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Assessing Acinetobacter baumannii Virulence and Persistence in a Murine Model of Lung Infection.
Palmer LD, Green ER, Sheldon JR, Skaar EP
(2019) Methods Mol Biol 1946: 289-305
MeSH Terms: Acinetobacter Infections, Acinetobacter baumannii, Acute Disease, Animals, Bacterial Load, Biopsy, Disease Models, Animal, Flow Cytometry, Immunity, Immunohistochemistry, Mice, Pneumonia, Bacterial, Virulence
Show Abstract · Added April 2, 2019
Acinetobacter baumannii is a Gram-negative opportunistic pathogen and a leading cause of ventilator-associated pneumonia. Murine models of A. baumannii lung infection allow researchers to experimentally assess A. baumannii virulence and host response. Intranasal administration of A. baumannii models acute lung infection. This chapter describes the methods to test A. baumannii virulence in a murine model of lung infection, including assessing the competitive index of a bacterial mutant and the associated inflammatory responses.
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1 Members
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13 MeSH Terms
Single-Cell Mass Cytometry of Archived Human Epithelial Tissue for Decoding Cancer Signaling Pathways.
Scurrah CR, Simmons AJ, Lau KS
(2019) Methods Mol Biol 1884: 215-229
MeSH Terms: Animals, Cryopreservation, Epithelial Cells, Epithelium, Fixatives, Flow Cytometry, Formaldehyde, Humans, Mass Spectrometry, Mice, Neoplasms, Paraffin Embedding, Signal Transduction, Single-Cell Analysis, Tissue Fixation
Show Abstract · Added December 14, 2018
The emerging phenomenon of cellular heterogeneity in tissue requires single-cell resolution studies. A specific challenge for suspension-based single-cell analysis is the preservation of intact cell states when single cells are isolated from tissue contexts, in order to enable downstream analyses to extract accurate, native information. We have developed DISSECT (Disaggregation for Intracellular Signaling in Single Epithelial Cells from Tissue) coupled to mass cytometry (CyTOF: Cytometry by Time-of-Flight), an experimental approach for profiling intact signaling states of single cells from epithelial tissue specimens. We have previously applied DISSECT-CyTOF to fresh mouse intestinal samples and to Formalin-Fixed, Paraffin-Embedded (FFPE) human colorectal cancer specimens. Here, we present detailed protocols for each of these procedures, as well as a new method for applying DISSECT to cryopreserved tissue slices. We present example data for using DISSECT on a cryopreserved specimen of the human colon to profile its immune and epithelial composition. These techniques can be used for high-resolution studies for monitoring disease-related alternations in different cellular compartments using specimens stored in cryopreserved or FFPE tissue banks.
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15 MeSH Terms
Generating Quantitative Cell Identity Labels with Marker Enrichment Modeling (MEM).
Diggins KE, Gandelman JS, Roe CE, Irish JM
(2018) Curr Protoc Cytom 83: 10.21.1-10.21.28
MeSH Terms: Animals, Electronic Data Processing, Flow Cytometry, Humans, Machine Learning, Models, Theoretical
Show Abstract · Added January 19, 2018
Multiplexed single-cell experimental techniques like mass cytometry measure 40 or more features and enable deep characterization of well-known and novel cell populations. However, traditional data analysis techniques rely extensively on human experts or prior knowledge, and novel machine learning algorithms may generate unexpected population groupings. Marker enrichment modeling (MEM) creates quantitative identity labels based on features enriched in a population relative to a reference. While developed for cell type analysis, MEM labels can be generated for a wide range of multidimensional data types, and MEM works effectively with output from expert analysis and diverse machine learning algorithms. MEM is implemented as an R package and includes three steps: (1) calculation of MEM values that quantify each feature's relative enrichment in the population, (2) reporting of MEM labels as a heatmap or as a text label, and (3) quantification of MEM label similarity between populations. The protocols here show MEM analysis using datasets from immunology and oncology. These MEM implementations provide a way to characterize population identity and novelty in the context of computational and expert analyses. © 2018 by John Wiley & Sons, Inc.
Copyright © 2018 John Wiley & Sons, Inc.
2 Communities
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6 MeSH Terms
Discovery of human cell selective effector molecules using single cell multiplexed activity metabolomics.
Earl DC, Ferrell PB, Leelatian N, Froese JT, Reisman BJ, Irish JM, Bachmann BO
(2018) Nat Commun 9: 39
MeSH Terms: Aged, Bone Marrow, Cell Extracts, Chromatography, Liquid, DNA Damage, Female, Flow Cytometry, Humans, Leukemia, Leukemia, Myeloid, Acute, Lymphocytes, Male, Mass Spectrometry, Metabolome, Metabolomics, Monocytes, Signal Transduction, Streptomyces, Tumor Cells, Cultured, Young Adult
Show Abstract · Added January 4, 2018
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.
