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https://www.readbyqxmd.com/read/28414312/high-resolution-myogenic-lineage-mapping-by-single-cell-mass-cytometry
#1
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...
April 17, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28407030/intratumoral-heterogeneity-pathways-to-treatment-resistance-and-relapse-in-human-glioblastoma
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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...
February 10, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28167507/parp-inhibitor-upregulates-pd-l1-expression-and-enhances-cancer-associated-immunosuppression
#10
Shiping Jiao, Weiya Xia, Hirohito Yamaguchi, Yongkun Wei, Mei-Kuang Chen, Jung-Mao Hsu, Jennifer L Hsu, Wen-Hsuan Yu, Yi Du, Heng-Huan Lee, Chia-Wei Li, Chao-Kai Chou, Seung-Oe Lim, Shih-Shin Chang, Jennifer K Litton, Banu Arun, Gabriel N Hortobagyi, Mien-Chie Hung
PURPOSE: To explore whether a crosstalk exists between PARP inhibition and PD-L1/ PD-1 immune checkpoint axis, and determine if blockade of PD-L1/ PD-1 potentiates PARP inhibitor (PARPi) in tumor suppression. EXPERIMENTAL DESIGN: Breast cancer cell lines, xenograft tumors and syngeneic tumors treated with PARPi were assessed for PD-L1 expression by immunoblotting, immunohistochemistry and FACS analyses. The phospho-kinase antibody array screen was used to explore the underlying mechanism of PARPi-induced PD-L1 upregulation...
February 6, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28148223/effect-of-cryopreservation-on-delineation-of-immune-cell-subpopulations-in-tumor-specimens-as-determinated-by-multiparametric-single-cell-mass-cytometry-analysis
#11
Elma Kadić, Raymond J Moniz, Ying Huo, An Chi, Ilona Kariv
BACKGROUND: Comprehensive understanding of cellular immune subsets involved in regulation of tumor progression is central to the development of cancer immunotherapies. Single cell immunophenotyping has historically been accomplished by flow cytometry (FC) analysis, enabling the analysis of up to 18 markers. Recent advancements in mass cytometry (MC) have facilitated detection of over 50 markers, utilizing high resolving power of mass spectrometry (MS). This study examined an analytical and operational feasibility of MC for an in-depth immunophenotyping analysis of the tumor microenvironment, using the commercial CyTOF™ instrument, and further interrogated challenges in managing the integrity of tumor specimens...
February 2, 2017: BMC Immunology
https://www.readbyqxmd.com/read/28124752/automation-of-sample-preparation-for-mass-cytometry-barcoding-in-support-of-clinical-research-protocol-optimization
#12
Ala F Nassar, Adam V Wisnewski, Khadir Raddassi
Analysis of multiplexed assays is highly important for clinical diagnostics and other analytical applications. Mass cytometry enables multi-dimensional, single-cell analysis of cell type and state. In mass cytometry, the rare earth metals used as reporters on antibodies allow determination of marker expression in individual cells. Barcode-based bioassays for CyTOF are able to encode and decode for different experimental conditions or samples within the same experiment, facilitating progress in producing straightforward and consistent results...
January 26, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28073775/dasatinib-changes-immune-cell-profiles-concomitant-with-reduced-tumor-growth-in-several-murine-solid-tumor-models
#13
Can Hekim, Mette Ilander, Jun Yan, Erin Michaud, Richard Smykla, Markus Vähä-Koskela, Paula Savola, Siri Tähtinen, Leena Saikko, Akseli Hemminki, Panu E Kovanen, Kimmo Porkka, Francis Y F Lee, Satu Mustjoki
Dasatinib, a broad-range tyrosine kinase inhibitor, induces rapid mobilization of lymphocytes and clonal expansion of cytotoxic cells in leukemia patients. Here, we investigated whether dasatinib could induce beneficial immunomodulatory effects in solid tumor models. The effects on tumor growth and on the immune system were studied in four different syngeneic mouse models (B16.OVA melanoma, 1956 sarcoma, MC38 colon, and 4T1 breast carcinoma). Both peripheral blood (PB) and tumor samples were immunophenotyped during treatment...
February 2017: Cancer Immunology Research
https://www.readbyqxmd.com/read/28042144/novel-bet-protein-proteolysis-targeting-chimera-exerts-superior-lethal-activity-than-bromodomain-inhibitor-beti-against-post-myeloproliferative-neoplasm-secondary-s-aml-cells
#14
D T Saenz, W Fiskus, Y Qian, T Manshouri, K Rajapakshe, K Raina, K G Coleman, A P Crew, A Shen, C P Mill, B Sun, P Qiu, T M Kadia, N Pemmaraju, C DiNardo, M-S Kim, A J Nowak, C Coarfa, C M Crews, S Verstovsek, K N Bhalla
The PROTAC (proteolysis-targeting chimera) ARV-825 recruits bromodomain and extraterminal (BET) proteins to the E3 ubiquitin ligase cereblon, leading to degradation of BET proteins, including BRD4. Although the BET-protein inhibitor (BETi) OTX015 caused accumulation of BRD4, treatment with equimolar concentrations of ARV-825 caused sustained and profound depletion (>90%) of BRD4 and induced significantly more apoptosis in cultured and patient-derived (PD) CD34+ post-MPN sAML cells, while relatively sparing the CD34+ normal hematopoietic progenitor cells...
