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https://www.readbyqxmd.com/read/29444438/commonly-occurring-cell-subsets-in-high-grade-serous-ovarian-tumors-identified-by-single-cell-mass-cytometry
#1
Veronica D Gonzalez, Nikolay Samusik, Tiffany J Chen, Erica S Savig, Nima Aghaeepour, David A Quigley, Ying-Wen Huang, Valeria Giangarrà, Alexander D Borowsky, Neil E Hubbard, Shih-Yu Chen, Guojun Han, Alan Ashworth, Thomas J Kipps, Jonathan S Berek, Garry P Nolan, Wendy J Fantl
We have performed an in-depth single-cell phenotypic characterization of high-grade serous ovarian cancer (HGSOC) by multiparametric mass cytometry (CyTOF). Using a CyTOF antibody panel to interrogate features of HGSOC biology, combined with unsupervised computational analysis, we identified noteworthy cell types co-occurring across the tumors. In addition to a dominant cell subset, each tumor harbored rarer cell phenotypes. One such group co-expressed E-cadherin and vimentin (EV), suggesting their potential role in epithelial mesenchymal transition, which was substantiated by pairwise correlation analyses...
February 13, 2018: Cell Reports
https://www.readbyqxmd.com/read/29370157/mass-cytometry-analysis-of-immune-cells-in-the-brain
#2
Ben Korin, Tania Dubovik, Asya Rolls
Immune cells comprise a diverse and dynamic cell population that is responsible for a broad range of immunological activities. They act in concert with other immune and nonimmune cells via cytokine-mediated communication and direct cell-cell interactions. Understanding the complex immune network requires a broad characterization of its individual cellular components. This is especially relevant for the brain compartment, which is an active immunological site, composed of resident and infiltrating immune cells that affect brain development, tissue homeostasis and neuronal activity...
February 2018: Nature Protocols
https://www.readbyqxmd.com/read/29305968/alternatives-to-current-flow-cytometry-data-analysis-for-clinical-and-research-studies
#3
REVIEW
Carmen Gondhalekar, Bartek Rajwa, Valery Patsekin, Kathy Ragheb, Jennifer Sturgis, J Paul Robinson
Flow cytometry has well-established methods for data analysis based on traditional data collection techniques. These techniques typically involved manual insertion of tube samples into an instrument that, historically, could only measure 1-3 colors. The field has since evolved to incorporate new technologies for faster and highly automated sample preparation and data collection. For example, the use of microwell plates on benchtop instruments is now a standard on virtually every new instrument, and so users can easily accumulate multiple data sets quickly...
January 3, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29281633/scalable-multi-sample-single-cell-data-analysis-by-partition-assisted-clustering-and-multiple-alignments-of-networks
#4
Ye Henry Li, Dangna Li, Nikolay Samusik, Xiaowei Wang, Leying Guan, Garry P Nolan, Wing Hung Wong
Mass cytometry (CyTOF) has greatly expanded the capability of cytometry. It is now easy to generate multiple CyTOF samples in a single study, with each sample containing single-cell measurement on 50 markers for more than hundreds of thousands of cells. Current methods do not adequately address the issues concerning combining multiple samples for subpopulation discovery, and these issues can be quickly and dramatically amplified with increasing number of samples. To overcome this limitation, we developed Partition-Assisted Clustering and Multiple Alignments of Networks (PAC-MAN) for the fast automatic identification of cell populations in CyTOF data closely matching that of expert manual-discovery, and for alignments between subpopulations across samples to define dataset-level cellular states...
December 27, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29205767/atomic-mass-tag-of-bismuth-209-for-increasing-the-immunoassay-multiplexing-capacity-of-mass-cytometry
#5
Guojun Han, Shih-Yu Chen, Veronica D Gonzalez, Eli R Zunder, Wendy J Fantl, Garry P Nolan
Mass cytometry (or CyTOF) is an atomic mass spectrometry-based single-cell immunoassay technology, which has provided an increasingly systematic and sophisticated view in basic biological and clinical studies. Using elemental reporters composed of stable heavy metal isotopes, more than 50 cellular parameters are measured simultaneously. However, this current multiplexing does not meet the theoretical capability of CyTOF instrumentation with 135 detectable channels, primarily due to the limitation of available chemistries for conjugating elemental mass tags to affinity reagents...
December 4, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/29175391/integrated-functional-and-mass-spectrometry-based-flow-cytometric-phenotyping-to-describe-the-immune-microenvironment-in-acute-myeloid-leukemia
#6
Adam J Lamble, Matthew Dietz, Ted Laderas, Shannon McWeeney, Evan F Lind
A hallmark of the development of cancer is its ability to avoid detection and elimination by the immune system. There are many identified mechanisms of this immune evasion that can be measured both phenotypically and functionally. Functional studies directly show the ability of the tumor microenvironment to suppress immune responses, typically measured as lymphocyte proliferation, cytokine production or killing ability. While a direct measurement of function is ideal, these assays require ex vivo activation which may not accurately mimic in vivo conditions...