3 Communities
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20 MeSH Terms
Prominin-1 Is a Novel Regulator of Autophagy in the Human Retinal Pigment Epithelium.
Bhattacharya S, Yin J, Winborn CS, Zhang Q, Yue J, Chaum E
(2017) Invest Ophthalmol Vis Sci 58: 2366-2387
MeSH Terms: AC133 Antigen, Adult, Aged, Animals, Autophagy, Blotting, Western, Cells, Cultured, Female, Flow Cytometry, Gene Expression Regulation, Humans, Immunoprecipitation, Macular Degeneration, Male, Microscopy, Confocal, Middle Aged, RNA, Rabbits, Real-Time Polymerase Chain Reaction, Retinal Pigment Epithelium, Signal Transduction, Young Adult
Show Abstract · Added June 11, 2018
Purpose - Prominin-1 (Prom1) is a transmembrane glycoprotein, which is expressed in stem cell lineages, and has recently been implicated in cancer stem cell survival. Mutations in the Prom1 gene have been shown to disrupt photoreceptor disk morphogenesis and cause an autosomal dominant form of Stargardt-like macular dystrophy (STGD4). Despite the apparent structural role of Prom1 in photoreceptors, its role in other cells of the retina is unknown. The purpose of this study is to investigate the role of Prom1 in the highly metabolically active cells of the retinal pigment epithelium (RPE).
Methods - Lentiviral siRNA and the genome editing CRISPR/Cas9 system were used to knockout Prom1 in primary RPE and ARPE-19 cells, respectively. Western blotting, confocal microscopy, and flow sight imaging cytometry assays were used to quantify autophagy flux. Immunoprecipitation was used to detect Prom1 interacting proteins.
Results - Our studies demonstrate that Prom1 is primarily a cytosolic protein in the RPE. Stress signals and physiological aging robustly increase autophagy with concomitant upregulation of Prom1 expression. Knockout of Prom1 increased mTORC1 and mTORC2 signaling, decreased autophagosome trafficking to the lysosome, increased p62 accumulation, and inhibited autophagic puncta induced by activators of autophagy. Conversely, ectopic overexpression of Prom1 inhibited mTORC1 and mTORC2 activities, and potentiated autophagy flux. Through interactions with p62 and HDAC6, Prom1 regulates autophagosome maturation and trafficking, suggesting a new cytoplasmic role of Prom1 in RPE function.
Conclusions - Our results demonstrate that Prom1 plays a key role in the regulation of autophagy via upstream suppression of mTOR signaling and also acting as a component of a macromolecular scaffold involving p62 and HDAC6.
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MeSH Terms
Mass cytometry deep phenotyping of human mononuclear phagocytes and myeloid-derived suppressor cells from human blood and bone marrow.
Roussel M, Ferrell PB, Greenplate AR, Lhomme F, Le Gallou S, Diggins KE, Johnson DB, Irish JM
(2017) J Leukoc Biol 102: 437-447
MeSH Terms: Dendritic Cells, Flow Cytometry, Humans, Lymphocyte Culture Test, Mixed, Macrophages, Monocytes, Myeloid-Derived Suppressor Cells, Phagocytes, Phenotype
Show Abstract · Added April 13, 2017
The monocyte phagocyte system (MPS) includes numerous monocyte, macrophage, and dendritic cell (DC) populations that are heterogeneous, both phenotypically and functionally. In this study, we sought to characterize those diverse MPS phenotypes with mass cytometry (CyTOF). To identify a deep phenotype of monocytes, macrophages, and DCs, a panel was designed to measure 38 identity, activation, and polarization markers, including CD14, CD16, HLA-DR, CD163, CD206, CD33, CD36, CD32, CD64, CD13, CD11b, CD11c, CD86, and CD274. MPS diversity was characterized for 1) circulating monocytes from healthy donors, 2) monocyte-derived macrophages further polarized in vitro (i.e., M-CSF, GM-CSF, IL-4, IL-10, IFN-γ, or LPS long-term stimulations), 3) monocyte-derived DCs, and 4) myeloid-derived suppressor cells (MDSCs), generated in vitro from bone marrow and/or peripheral blood. Known monocyte subsets were detected in peripheral blood to validate the panel and analysis pipeline. Then, using various culture conditions and stimuli before CyTOF analysis, we constructed a multidimensional framework for the MPS compartment, which was registered against historical M1 or M2 macrophages, monocyte subsets, and DCs. Notably, MDSCs generated in vitro from bone marrow expressed more S100A9 than when generated from peripheral blood. Finally, to test the approach in vivo, peripheral blood from patients with melanoma ( = 5) was characterized and observed to be enriched for MDSCs with a phenotype of CD14HLA-DRS100A9 (3% of PBMCs in healthy donors, 15.5% in patients with melanoma, < 0.02). In summary, mass cytometry comprehensively characterized phenotypes of human monocyte, MDSC, macrophage, and DC subpopulations in both in vitro models and patients.
