID: PMC5917007 DOI: 10.3389/fphys.2018.00397] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/04/2018] [Indexed: 11/24/2022] Open
Abstract
Long QT Syndrome (LQTS) is an acquired or inherited disorder characterized by prolonged QT interval, exertion-triggered arrhythmias, and sudden cardiac death. One of the most prevalent hereditary LQTS subtypes, LQT2, results from loss-of-function mutations in the hERG channel, which conducts IKr, the rapid component of the delayed rectifier K+ current, critical for cardiac repolarization. The majority of LQT2 mutations result in Class 2 deficits characterized by impaired maturation and trafficking of hERG channels. Here, we have developed a high-throughput flow cytometric assay to analyze the surface and total expression of wild-type (WT) and mutant hERG channels with single-cell resolution. To test our method, we focused on 16 LQT2 mutations in the hERG Per-Arnt-Sim (PAS) domain that were previously studied via a widely used biochemical approach that compares levels of 135-kDa immature and 155-kDa fully glycosylated hERG protein to infer surface expression. We confirmed that LQT2 mutants expressed in HEK293 cells displayed a decreased surface density compared to WT hERG, and were differentially rescued by low temperature. However, we also uncovered some notable differences from the findings obtained via the biochemical approach. In particular, three mutations (N33T, R56Q, and A57P) with apparent WT-like hERG glycosylation patterns displayed up to 50% decreased surface expression. Furthermore, despite WT-like levels of complex glycosylation, these mutants have impaired forward trafficking, and exhibit varying half-lives at the cell surface. The results highlight utility of the surface labeling/flow cytometry approach to quantitatively assess trafficking deficiencies associated with LQT2 mutations, to discern underlying mechanisms, and to report on interventions that rescue deficits in hERG surface expression.
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Affiliation(s)
- Scott A Kanner
- Doctoral Program in Neurobiology and Behavior, Columbia University College of Physicians and Surgeons, New York, NY, United States
| | - Ananya Jain
- Department of Physiology and Cellular Biophysics, Columbia University College of Physicians and Surgeons, New York, NY, United States
| | - Henry M Colecraft
- Doctoral Program in Neurobiology and Behavior, Columbia University College of Physicians and Surgeons, New York, NY, United States.,Department of Physiology and Cellular Biophysics, Columbia University College of Physicians and Surgeons, New York, NY, United States.,Department of Pharmacology, Columbia University College of Physicians and Surgeons, New York, NY, United States
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134
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Reichard A, Wanner N, Stuehr E, Alemagno M, Weiss K, Queisser K, Erzurum S, Asosingh K. Quantification of airway fibrosis in asthma by flow cytometry. Cytometry A 2018; 93:952-958. [PMID: 29659138 DOI: 10.1002/cyto.a.23373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/23/2018] [Accepted: 03/20/2018] [Indexed: 01/31/2023]
Abstract
Airway fibrosis is a prominent feature of asthma, contributing to the detrimental consequences of the disease. Fibrosis in the airway is the result of collagen deposition in the reticular lamina layer of the subepithelial tissue. Myofibroblasts are the leading cell type involved with this collagen deposition. Established methods of collagen deposition quantification present various issues, most importantly their inability to quantify current collagen biosynthesis occurring in airway myofibroblasts. Here, a novel method to quantify myofibroblast collagen expression in asthmatic lungs is described. Single cell suspensions of lungs harvested from C57BL/6 mice in a standard house dust mite model of asthma were employed to establish a flow cytometric method and compare collagen production in asthmatic and non-asthmatic lungs. Cells found to be CD45- αSMA+ , indicative of myofibroblasts, were gated, and median fluorescence intensity of the anti-collagen-I antibody labeling the cells was calculated. Lung myofibroblasts with no, medium, or high levels of collagen-I expression were distinguished. In asthmatic animals, collagen-I levels were increased in both medium and high expressers, and the number of myofibroblasts with high collagen-I content was elevated. Our findings determined that quantification of collagen-I deposition in myofibroblastic lung cells by flow cytometry is feasible in mouse models of asthma and indicative of increased collagen-I expression by asthmatic myofibroblasts. © 2018 International Society for Advancement of Cytometry.
