1
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Mudrak DA, Navolokin NA, Maslyakova GN. [Morphology of Hassall's corpuscles and their microenvironment in neonates with increased thymus weight]. Arkh Patol 2024; 86:13-20. [PMID: 38319267 DOI: 10.17116/patol20248601113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
OBJECTIVE To study morphological features of Hassall's corpuscles (HC) and their microenvironment in newborns with increased thymus mass. MATERIAL AND METHODS The study was carried out on autopsy material of children of the first month of life. Based on the thymic index (TI), 2 groups were identified: with normal (conditional norm) and increased TI value (increased thymus weight). The standard method of histological staining and immunohistochemical methods with antibodies to Pan-CK, CK19, CD68, CD3 and p53 were used in the study. The classification proposed by A.G. Beloveshkin (2013) was used to determine the degree of maturity of HC. Nonparametric Mann-Whitney test was used to determine statistically significant differences in the groups. RESULTS In the group of children with increased thymus weight, the number of HC decreased by 20%. It was found that the proportion of progressive and mature corpuscles in this group was reduced by 2.3 and 1.6 times, respectively, compared to the group of children with normal thymus weight, while the proportion of regressive corpuscles increased almost 2-fold. In the HC microenvironment, there is an increase in the total number of thymocytes, combined with a decrease in the expression of CD68, CD3 and p53 in them. A sharp decrease in CK19-expressing cells in this group is accompanied by a disruption in the formation of reticular structures characteristic of the comparison group. CONCLUSION In the thymus with increased mass, the structural and functional organization changes: along with an increase in the total number of thymocytes in the cortical layer and a decrease in the number of macrophages, epithelial cells and HC (with a predominance of regressive corpuscles), disturbances in the processes of maturation, apoptosis and negative selection of lymphocytes occur, which can lead to development of immunogenesis disorders.
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Affiliation(s)
- D A Mudrak
- Saratov State Medical University named after V.I. Razumovsky, Saratov, Russia
| | - N A Navolokin
- Saratov State Medical University named after V.I. Razumovsky, Saratov, Russia
| | - G N Maslyakova
- Saratov State Medical University named after V.I. Razumovsky, Saratov, Russia
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2
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Flores BCT, Chawla S, Ma N, Sanada C, Kujur PK, Yeung R, Bellon MB, Hukari K, Fowler B, Lynch M, Chinen LTD, Ramalingam N, Sengupta D, Jeffrey SS. Microfluidic live tracking and transcriptomics of cancer-immune cell doublets link intercellular proximity and gene regulation. Commun Biol 2022; 5:1231. [DOI: 10.1038/s42003-022-04205-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 11/01/2022] [Indexed: 11/15/2022] Open
Abstract
AbstractCell–cell communication and physical interactions play a vital role in cancer initiation, homeostasis, progression, and immune response. Here, we report a system that combines live capture of different cell types, co-incubation, time-lapse imaging, and gene expression profiling of doublets using a microfluidic integrated fluidic circuit that enables measurement of physical distances between cells and the associated transcriptional profiles due to cell–cell interactions. We track the temporal variations in natural killer—triple-negative breast cancer cell distances and compare them with terminal cellular transcriptome profiles. The results show the time-bound activities of regulatory modules and allude to the existence of transcriptional memory. Our experimental and bioinformatic approaches serve as a proof of concept for interrogating live-cell interactions at doublet resolution. Together, our findings highlight the use of our approach across different cancers and cell types.
