Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level

Nicolle H R Litjens; Anton W Langerak; Zakia Azmani; Xander den Dekker; Michiel G H Betjes; Rutger W W Brouwer; Wilfred F J van IJcken

doi:10.1007/978-1-0716-2115-8_14

Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level

Nicolle H R Litjens, Anton W Langerak, Zakia Azmani, Xander den Dekker, Michiel G H Betjes, Rutger W W Brouwer, Wilfred F J van IJcken^*

^*Corresponding author for this work

Research output: Chapter/Conference proceeding › Chapter › Academic

2 Downloads (Pure)

Abstract

With the advent of next-generation sequencing (NGS) methodologies, the total repertoires of B and T cells can be disclosed in much more detail than ever before. Even though many of these strategies do provide in-depth and high-resolution information of the immunoglobulin (IG) and/or T-cell receptor (TR) repertoire, one clear disadvantage is that the IG/TR profiles cannot be connected to individual cells. Single-cell technologies do allow to study the IG/TR repertoire at the individual cell level. This is especially relevant in cell samples in which much heterogeneity of the cell population is expected. By combining the IG/TR repertoire with transcriptome data, the reactivity of the B or T cell can be associated with activation or maturation stages. An additional advantage of such single-cell technologies is that the combination of both IG and both TR chains can be studied on a per cell basis, which better reflects the antigen receptor reactivity of cells. Here we present the ICELL8 single-cell method for the parallel analysis of the TR repertoire and transcriptome, which is especially useful in samples that contain relatively few cells.

Original language	English
Title of host publication	Methods in Molecular Biology
Subtitle of host publication	Methods and Protocols
Publisher	Humana Press
Pages	231-259
Number of pages	29
Volume	2453
Edition	1
ISBN (Electronic)	978-1-0716-2115-8
ISBN (Print)	978-1-0716-2114-1
DOIs	https://doi.org/10.1007/978-1-0716-2115-8_14
Publication status	Published - 28 May 2022

Publication series

Series	Methods in Molecular Biology
ISSN	1064-3745

Bibliographical note

Funding Information:
We would like to thank Maaike de Bie, Amy van der List, and Mariska Klepper for technical assistance.

Publisher Copyright:
© 2022, The Author(s).

Access to Document

10.1007/978-1-0716-2115-8_14Licence: CC BY

978-1-0716-2115-8_14Final published version, 916 KBLicence: CC BY

Cite this

Litjens, N. H. R., Langerak, A. W., Azmani, Z., den Dekker, X., Betjes, M. G. H., Brouwer, R. W. W., & van IJcken, W. F. J. (2022). Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level. In Methods in Molecular Biology: Methods and Protocols (1 ed., Vol. 2453, pp. 231-259). Humana Press. Methods in Molecular Biology https://doi.org/10.1007/978-1-0716-2115-8_14

@inbook{3eff2f08043a443a931f73f60df9b90f,

title = "Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level",

abstract = "With the advent of next-generation sequencing (NGS) methodologies, the total repertoires of B and T cells can be disclosed in much more detail than ever before. Even though many of these strategies do provide in-depth and high-resolution information of the immunoglobulin (IG) and/or T-cell receptor (TR) repertoire, one clear disadvantage is that the IG/TR profiles cannot be connected to individual cells. Single-cell technologies do allow to study the IG/TR repertoire at the individual cell level. This is especially relevant in cell samples in which much heterogeneity of the cell population is expected. By combining the IG/TR repertoire with transcriptome data, the reactivity of the B or T cell can be associated with activation or maturation stages. An additional advantage of such single-cell technologies is that the combination of both IG and both TR chains can be studied on a per cell basis, which better reflects the antigen receptor reactivity of cells. Here we present the ICELL8 single-cell method for the parallel analysis of the TR repertoire and transcriptome, which is especially useful in samples that contain relatively few cells.",

author = "Litjens, {Nicolle H R} and Langerak, {Anton W} and Zakia Azmani and {den Dekker}, Xander and Betjes, {Michiel G H} and Brouwer, {Rutger W W} and {van IJcken}, {Wilfred F J}",

note = "Funding Information: We would like to thank Maaike de Bie, Amy van der List, and Mariska Klepper for technical assistance. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = may,

