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https://www.readbyqxmd.com/read/28730492/analysis-of-signaling-networks-at-the-single-cell-level-using-mass-cytometry
#1
Shovik Bandyopadhyay, Daniel A C Fisher, Olga Malkova, Stephen T Oh
Mass cytometry is a powerful technology that enables the measurement of >40 parameters at the single-cell level. The inherent spectral limitations of fluorescent flow cytometry are circumvented by the use of antibodies conjugated to metal isotope reporters, which are measured quantitatively using a CyTOF mass cytometer. The high dimensionality of mass cytometry is particularly useful for the analysis of cell signaling networks in complex biological samples. We describe here methods for cell preparation, antibody staining, data acquisition, and analysis of multidimensional data from a mass cytometry experiment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28679950/high-dimensional-cytof-analysis-of-dengue-virus-infected-human-dcs-reveals-distinct-viral-signatures
#2
Rebecca E Hamlin, Adeeb Rahman, Theodore R Pak, Kevin Maringer, Ignacio Mena, Dabeiba Bernal-Rubio, Uma Potla, Ana M Maestre, Anthony C Fredericks, El-Ad D Amir, Andrew Kasarskis, Irene Ramos, Miriam Merad, Ana Fernandez-Sesma
Dengue virus (DENV) is the most prevalent mosquito-borne virus causing human disease. Of the 4 DENV serotypes, epidemiological data suggest that DENV-2 secondary infections are associated with more severe disease than DENV-4 infections. Mass cytometry by time-of-flight (CyTOF) was used to dissect immune changes induced by DENV-2 and DENV-4 in human DCs, the initial targets of primary infections that likely affect infection outcomes. Strikingly, DENV-4 replication peaked earlier and promoted stronger innate immune responses, with increased expression of DC activation and migration markers and increased cytokine production, compared with DENV-2...
July 6, 2017: JCI Insight
https://www.readbyqxmd.com/read/28678421/cytof-mass-cytometry-for-click-proliferation-assays
#3
Vinko Tosevski, Egor Ulashchik, Andrea Trovato, Paolo Cappella
Novel cell analyzers, including polychromatic flow cytometers and isotopical cytometry by time of flight (CyTOF) mass cytometers, enable simultaneous measurement of virtually bondless characteristics at the single-cell level. BrdU assays for quantifying cellular proliferation are common but have several limitations, including the need for a DNA denaturation step and inability to simultaneously resolve multiple parameters and phenotypic complexity. Click chemistry reactions have become popular in the past decade, as they can resolve these issues...
July 5, 2017: Current Protocols in Cytometry
https://www.readbyqxmd.com/read/28663787/cytof-workflow-differential-discovery-in-high-throughput-high-dimensional-cytometry-datasets
#4
Malgorzata Nowicka, Carsten Krieg, Lukas M Weber, Felix J Hartmann, Silvia Guglietta, Burkhard Becher, Mitchell P Levesque, Mark D Robinson
High dimensional mass and flow cytometry (HDCyto) experiments have become a method of choice for high throughput interrogation and characterization of cell populations.Here, we present an R-based pipeline for differential analyses of HDCyto data, largely based on Bioconductor packages. We computationally define cell populations using FlowSOM clustering, and facilitate an optional but reproducible strategy for manual merging of algorithm-generated clusters. Our workflow offers different analysis paths, including association of cell type abundance with a phenotype or changes in signaling markers within specific subpopulations, or differential analyses of aggregated signals...
2017: F1000Research
https://www.readbyqxmd.com/read/28662063/rna-seq-and-cytof-immuno-profiling-of-regenerating-lacrimal-glands-identifies-a-novel-subset-of-cells-expressing-muscle-related-proteins
#5
Dillon Hawley, Jian Ding, Suharika Thotakura, Scott Haskett, Hema Aluri, Claire Kublin, Audrey Michel, Lisa Clapisson, Michael Mingueneau, Driss Zoukhri
The purpose of the present studies was to use CyTOF and RNA-Seq technologies to identify cells and genes involved in lacrimal gland repair that could be targeted to treat diseases of lacrimal gland dysfunction. Lacrimal glands of female BALB/c mice were experimentally injured by intra-glandular injection of interleukin 1 alpha (IL-1α). The lacrimal glands were harvested at various time points following injury (1 to 14 days) and used to either prepare single cell suspensions for CyTOF immuno-phenotyping analyses or to extract RNA for gene expression studies using RNA-Seq...