November 23, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/29174717/comparison-of-cytof-assays-across-sites-results-of-a-six-center-pilot-study
#7
Michael D Leipold, Gerlinde Obermoser, Craig Fenwick, Katja Kleinstuber, Narges Rashidi, John P McNevin, Allison N Nau, Lisa E Wagar, Virginie Rozot, Mark M Davis, Stephen DeRosa, Giuseppe Pantaleo, Thomas J Scriba, Bruce D Walker, Lars R Olsen, Holden T Maecker
For more than five years, high-dimensional mass cytometry has been employed to study immunology. However, these studies have typically been performed in one laboratory on one or few instruments. We present the results of a six-center study using healthy control human peripheral blood mononuclear cells (PBMCs) and commercially available reagents to test the intra-site and inter-site variation of mass cytometers and operators. We used prestained controls generated by the primary center as a reference to compare against samples stained at each individual center...
November 22, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/29156825/targeting-p-selectin-blocks-neuroblastoma-growth
#8
Riitta Nolo, Shelley Herbrich, Arvind Rao, Patrick Zweidler-McKay, Sankaranarayanan Kannan, Vidya Gopalakrishnan
Selectins and their ligands have been implicated in tumor growth and progression in carcinomas, but their role in neuroblastoma has not been systematically examined. In the current study we evaluated L-, P- and E-selectin binding to neuroblastoma cells and the expression of some of their known ligands, namely CD44, CD24 and P-selectin glycoprotein ligand-1 (PSGL-1). Genetic loss of PSGL-1 or CD24 and pharmacological inhibition of P-selectin reduced P-selectin binding to neuroblastoma cells in vitro. Targeting P-selectin using specific antibodies promoted a significant reduction in the growth of neuroblastoma tumors in vivo...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29128078/applications-of-mass-cytometry-in-clinical-medicine-the-promise-and-perils-of-clinical-cytof
#9
REVIEW
Gregory K Behbehani
Mass cytometry is a novel technology similar to flow cytometry in which antibodies are tagged with heavy metal molecules rather than fluorophores and then detected with time-of-flight mass spectrometry. This enables measurement of up to 50 simultaneous parameters with no autofluorescent background and little or no spillover or required compensation. Mass cytometry has tremendous potential for the analysis of highly complex clinical samples for the diagnosis and monitoring of malignant and autoimmune disorders...
December 2017: Clinics in Laboratory Medicine
https://www.readbyqxmd.com/read/29093262/human-regulatory-t-cells-undergo-self-inflicted-damage-via-granzyme-pathways-upon-activation
#10
Esilida Sula Karreci, Siawosh K Eskandari, Farokh Dotiwala, Sujit K Routray, Ahmed T Kurdi, Jean Pierre Assaker, Pavlo Luckyanchykov, Albana B Mihali, Omar Maarouf, Thiago J Borges, Abdullah Alkhudhayri, Kruti R Patel, Amr Radwan, Irene Ghobrial, Martina McGrath, Anil Chandraker, Leonardo V Riella, Wassim Elyaman, Reza Abdi, Judy Lieberman, Jamil Azzi
Tregs hold great promise as a cellular therapy for multiple immunologically mediated diseases, given their ability to control immune responses. The success of such strategies depends on the expansion of healthy, suppressive Tregs ex vivo and in vivo following the transfer. In clinical studies, levels of transferred Tregs decline sharply in the blood within a few days of the transfer. Tregs have a high rate of apoptosis. Here, we describe a new mechanism of Treg self-inflicted damage. We show that granzymes A and -B (GrA and GrB), which are highly upregulated in human Tregs upon stimulation, leak out of cytotoxic granules to induce cleavage of cytoplasmic and nuclear substrates, precipitating apoptosis in target cells...
November 2, 2017: JCI Insight
https://www.readbyqxmd.com/read/29071674/mass-cytometry-assays-for-antigen-specific-t-cells-using-cytof
#11
Dongxia Lin, Holden T Maecker
T Cells specific for a single antigen tend to be rare, even after expansion of memory cells. They are commonly detected by in vitro stimulation with peptides or protein, followed by staining for intracellular cytokines. In this protocol, we use CyTOF(®) mass cytometry to collect single-cell data on a large number of cytokines/chemokines, as well as cell-surface proteins that characterize T cells and other immune cells. We also include a method for magnetic bead enrichment of antigen-stimulated T cells, based on their expression of CD154 and CD69...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29036374/gating-mass-cytometry-data-by-deep-learning
#12
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...
November 1, 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
#13
Marij J P Welters, Wenbo Ma, Saskia J Santegoets, Renske Goedemans, Ilina Ehsan, Ekaterina 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
#14
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
#15
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
#16
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
#17
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...
November 6, 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
#18
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
#19
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
#20
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
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