TCRβ rearrangements without a D segment are common, abundant, and public

Peter C. de Greef; Rob J. de Boer

doi:10.1073/pnas.2104367118

TCRβ rearrangements without a D segment are common, abundant, and public

Peter C. de Greef^*
, Rob J. de Boer

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

T cells play an important role in adaptive immunity. An enormous clonal diversity of T cells with a different specificity, encoded by the T cell receptor (TCR), protect the body against infection. Most TCRβ chains are generated from a V, D, and J segment during recombination in the thymus. Although complete absence of the D segment is not easily detectable from sequencing data, we find convincing evidence for a substantial proportion of TCRβ rearrangements lacking a D segment. Additionally, sequences without a D segment are more likely to be abundant within individuals and/or shared between individuals. Our analysis indicates that such sequences are preferentially generated during fetal development and persist within the elderly. Summarizing, TCRβ rearrangements without a D segment are not uncommon, and tend to allow for TCRβ chains with a high abundance in the naive repertoire.

Original language	English
Article number	e2104367118
Pages (from-to)	1-7
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	118
Issue number	39
DOIs	https://doi.org/10.1073/pnas.2104367118
Publication status	Published - 28 Sept 2021

Bibliographical note

Funding Information:
ACKNOWLEDGMENTS This work was supported by The Netherlands Organization for Scientific Research Graduate Program 22.005.023 (to P.C.d.G.). We gratefully acknowledge all authors involved in generating the TCR sequencing datasets we studied, for providing access to their data.

Publisher Copyright:
© 2021 National Academy of Sciences. All rights reserved.

Funding

ACKNOWLEDGMENTS This work was supported by The Netherlands Organization for Scientific Research Graduate Program 22.005.023 (to P.C.d.G.). We gratefully acknowledge all authors involved in generating the TCR sequencing datasets we studied, for providing access to their data.

Keywords

Immune repertoire
T cell receptor
V(D)J recombination

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10.1073/pnas.2104367118Licence: CC BY

e2104367118.fullFinal published version, 1.04 MBLicence: CC BY

Cite this

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title = "TCRβ rearrangements without a D segment are common, abundant, and public",

abstract = "T cells play an important role in adaptive immunity. An enormous clonal diversity of T cells with a different specificity, encoded by the T cell receptor (TCR), protect the body against infection. Most TCRβ chains are generated from a V, D, and J segment during recombination in the thymus. Although complete absence of the D segment is not easily detectable from sequencing data, we find convincing evidence for a substantial proportion of TCRβ rearrangements lacking a D segment. Additionally, sequences without a D segment are more likely to be abundant within individuals and/or shared between individuals. Our analysis indicates that such sequences are preferentially generated during fetal development and persist within the elderly. Summarizing, TCRβ rearrangements without a D segment are not uncommon, and tend to allow for TCRβ chains with a high abundance in the naive repertoire.",

keywords = "Immune repertoire, T cell receptor, V(D)J recombination",

author = "\{de Greef\}, \{Peter C.\} and \{de Boer\}, \{Rob J.\}",

note = "Funding Information: ACKNOWLEDGMENTS This work was supported by The Netherlands Organization for Scientific Research Graduate Program 22.005.023 (to P.C.d.G.). We gratefully acknowledge all authors involved in generating the TCR sequencing datasets we studied, for providing access to their data. Publisher Copyright: {\textcopyright} 2021 National Academy of Sciences. All rights reserved.",

year = "2021",

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doi = "10.1073/pnas.2104367118",

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AU - de Greef, Peter C.

AU - de Boer, Rob J.

N1 - Funding Information: ACKNOWLEDGMENTS This work was supported by The Netherlands Organization for Scientific Research Graduate Program 22.005.023 (to P.C.d.G.). We gratefully acknowledge all authors involved in generating the TCR sequencing datasets we studied, for providing access to their data. Publisher Copyright: © 2021 National Academy of Sciences. All rights reserved.

PY - 2021/9/28

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N2 - T cells play an important role in adaptive immunity. An enormous clonal diversity of T cells with a different specificity, encoded by the T cell receptor (TCR), protect the body against infection. Most TCRβ chains are generated from a V, D, and J segment during recombination in the thymus. Although complete absence of the D segment is not easily detectable from sequencing data, we find convincing evidence for a substantial proportion of TCRβ rearrangements lacking a D segment. Additionally, sequences without a D segment are more likely to be abundant within individuals and/or shared between individuals. Our analysis indicates that such sequences are preferentially generated during fetal development and persist within the elderly. Summarizing, TCRβ rearrangements without a D segment are not uncommon, and tend to allow for TCRβ chains with a high abundance in the naive repertoire.

AB - T cells play an important role in adaptive immunity. An enormous clonal diversity of T cells with a different specificity, encoded by the T cell receptor (TCR), protect the body against infection. Most TCRβ chains are generated from a V, D, and J segment during recombination in the thymus. Although complete absence of the D segment is not easily detectable from sequencing data, we find convincing evidence for a substantial proportion of TCRβ rearrangements lacking a D segment. Additionally, sequences without a D segment are more likely to be abundant within individuals and/or shared between individuals. Our analysis indicates that such sequences are preferentially generated during fetal development and persist within the elderly. Summarizing, TCRβ rearrangements without a D segment are not uncommon, and tend to allow for TCRβ chains with a high abundance in the naive repertoire.

KW - Immune repertoire

KW - T cell receptor

KW - V(D)J recombination

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ER -

TCRβ rearrangements without a D segment are common, abundant, and public

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Bibliographical note

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Keywords

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