2017: PloS One
https://www.readbyqxmd.com/read/28615538/expression-of-lag-3-defines-exhaustion-of-intratumoral-pd-1-t-cells-and-correlates-with-poor-outcome-in-follicular-lymphoma
#6
Zhi-Zhang Yang, Hyo Jin Kim, Jose C Villasboas, Ya-Ping Chen, Tammy Price-Troska, Shahrzad Jalali, Mara Wilson, Anne J Novak, Stephen M Ansell
Exhausted T-cells in follicular lymphoma (FL) typically express PD-1, but expression of PD-1 is not limited to exhausted cells. Although expected to be functionally suppressed, we found that the population of intratumoral PD-1+ T cells were predominantly responsible for production of cytokines and granules. This surprising finding prompted us to explore the involvement of LAG-3 to specifically identify functionally exhausted T cells. We found that LAG-3 was expressed on a subset of intratumoral T cells from FL and LAG-3+ T cells almost exclusively came from PD-1+ population...
May 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28597073/beta-cell-heterogeneity-an-evolving-concept
#7
REVIEW
Dana Avrahami, Agnes Klochendler, Yuval Dor, Benjamin Glaser
Beta cells are primarily defined by their ability to produce insulin and secrete it in response to appropriate stimuli. It has been known for some time, however, that beta cells are not functionally identical to each other and that the rates of insulin synthesis and release differ from cell to cell, although the functional significance of this variability remains unclear. Recent studies have used heterogeneous gene expression to isolate and evaluate different subpopulations of beta cells and to demonstrate alterations in these subpopulations in diabetes...
June 8, 2017: Diabetologia
https://www.readbyqxmd.com/read/28500913/myb-fusions-and-cd-markers-as-tools-for-authentication-and-purification-of-cancer-stem-cells-from-salivary-adenoid-cystic-carcinoma
#8
Alex Panaccione, Yi Zhang, Molly Ryan, Christopher A Moskaluk, Karen S Anderson, Wendell G Yarbrough, Sergey V Ivanov
Cancer stem cells (CSC) are considered the major cause of aggressive tumor behavior, recurrence, metastases, and resistance to radiation, making them an attractive therapeutic target. However, isolation of CSC from tumor tissue and their characterization are challenging due to uncertainty about their molecular markers and conditions for their propagation. Adenoid cystic carcinoma (ACC), which arises predominantly in the salivary glands, is a slow-growing but relentless tumor that frequently invades nerves and metastasizes...
May 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28498568/reconstitution-of-immune-cell-populations-in-multiple-sclerosis-patients-after-autologous-stem-cell-transplantation
#9
REVIEW
F G Karnell, D Lin, S Motley, T Duhen, N Lim, D J Campbell, L A Turka, H T Maecker, K M Harris
Multiple sclerosis is an inflammatory T cell-mediated autoimmune disease. In a Phase II clinical trial, high-dose immunosuppressive therapy combined with autologous CD34(+) haematopoietic stem cell transplant resulted in 69·2% of subjects remaining disease-free without evidence of relapse, loss of neurological function or new magnetic resonance imaging (MRI) lesions to year 5 post-treatment. A combination of CyTOF mass cytometry and multi-parameter flow cytometry was used to explore the reconstitution kinetics of immune cell subsets in the periphery post-haematopoietic cell transplant (HSCT) and the impact of treatment on the phenotype of circulating T cells in this study population...