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Affiliation(s)
- Andrew Reichard
- Department of Inflammation and Immunity, The Cleveland Clinic, Cleveland, Ohio
| | - Nicholas Wanner
- Department of Inflammation and Immunity, The Cleveland Clinic, Cleveland, Ohio
| | - Eric Stuehr
- Department of Inflammation and Immunity, The Cleveland Clinic, Cleveland, Ohio
| | - Mario Alemagno
- Department of Inflammation and Immunity, The Cleveland Clinic, Cleveland, Ohio
| | - Kelly Weiss
- Department of Inflammation and Immunity, The Cleveland Clinic, Cleveland, Ohio
| | - Kimberly Queisser
- Department of Inflammation and Immunity, The Cleveland Clinic, Cleveland, Ohio
| | - Serpil Erzurum
- Department of Inflammation and Immunity, The Cleveland Clinic, Cleveland, Ohio.,Respiratory Institute, The Cleveland Clinic, Cleveland, Ohio
| | - Kewal Asosingh
- Department of Inflammation and Immunity, The Cleveland Clinic, Cleveland, Ohio.,Flow Cytometry Core, Lerner Research Institute The Cleveland Clinic, Cleveland, Ohio
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135
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Deng Y, Kizer M, Rada M, Sage J, Wang X, Cheon DJ, Chung AJ. Intracellular Delivery of Nanomaterials via an Inertial Microfluidic Cell Hydroporator. NANO LETTERS 2018; 18:2705-2710. [PMID: 29569926 DOI: 10.1021/acs.nanolett.8b00704] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The introduction of nanomaterials into cells is an indispensable process for studies ranging from basic biology to clinical applications. To deliver foreign nanomaterials into living cells, traditionally endocytosis, viral and lipid nanocarriers or electroporation are mainly employed; however, they critically suffer from toxicity, inconsistent delivery, and low throughput and are time-consuming and labor-intensive processes. Here, we present a novel inertial microfluidic cell hydroporator capable of delivering a wide range of nanomaterials to various cell types in a single-step without the aid of carriers or external apparatus. The platform inertially focuses cells into the channel center and guides cells to collide at a T-junction. Controlled compression and shear forces generate transient membrane discontinuities that facilitate passive diffusion of external nanomaterials into the cell cytoplasm while maintaining high cell viability. This hydroporation method shows superior delivery efficiency, is high-throughput, and has high controllability; moreover, its extremely simple and low-cost operation provides a powerful and practical strategy in the applications of cellular imaging, biomanufacturing, cell-based therapies, regenerative medicine, and disease diagnosis.
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Affiliation(s)
| | | | - Miran Rada
- Department of Regenerative and Cancer Cell Biology , Albany Medical College (AMC) , Albany , New York 12208 , United States
| | - Jessica Sage
- Department of Regenerative and Cancer Cell Biology , Albany Medical College (AMC) , Albany , New York 12208 , United States
| | | | - Dong-Joo Cheon
- Department of Regenerative and Cancer Cell Biology , Albany Medical College (AMC) , Albany , New York 12208 , United States
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136
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Individually addressable and dynamic DNA gates for multiplexed cell sorting. Proc Natl Acad Sci U S A 2018; 115:4357-4362. [PMID: 29632190 DOI: 10.1073/pnas.1714820115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to analyze and isolate cells based on the expression of specific surface markers has increased our understanding of cell biology and produced numerous applications for biomedicine. However, established cell-sorting platforms rely on labels that are limited in number due to biophysical constraints, such as overlapping emission spectra of fluorophores in FACS. Here, we establish a framework built on a system of orthogonal and extensible DNA gates for multiplexed cell sorting. These DNA gates label target cell populations by antibodies to allow magnetic bead isolation en masse and then selectively unlock by strand displacement to sort cells. We show that DNA gated sorting (DGS) is triggered to completion within minutes on the surface of cells and achieves target cell purity, viability, and yield equivalent to that of commercial magnetic sorting kits. We demonstrate multiplexed sorting of three distinct immune cell populations (CD8+, CD4+, and CD19+) from mouse splenocytes to high purity and show that recovered CD8+ T cells retain proliferative potential and target cell-killing activity. To broaden the utility of this platform, we implement a double positive sorting scheme using DNA gates on peptide-MHC tetramers to isolate antigen-specific CD8+ T cells from mice infected with lymphocytic choriomeningitis virus (LCMV). DGS can potentially be expanded with fewer biophysical constraints to large families of DNA gates for applications that require analysis of complex cell populations, such as host immune responses to disease.