© Society for Leukocyte Biology.
3 Communities
1 Members
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9 MeSH Terms
Preparing Viable Single Cells from Human Tissue and Tumors for Cytomic Analysis.
Leelatian N, Doxie DB, Greenplate AR, Sinnaeve J, Ihrie RA, Irish JM
(2017) Curr Protoc Mol Biol 118: 25C.1.1-25C.1.23
MeSH Terms: Cell Separation, Cryopreservation, Flow Cytometry, Humans, Neoplasms, Single-Cell Analysis
Show Abstract · Added April 4, 2017
Mass cytometry is a single-cell biology technique that samples >500 cells per second, measures >35 features per cell, and is sensitive across a dynamic range of >10 relative intensity units per feature. This combination of technical assets has powered a series of recent cytomic studies where investigators used mass cytometry to measure protein and phospho-protein expression in millions of cells, characterize rare cell types in healthy and diseased tissues, and reveal novel, unexpected cells. However, these advances largely occurred in studies of blood, lymphoid tissues, and bone marrow, since the cells in these tissues are readily obtained in single-cell suspensions. This unit establishes a primer for single-cell analysis of solid tumors and tissues, and has been tested with mass cytometry. The cells obtained from these protocols can be fixed for study, cryopreserved for long-term storage, or perturbed ex vivo to dissect responses to stimuli and inhibitors. © 2017 by John Wiley & Sons, Inc.
Copyright © 2017 John Wiley & Sons, Inc.
3 Communities
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6 MeSH Terms
Myc enhances B-cell receptor signaling in precancerous B cells and confers resistance to Btk inhibition.
Moyo TK, Wilson CS, Moore DJ, Eischen CM
(2017) Oncogene 36: 4653-4661
MeSH Terms: Agammaglobulinaemia Tyrosine Kinase, Animals, B-Lymphocytes, CD79 Antigens, Cell Proliferation, Flow Cytometry, Humans, Lymphoma, Non-Hodgkin, Male, Mice, Mice, Inbred C57BL, Mitogen-Activated Protein Kinase 3, Phosphatidylinositol 3-Kinases, Phospholipase C gamma, Phosphorylation, Precancerous Conditions, Protein-Tyrosine Kinases, Proto-Oncogene Proteins c-myc, Pyrazoles, Pyrimidines, Receptors, Antigen, B-Cell, Splenic Neoplasms, Syk Kinase
Show Abstract · Added April 6, 2017
Dysregulation of the oncogenic transcription factor MYC induces B-cell transformation and is a driver for B-cell non-Hodgkin lymphoma (B-NHL). MYC overexpression in B-NHL is associated with more aggressive phenotypes and poor prognosis. Although genomic studies suggest a link between MYC overexpression and B-cell receptor (BCR) signaling molecules in B-NHL, signaling pathways essential to Myc-mediated B-cell transformation have not been fully elucidated. We utilized intracellular phospho-flow cytometry to investigate the relationship between Myc and BCR signaling in pre-malignant B cells. Utilizing the Eμ-myc mouse model, where Myc is overexpressed specifically in B cells, both basal and stimulated BCR signaling were increased in precancerous B lymphocytes from Eμ-myc mice compared with wild-type littermates. B cells overexpressing Myc displayed constitutively higher levels of activated CD79α, Btk, Plcγ2 and Erk1/2. Notably, Myc-overexpressing B cells maintained elevated BCR signaling despite treatment with ibrutinib, a Bruton's tyrosine kinase inhibitor. Furthermore, PI3K/Akt pathway signaling was also increased in Eμ-myc B cells, and this increase was partially suppressed with ibrutinib. In addition, experiments with Btk-null B cells revealed off-target effects of ibrutinib on BCR signaling. Our data show that in pre-malignant B cells, Myc overexpression is sufficient to activate BCR and PI3K/Akt signaling pathways and further enhances signaling following BCR ligation. Therefore, our results indicate that precancerous B cells have already acquired enhanced survival and growth capabilities before transformation, and that elevated MYC levels confer resistance to pharmacologic inhibitors of BCR signaling, which has significant implications for B-NHL treatment.