May 12, 2017: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/28497484/cd44-variant-isoform-9-emerges-in-response-to-injury-and-contributes-to-the-regeneration-of-the-gastric-epithelium
#10
Nina Bertaux-Skeirik, Mark Wunderlich, Emma Teal, Jayati Chakrabarti, Jacek Biesiada, Maxime Mahe, Nambirajan Sundaram, Joel Gabre, Jennifer Hawkins, Jian Gao, Amy C Engevik, Li Yang, Jiang Wang, James R Goldenring, Joseph E Qualls, Mario Medvedovic, Michael A Helmrath, Tayyab Diwan, James C Mulloy, Yana Zavros
Cluster-of-differentiation gene 44, in particular CD44 variant isoform 9 (CD44v9), emerges during regeneration of the gastric epithelium in response to injury. In particular, CD44v9 is expressed within Spasmolytic Polypeptide/TFF2-Expressing Metaplasia (SPEM) glands during gastric repair, but the function is unknown. Here we tested the hypothesis that age dependent expression of CD44v9 marks a regenerative cell lineage responsive to infiltrating macrophages during regeneration of the gastric epithelium. Acetic acid injury was induced in CD44-deficient (CD44KO) and C57BL/6 (BL6) mice...
May 12, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28473638/mapping-the-human-dc-lineage-through-the-integration-of-high-dimensional-techniques
#11
Peter See, Charles-Antoine Dutertre, Jinmiao Chen, Patrick Günther, Naomi McGovern, Sergio Erdal Irac, Merry Gunawan, Marc Beyer, Kristian Händler, Kaibo Duan, Hermi Rizal Bin Sumatoh, Nicolas Ruffin, Mabel Jouve, Ester Gea-Mallorquí, Raoul C M Hennekam, Tony Lim, Chan Chung Yip, Ming Wen, Benoit Malleret, Ivy Low, Nurhidaya Binte Shadan, Charlene Foong Shu Fen, Alicia Tay, Josephine Lum, Francesca Zolezzi, Anis Larbi, Michael Poidinger, Jerry K Y Chan, Qingfeng Chen, Laurent Renia, Muzlifah Haniffa, Philippe Benaroch, Andreas Schlitzer, Joachim L Schultze, Evan W Newell, Florent Ginhoux
Dendritic cells (DC) are professional antigen-presenting cells that orchestrate immune responses. The human DC population comprises two main functionally specialized lineages, whose origins and differentiation pathways remain incompletely defined. Here, we combine two high-dimensional technologies-single-cell mRNA sequencing and cytometry by time-of-flight (CyTOF), to identify human blood CD123(+)CD33(+)CD45RA(+) DC precursors (pre-DC). Pre-DC share surface markers with plasmacytoid DC (pDC) but have distinct functional properties that were previously attributed to pDC...
May 4, 2017: Science
https://www.readbyqxmd.com/read/28414312/high-resolution-myogenic-lineage-mapping-by-single-cell-mass-cytometry
#12
Ermelinda Porpiglia, Nikolay Samusik, Andrew Tri Van Ho, Benjamin D Cosgrove, Thach Mai, Kara L Davis, Astraea Jager, Garry P Nolan, Sean C Bendall, Wendy J Fantl, Helen M Blau
Muscle regeneration is a dynamic process during which cell state and identity change over time. A major roadblock has been a lack of tools to resolve a myogenic progression in vivo. Here we capitalize on a transformative technology, single-cell mass cytometry (CyTOF), to identify in vivo skeletal muscle stem cell and previously unrecognized progenitor populations that precede differentiation. We discovered two cell surface markers, CD9 and CD104, whose combined expression enabled in vivo identification and prospective isolation of stem and progenitor cells...
May 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28407030/intratumoral-heterogeneity-pathways-to-treatment-resistance-and-relapse-in-human-glioblastoma
#13
M A Qazi, P Vora, C Venugopal, S S Sidhu, J Moffat, C Swanton, S K Singh
Intratumoral heterogeneity (ITH) has increasingly being described for multiple cancers as the root cause of therapy resistance. Recent studies have started to explore the scope of ITH in glioblastoma (GBM), a highly aggressive and fatal form of brain tumor, to explain its inevitable therapy resistance and disease relapse. In this review, we detail the emerging data that explores the extensive genetic, cellular and functional ITH present in GBM. We discuss current experimental models of human GBM recurrence and suggest harnessing new technologies (CRISPR-Cas9 screening, CyTOF, cellular barcoding, single cell analysis) to delineate GBM ITH and identify treatment-refractory cell populations, thus opening new therapeutic windows...
April 12, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28400539/mass-cytometry-deep-phenotyping-of-human-mononuclear-phagocytes-and-myeloid-derived-suppressor-cells-from-human-blood-and-bone-marrow
#14
Mikael Roussel, P Brent Ferrell, Allison R Greenplate, Faustine Lhomme, Simon Le Gallou, Kirsten E Diggins, Douglas B Johnson, Jonathan M Irish
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...
