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https://www.readbyqxmd.com/read/29036374/gating-mass-cytometry-data-by-deep-learning
#1
Huamin Li, Uri Shaham, Kelly P Stanton, Yi Yao, Ruth R Montgomery, Yuval Kluger
Motivation: Mass cytometry or CyTOF is an emerging technology for high-dimensional multiparameter single cell analysis that overcomes many limitations of fluorescence-based flow cytometry. New methods for analyzing CyTOF data attempt to improve automation, scalability, performance and interpretation of data generated in large studies. Assigning individual cells into discrete groups of cell types (gating) involves time-consuming sequential manual steps, untenable for larger studies. Results: We introduce DeepCyTOF, a standardization approach for gating, based on deep learning techniques...
July 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29018052/intratumoral-hpv16-specific-t-cells-constitute-a-type-1-oriented-tumor-microenvironment-to-improve-survival-in-hpv16-driven-oropharyngeal-cancer
#2
Marij J P Welters, Wenbo Ma, Saskia J Santegoets, Renske Goedemans, Ilina Ehsan, Katja S Jordanova, Vanessa J van Ham, Vincent van Unen, Frits Koning, Sylvia I van Egmond, Pornpimol Charoentong, Zlatko Trajanoski, Lilly-Ann van der Velden, Sjoerd H van der Burg
PURPOSE: Human papilloma virus (HPV)-associated oropharyngeal squamous cell cancer (OPSCC) has a much better prognosis than HPV-negative OPSCC and this is linked to dense tumor immune infiltration. Since the viral antigens may trigger potent immunity, we studied the relationship between the presence of intratumoral HPV-specific T-cell responses, the immune contexture in tumor microenvironment and clinical outcome. EXPERIMENTAL DESIGN: To this purpose an in-depth analysis of tumor-infiltrating immune cells in a prospective cohort of 97 HPV16-positive and -negative OPSCC patients was performed using functional T-cell assays, mass cytometry (CyTOF), flow cytometry and fluorescent immunostaining of tumor tissues...
October 10, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28994825/clustergrammer-a-web-based-heatmap-visualization-and-analysis-tool-for-high-dimensional-biological-data
#3
Nicolas F Fernandez, Gregory W Gundersen, Adeeb Rahman, Mark L Grimes, Klarisa Rikova, Peter Hornbeck, Avi Ma'ayan
Most tools developed to visualize hierarchically clustered heatmaps generate static images. Clustergrammer is a web-based visualization tool with interactive features such as: zooming, panning, filtering, reordering, sharing, performing enrichment analysis, and providing dynamic gene annotations. Clustergrammer can be used to generate shareable interactive visualizations by uploading a data table to a web-site, or by embedding Clustergrammer in Jupyter Notebooks. The Clustergrammer core libraries can also be used as a toolkit by developers to generate visualizations within their own applications...
October 10, 2017: Scientific Data
https://www.readbyqxmd.com/read/28977875/expression-of-lag-3-defines-exhaustion-of-intratumoral-pd-1-t-cells-and-correlates-with-poor-outcome-in-follicular-lymphoma
#4
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...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28967988/cytof-measurement-of-immunocompetence-across-major-immune-cell-types
#5
Priyanka B Subrahmanyam, Holden T Maecker
The central role of the immune system is becoming appreciated in a wide variety of diseases. Cancer immunotherapy is one area that has yielded much recent success, although not all patients benefit equally. At the same time, recent studies have highlighted the heterogeneity of the human immune system. Despite this heterogeneity, we do not routinely measure immune competence in clinical practice, and there are no consensus assays of healthy immune function. Using mass cytometry (CyTOF), we can simultaneously detect ∼40 markers to identify various cell subsets and determine their function by the expression of cytokines, cytotoxicity, and activation markers...