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3
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Cui J, Meshesha M, Churgulia N, Merlo C, Fuchs E, Breakey J, Jones J, Stivers JT. Replication-competent HIV-1 in human alveolar macrophages and monocytes despite nucleotide pools with elevated dUTP. Retrovirology 2022; 19:21. [PMID: 36114511 PMCID: PMC9482235 DOI: 10.1186/s12977-022-00607-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/23/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Although CD4+ memory T cells are considered the primary latent reservoir for HIV-1, replication competent HIV has been detected in tissue macrophages in both animal and human studies. During in vitro HIV infection, the depleted nucleotide pool and high dUTP levels in monocyte derived macrophages (MDM) leads to proviruses with high levels of dUMP, which has been implicated in viral restriction or reduced transcription depending on the uracil base excision repair (UBER) competence of the macrophage. Incorporated dUMP has also been detected in viral DNA from circulating monocytes (MC) and alveolar macrophages (AM) of HIV infected patients on antiretroviral therapy (ART), establishing the biological relevance of this phenotype but not the replicative capacity of dUMP-containing proviruses. RESULTS As compared to in vitro differentiated MDM, AM from normal donors had sixfold lower levels of dTTP and a sixfold increased dUTP/dTTP, indicating a highly restrictive dNTP pool for reverse transcription. Expression of uracil DNA glycosylase (UNG) was eightfold lower in AM compared to the already low levels in MDM. Accordingly, ~ 80% of HIV proviruses contained dUMP, which persisted for at least 14-days due to low UNG excision activity. Unlike MDM, AM expression levels of UNG and SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) increased over 14 days post-HIV infection, while dUTP nucleotidohydrolase (DUT) expression decreased. These AM-specific effects suggest a restriction response centered on excising uracil from viral DNA copies and increasing relative dUTP levels. Despite the restrictive nucleotide pools, we detected rare replication competent HIV in AM, peripheral MC, and CD4+ T cells from ART-treated donors. CONCLUSIONS These findings indicate that the potential integration block of incorporated dUMP is not realized during in vivo infection of AM and MC due to the near absence of UBER activity. In addition, the increased expression of UNG and SAMHD1 in AM post-infection is too slow to prevent integration. Accordingly, dUMP persists in integrated viruses, which based on in vitro studies, can lead to transcriptional silencing. This possible silencing outcome of persistent dUMP could promote viral latency until the repressive effects of viral dUMP are reversed.
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Affiliation(s)
- Junru Cui
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185 USA
| | - Mesfin Meshesha
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185 USA
| | - Natela Churgulia
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185 USA
| | - Christian Merlo
- grid.21107.350000 0001 2171 9311Division of Pulmonary and Critical Care, Johns Hopkins University School of Medicine, 1830 E. Monument Street/5th Floor, Baltimore, MD 21205 USA
| | - Edward Fuchs
- grid.21107.350000 0001 2171 9311Division of Clinical Pharmacology, Drug Development Unit, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Blalock 569, Baltimore, MD 21287 USA
| | - Jennifer Breakey
- grid.21107.350000 0001 2171 9311Division of Clinical Pharmacology, Drug Development Unit, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Blalock 569, Baltimore, MD 21287 USA
| | - Joyce Jones
- grid.21107.350000 0001 2171 9311Division of Infectious Diseases, Johns Hopkins University School of Medicine, 1830 E. Monument Street, Baltimore, MD 21205 USA
| | - James T. Stivers
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185 USA
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4
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Lee JH, Park ES, Choi JR, Matthews K, Lam AV, Deng X, Duffy SP, Ma H. See-N-Seq: RNA sequencing of target single cells identified by microscopy via micropatterning of hydrogel porosity. Commun Biol 2022; 5:768. [PMID: 35908100 PMCID: PMC9338959 DOI: 10.1038/s42003-022-03703-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 07/12/2022] [Indexed: 11/30/2022] Open
Abstract
Single cell RNA sequencing has the potential to elucidate transcriptional programs underlying key cellular phenotypes and behaviors. However, many cell phenotypes are incompatible with indiscriminate single cell sequencing because they are rare, transient, or can only be identified by imaging. Existing methods for isolating cells based on imaging for single cell sequencing are technically challenging, time-consuming, and prone to loss because of the need to physically transport single cells. Here, we developed See-N-Seq, a method to rapidly screen cells in microwell plates in order to isolate RNA from specific single cells without needing to physically extract each cell. Our approach involves encapsulating the cell sample in a micropatterned hydrogel with spatially varying porosity to selectively expose specific cells for targeted RNA extraction. Extracted RNA can then be captured, barcoded, reverse transcribed, amplified, and sequenced at high-depth. We used See-N-Seq to isolate and sequence RNA from cell-cell conjugates forming an immunological synapse between T-cells and antigen presenting cells. In the hours after synapsing, we found time-dependent bifurcation of single cell transcriptomic profiles towards Type 1 and Type 2 helper T-cells lineages. Our results demonstrate how See-N-Seq can be used to associate transcriptomic data with specific functions and behaviors in single cells. A selective sequencing method, termed SeeN-Seq, is presented to link morphological phenotypes to single-cell RNAseq using UV laser patterning of hydrogel porosity.