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137
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Uchiyama S, Tsuji T, Kawamoto K, Okano K, Fukatsu E, Noro T, Ikado K, Yamada S, Shibata Y, Hayashi T, Inada N, Kato M, Koizumi H, Tokuyama H. A Cell‐Targeted Non‐Cytotoxic Fluorescent Nanogel Thermometer Created with an Imidazolium‐Containing Cationic Radical Initiator. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801495] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Seiichi Uchiyama
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toshikazu Tsuji
- Central Laboratories for Key Technologies KIRIN Company Limited 1-13-5 Fukuura Kanazawa-ku Yokohama Kanagawa 236-0004 Japan
| | - Kyoko Kawamoto
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kentaro Okano
- Graduate School of Pharmaceutical Sciences Tohoku University Sendai Miyagi 980-8578 Japan
- Department of Chemical Science and Engineering Kobe University Kobe Hyogo 657-8501 Japan
| | - Eiko Fukatsu
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takahiro Noro
- Graduate School of Pharmaceutical Sciences Tohoku University Sendai Miyagi 980-8578 Japan
| | - Kumiko Ikado
- Central Laboratories for Key Technologies KIRIN Company Limited 1-13-5 Fukuura Kanazawa-ku Yokohama Kanagawa 236-0004 Japan
| | - Sayuri Yamada
- Central Laboratories for Key Technologies KIRIN Company Limited 1-13-5 Fukuura Kanazawa-ku Yokohama Kanagawa 236-0004 Japan
| | - Yuka Shibata
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Teruyuki Hayashi
- The Graduate School of Biological Sciences Nara Institute of Science and Technology Ikoma Nara 630-0192 Japan
- Department of Nutrition Koshien University 10-1 Momijigaoka Takarazuka Hyogo 665-0006 Japan
| | - Noriko Inada
- The Graduate School of Biological Sciences Nara Institute of Science and Technology Ikoma Nara 630-0192 Japan
| | - Masaru Kato
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Hideki Koizumi
- Central Laboratories for Key Technologies KIRIN Company Limited 1-13-5 Fukuura Kanazawa-ku Yokohama Kanagawa 236-0004 Japan
| | - Hidetoshi Tokuyama
- Graduate School of Pharmaceutical Sciences Tohoku University Sendai Miyagi 980-8578 Japan
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138
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Uchiyama S, Tsuji T, Kawamoto K, Okano K, Fukatsu E, Noro T, Ikado K, Yamada S, Shibata Y, Hayashi T, Inada N, Kato M, Koizumi H, Tokuyama H. A Cell‐Targeted Non‐Cytotoxic Fluorescent Nanogel Thermometer Created with an Imidazolium‐Containing Cationic Radical Initiator. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/anie.201801495] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Seiichi Uchiyama
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toshikazu Tsuji
- Central Laboratories for Key Technologies KIRIN Company Limited 1-13-5 Fukuura Kanazawa-ku Yokohama Kanagawa 236-0004 Japan
| | - Kyoko Kawamoto
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kentaro Okano
- Graduate School of Pharmaceutical Sciences Tohoku University Sendai Miyagi 980-8578 Japan
- Department of Chemical Science and Engineering Kobe University Kobe Hyogo 657-8501 Japan
| | - Eiko Fukatsu
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takahiro Noro
- Graduate School of Pharmaceutical Sciences Tohoku University Sendai Miyagi 980-8578 Japan
| | - Kumiko Ikado
- Central Laboratories for Key Technologies KIRIN Company Limited 1-13-5 Fukuura Kanazawa-ku Yokohama Kanagawa 236-0004 Japan
| | - Sayuri Yamada
- Central Laboratories for Key Technologies KIRIN Company Limited 1-13-5 Fukuura Kanazawa-ku Yokohama Kanagawa 236-0004 Japan
| | - Yuka Shibata
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Teruyuki Hayashi
- The Graduate School of Biological Sciences Nara Institute of Science and Technology Ikoma Nara 630-0192 Japan
- Department of Nutrition Koshien University 10-1 Momijigaoka Takarazuka Hyogo 665-0006 Japan
| | - Noriko Inada
- The Graduate School of Biological Sciences Nara Institute of Science and Technology Ikoma Nara 630-0192 Japan
| | - Masaru Kato
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Hideki Koizumi
- Central Laboratories for Key Technologies KIRIN Company Limited 1-13-5 Fukuura Kanazawa-ku Yokohama Kanagawa 236-0004 Japan
| | - Hidetoshi Tokuyama