October 2, 2017: Current Protocols in Cytometry
https://www.readbyqxmd.com/read/28951494/sting-associated-vasculopathy-develops-independently-of-irf3-in-mice
#6
James D Warner, Ricardo A Irizarry-Caro, Brock G Bennion, Teresa L Ai, Amber M Smith, Cathrine A Miner, Tomomi Sakai, Vijay K Gonugunta, Jianjun Wu, Derek J Platt, Nan Yan, Jonathan J Miner
Patients with stimulator of interferon genes (STING)-associated vasculopathy with onset in infancy (SAVI) develop systemic inflammation characterized by vasculopathy, interstitial lung disease, ulcerative skin lesions, and premature death. Autosomal dominant mutations in STING are thought to trigger activation of IRF3 and subsequent up-regulation of interferon (IFN)-stimulated genes (ISGs) in patients with SAVI. We generated heterozygous STING N153S knock-in mice as a model of SAVI. These mice spontaneously developed inflammation within the lung, hypercytokinemia, T cell cytopenia, skin ulcerations, and premature death...
September 26, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28882613/average-overlap-frequency-a-simple-metric-to-evaluate-staining-quality-and-community-identification-in-high-dimensional-mass-cytometry-experiments
#7
El-Ad David Amir, Xinzheng V Guo, Oksana Mayovska, Adeeb H Rahman
High dimensional cytometry now allows measurement of over 50 parameters in a single sample, and is typically visualized using sophisticated dimensionality-reducing methods and analyzed with automated clustering algorithms. While these tools facilitate the identification and presentation of key findings, it remains challenging to effectively monitor and report the staining quality of individual markers. We present the Average Overlap Frequency (AOF), a simple and efficient metric to evaluate and quantify the robustness of staining and clustering quality in high-dimensional data...
September 4, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28783660/tumor-immune-landscape-paintings-from-the-cytof-period
#8
Andrew Lichtman
Early lung cancer patients harbor cancer-permissive innate immunity in the tumor microenvironment.
June 2, 2017: Science Immunology
https://www.readbyqxmd.com/read/28774561/personalized-vaccinology-a-review
#9
G A Poland, I G Ovsyannikova, R B Kennedy
At the current time, the field of vaccinology remains empirical in many respects. Vaccine development, vaccine immunogenicity, and vaccine efficacy have, for the most part, historically been driven by an empiric "isolate-inactivate-inject" paradigm. In turn, a population-level public health paradigm of "the same dose for everyone for every disease" model has been the normative thinking in regard to prevention of vaccine-preventable infectious diseases. In addition, up until recently, no vaccines had been designed specifically to overcome the immunosenescence of aging, consistent with a post-WWII mentality of developing vaccines and vaccine programs for children...
July 31, 2017: Vaccine
https://www.readbyqxmd.com/read/28769897/mass-cytometry-for-detection-of-silver-at-the-bacterial-single-cell-level
#10
Yuting Guo, Sabine Baumgart, Hans-Joachim Stärk, Hauke Harms, Susann Müller
Background: Mass cytometry (Cytometry by Time of Flight, CyTOF) allows single-cell characterization on the basis of specific metal-based cell markers. In addition, other metals in the mass range such as silver can be detected per cell. Bacteria are known to be sensible to silver and a protocol was developed to measure both the number of affected cells per population and the quantities of silver per cell. Methods: For mass cytometry ruthenium red was used as a marker for all cells of a population while parallel application of cisplatin discriminated live from dead cells...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28760671/application-of-phospho-cytof-to-characterize-immune-activation-in-patients-with-sickle-cell-disease-in-an-ex-vivo-model-of-thrombosis
#11
Jeffrey Glassberg, Adeeb H Rahman, Mohammad Zafar, Caroline Cromwell, Alexa Punzalan, Juan Jose Badimon, Louis Aledort
Sickle cell disease (SCD) is a genetic disease caused by mutations in the beta globin gene, and inflammation plays a key role in driving many aspects of disease pathology. Early immune activation is believed to be associated with hemodynamic stresses and thrombus formation as cells traffic through blood vessels. We applied an extracorporeal perfusion system to model these effects ex vivo, and combined this with a phospho-CyTOF workflow to comprehensively evaluate single-cell signatures of early activation across all major circulating immune subsets...