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Affiliation(s)
- Jeong Hyun Lee
- Department of Mechanical Engineering, University of British Columbia, Vancouver, BC, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Emily S Park
- Department of Mechanical Engineering, University of British Columbia, Vancouver, BC, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Jane Ru Choi
- Department of Mechanical Engineering, University of British Columbia, Vancouver, BC, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Kerryn Matthews
- Department of Mechanical Engineering, University of British Columbia, Vancouver, BC, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Alice V Lam
- Department of Mechanical Engineering, University of British Columbia, Vancouver, BC, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Xiaoyan Deng
- Department of Mechanical Engineering, University of British Columbia, Vancouver, BC, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Simon P Duffy
- Department of Mechanical Engineering, University of British Columbia, Vancouver, BC, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada.,British Columbia Institute of Technology, Vancouver, BC, Canada
| | - Hongshen Ma
- Department of Mechanical Engineering, University of British Columbia, Vancouver, BC, Canada. .,Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada. .,School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada. .,Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, BC, Canada.
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5
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Liu Y, Segura T. Biomaterials-Mediated Regulation of Macrophage Cell Fate. Front Bioeng Biotechnol 2020; 8:609297. [PMID: 33363135 PMCID: PMC7759630 DOI: 10.3389/fbioe.2020.609297] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/23/2020] [Indexed: 01/28/2023] Open
Abstract
Endogenous regeneration aims to rebuild and reinstate tissue function through enlisting natural self-repairing processes. Promoting endogenous regeneration by reducing tissue-damaging inflammatory responses while reinforcing self-resolving inflammatory processes is gaining popularity. In this approach, the immune system is recruited as the principal player to deposit a pro-reparative matrix and secrete pro-regenerative cytokines and growth factors. The natural wound healing cascade involves many immune system players (neutrophils, macrophages, T cells, B cells, etc.) that are likely to play important and indispensable roles in endogenous regeneration. These cells support both the innate and adaptive arms of the immune system and collectively orchestrate host responses to tissue damage. As the early responders during the innate immune response, macrophages have been studied for decades in the context of inflammatory and foreign body responses and were often considered a cell type to be avoided. The view on macrophages has evolved and it is now understood that macrophages should be directly engaged, and their phenotype modulated, to guide the timely transition of the immune response and reparative environment. One way to achieve this is to design immunomodulating biomaterials that can be placed where endogenous regeneration is desired and actively direct macrophage polarization. Upon encountering these biomaterials, macrophages are trained to perform more pro-regenerative roles and generate the appropriate environment for later stages of regeneration since they bridge the innate immune response and the adaptive immune response. This new design paradigm necessitates the understanding of how material design elicits differential macrophage phenotype activation. This review is focused on the macrophage-material interaction and how to engineer biomaterials to steer macrophage phenotypes for better tissue regeneration.
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Affiliation(s)
- Yining Liu
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Tatiana Segura
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
- Department of Neurology, Duke University, Durham, NC, United States
- Department of Dermatology, Duke University, Durham, NC, United States
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6
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Temporal TGF-β Supergene Family Signalling Cues Modulating Tissue Morphogenesis: Chondrogenesis within a Muscle Tissue Model? Int J Mol Sci 2020; 21:ijms21144863. [PMID: 32660137 PMCID: PMC7402331 DOI: 10.3390/ijms21144863] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022] Open
Abstract
Temporal translational signalling cues modulate all forms of tissue morphogenesis. However, if the rules to obtain specific tissues rely upon specific ligands to be active or inactive, does this mean we can engineer any tissue from another? The present study focused on the temporal effect of “multiple” morphogen interactions on muscle tissue to figure out if chondrogenesis could be induced, opening up the way for new tissue models or therapies. Gene expression and histomorphometrical analysis of muscle tissue exposed to rat bone morphogenic protein 2 (rBMP-2), rat transforming growth factor beta 3 (rTGF-β3), and/or rBMP-7, including different combinations applied briefly for 48 h or continuously for 30 days, revealed that a continuous rBMP-2 stimulation seems to be critical to initiate a chondrogenesis response that was limited to the first seven days of culture, but only in the absence of rBMP-7 and/or rTGF-β3. After day 7, unknown modulatory effects retard rBMP-2s’ effect where only through the paired-up addition of rBMP-7 and/or rTGF-β3 a chondrogenesis-like reaction seemed to be maintained. This new tissue model, whilst still very crude in its design, is a world-first attempt to better understand how multiple morphogens affect tissue morphogenesis with time, with our goal being to one day predict the chronological order of what signals have to be applied, when, for how long, and with which other signals to induce and maintain a desired tissue morphogenesis.