- Graduate School of Pharmaceutical Sciences Tohoku University Sendai Miyagi 980-8578 Japan
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139
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Rehage N, Davydova E, Conrad C, Behrens G, Maiser A, Stehklein JE, Brenner S, Klein J, Jeridi A, Hoffmann A, Lee E, Dianzani U, Willemsen R, Feederle R, Reiche K, Hackermüller J, Leonhardt H, Sharma S, Niessing D, Heissmeyer V. Binding of NUFIP2 to Roquin promotes recognition and regulation of ICOS mRNA. Nat Commun 2018; 9:299. [PMID: 29352114 PMCID: PMC5775257 DOI: 10.1038/s41467-017-02582-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 12/12/2017] [Indexed: 12/02/2022] Open
Abstract
The ubiquitously expressed RNA-binding proteins Roquin-1 and Roquin-2 are essential for appropriate immune cell function and postnatal survival of mice. Roquin proteins repress target mRNAs by recognizing secondary structures in their 3'-UTRs and by inducing mRNA decay. However, it is unknown if other cellular proteins contribute to target control. To identify cofactors of Roquin, we used RNA interference to screen ~1500 genes involved in RNA-binding or mRNA degradation, and identified NUFIP2 as a cofactor of Roquin-induced mRNA decay. NUFIP2 binds directly and with high affinity to Roquin, which stabilizes NUFIP2 in cells. Post-transcriptional repression of human ICOS by endogenous Roquin proteins requires two neighboring non-canonical stem-loops in the ICOS 3'-UTR. This unconventional cis-element as well as another tandem loop known to confer Roquin-mediated regulation of the Ox40 3'-UTR, are bound cooperatively by Roquin and NUFIP2. NUFIP2 therefore emerges as a cofactor that contributes to mRNA target recognition by Roquin.
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Affiliation(s)
- Nina Rehage
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, 81377, München, Germany
| | - Elena Davydova
- Group Intracellular Transport and RNA Biology, Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Christine Conrad
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
| | - Gesine Behrens
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
| | - Andreas Maiser
- Center for Integrated Protein Science at the Department of Biology, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Jenny E Stehklein
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, 81377, München, Germany
| | - Sven Brenner
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, 81377, München, Germany
| | - Juliane Klein
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
| | - Aicha Jeridi
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, 81377, München, Germany
| | - Anne Hoffmann
- Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Eunhae Lee
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- The Functional Genomics Center, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Umberto Dianzani
- Department of Health Sciences, Universita' del Piemonte Orientale, via Solaroli 17, 28100, Novara, Italy
| | - Rob Willemsen
- CBG Department of Clinical Genetics, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | - Regina Feederle
- Monoclonal Antibody Core Facility and Research Group, Institute for Diabetes and Obesity, Helmholtz Zentrum München, Marchioninistrasse 25, 81377, München, Germany
| | - Kristin Reiche
- Bioinformatic Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology- IZI, 04103, Leipzig, Germany
| | - Jörg Hackermüller
- Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Heinrich Leonhardt
- Center for Integrated Protein Science at the Department of Biology, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Sonia Sharma
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- The Functional Genomics Center, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
| | - Dierk Niessing
- Group Intracellular Transport and RNA Biology, Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
- Department of Cell Biology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany.
- Institute of Pharmaceutical Biotechnology, Ulm University, James Franck Ring N27, 89081, Ulm, Germany.
| | - Vigo Heissmeyer
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany.
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, 81377, München, Germany.