day = "28",

doi = "10.1007/978-1-0716-2115-8_14",

language = "English",

isbn = "978-1-0716-2114-1",

volume = "2453",

series = "Methods in Molecular Biology",

publisher = "Humana Press",

pages = "231--259",

booktitle = "Methods in Molecular Biology",

address = "United States",

edition = "1",

}

Litjens, NHR , Langerak, AW, Azmani, Z, den Dekker, X , Betjes, MGH, Brouwer, RWW & van IJcken, WFJ 2022, Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level. in Methods in Molecular Biology: Methods and Protocols. 1 edn, vol. 2453, Humana Press, Methods in Molecular Biology, pp. 231-259. https://doi.org/10.1007/978-1-0716-2115-8_14

Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level. / Litjens, Nicolle H R ; Langerak, Anton W; Azmani, Zakia et al.
Methods in Molecular Biology: Methods and Protocols. Vol. 2453 1. ed. Humana Press, 2022. p. 231-259 (Methods in Molecular Biology).

Research output: Chapter/Conference proceeding › Chapter › Academic

TY - CHAP

T1 - Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level

AU - Litjens, Nicolle H R

AU - Langerak, Anton W

AU - Azmani, Zakia

AU - den Dekker, Xander

AU - Betjes, Michiel G H

AU - Brouwer, Rutger W W

AU - van IJcken, Wilfred F J

PY - 2022/5/28

Y1 - 2022/5/28

N2 - With the advent of next-generation sequencing (NGS) methodologies, the total repertoires of B and T cells can be disclosed in much more detail than ever before. Even though many of these strategies do provide in-depth and high-resolution information of the immunoglobulin (IG) and/or T-cell receptor (TR) repertoire, one clear disadvantage is that the IG/TR profiles cannot be connected to individual cells. Single-cell technologies do allow to study the IG/TR repertoire at the individual cell level. This is especially relevant in cell samples in which much heterogeneity of the cell population is expected. By combining the IG/TR repertoire with transcriptome data, the reactivity of the B or T cell can be associated with activation or maturation stages. An additional advantage of such single-cell technologies is that the combination of both IG and both TR chains can be studied on a per cell basis, which better reflects the antigen receptor reactivity of cells. Here we present the ICELL8 single-cell method for the parallel analysis of the TR repertoire and transcriptome, which is especially useful in samples that contain relatively few cells.

AB - With the advent of next-generation sequencing (NGS) methodologies, the total repertoires of B and T cells can be disclosed in much more detail than ever before. Even though many of these strategies do provide in-depth and high-resolution information of the immunoglobulin (IG) and/or T-cell receptor (TR) repertoire, one clear disadvantage is that the IG/TR profiles cannot be connected to individual cells. Single-cell technologies do allow to study the IG/TR repertoire at the individual cell level. This is especially relevant in cell samples in which much heterogeneity of the cell population is expected. By combining the IG/TR repertoire with transcriptome data, the reactivity of the B or T cell can be associated with activation or maturation stages. An additional advantage of such single-cell technologies is that the combination of both IG and both TR chains can be studied on a per cell basis, which better reflects the antigen receptor reactivity of cells. Here we present the ICELL8 single-cell method for the parallel analysis of the TR repertoire and transcriptome, which is especially useful in samples that contain relatively few cells.

UR - http://www.scopus.com/inward/record.url?scp=85131107971&partnerID=8YFLogxK

U2 - 10.1007/978-1-0716-2115-8_14

DO - 10.1007/978-1-0716-2115-8_14

M3 - Chapter

C2 - 35622330

SN - 978-1-0716-2114-1

VL - 2453

T3 - Methods in Molecular Biology

SP - 231

EP - 259

BT - Methods in Molecular Biology

PB - Humana Press

ER -

Litjens NHR , Langerak AW, Azmani Z, den Dekker X , Betjes MGH, Brouwer RWW et al. Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level. In Methods in Molecular Biology: Methods and Protocols. 1 ed. Vol. 2453. Humana Press. 2022. p. 231-259. (Methods in Molecular Biology). doi: 10.1007/978-1-0716-2115-8_14

Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level

Abstract

Publication series

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this