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7
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Abstract
Macrophages are motile cells that roam the extracellular spaces within organs or the body cavity and carry out essential functions in organ development and immunity. New work published in The EMBO Journal adds surprising new insights into the heterogeneity of Drosophila macrophages revealing many similarities to their vertebrate counterparts.
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Affiliation(s)
- Volker Hartenstein
- Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA, USA
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8
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Carlon-Andres I, Padilla-Parra S. Quantitative FRET-FLIM-BlaM to Assess the Extent of HIV-1 Fusion in Live Cells. Viruses 2020; 12:E206. [PMID: 32059513 PMCID: PMC7077196 DOI: 10.3390/v12020206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 11/16/2022] Open
Abstract
The first steps of human immunodeficiency virus (HIV) infection go through the engagement of HIV envelope (Env) with CD4 and coreceptors (CXCR4 or CCR5) to mediate viral membrane fusion between the virus and the host. New approaches are still needed to better define both the molecular mechanistic underpinnings of this process but also the point of fusion and its kinetics. Here, we have developed a new method able to detect and quantify HIV-1 fusion in single live cells. We present a new approach that employs fluorescence lifetime imaging microscopy (FLIM) to detect Förster resonance energy transfer (FRET) when using the β-lactamase (BlaM) assay. This novel approach allows comparing different populations of single cells regardless the concentration of CCF2-AM FRET reporter in each cell, and more importantly, is able to determine the relative amount of viruses internalized per cell. We have applied this approach in both reporter TZM-bl cells and primary T cell lymphocytes.
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Affiliation(s)
| | - Sergi Padilla-Parra
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, UK;
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9
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Abstract
Given the many cell types and molecular components of the human immune system, along with vast variations across individuals, how should we go about developing causal and predictive explanations of immunity? A central strategy in human studies is to leverage natural variation to find relationships among variables, including DNA variants, epigenetic states, immune phenotypes, clinical descriptors, and others. Here, we focus on how natural variation is used to find patterns, infer principles, and develop predictive models for two areas: (a) immune cell activation-how single-cell profiling boosts our ability to discover immune cell types and states-and (b) antigen presentation and recognition-how models can be generated to predict presentation of antigens on MHC molecules and their detection by T cell receptors. These are two examples of a shift in how we find the drivers and targets of immunity, especially in the human system in the context of health and disease.
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Affiliation(s)
- Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02129, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Siranush Sarkizova
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02142, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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10
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Marcotti S, Reilly GC, Lacroix D. Effect of cell sample size in atomic force microscopy nanoindentation. J Mech Behav Biomed Mater 2019; 94:259-266. [PMID: 30928670 DOI: 10.1016/j.jmbbm.2019.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/21/2018] [Accepted: 03/17/2019] [Indexed: 11/25/2022]
Abstract
Single-cell technologies are powerful tools to evaluate cell characteristics. In particular, Atomic Force Microscopy (AFM) nanoindentation experiments have been widely used to study single cell mechanical properties. One important aspect related to single cell techniques is the need for sufficient statistical power to obtain reliable results. This aspect is often overlooked in AFM experiments were sample sizes are arbitrarily set. The aim of the present work was to propose a tool for sample size estimation in the context of AFM nanoindentation experiments of single cell. To this aim, a retrospective approach was used by acquiring a large dataset of experimental measurements on four bone cell types and by building saturation curves for increasing sample sizes with a bootstrap resampling method. It was observed that the coefficient of variation (CV%) decayed with a function of the form y = axb with similar parameters for all samples tested and that sample sizes of 21 and 83 cells were needed for the specific cells and protocol employed if setting a maximum threshold on CV% of 10% or 5%, respectively. The developed tool is made available as an open-source repository and guidelines are provided for its use for AFM nanoindentation experimental design.
