Mass cytometry as a tool in target validation and drug discovery

Methods in Enzymology - Tập 690 - Trang 541-574 - 2023
Edmund C.R. Watson1,2, Warren Baker1,2, David Ahern3, Danson Loi1,2, Adam P. Cribbs1,2, Udo Oppermann1,2
1Botnar Research Centre, NIHR Biomedical Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom
2Oxford Translational Myeloma Centre, Botnar Research Centre, University of Oxford, United Kingdom
3Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom

Tài liệu tham khảo

Bandura, 2009, Mass cytometry: Technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry, Analytical Chemistry, 81, 6813, 10.1021/ac901049w Behbehani, 2012, Single‐cell mass cytometry adapted to measurements of the cell cycle, Cytometry Part A, 81A, 552, 10.1002/cyto.a.22075 Bendall, 2014, Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development, Cell, 157, 714, 10.1016/j.cell.2014.04.005 Bodenmiller, 2012, Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators, Nature Biotechnology, 30, 858, 10.1038/nbt.2317 Braanker, 2021, How to prepare spectral flow cytometry datasets for high dimensional data analysis: A practical workflow, Frontiers in Immunology, 12 Crowell, H. L., Zanotelli, V. R. T., Chevrier, S., & Robinson, M. D. (2022). CATALYST: Cytometry dATa anALYSis tools. Retrieved from 〈https://github.com/HelenaLC/CATALYST〉. Finak, 2014, OpenCyto: An open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis, PLoS Computational Biology, 10, 10.1371/journal.pcbi.1003806 Guo, 2020, Mass cytometry analysis reveals a distinct immune environment in peritoneal fluid in endometriosis: A characterisation study, BMC Medicine, 18, 3, 10.1186/s12916-019-1470-y Hartmann, 2019, Comprehensive immune monitoring of clinical trials to advance human immunotherapy, Cell Reports, 28, 819, 10.1016/j.celrep.2019.06.049 Iyer, 2022, CyTOF® for the masses, Frontiers in Immunology, 13, 10.3389/fimmu.2022.815828 Krieg, 2018, High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy, Nature Medicine, 24, 144, 10.1038/nm.4466 Kuett, 2022, Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment, Nature Cancer, 3, 122, 10.1038/s43018-021-00301-w Lai, 2015, A CD45–based barcoding approach to multiplex mass‐cytometry (CyTOF), Cytometry Part A, 87, 369, 10.1002/cyto.a.22640 Levine, 2015, Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis, Cell, 162, 184, 10.1016/j.cell.2015.05.047 Newell, 2012, Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes, Immunity, 36, 142, 10.1016/j.immuni.2012.01.002 Olsen, 2019, The anatomy of single cell mass cytometry data, Cytometry Part A, 95, 156, 10.1002/cyto.a.23621 Ornatsky, 2008, Study of cell antigens and intracellular DNA by identification of element-containing labels and metallointercalators using inductively coupled plasma mass spectrometry, Analytical Chemistry, 80, 2539, 10.1021/ac702128m Ornatsky, 2010, Highly multiparametric analysis by mass cytometry, Journal of Immunological Methods, 361, 1, 10.1016/j.jim.2010.07.002 Picot, 2012, Flow cytometry: Retrospective, fundamentals and recent instrumentation, Cytotechnology, 64, 109, 10.1007/s10616-011-9415-0 Plückthun, 2015, Designed Ankyrin Repeat Proteins (DARPins): Binding proteins for research, diagnostics, and therapy, Annual Review of Pharmacology and Toxicology, 55, 489, 10.1146/annurev-pharmtox-010611-134654 R Core Team (2022). R: A language and environment for statistical computing. Retrieved from 〈https://www.R-project.org/〉. Sahaf, 2019, Biomarkers for immunotherapy of cancer, methods and protocols, Methods in Molecular Biology, 2055, 351, 10.1007/978-1-4939-9773-2_16 Schulz, 2019, Stabilizing antibody cocktails for mass cytometry, Cytometry Part A, 95, 910, 10.1002/cyto.a.23781 Spitzer, 2016, Mass cytometry: Single cells, many features, Cell, 165, 780, 10.1016/j.cell.2016.04.019 Spitzer, 2015, An interactive reference framework for modeling a dynamic immune system, Science (New York, N. Y.), 349, 1259425, 10.1126/science.1259425 Ståhl, 2017, Affibody molecules in biotechnological and medical applications, Trends in Biotechnology, 35, 691, 10.1016/j.tibtech.2017.04.007 StandardBioTools. (2021a). Cell-ID 20-Plex Pd barcoding kit user guide. Retrieved July 5, 2023, from 〈https://www.standardbio.com/asset/692〉. StandardBioTools. (2021b). Maxpar antibody labeling user guide. Retrieved March 27, 2023, from 〈https://fluidigm.my.salesforce.com/sfc/p/#700000009DAw/a/4u0000019hJc/bT0Mr1sBIRKJDSm14.zvdfrWEJd_QAmX.36RviKDyO8〉. StandardBioTools. (2022a). Maxpar cell surface staining with fresh fix. Retrieved April 2, 2023, from 〈https://fluidigm.my.salesforce.com/sfc/p/#700000009DAw/a/4u0000019gwY/kAt2wPkiFPIVRiyUicKj_aVUlQjgfgei0lAKG6I2WWY〉. StandardBioTools. (2022b). Maxpar cytoplasmic/secreted antigen staining with fresh fix. Retrieved July 5, 2023, from 〈https://fluidigm.my.salesforce.com/sfc/p/#700000009DAw/a/4u0000019gwS/aIjEtbnLznwN.KbwUA9R1_PqDEgUs8hUhhCFl2vCOGM〉. StandardBioTools. (2022c). Maxpar nuclear antigen staining with fresh fix. Retrieved April 5, 2023, from 〈https://fluidigm.my.salesforce.com/sfc/p/#700000009DAw/a/4u0000019gvy/k1.CbKFY8JN7swG2ZVHybPpEZldzMpDAZnJYQvxyrrc〉. Takahashi, 2017, Mass cytometry panel optimization through the designed distribution of signal interference, Cytometry Part A, 91, 39, 10.1002/cyto.a.22977 Wickham, 2016 Zunder, 2015, A continuous molecular roadmap to iPSC reprogramming through progression analysis of single-cell mass cytometry, Cell Stem Cell, 16, 323, 10.1016/j.stem.2015.01.015