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140
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Supermultiplexed optical imaging and barcoding with engineered polyynes. Nat Methods 2018; 15:194-200. [PMID: 29334378 PMCID: PMC5831481 DOI: 10.1038/nmeth.4578] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/05/2017] [Indexed: 12/19/2022]
Abstract
Optical multiplexing has a large impact in photonics, the life sciences and biomedicine. However, current technology is limited by a 'multiplexing ceiling' from existing optical materials. Here we engineered a class of polyyne-based materials for optical supermultiplexing. We achieved 20 distinct Raman frequencies, as 'Carbon rainbow', through rational engineering of conjugation length, bond-selective isotope doping and end-capping substitution of polyynes. With further probe functionalization, we demonstrated ten-color organelle imaging in individual living cells with high specificity, sensitivity and photostability. Moreover, we realized optical data storage and identification by combinatorial barcoding, yielding to our knowledge the largest number of distinct spectral barcodes to date. Therefore, these polyynes hold great promise in live-cell imaging and sorting as well as in high-throughput diagnostics and screening.
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141
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Duensing TD, Watson SR. Antibody Screening Using High-Throughput Flow Cytometry. Cold Spring Harb Protoc 2018; 2018:2018/1/pdb.top093773. [PMID: 29295907 DOI: 10.1101/pdb.top093773] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Because molecular targets addressable with antibody therapeutics are present on the surface of cells or in circulation, they are ideal for screening by cell- or bead-based assays using flow cytometry, a powerful, high-content analysis technique for cells, beads, and other particles in suspension. The ability to analyze thousands of cells per second, combined with multiplexing capabilities, has made this technology indispensable for laboratories performing antibody development work. Advances in this field, particularly in the areas of plate-based sampling and high-throughput flow cytometry, are enabling the use of this technology earlier in the antibody development and discovery process.
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142
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Earl DC, Ferrell PB, Leelatian N, Froese JT, Reisman BJ, Irish JM, Bachmann BO. Discovery of human cell selective effector molecules using single cell multiplexed activity metabolomics. Nat Commun 2018; 9:39. [PMID: 29295987 PMCID: PMC5750220 DOI: 10.1038/s41467-017-02470-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 12/01/2017] [Indexed: 01/06/2023] Open
Abstract
Discovering bioactive metabolites within a metabolome is challenging because there is generally little foreknowledge of metabolite molecular and cell-targeting activities. Here, single-cell response profiles and primary human tissue comprise a response platform used to discover novel microbial metabolites with cell-type-selective effector properties in untargeted metabolomic inventories. Metabolites display diverse effector mechanisms, including targeting protein synthesis, cell cycle status, DNA damage repair, necrosis, apoptosis, or phosphoprotein signaling. Arrayed metabolites are tested against acute myeloid leukemia patient bone marrow and molecules that specifically targeted blast cells or nonleukemic immune cell subsets within the same tissue biopsy are revealed. Cell-targeting polyketides are identified in extracts from biosynthetically prolific bacteria, including a previously unreported leukemia blast-targeting anthracycline and a polyene macrolactam that alternates between targeting blasts or nonmalignant cells by way of light-triggered photochemical isomerization. High-resolution cell profiling with mass cytometry confirms response mechanisms and is used to validate initial observations.
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Affiliation(s)
- David C Earl
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA
| | - P Brent Ferrell
- Department of Medicine, Vanderbilt University Medical Center, 1161 21st Avenue South, D-3100 Medical Center North, Nashville, TN, 37232, USA
| | - Nalin Leelatian
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37232, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2220 Pierce Avenue, Nashville, TN, 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, D-2220 Medical Center North, Nashville, TN, 37232, USA
| | - Jordan T Froese
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA
| | - Benjamin J Reisman
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37232, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2220 Pierce Avenue, Nashville, TN, 37232, USA.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, D-2220 Medical Center North, Nashville, TN, 37232, USA.
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA.
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143
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Abstract
Cancer immunotherapy fights against cancer by modulating the immune response and is delivering encouraging results in clinical treatments. However, it is challenging to achieve durable response in all cancer patients during treatment due to the diversity and dynamic nature of immune system as well as inter- and intratumor heterogeneity. A comprehensive assessment of system immunity and tumor microenvironment is crucial for effective and safe cancer therapy, which can potentially be resolved by single-cell proteomic analysis. Single-cell proteomic technologies enable system-wide profiling of protein levels in a number of single cells within the immune system and tumor microenvironment, and thereby provide direct assessment of the functional state of the immune cells and tumor-immune interaction that could be used to evaluate efficacy of immunotherapy and to improve clinical outcome. In this chapter, we summarized current single-cell proteomic technologies and their applications in cancer immunotherapy.