January 31, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28039862/isolation-and-high-dimensional-phenotyping-of-gastrointestinal-immune-cells
#15
Bruna A David, Stephen Rubino, Thais G Moreira, Maria Alice Freitas-Lopes, Alan M Araújo, Nicole E Paul, Rafael M Rezende, Gustavo B Menezes
The gastrointestinal immune system plays a pivotal role in the host relationship with food antigens, the homeostatic microbiome and enteric pathogens. Here, we describe how to collect and process liver and intestinal samples to efficiently isolate and analyse resident immune cells. Furthermore, we describe a step-by-step methodology showing how to high-dimensionally immunophenotype resident leucocytes using cytometry by time-of-flight, providing a well-characterized antibody platform that allows the identification of every leucocyte subset simultaneously...
May 2017: Immunology
https://www.readbyqxmd.com/read/27997758/comprehensive-mass-cytometry-analysis-of-cell-cycle-activation-and-co-inhibitory-receptors-expression-in-cd4-t-cells-from-healthy-and-hiv-infected-individuals
#16
REVIEW
Aurélien Corneau, Antonio Cosma, Sophie Even, Christine Katlama, Roger Legrand, Véronique Frachet, Catherine Blanc, Brigitte Autran
RATIONALE: Mass cytometry allows large multiplex analysis of cell cycle stages together with differentiation, activation and exhaustion markers, allowing further assessment of the quiescence status of resting CD4 T cells. METHODS: peripheral blood CD4 T lymphocytes from 8 individuals, 4 healthy donors (HD) and 4 HIV-infected on anti-retroviral treatment (T) were stained with the same 26 monoclonal antibodies and dyes targeting surface and intra-cellular markers of differentiation, activation, exhaustion and cell cycle stages...
December 20, 2016: Cytometry. Part B, Clinical Cytometry
https://www.readbyqxmd.com/read/27994939/pointwise-mutual-information-quantifies-intratumor-heterogeneity-in-tissue-sections-labeled-with-multiple-fluorescent-biomarkers
#17
Daniel M Spagnolo, Rekha Gyanchandani, Yousef Al-Kofahi, Andrew M Stern, Timothy R Lezon, Albert Gough, Dan E Meyer, Fiona Ginty, Brion Sarachan, Jeffrey Fine, Adrian V Lee, D Lansing Taylor, S Chakra Chennubhotla
BACKGROUND: Measures of spatial intratumor heterogeneity are potentially important diagnostic biomarkers for cancer progression, proliferation, and response to therapy. Spatial relationships among cells including cancer and stromal cells in the tumor microenvironment (TME) are key contributors to heterogeneity. METHODS: We demonstrate how to quantify spatial heterogeneity from immunofluorescence pathology samples, using a set of 3 basic breast cancer biomarkers as a test case...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27992111/comparison-of-clustering-methods-for-high-dimensional-single-cell-flow-and-mass-cytometry-data
#18
Lukas M Weber, Mark D Robinson
Recent technological developments in high-dimensional flow cytometry and mass cytometry (CyTOF) have made it possible to detect expression levels of dozens of protein markers in thousands of cells per second, allowing cell populations to be characterized in unprecedented detail. Traditional data analysis by "manual gating" can be inefficient and unreliable in these high-dimensional settings, which has led to the development of a large number of automated analysis methods. Methods designed for unsupervised analysis use specialized clustering algorithms to detect and define cell populations for further downstream analysis...
December 2016: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/27933753/mass-cytometry-of-follicular-lymphoma-tumors-reveals-intrinsic-heterogeneity-in-proteins-including-hla-dr-and-a-deficit-in-non-malignant-plasmablast-and-germinal-center-b-cell-populations
#19
Cara Ellen Wogsland, Allison Rae Greenplate, Arne Kolstad, June Helen Myklebust, Jonathan Michael Irish, Kanutte Huse
BACKGROUND: Follicular lymphoma (FL) is an indolent non-Hodgkin lymphoma that has a risk of transformation to more aggressive lymphoma. Relatively little is known about the non-malignant B-cell and T-cell subset composition within the tumor microenvironment and whether altered phenotypes are associated with patterns of lymphoma B-cell heterogeneity. METHODS: Two mass cytometry (CyTOF) panels were designed to immunophenotype B and T cells in FL tumors. Populations of malignant B cells, non-malignant B cells, and T cells from each FL tumor were identified and their phenotypes compared to B and T cells from healthy human tonsillar tissue...
December 9, 2016: Cytometry. Part B, Clinical Cytometry
https://www.readbyqxmd.com/read/27933748/exploring-glucocorticoid-receptor-agonists-mechanism-of-action-through-mass-cytometry-and-radial-visualizations
#20
Yann Abraham, Bertran Gerrits, Marie-Gabrielle Ludwig, Michael Rebhan, Caroline Gubser Keller
Recent advances in combining flow cytometry and mass spectrometry have led to the development of mass cytometry, allowing for the interrogation of complex cell populations on an unprecedented scale. The volumes and high dimensionality of mass cytometry data pose significant challenges in terms of analysis and visualization. We implement a method called Radviz (1-3), where multidimensional single cell data can be visualized as a projection that maintains the original dimensions and data complexity whilst facilitating analysis and visualization...
December 9, 2016: Cytometry. Part B, Clinical Cytometry
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