April 11, 2017: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/28340685/research-techniques-made-simple-experimental-methodology-for-single-cell-mass-cytometry
#15
Tiago R Matos, Hongye Liu, Jerome Ritz
Growing recognition of the complexity of interactions within cellular systems has fueled the development of mass cytometry. The precision of time-of-flight mass spectrometry combined with the labeling of specific ligands with mass tags enables detection and quantification of more than 40 markers at a single-cell resolution. The 135 available detection channels allow simultaneous study of additional characteristics of complex biological systems across millions of cells. Cutting-edge mass cytometry by time-of-flight (CyTOF) can profoundly affect our knowledge of cell population heterogeneity and hierarchy, cellular state, multiplexed signaling pathways, proteolysis products, and mRNA transcripts...
April 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28321124/combined-inhibition-of-%C3%AE-catenin-and-bcr-abl-synergistically-targets-tyrosine-kinase-inhibitor-resistant-blast-crisis-chronic-myeloid-leukemia-blasts-and-progenitors-in-vitro-and-in-vivo
#16
H Zhou, P Y Mak, H Mu, D H Mak, Z Zeng, J Cortes, Q Liu, M Andreeff, B Z Carter
Tyrosine kinase inhibitor (TKI) resistance and progression to blast crisis (BC), both related to persistent β-catenin activation, remain formidable challenges for chronic myeloid leukemia (CML). We observed overexpression of β-catenin in BC-CML stem/progenitor cells, particularly in granulocyte-macrophage progenitors, and highest among a novel CD34(+)CD38(+)CD123(hi)Tim-3(hi) subset as determined by CyTOF analysis. Co-culture with mesenchymal stromal cells (MSCs) induced the expression of β-catenin and its target CD44 in CML cells...
April 18, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28268852/distance-metric-learning-using-random-forest-for-cytometry-data
#17
M Baran Pouyan, J Birjandtalab, M Nourani
Visualization and clustering of single-cell mass cytometry (CyTOF) data are analytic techniques to identify different cell types. Most of such techniques, such as Euclidean norm, lose their effectiveness when the data dimension increases due to the curse of dimensionality. In this paper, we propose a new cell distance (called CytoRFD) that works based on Random Forest (RF) concept. The experimental results show that the proposed distance can achieve a much higher quality and effectiveness in large data analysis than traditional metrics specially for CyTOF data...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227050/distance-metric-learning-using-random-forest-for-cytometry-data
#18
M Baran Pouyan, J Birjandtalab, M Nourani, M Baran Pouyan, J Birjandtalab, M Nourani, M Baran Pouyan, J Birjandtalab, M Nourani
Visualization and clustering of single-cell mass cytometry (CyTOF) data are analytic techniques to identify different cell types. Most of such techniques, such as Euclidean norm, lose their effectiveness when the data dimension increases due to the curse of dimensionality. In this paper, we propose a new cell distance (called CytoRFD) that works based on Random Forest (RF) concept. The experimental results show that the proposed distance can achieve a much higher quality and effectiveness in large data analysis than traditional metrics specially for CyTOF data...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28198832/cytof-analysis-of-anti-tumor-responses
#19
Laurie A Dempsey
No abstract text is available yet for this article.
February 15, 2017: Nature Immunology
https://www.readbyqxmd.com/read/28192147/systemic-innate-immune-activation-in-food-protein-induced-enterocolitis-syndrome
#20
Ritobrata Goswami, Ana Belen Blazquez, Roman Kosoy, Adeeb Rahman, Anna Nowak-Węgrzyn, M Cecilia Berin
BACKGROUND: Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated food allergy of infancy whose pathophysiology is poorly understood. OBJECTIVES: We set out to identify and phenotype allergen-responsive cells in peripheral blood of a cohort of subjects undergoing supervised food challenge for FPIES. METHODS: We profiled antigen-responsive cells in PBMCs by flow cytometry, and examined cells in whole blood obtained before and after challenge by CyTOF mass cytometry and RNAseq...
June 2017: Journal of Allergy and Clinical Immunology
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