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.

Basic information

Original name

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

Authors

JAROUŠEK, Radim (203 Czech Republic, belonging to the institution), Antónia MIKULOVÁ (703 Slovakia, belonging to the institution), Petra DAĎOVÁ (203 Czech Republic, belonging to the institution), Petr TAUŠ (203 Czech Republic, belonging to the institution), Terézia KURUCOVÁ (703 Slovakia, belonging to the institution), Karla PLEVOVÁ (203 Czech Republic, belonging to the institution), Boris TICHÝ (203 Czech Republic, belonging to the institution) and Lukáš KUBALA (203 Czech Republic, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.100

RIV identification code

RIV/00216224:14310/22:00127718

Organization unit

Faculty of Science

DOI

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

UT WoS

000828701100002

Keywords in English

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

Abstract

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.

Links

EF16_025/0007381, research and development project

Name: Preklinická progrese nových organických sloučenin s cílenou biologickou aktivitou

NU20-08-00314, research and development project

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

Investor: Ministry of Health of the CR, Subprogram 1 - standard

90132, large research infrastructures

Name: NCMG II

Citovat

JAROUŠEK, Radim, Antónia MIKULOVÁ, Petra DAĎOVÁ, Petr TAUŠ, Terézia KURUCOVÁ, Karla PLEVOVÁ, Boris TICHÝ and 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, vol. 1869, No 10, p. 1-17. ISSN 0167-4889. Available from: 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 and 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, vol.~1869, No~10, p.~1-17. ISSN~0167-4889. Available from: https://dx.doi.org/10.1016/j.bbamcr.2022.119321.

Detailed Information on Publication Record