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23 MeSH Terms
The Cytokine Response to Lipopolysaccharide Does Not Predict the Host Response to Infection.
Fensterheim BA, Guo Y, Sherwood ER, Bohannon JK
(2017) J Immunol 198: 3264-3273
MeSH Terms: Animals, Cytokines, Disease Models, Animal, Flow Cytometry, Ligands, Lipid A, Lipopolysaccharides, Male, Mice, Mice, Inbred BALB C, Mice, Inbred C57BL, Poly I-C, Pseudomonas Infections, Pseudomonas aeruginosa, Toll-Like Receptors
Show Abstract · Added April 10, 2017
The magnitude of the LPS-elicited cytokine response is commonly used to assess immune function in critically ill patients. A suppressed response, known as endotoxin tolerance, is associated with worse outcomes, yet endotoxin tolerance-inducing TLR4 ligands are known to protect animals from infection. Thus, it remains unknown whether the magnitude of the LPS-elicited cytokine response provides an accurate assessment of antimicrobial immunity. To address this, the ability of diverse TLR ligands to modify the LPS-elicited cytokine response and resistance to infection were assessed. Priming of mice with LPS, monophosphoryl lipid A (MPLA), or poly(I:C) significantly reduced plasma LPS-elicited proinflammatory cytokines, reflecting endotoxin tolerance, whereas CpG-ODN-primed mice showed augmented cytokine production. In contrast, LPS, MPLA, and CpG-ODN, but not poly(I:C), improved the host response to a infection. Mice primed with protective TLR ligands, including CpG-ODN, showed reduced plasma cytokines during infection. The protection imparted by TLR ligands persisted for up to 15 d yet was independent of the adaptive immune system. In bone marrow-derived macrophages, protective TLR ligands induced a persistent metabolic phenotype characterized by elevated glycolysis and oxidative metabolism as well as augmented size, granularity, phagocytosis, and respiratory burst. Sustained augmentation of glycolysis in TLR-primed cells was dependent, in part, on hypoxia-inducible factor 1-α and was essential for increased phagocytosis. In conclusion, the magnitude of LPS-elicited cytokine production is not indicative of antimicrobial immunity after exposure to TLR ligands. Additionally, protective TLR ligands induce sustained augmentation of phagocyte metabolism and antimicrobial function.
Copyright © 2017 by The American Association of Immunologists, Inc.
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15 MeSH Terms
A signalling cascade of IL-33 to IL-13 regulates metaplasia in the mouse stomach.
Petersen CP, Meyer AR, De Salvo C, Choi E, Schlegel C, Petersen A, Engevik AC, Prasad N, Levy SE, Peebles RS, Pizarro TT, Goldenring JR
(2018) Gut 67: 805-817
MeSH Terms: Animals, Flow Cytometry, Gastric Mucosa, Immunohistochemistry, Interleukin-13, Interleukin-33, Macrophages, Metaplasia, Mice, Mice, Inbred C57BL, Mice, Knockout, Parietal Cells, Gastric, Peptides, Real-Time Polymerase Chain Reaction, Receptors, Interleukin, Signal Transduction, Stomach
Show Abstract · Added April 18, 2017
OBJECTIVE - Alternatively activated macrophages (M2) are associated with the progression of spasmolytic polypeptide-expressing metaplasia (SPEM) in the stomach. However, the precise mechanism(s) and critical mediators that induce SPEM are unknown.
DESIGN - To determine candidate genes important in these processes, macrophages from the stomach corpus of mice with SPEM (DMP-777-treated) or advanced SPEM (L635-treated) were isolated and RNA sequenced. Effects on metaplasia development after acute parietal cell loss induced by L635 were evaluated in interleukin (IL)-33, IL-33 receptor (ST2) and IL-13 knockout (KO) mice.
RESULTS - Profiling of metaplasia-associated macrophages in the stomach identified an M2a-polarised macrophage population. Expression of IL-33 was significantly upregulated in macrophages associated with advanced SPEM. L635 induced metaplasia in the stomachs of wild-type mice, but not in the stomachs of IL-33 and ST2 KO mice. While IL-5 and IL-9 were not required for metaplasia induction, IL-13 KO mice did not develop metaplasia in response to L635. Administration of IL-13 to ST2 KO mice re-established the induction of metaplasia following acute parietal cell loss.
CONCLUSIONS - Metaplasia induction and macrophage polarisation after parietal cell loss is coordinated through a cytokine signalling network of IL-33 and IL-13, linking a combined response to injury by both intrinsic mucosal mechanisms and infiltrating M2 macrophages.
Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.
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17 MeSH Terms