Evidence map›Paper›PMID 39731734›Full record

ArticleCell reports2025

The T cell receptor sequence influences the likelihood of T cell memory formation.

Kaitlyn A Lagattuta, Ayano C Kohlgruber, Nouran S Abdelfattah, Aparna Nathan, Laurie Rumker, Michael E Birnbaum, Stephen J Elledge, Soumya Raychaudhuri

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. Article
  5. Article
  6. Article
  7. Development of αβ and γδ T Cells in the Thymus and Methods of Analysis.International journal of molecular sciences · 2025
    Review
  8. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Kaitlyn A LagattutaCenter for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Ayano C KohlgruberDivision of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Division of Immunology, Boston Children's Hospital, Boston, MA, USA.
Nouran S AbdelfattahDivision of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
Aparna NathanCenter for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Laurie RumkerCenter for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Michael E BirnbaumKoch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
Stephen J ElledgeDivision of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Soumya RaychaudhuriCenter for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. Electronic address: soumya@broadinstitute.org.

Funding

Medical Scientist Training ProgramT32GM007753 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI WALENSKY, LOREN DAVID · 1985 to 2021
$50.0M
Metabolomics Core U19AI111224 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI MOODY, DAVID BRANCH, MURRAY, MEGAN B · 2015 to 2021
$20.4M
Role of fibroblastic stromal cells and notch signaling in tissue inflammation in RA and SLEP01AI148102 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI Nir Hacohen · 2021 to 2026
$17.3M
Medical Scientist Training ProgramT32GM144273 · NIGMS · HARVARD MEDICAL SCHOOL · PI David Shumway Jones, Jacqueline A. Lees · 2022 to 2026
$14.7M
Discovery and Functional Impact of Common and Rare Variants in RAR01AR063759 · NIAMS · BRIGHAM AND WOMEN'S HOSPITAL · PI Soumya Raychaudhuri · 2013 to 2026
$5.4M
Integrative analysis of high dimensional tissue molecular data to define key biological systems in autoimmune diseases (SBC)UC2AR081023 · NIAMS · BRIGHAM AND WOMEN'S HOSPITAL · PI Soumya Raychaudhuri · 2022 to 2026
$4.8M
RA-SLE Molecular Deconstruction Leadership CenterUH2AR067677 · NIAMS · BRIGHAM AND WOMEN'S HOSPITAL · PI BRENNER, MICHAEL B., RAYCHAUDHURI, SOUMYA · 2014 to 2020
$4.3M
Predicting the impact of genetic variants, genes and pathways on human DiseaseU01HG012009 · NHGRI · BRIGHAM AND WOMEN'S HOSPITAL · PI ALKES L PRICE, Soumya Raychaudhuri · 2021 to 2026
$4.2M
Functionally specialized components of disease heritability in ENCODE dataU01HG009379 · NHGRI · HARVARD SCHOOL OF PUBLIC HEALTH · PI PRICE, ALKES L, RAYCHAUDHURI, SOUMYA · 2017 to 2021
$2.5M
Repertoire-scale T cell antigen identification via peptide-MHC lentivirus displayDP2AI158126 · NIAID · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BIRNBAUM, MICHAEL · 2020 to 2020
$2.3M
Analysis of the Mammalian DNA Damage ResponseR01CA234600 · NCI · BRIGHAM AND WOMEN'S HOSPITAL · PI ELLEDGE, STEPHEN J · 2019 to 2023
$2.0M
Integrative modelling of single-cell data to elucidate the genetic architecture of complex diseaseR01HG013083 · NHGRI · DANA-FARBER CANCER INST · PI ALEXANDER GUSEV, ALKES L PRICE · 2024 to 2026
$1.5M
Cancer Research UK CGCATF-2023/100005NCI NIH HHS R01 CA234600NHGRI NIH HHS R01 HG013083NHGRI NIH HHS R56 HG013083NHGRI NIH HHS U01 HG009379NHGRI NIH HHS U01 HG012009NIAID NIH HHS DP2 AI158126NIAID NIH HHS F30 AI157385NIAID NIH HHS F30 AI176724NIAID NIH HHS P01 AI148102NIAID NIH HHS U19 AI111224NIAMS NIH HHS R01 AR063759NIAMS NIH HHS UC2 AR081023NIAMS NIH HHS UH2 AR067677NIGMS NIH HHS T32 GM007753NIGMS NIH HHS T32 GM144273
6 · The paper itself

Abstract

The amino acid sequence of the T cell receptor (TCR) varies between T cells of an individual's immune system. Particular TCR residues nearly guarantee mucosal-associated invariant T (MAIT) and natural killer T (NKT) cell transcriptional fates. To define how the TCR sequence affects T cell fates, we analyze the paired αβTCR sequence and transcriptome of 961,531 single cells. We find that hydrophobic complementarity-determining region (CDR)3 residues promote regulatory T cell fates in both the CD8 and CD4 lineages. Most strikingly, we find a set of TCR sequence features that promote the T cell transition from naive to memory. We quantify the extent of these features through our TCR scoring function "TCR-mem." Using TCR transduction experiments, we demonstrate that increased TCR-mem promotes T cell activation, even among T cells that recognize the same antigen. Our results reveal a common set of TCR sequence features that enable T cell activation and immunological memory.

Indexed as

Immunologic MemoryMemory T CellsReceptors, Antigen, T-CellAmino Acid SequenceAnimalsCD8-Positive T-LymphocytesComplementarity Determining RegionsLymphocyte ActivationMiceMice, Inbred C57BLReceptors, Antigen, T-Cell, alpha-betaComplementarity Determining RegionsReceptors, Antigen, T-CellReceptors, Antigen, T-Cell, alpha-betaactivationCP: ImmunologyimmunologymemoryT-cellsTCRtranscriptomics

Identifiers

PMID39731734
PMCPMC11785489

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.