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Affiliation(s)
- Stefania Marcotti
- Insigneo Institute for in silico Medicine, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK; Department of Mechanical Engineering, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, UK.
| | - Gwendolen C Reilly
- Insigneo Institute for in silico Medicine, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK; Department of Materials Science and Engineering, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
| | - Damien Lacroix
- Insigneo Institute for in silico Medicine, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK; Department of Mechanical Engineering, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
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11
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Haenseler W, Rajendran L. Concise Review: Modeling Neurodegenerative Diseases with Human Pluripotent Stem Cell-Derived Microglia. Stem Cells 2019; 37:724-730. [PMID: 30801863 PMCID: PMC6849818 DOI: 10.1002/stem.2995] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/25/2019] [Accepted: 02/03/2019] [Indexed: 12/11/2022]
Abstract
Inflammation of the brain and the consequential immunological responses play pivotal roles in neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal dementia (FTD). Microglia, the resident macrophage cells of the brain, have also emerged as key players in neuroinflammation. As primary human microglia from living subjects are normally not accessible to researchers, there is a pressing need for an alternative source of authentic human microglia which allows modeling of neurodegeneration in vitro. Several protocols for induced pluripotent stem cell (iPSC)‐derived microglia have recently been developed and provide unlimited access to patient‐derived material. In this present study, we give an overview of iPSC‐derived microglia models in monoculture and coculture systems, their advantages and limitations, and how they have already been used for disease phenotyping. Furthermore, we outline some of the gene engineering tools to generate isogenic controls, the creation of gene knockout iPSC lines, as well as covering reporter cell lines, which could help to elucidate complex cell interaction mechanisms in the microglia/neuron coculture system, for example, microglia‐induced synapse loss. Finally, we deliberate on how said cocultures could aid in personalized drug screening to identify patient‐specific therapies against neurodegeneration. stem cells2019;37:724–730
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Affiliation(s)
- Walther Haenseler
- Systems and Cell Biology of Neurodegeneration, IREM, University of Zurich, Schlieren, Switzerland
| | - Lawrence Rajendran
- Systems and Cell Biology of Neurodegeneration, IREM, University of Zurich, Schlieren, Switzerland.,UK-Dementia Research Institute (UK-DRI), Maurice Wohl Basic & Clinical Neuroscience Institute, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, United Kingdom
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12
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Sanada CD, Ooi AT. Single-Cell Dosing and mRNA Sequencing of Suspension and Adherent Cells Using the Polaris TM System. Methods Mol Biol 2019; 1979:185-195. [PMID: 31028639 DOI: 10.1007/978-1-4939-9240-9_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Single-cell functional analysis provides a natural next step in the now widely adopted single-cell mRNA sequencing studies. Functional studies can be designed to study cellular context by using single-cell culture, perturbation, manipulation, or treatment. Here we present a method for a functional study of 48 single cells by single-cell isolation, dosing, and mRNA sequencing with an integrated fluidic circuit (IFC) on the Fluidigm® Polaris™ system. The major procedures required to execute this protocol are (1) cell preparation and staining; (2) priming, single-cell selection, cell dosing, cell staining, and cDNA generation on the Polaris IFC; and (3) preparation and sequencing of single-cell mRNA-seq libraries. The cell preparation and staining steps employ the use of a universal tracking dye to trace all cells that enter the IFC, while additional fluorescence dyes chosen by the user can be used to differentiate cell types in the overall mix. The steps on the Polaris IFC follow standard protocols, which are also described in the Fluidigm user documentation. The library preparation step adds Illumina® Nextera® XT indexes to the cDNA generated on the Polaris IFC. The resulting sequencing libraries can be sequenced on any Illumina sequencing platform.
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Affiliation(s)
| | - Aik T Ooi
- Fluidigm Corporation, South San Francisco, CA, USA
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13
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Vegh P, Haniffa M. The impact of single-cell RNA sequencing on understanding the functional organization of the immune system. Brief Funct Genomics 2018; 17:265-272. [PMID: 29547972 PMCID: PMC6063276 DOI: 10.1093/bfgp/ely003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Application of single-cell genomics technologies has revolutionized our approach to study the immune system. Unravelling the functional diversity of immune cells and their coordinated response is key to understanding immunity. Single-cell transcriptomics technologies provide high-dimensional assessment of the transcriptional states of immune cells and have been successfully applied to discover new immune cell types, reveal haematopoietic lineages, identify gene modules dictating immune responses and investigate lymphocyte antigen receptor diversity. In this review, we discuss the impact and applications of single-cell RNA sequencing technologies in immunology.
