Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires

An individual’s T-cell repertoire constantly changes under the influence of external and internal factors. Cells that do not receive a stimulatory signal die, while those that encounter and recognize a pathogen or receive a co-stimulatory signal divide, resulting in clonal expansions. T-cell clones...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Anastasia V. Pavlova [verfasserIn] Ivan V. Zvyagin [verfasserIn] Mikhail Shugay [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2024

Schlagwörter:	T cell repertoire analysis adaptive immune receptor repertoire (AIRR) T cell receptor (TCR) clonal tracking hematopoietic (stem) cell transplantation (HCST) immune reconstitution

Übergeordnetes Werk:	In: Frontiers in Immunology - Frontiers Media S.A., 2011, 15(2024)
Übergeordnetes Werk:	volume:15 ; year:2024

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fimmu.2024.1321603

Katalog-ID:	DOAJ09985225X

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520			\|a An individual’s T-cell repertoire constantly changes under the influence of external and internal factors. Cells that do not receive a stimulatory signal die, while those that encounter and recognize a pathogen or receive a co-stimulatory signal divide, resulting in clonal expansions. T-cell clones can be traced by monitoring the presence of their unique T-cell receptor (TCR) sequence, which is assembled de novo through a process known as V(D)J rearrangement. Tracking T cells can provide valuable insights into the survival of cells after hematopoietic stem cell transplantation (HSCT) or cancer treatment response and can indicate the induction of protective immunity by vaccination. In this study, we report a bioinformatic method for quantifying the T-cell repertoire dynamics from TCR sequencing data. We demonstrate its utility by measuring the T-cell repertoire stability in healthy donors, by quantifying the effect of donor lymphocyte infusion (DLI), and by tracking the fate of the different T-cell subsets in HSCT patients and the expansion of pathogen-specific clones in vaccinated individuals.
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allfieldsSound	10.3389/fimmu.2024.1321603 doi (DE-627)DOAJ09985225X (DE-599)DOAJaf5032eadcf744bdb530be0a40851f29 DE-627 ger DE-627 rakwb eng RC581-607 Anastasia V. Pavlova verfasserin aut Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier An individual’s T-cell repertoire constantly changes under the influence of external and internal factors. Cells that do not receive a stimulatory signal die, while those that encounter and recognize a pathogen or receive a co-stimulatory signal divide, resulting in clonal expansions. T-cell clones can be traced by monitoring the presence of their unique T-cell receptor (TCR) sequence, which is assembled de novo through a process known as V(D)J rearrangement. Tracking T cells can provide valuable insights into the survival of cells after hematopoietic stem cell transplantation (HSCT) or cancer treatment response and can indicate the induction of protective immunity by vaccination. In this study, we report a bioinformatic method for quantifying the T-cell repertoire dynamics from TCR sequencing data. We demonstrate its utility by measuring the T-cell repertoire stability in healthy donors, by quantifying the effect of donor lymphocyte infusion (DLI), and by tracking the fate of the different T-cell subsets in HSCT patients and the expansion of pathogen-specific clones in vaccinated individuals. T cell repertoire analysis adaptive immune receptor repertoire (AIRR) T cell receptor (TCR) clonal tracking hematopoietic (stem) cell transplantation (HCST) immune reconstitution Immunologic diseases. Allergy Anastasia V. Pavlova verfasserin aut Ivan V. Zvyagin verfasserin aut Ivan V. Zvyagin verfasserin aut Ivan V. Zvyagin verfasserin aut Mikhail Shugay verfasserin aut Mikhail Shugay verfasserin aut In Frontiers in Immunology Frontiers Media S.A., 2011 15(2024) (DE-627)657998354 (DE-600)2606827-8 16643224 nnns volume:15 year:2024 https://doi.org/10.3389/fimmu.2024.1321603 kostenfrei https://doaj.org/article/af5032eadcf744bdb530be0a40851f29 kostenfrei https://www.frontiersin.org/articles/10.3389/fimmu.2024.1321603/full kostenfrei https://doaj.org/toc/1664-3224 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 15 2024
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topic_facet	T cell repertoire analysis adaptive immune receptor repertoire (AIRR) T cell receptor (TCR) clonal tracking hematopoietic (stem) cell transplantation (HCST) immune reconstitution Immunologic diseases. Allergy
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callnumber-first	R - Medicine
author	Anastasia V. Pavlova
spellingShingle	Anastasia V. Pavlova misc RC581-607 misc T cell repertoire analysis misc adaptive immune receptor repertoire (AIRR) misc T cell receptor (TCR) misc clonal tracking misc hematopoietic (stem) cell transplantation (HCST) misc immune reconstitution misc Immunologic diseases. Allergy Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires
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topic_title	RC581-607 Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires T cell repertoire analysis adaptive immune receptor repertoire (AIRR) T cell receptor (TCR) clonal tracking hematopoietic (stem) cell transplantation (HCST) immune reconstitution