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144
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Evidence of microglial activation following exposure to serum from first-onset drug-naïve schizophrenia patients. Brain Behav Immun 2018; 67:364-373. [PMID: 28988033 DOI: 10.1016/j.bbi.2017.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/18/2017] [Accepted: 10/02/2017] [Indexed: 01/29/2023] Open
Abstract
Abnormal activation of brain microglial cells is widely implicated in the pathogenesis of schizophrenia. Previously the pathophysiology of microglial activation was considered to be intrinsic to the central nervous system. We hypothesised that due to their perivascular localization, microglia can also be activated by factors present in circulating blood. Through application of high-content functional screening, we show that peripheral blood serum from first-onset drug-naïve schizophrenia patients is sufficient to provoke microglial cell signalling network responses in vitro which are indicative of proinflammatory activation. We further explore the composition of the serum for the presence of analytes, with the potential to activate microglia, and the utility of the resultant microglial cellular phenotype for novel drug discovery.
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145
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Spurgeon BEJ, Naseem KM. High-Throughput Signaling Profiling in Blood Platelets by Multiplexed Phosphoflow Cytometry. Methods Mol Biol 2018; 1812:95-111. [PMID: 30171574 DOI: 10.1007/978-1-4939-8585-2_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Multiplexed phosphoflow cytometry is a novel method that provides rapid and quantitative readouts on intracellular phosphoprotein signaling. In this approach, flow cytometry is combined with fluorescent cell barcoding (FCB) to facilitate high-throughput analyses of signaling events. After stimulation, fixed and permeabilized platelets are labeled with distinct dye intensities to create unique fluorescent signatures for individual samples. These uniquely labeled samples can be combined for simultaneous antibody staining and acquisition. During software analysis, multiplexed samples can be differentiated by their distinct fluorescence intensities and analyzed as if they had been acquired individually. Multiplexing eliminates intersample variation, increases statistical robustness, and allows 4-96 samples to be processed with no appreciable increase in antibody consumption or runtime. The method can be performed on washed platelets, platelet-rich plasma (PRP), and whole blood. Its inherent versatility can fulfil wide-ranging experimental requirements from simple dose titrations to complex pharmacologic screens.
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Affiliation(s)
- Benjamin E J Spurgeon
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Khalid M Naseem
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK.
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146
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Caen O, Schütz S, Jammalamadaka MSS, Vrignon J, Nizard P, Schneider TM, Baret JC, Taly V. High-throughput multiplexed fluorescence-activated droplet sorting. MICROSYSTEMS & NANOENGINEERING 2018; 4:33. [PMID: 31057921 PMCID: PMC6220162 DOI: 10.1038/s41378-018-0033-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/05/2018] [Accepted: 07/05/2018] [Indexed: 05/02/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) is one of the most important features provided by droplet-based microfluidics. However, to date, it does not allow to compete with the high-throughput multiplexed sorting capabilities offered by flow cytometery. Here, we demonstrate the use of a dielectrophoretic-based FADS, allowing to sort up to five different droplet populations simultaneously. Our system provides means to select droplets of different phenotypes in a single experimental run to separate initially heterogeneous populations. Our experimental results are rationalized with the help of a numerical model of the actuation of droplets in electric fields providing guidelines for the prediction of sorting designs for upscaled or downscaled microsystems.
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Affiliation(s)
- Ouriel Caen
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Simon Schütz
- Emergent Complexity in Physical Systems Laboratory (ECPS), Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - M. S. Suryateja Jammalamadaka
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Jérémy Vrignon
- CNRS, University Bordeaux, CRPP, UMR 5031, 115 Avenue Schweitzer, 33600 Pessac, France
| | - Philippe Nizard
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Tobias M. Schneider
- Emergent Complexity in Physical Systems Laboratory (ECPS), Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jean-Christophe Baret
- CNRS, University Bordeaux, CRPP, UMR 5031, 115 Avenue Schweitzer, 33600 Pessac, France
| | - Valérie Taly
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
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147
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Murphy TW, Zhang Q, Naler LB, Ma S, Lu C. Recent advances in the use of microfluidic technologies for single cell analysis. Analyst 2017; 143:60-80. [PMID: 29170786 PMCID: PMC5839671 DOI: 10.1039/c7an01346a] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The inherent heterogeneity in cell populations has become of great interest and importance as analytical techniques have improved over the past decades. With the advent of personalized medicine, understanding the impact of this heterogeneity has become an important challenge for the research community. Many different microfluidic approaches with varying levels of throughput and resolution exist to study single cell activity. In this review, we take a broad view of the recent microfluidic developments in single cell analysis based on microwell, microchamber, and droplet platforms. We cover physical, chemical, and molecular biology approaches for cellular and molecular analysis including newly emerging genome-wide analysis.