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Affiliation(s)
- Peter Vegh
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Muzlifah Haniffa
- Department of Dermatology, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
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14
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Shamaei M, Mortaz E, Pourabdollah M, Garssen J, Tabarsi P, Velayati A, Adcock IM. Evidence for M2 macrophages in granulomas from pulmonary sarcoidosis: A new aspect of macrophage heterogeneity. Hum Immunol 2017; 79:63-69. [PMID: 29107084 DOI: 10.1016/j.humimm.2017.10.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/11/2017] [Accepted: 10/24/2017] [Indexed: 11/15/2022]
Abstract
BACKGROUND Sarcoidosis is a granulomatous disease of unknown etiology. Macrophages play a key role in granuloma formation with the T cells, having a significant impact on macrophage polarization (M1 and M2) and the cellular composition of the granuloma. This study evaluates macrophage polarization in granulomas in pulmonary sarcoidosis. MATERIALS AND METHODS Tissue specimens from the Department of Pathology biobank at the Masih Daneshvari Hospital were obtained. Paraffin sections from 10 sarcoidosis patients were compared with those from 12 cases of tuberculosis using immunohistochemical staining. These sections consisted of mediastinal lymph nodes and transbronchial lung biopsy (TBLB) for sarcoidosis patients versus pleural tissue, neck, axillary lymph nodes and TBLB for tuberculosis patients. The sections were stained for T-cells (CD4+, CD8+) and mature B lymphocytes (CD22+). CD14+ and CD68+ staining was used as a marker of M1 macrophages and CD163+ as a marker for M2 macrophages. RESULTS Immunohistochemical staining revealed a 4/1 ratio of CD4+/CD8+ T-cells in sarcoidosis granuloma sections and a 3/1 ratio in tuberculosis sections. There was no significance difference in single CD4+, CD8+, CD22+, CD14+ and CD68+ staining between sarcoidosis and tuberculosis sections. CD163 expression was significantly increased in sarcoidosis sections compared with those from tuberculosis subjects. CONCLUSION Enhanced CD163+ staining indicates a shift towards M2 macrophage subsets in granulomas from sarcoidosis patients. Further research is required to determine the functional role of M2 macrophages in the immunopathogenesis of sarcoidosis.
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Affiliation(s)
- Masoud Shamaei
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Esmaeil Mortaz
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran; Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Mihan Pourabdollah
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands; Nutricia Research Centre for Specialized Nutrition, Utrecht, Netherlands
| | - Payam Tabarsi
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aliakbar Velayati
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ian M Adcock
- Airways Disease Section, National Heart & Lung Institute, Imperial College London, London, UK; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia.
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15
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Hedlund E, Deng Q. Single-cell RNA sequencing: Technical advancements and biological applications. Mol Aspects Med 2017; 59:36-46. [PMID: 28754496 DOI: 10.1016/j.mam.2017.07.003] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022]
Abstract
Cells are the basic building blocks of organisms and each cell is unique. Single-cell RNA sequencing has emerged as an indispensable tool to dissect the cellular heterogeneity and decompose tissues into cell types and/or cell states, which offers enormous potential for de novo discovery. Single-cell transcriptomic atlases provide unprecedented resolution to reveal complex cellular events and deepen our understanding of biological systems. In this review, we summarize and compare single-cell RNA sequencing technologies, that were developed since 2009, to facilitate a well-informed choice of method. The applications of these methods in different biological contexts are also discussed. We anticipate an ever-increasing role of single-cell RNA sequencing in biology with further improvement in providing spatial information and coupling to other cellular modalities. In the future, such biological findings will greatly benefit medical research.
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Affiliation(s)
- Eva Hedlund
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Qiaolin Deng
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
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16
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Wang W, Gao D, Wang X. Can single-cell RNA sequencing crack the mystery of cells? Cell Biol Toxicol 2017; 34:1-6. [DOI: 10.1007/s10565-017-9404-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/28/2017] [Indexed: 12/15/2022]
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