topic	misc RC581-607 misc T cell repertoire analysis misc adaptive immune receptor repertoire (AIRR) misc T cell receptor (TCR) misc clonal tracking misc hematopoietic (stem) cell transplantation (HCST) misc immune reconstitution misc Immunologic diseases. Allergy
topic_unstemmed	misc RC581-607 misc T cell repertoire analysis misc adaptive immune receptor repertoire (AIRR) misc T cell receptor (TCR) misc clonal tracking misc hematopoietic (stem) cell transplantation (HCST) misc immune reconstitution misc Immunologic diseases. Allergy
topic_browse	misc RC581-607 misc T cell repertoire analysis misc adaptive immune receptor repertoire (AIRR) misc T cell receptor (TCR) misc clonal tracking misc hematopoietic (stem) cell transplantation (HCST) misc immune reconstitution misc Immunologic diseases. Allergy
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title	Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires
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title_full	Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires
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author_browse	Anastasia V. Pavlova Ivan V. Zvyagin Mikhail Shugay
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title_sort	detecting t-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires
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title_auth	Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires
abstract	An individual’s T-cell repertoire constantly changes under the influence of external and internal factors. Cells that do not receive a stimulatory signal die, while those that encounter and recognize a pathogen or receive a co-stimulatory signal divide, resulting in clonal expansions. T-cell clones can be traced by monitoring the presence of their unique T-cell receptor (TCR) sequence, which is assembled de novo through a process known as V(D)J rearrangement. Tracking T cells can provide valuable insights into the survival of cells after hematopoietic stem cell transplantation (HSCT) or cancer treatment response and can indicate the induction of protective immunity by vaccination. In this study, we report a bioinformatic method for quantifying the T-cell repertoire dynamics from TCR sequencing data. We demonstrate its utility by measuring the T-cell repertoire stability in healthy donors, by quantifying the effect of donor lymphocyte infusion (DLI), and by tracking the fate of the different T-cell subsets in HSCT patients and the expansion of pathogen-specific clones in vaccinated individuals.
abstractGer	An individual’s T-cell repertoire constantly changes under the influence of external and internal factors. Cells that do not receive a stimulatory signal die, while those that encounter and recognize a pathogen or receive a co-stimulatory signal divide, resulting in clonal expansions. T-cell clones can be traced by monitoring the presence of their unique T-cell receptor (TCR) sequence, which is assembled de novo through a process known as V(D)J rearrangement. Tracking T cells can provide valuable insights into the survival of cells after hematopoietic stem cell transplantation (HSCT) or cancer treatment response and can indicate the induction of protective immunity by vaccination. In this study, we report a bioinformatic method for quantifying the T-cell repertoire dynamics from TCR sequencing data. We demonstrate its utility by measuring the T-cell repertoire stability in healthy donors, by quantifying the effect of donor lymphocyte infusion (DLI), and by tracking the fate of the different T-cell subsets in HSCT patients and the expansion of pathogen-specific clones in vaccinated individuals.
abstract_unstemmed	An individual’s T-cell repertoire constantly changes under the influence of external and internal factors. Cells that do not receive a stimulatory signal die, while those that encounter and recognize a pathogen or receive a co-stimulatory signal divide, resulting in clonal expansions. T-cell clones can be traced by monitoring the presence of their unique T-cell receptor (TCR) sequence, which is assembled de novo through a process known as V(D)J rearrangement. Tracking T cells can provide valuable insights into the survival of cells after hematopoietic stem cell transplantation (HSCT) or cancer treatment response and can indicate the induction of protective immunity by vaccination. In this study, we report a bioinformatic method for quantifying the T-cell repertoire dynamics from TCR sequencing data. We demonstrate its utility by measuring the T-cell repertoire stability in healthy donors, by quantifying the effect of donor lymphocyte infusion (DLI), and by tracking the fate of the different T-cell subsets in HSCT patients and the expansion of pathogen-specific clones in vaccinated individuals.
collection_details	GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700
title_short	Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires
url	https://doi.org/10.3389/fimmu.2024.1321603 https://doaj.org/article/af5032eadcf744bdb530be0a40851f29 https://www.frontiersin.org/articles/10.3389/fimmu.2024.1321603/full https://doaj.org/toc/1664-3224
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Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires

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