Single-cell RNA sequencing analysis of T helper cell
differentiation and heterogeneity

J 2022

Single-cell RNA sequencing analysis of T helper cell differentiation and heterogeneity

JAROUŠEK, Radim, Antónia MIKULOVÁ, Petra DAĎOVÁ, Petr TAUŠ, Terézia KURUCOVÁ et. al.

Základní údaje

Originální název

Single-cell RNA sequencing analysis of T helper cell differentiation and heterogeneity

Autoři

JAROUŠEK, Radim (203 Česká republika, domácí), Antónia MIKULOVÁ (703 Slovensko, domácí), Petra DAĎOVÁ (203 Česká republika, domácí), Petr TAUŠ (203 Česká republika, domácí), Terézia KURUCOVÁ (703 Slovensko, domácí), Karla PLEVOVÁ (203 Česká republika, domácí), Boris TICHÝ (203 Česká republika, domácí) a Lukáš KUBALA (203 Česká republika, domácí)

Vydání

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Elsevier B.V. 2022, 0167-4889

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.100

Kód RIV

RIV/00216224:14310/22:00127718

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1016/j.bbamcr.2022.119321

UT WoS

000828701100002

Klíčová slova anglicky

Thelpercells; Activation; Differentiation; Plasticity; Single-cellRNAsequencing; Geneexpressionprofiling; Signaturegenes; Differentialexpression; Cellcycleregression; Correctionforbatcheffect; Dataanalysis

Štítky

14110323, CF GEN, podil, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 15. 10. 2024 14:37, Ing. Martina Blahová

Anotace

V originále

Single-cell transcriptomics has emerged as a powerful tool to investigate cells' biological landscape and focus on the expression profile of individual cells. Major advantage of this approach is an analysis of highly complex and heterogeneous cell populations, such as a specific subpopulation of T helper cells that are known to differentiate into distinct subpopulations. The need for distinguishing the specific expression profile is even more important considering the T cell plasticity. However, importantly, the universal pipelines for single-cell analysis are usually not sufficient for every cell type. Here, the aims are to analyze the diversity of T cell phenotypes employing classical in vitro cytokine-mediated differentiation of human T cells isolated from human peripheral blood by single-cell transcriptomic approach with support of labelled antibodies and a comprehensive bioinformatics analysis using combination of Seurat, Nebulosa, GGplot and others. The results showed high expression similarities between Th1 and Th17 phenotype and very distinct Th2 expression profile. In a case of Th2 highly specific marker genes SPINT2, TRIB3 and CST7 were expressed. Overall, our results demonstrate how donor difference, Th plasticity and cell cycle influence the expression profiles of distinct T cell populations. The results could help to better understand the importance of each step of the analysis when working with T cell single-cell data and observe the results in a more practical way by using our analyzed datasets.

Návaznosti

EF16_025/0007381, projekt VaV

Název: Preklinická progrese nových organických sloučenin s cílenou biologickou aktivitou

NU20-08-00314, projekt VaV

Název: Single cell analýza: moderní nástroj pro studium klonální evoluce u pacientů s chronickou lymfocytární leukémií s vysokým rizikem (Akronym: Single cell analysis of CLL cells)

Investor: Ministerstvo zdravotnictví ČR, Single cell analysis: a modern tool to study clonal evolution in high-risk patients with chronic lymphocytic leukemia, Podprogram 1 - standardní

90132, velká výzkumná infrastruktura

Název: NCMG II

Citovat

JAROUŠEK, Radim, Antónia MIKULOVÁ, Petra DAĎOVÁ, Petr TAUŠ, Terézia KURUCOVÁ, Karla PLEVOVÁ, Boris TICHÝ a Lukáš KUBALA. Single-cell RNA sequencing analysis of T helper cell differentiation and heterogeneity. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. Elsevier B.V., 2022, roč. 1869, č. 10, s. 1-17. ISSN 0167-4889. Dostupné z: https://dx.doi.org/10.1016/j.bbamcr.2022.119321.

