A unique human cord blood CD8 + CD45RA + CD27 + CD161 + T-cell subset identified by flow cytometric data analysis using Seurat.

Autor: Reyes JGA; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.; Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia.; Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia., Ni D; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.; Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia.; Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia., Santner-Nanan B; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.; Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia.; Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia., Pinget GV; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.; Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia., Kraftova L; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.; Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia.; Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic.; Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic., Ashhurst TM; Sydney Cytometry Core Research Facility, Charles Perkins Centre, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia., Marsh-Wakefield F; Liver Injury and Cancer Program, Centenary Institute, Sydney, New South Wales, Australia.; Human Cancer and Viral Immunology Laboratory, The University of Sydney, Sydney, New South Wales, Australia., Wishart CL; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.; Viral immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.; Ramaciotti Facility for Human System Biology, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia., Tan J; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia., Hsu P; Kids Research, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.; Discipline of Child and Adolescent Health, The University of Sydney, Sydney, New South Wales, Australia., King NJC; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.; Sydney Cytometry Core Research Facility, Charles Perkins Centre, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia.; Viral immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.; Ramaciotti Facility for Human System Biology, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia.; The University of Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia.; Sydney Nano, The University of Sydney, Sydney, New South Wales, Australia., Macia L; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.; Sydney Cytometry Core Research Facility, Charles Perkins Centre, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia.; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia., Nanan R; Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.; Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia.; Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia.
Jazyk: angličtina
Zdroj: Immunology [Immunology] 2024 Sep; Vol. 173 (1), pp. 106-124. Date of Electronic Publication: 2024 May 26.
DOI: 10.1111/imm.13803
Abstrakt: Advances in single-cell level analytical techniques, especially cytometric approaches, have led to profound innovation in biomedical research, particularly in the field of clinical immunology. This has resulted in an expansion of high-dimensional data, posing great challenges for comprehensive and unbiased analysis. Conventional manual analysis is thus becoming untenable to handle these challenges. Furthermore, most newly developed computational methods lack flexibility and interoperability, hampering their accessibility and usability. Here, we adapted Seurat, an R package originally developed for single-cell RNA sequencing (scRNA-seq) analysis, for high-dimensional flow cytometric data analysis. Based on a 20-marker antibody panel and analyses of T-cell profiles in both adult blood and cord blood (CB), we showcased the robust capacity of Seurat in flow cytometric data analysis, which was further validated by Spectre, another high-dimensional cytometric data analysis package, and conventional manual analysis. Importantly, we identified a unique CD8 + T-cell population defined as CD8 + CD45RA + CD27 + CD161 + T cell that was predominantly present in CB. We characterised its IFN-γ-producing and potential cytotoxic properties using flow cytometry experiments and scRNA-seq analysis from a published dataset. Collectively, we identified a unique human CB CD8 + CD45RA + CD27 + CD161 + T-cell subset and demonstrated that Seurat, a widely used package for scRNA-seq analysis, possesses great potential to be repurposed for cytometric data analysis. This facilitates an unbiased and thorough interpretation of complicated high-dimensional data using a single analytical pipeline and opens a novel avenue for data-driven investigation in clinical immunology.
(© 2024 The Authors. Immunology published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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