July 28, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28758994/high-dimensional-single-cell-characterization-of-the-brain-s-immune-compartment
#12
Ben Korin, Tamar L Ben-Shaanan, Maya Schiller, Tania Dubovik, Hilla Azulay-Debby, Nadia T Boshnak, Tamar Koren, Asya Rolls
The brain and its borders create a highly dynamic microenvironment populated with immune cells. Yet characterization of immune cells within the naive brain compartment remains limited. In this study, we used CyTOF mass cytometry to characterize the immune populations of the naive mouse brain using 44 cell surface markers. By comparing immune cell composition and cell profiles between the brain compartment and blood, we were able to characterize previously undescribed cell subsets of CD8 T cells, B cells, NK cells and dendritic cells in the naive brain...
September 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28747454/by-cytof-heterogeneity-of-human-monocytes
#13
EDITORIAL
P'ng Loke, Timothy B Niewold
No abstract text is available yet for this article.
August 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28746881/mass-cytometric-analysis-of-hiv-entry-replication-and-remodeling-in-tissue-cd4-t-cells
#14
Marielle Cavrois, Trambak Banerjee, Gourab Mukherjee, Nandhini Raman, Rajaa Hussien, Brandon Aguilar Rodriguez, Joshua Vasquez, Matthew H Spitzer, Nicole H Lazarus, Jennifer J Jones, Christina Ochsenbauer, Joseph M McCune, Eugene C Butcher, Ann M Arvin, Nandini Sen, Warner C Greene, Nadia R Roan
To characterize susceptibility to HIV infection, we phenotyped infected tonsillar T cells by single-cell mass cytometry and created comprehensive maps to identify which subsets of CD4+ T cells support HIV fusion and productive infection. By comparing HIV-fused and HIV-infected cells through dimensionality reduction, clustering, and statistical approaches to account for viral perturbations, we identified a subset of memory CD4+ T cells that support HIV entry but not viral gene expression. These cells express high levels of CD127, the IL-7 receptor, and are believed to be long-lived lymphocytes...
July 25, 2017: Cell Reports
https://www.readbyqxmd.com/read/28735481/single-cell-mass-cytometry-of-acute-myeloid-leukemia-and-leukemia-stem-progenitor-cells
#15
Zhihong Zeng, Marina Konopleva, Michael Andreeff
Mass cytometry time-of-flight (CyTOF) empowers us to understand acute myeloid leukemia (AML) biology at the single-cell level. This technology, combined with advanced data-analysis methods, enables identification and characterization of the rare AML stem/progenitor cells that play key roles in drug resistance and AML relapse. Here we provide a protocol for AML sample preparation for CyTOF and keynotes emphasizing critical steps in and troubleshooting strategies for this procedure.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28734132/high-dimensional-single-cell-mapping-of-cerium-distribution-in-the-lung-immune-microenvironment-of-an-active-smoker
#16
Adeeb H Rahman, Yonit Lavin, Soma Kobayashi, Andrew Leader, Miriam Merad
BACKGROUND: Mass cytometry leverages inductively coupled mass spectrometry to perform high dimensional single cell analyses using antibodies tagged with rare earth isotopes that are considered to be largely absent in biological samples. We have recently noted an unusual exception to this rule while analyzing tissue samples from patients undergoing surgical resection for early stage lung cancer, and here we present a detailed cytometric characterization of cerium in a clinical patient sample...
July 22, 2017: Cytometry. Part B, Clinical Cytometry
https://www.readbyqxmd.com/read/28730492/analysis-of-signaling-networks-at-the-single-cell-level-using-mass-cytometry
#17
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
#18
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
#19
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
#20
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
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