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Affiliation(s)
- Travis W Murphy
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA.
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148
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Kamalakshakurup G, Lee AP. High-efficiency single cell encapsulation and size selective capture of cells in picoliter droplets based on hydrodynamic micro-vortices. LAB ON A CHIP 2017; 17:4324-4333. [PMID: 29138790 DOI: 10.1039/c7lc00972k] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Single cell analysis has emerged as a paradigm shift in cell biology to understand the heterogeneity of individual cells in a clone for pathological interrogation. Microfluidic droplet technology is a compelling platform to perform single cell analysis by encapsulating single cells inside picoliter-nanoliter (pL-nL) volume droplets. However, one of the primary challenges for droplet based single cell assays is single cell encapsulation in droplets, currently achieved either randomly, dictated by Poisson statistics, or by hydrodynamic techniques. In this paper, we present an interfacial hydrodynamic technique which initially traps the cells in micro-vortices, and later releases them one-to-one into the droplets, controlled by the width of the outer streamline that separates the vortex from the flow through the streaming passage adjacent to the aqueous-oil interface (dgap). One-to-one encapsulation is achieved at a dgap equal to the radius of the cell, whereas complete trapping of the cells is realized at a dgap smaller than the radius of the cell. The unique feature of this technique is that it can perform 1. high efficiency single cell encapsulations and 2. size-selective capturing of cells, at low cell loading densities. Here we demonstrate these two capabilities with a 50% single cell encapsulation efficiency and size selective separation of platelets, RBCs and WBCs from a 10× diluted blood sample (WBC capture efficiency at 70%). The results suggest a passive, hydrodynamic micro-vortex based technique capable of performing high-efficiency single cell encapsulation for cell based assays.
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149
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High-throughput flow cytometry for drug discovery: principles, applications, and case studies. Drug Discov Today 2017; 22:1844-1850. [DOI: 10.1016/j.drudis.2017.09.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/01/2017] [Accepted: 09/08/2017] [Indexed: 12/31/2022]
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150
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Zimmermann S, Gretzinger S, Zimmermann PK, Bogsnes A, Hansson M, Hubbuch J. Cell Separation in Aqueous Two-Phase Systems - Influence of Polymer Molecular Weight and Tie-Line Length on the Resolution of Five Model Cell Lines. Biotechnol J 2017; 13. [PMID: 29087627 DOI: 10.1002/biot.201700250] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 10/16/2017] [Indexed: 12/29/2022]
Abstract
The availability of clinical-scale downstream processing strategies for cell-based products presents a critical juncture between basic research and clinical development. Aqueous two-phase systems (ATPS) facilitate the label-free, scalable, and cost-effective separation of cells, and are a versatile tool for downstream processing of cell-based therapeutics. Here, we report the application of a previously developed robotic screening platform, here extended to enable a multiplexed high-throughput cell partitioning analysis in ATPS. We investigated the influence of polymer molecular weight and tie-line length on the resolution of five model cell lines in "charge-sensitive" polyethylene-glycol (PEG)-dextran ATPS. We show, how these factors influence cell partitioning, and that the combination of low molecular weight PEGs and high molecular weight dextrans enable the highest resolution of the five cell lines. Furthermore, we demonstrate that the separability of each cell line from the mixture is highly dependent on the polymer molecular weight composition and tie-line length. Using a countercurrent distribution model we demonstrate that our screenings yielded conditions that theoretically enable the isolation of four of the five cell lines with high purity (>99.9%) and yield.
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Affiliation(s)
- Sarah Zimmermann
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Sarah Gretzinger
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Philipp K Zimmermann
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Are Bogsnes
- Biopharm Purification Development & Virology, Novo Nordisk A/SGentofte, Denmark
| | - Mattias Hansson
- Dr. M. Hansson, Diabetes Research, Novo Nordisk A/S, Måløv, Denmark
| | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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