Unsupervised Analysis of Flow Cytometry Data in a Clinical Setting Captures Cell Diversity and Allows Population Discovery.
Algorithms
Biomarkers
/ blood
Clinical Trials, Phase I as Topic
Cluster Analysis
Dendritic Cells
/ immunology
Flow Cytometry
Humans
Immunophenotyping
Leukocytes, Mononuclear
/ immunology
Longitudinal Studies
Male
Phenotype
Proof of Concept Study
Prostatic Neoplasms
/ blood
RNA-Seq
Time Factors
Transcriptome
Treatment Outcome
analytical immunology
data-driven analysis
flow cytometry
immune monitoring
unsupervised clustering
Journal
Frontiers in immunology
ISSN: 1664-3224
Titre abrégé: Front Immunol
Pays: Switzerland
ID NLM: 101560960
Informations de publication
Date de publication:
2021
2021
Historique:
received:
26
11
2020
accepted:
12
04
2021
entrez:
17
5
2021
pubmed:
18
5
2021
medline:
22
9
2021
Statut:
epublish
Résumé
Data obtained with cytometry are increasingly complex and their interrogation impacts the type and quality of knowledge gained. Conventional supervised analyses are limited to pre-defined cell populations and do not exploit the full potential of data. Here, in the context of a clinical trial of cancer patients treated with radiotherapy, we performed longitudinal flow cytometry analyses to identify multiple distinct cell populations in circulating whole blood. We cross-compared the results from state-of-the-art recommended supervised analyses with results from MegaClust, a high-performance data-driven clustering algorithm allowing fast and robust identification of cell-type populations. Ten distinct cell populations were accurately identified by supervised analyses, including main T, B, dendritic cell (DC), natural killer (NK) and monocytes subsets. While all ten subsets were also identified with MegaClust, additional cell populations were revealed (e.g. CD4
Identifiants
pubmed: 33995353
doi: 10.3389/fimmu.2021.633910
pmc: PMC8119773
doi:
Substances chimiques
Biomarkers
0
Types de publication
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
633910Informations de copyright
Copyright © 2021 Baumgaertner, Sankar, Herrera, Benedetti, Barras, Thierry, Dangaj, Kandalaft, Coukos, Xenarios, Guex and Harari.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
Proc ExploreDB17 (2017). 2017 May;2017:
pubmed: 29757329
Cell Rep. 2019 Jul 16;28(3):819-831.e4
pubmed: 31315057
Nat Rev Immunol. 2016 Jul;16(7):449-62
pubmed: 27320317
Eur J Immunol. 2016 Jan;46(1):34-43
pubmed: 26548301
Int J Lab Hematol. 2019 May;41 Suppl 1:56-62
pubmed: 31069980
Cytometry A. 2018 Jun;93(6):649-652
pubmed: 29473993
Cytometry A. 2015 Jul;87(7):636-45
pubmed: 25573116
Nat Rev Immunol. 2012 Feb 17;12(3):191-200
pubmed: 22343568
Cytometry A. 2018 Aug;93(8):793-802
pubmed: 30168890
Immunity. 2009 Oct 16;31(4):527-8
pubmed: 19833080
Transplant Res. 2013 Oct 25;2(1):17
pubmed: 24160259
Cancer Immunol Immunother. 2012 Jul;61(7):967-78
pubmed: 22714399
PLoS One. 2019 May 22;14(5):e0217163
pubmed: 31116766
J Immunol Methods. 2014 Sep;411:23-36
pubmed: 24925805
Cytometry A. 2013 Aug;83(8):728-38
pubmed: 23788464
Nat Methods. 2016 Jun;13(6):493-6
pubmed: 27183440
Cytometry A. 2016 Dec;89(12):1084-1096
pubmed: 27992111
Bioinformatics. 2013 May 15;29(10):1268-74
pubmed: 23539304
J Immunol. 2000 Dec 1;165(11):6037-46
pubmed: 11086035
J Transl Med. 2011 Jul 11;9:108
pubmed: 21745365
Nat Methods. 2013 Mar;10(3):228-38
pubmed: 23396282
J Immunother Cancer. 2015 Sep 15;3:44
pubmed: 26380089
Cell. 2015 Jul 2;162(1):184-97
pubmed: 26095251
Front Immunol. 2013 Dec 27;4:495
pubmed: 24416034
Immunity. 2018 Apr 17;48(4):812-830.e14
pubmed: 29628290
Brief Bioinform. 2009 May;10(3):297-314
pubmed: 19240124
Cell Rep. 2017 Dec 12;21(11):3190-3204
pubmed: 29241546
Nat Rev Immunol. 2017 Dec 22;18(1):78
pubmed: 29269765
Cancer Immunol Immunother. 2015 May;64(5):585-98
pubmed: 25854580
Immunology. 2018 May;154(1):3-20
pubmed: 29313948
Cytometry B Clin Cytom. 2018 Mar;94(2):342-353
pubmed: 27363684
Int J Radiat Oncol Biol Phys. 2019 Feb 1;103(2):320-334
pubmed: 30267761