@article{2243724,
   author = {Jaroušek, Radim and Mikulová, Antónia and Daďová, Petra and Tauš, Petr and Kurucová, Terézia and Plevová, Karla and Tichý, Boris and Kubala, Lukáš},
   article_number = {10},
   doi = {http://dx.doi.org/10.1016/j.bbamcr.2022.119321},
   keywords = {Thelpercells; Activation; Differentiation; Plasticity; Single-cellRNAsequencing; Geneexpressionprofiling; Signaturegenes; Differentialexpression; Cellcycleregression; Correctionforbatcheffect; Dataanalysis},
   language = {eng},
   issn = {0167-4889},
   journal = {Biochimica et Biophysica Acta (BBA) - Molecular Cell Research},
   title = {Single-cell RNA sequencing analysis of T helper cell differentiation and heterogeneity},
   url = {https://doi.org/10.1016/j.bbamcr.2022.119321},
   volume = {1869},
   year = {2022}
}

TY  - JOUR
ID  - 2243724
AU  - Jaroušek, Radim - Mikulová, Antónia - Daďová, Petra - Tauš, Petr - Kurucová, Terézia - Plevová, Karla - Tichý, Boris - Kubala, Lukáš
PY  - 2022
TI  - Single-cell RNA sequencing analysis of T helper cell differentiation and heterogeneity
JF  - Biochimica et Biophysica Acta (BBA) - Molecular Cell Research
VL  - 1869
IS  - 10
SP  - 1-17
EP  - 1-17
PB  - Elsevier B.V.
SN  - 01674889
KW  - Thelpercells
KW  - Activation
KW  - Differentiation
KW  - Plasticity
KW  - Single-cellRNAsequencing
KW  - Geneexpressionprofiling
KW  - Signaturegenes
KW  - Differentialexpression
KW  - Cellcycleregression
KW  - Correctionforbatcheffect
KW  - Dataanalysis
UR  - https://doi.org/10.1016/j.bbamcr.2022.119321
N2  - Single-cell transcriptomics has emerged as a powerful tool to investigate cells' biological landscape and focus on the expression profile of individual cells. Major advantage of this approach is an analysis of highly complex and heterogeneous cell populations, such as a specific subpopulation of T helper cells that are known to differentiate into distinct subpopulations. The need for distinguishing the specific expression profile is even more important considering the T cell plasticity. However, importantly, the universal pipelines for single-cell analysis are usually not sufficient for every cell type. Here, the aims are to analyze the diversity of T cell phenotypes employing classical in vitro cytokine-mediated differentiation of human T cells isolated from human peripheral blood by single-cell transcriptomic approach with support of labelled antibodies and a comprehensive bioinformatics analysis using combination of Seurat, Nebulosa, GGplot and others. The results showed high expression similarities between Th1 and Th17 phenotype and very distinct Th2 expression profile. In a case of Th2 highly specific marker genes SPINT2, TRIB3 and CST7 were expressed. Overall, our results demonstrate how donor difference, Th plasticity and cell cycle influence the expression profiles of distinct T cell populations. The results could help to better understand the importance of each step of the analysis when working with T cell single-cell data and observe the results in a more practical way by using our analyzed datasets.
ER  -

JAROUŠEK, Radim, Antónia MIKULOVÁ, Petra DAĎOVÁ, Petr TAUŠ, Terézia KURUCOVÁ, Karla PLEVOVÁ, Boris TICHÝ a Lukáš KUBALA. Single-cell RNA sequencing analysis of T helper cell differentiation and heterogeneity. \textit{Biochimica et Biophysica Acta (BBA) - Molecular Cell Research}. Elsevier B.V., 2022, roč.~1869, č.~10, s.~1-17. ISSN~0167-4889. Dostupné z: https://dx.doi.org/10.1016/j.bbamcr.2022.119321.

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