Evidence map›Paper›PMID 41676596›Full record

ArticlebioRxiv : the preprint server for biology2026

The CD8 immgenT framework as a universal reference of mouse CD8αβ T cell differentiation states.

Giovanni Galletti, Anna-Maria Globig, Olga Barreiro, Taylor A Heim, Shuozhi Liu, Samantha M Borys, Odhran Casey, Alexander Monell, Dhruv Patravali, Nicole E Scharping and 12 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

22 authors.

Giovanni GallettiSchool of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.ORCID 0000-0001-6613-2354
Anna-Maria GlobigAllen Institute for Immunology, Seattle, WA, USA.
Olga BarreiroDepartment of Immunology, Harvard Medical School, Boston, MA, USA.
Taylor A HeimKoch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.
Shuozhi LiuSchool of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
Samantha M BorysDepartment of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, USA.
Odhran CaseyDepartment of Immunology, Harvard Medical School, Boston, MA, USA.
Alexander MonellSchool of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
Dhruv PatravaliSchool of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
Nicole E ScharpingSchool of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
Sara QuonSchool of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
Kennidy K TakeharaSchool of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
Amir FerrySchool of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
Kitty P CheungSchool of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
Ellen DuongKoch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.
Tomoyo ShinkawaDepartment of Microbiology, University of Massachusetts Medical School, Worcester, MA, USA.
Stefani SprangerKoch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.ORCID 0000-0003-3257-4546
Samuel M BeharDepartment of Microbiology, University of Massachusetts Medical School, Worcester, MA, USA.ORCID 0000-0002-3374-6699
Susan M KaechAllen Institute for Immunology, Seattle, WA, USA.
Ananda W GoldrathSchool of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
David ZemmourDepartment of Pathology, University of Chicago, Chicago, IL, USA.
immgenT Project

Funding

Regulation of T cell immunity to viral infectionR01AI072117 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GOLDRATH, ANANDA W · 2008 to 2022
$5.4M
Systems-level identification of key regulators deciding immune cell stateR01AI150282 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI WANG, WEI · 2020 to 2024
$3.5M
T cell maintenance: molecular mediators of T cell differentiation and survivalR37AI067545 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Ananda W Goldrath · 2022 to 2026
$3.0M
Hypoxia, tuberculosis, and T cell dysfunctionR01AI172905 · NIAID · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI SAMUEL M BEHAR · 2023 to 2026
$3.0M
Tissue-specific adaptions to promote localized T cell memoryR01AI179952 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Ananda W Goldrath · 2024 to 2026
$1.8M
PROTECTIVE CD8 T CELL RESPONSES to TUBERCULOSISR01AI192333 · NIAID · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI SAMUEL M BEHAR · 2025 to 2026
$1.7M
Tumor-infiltrating T cell metabolic dysfunction and genetic reprogramming for effective immunotherapyK00CA222711 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SCHARPING, NICOLE E · 2020 to 2023
$360k
PD-1 Mediated Regulation of Salivary Gland IntegrityF31DE032593 · NIDCR · BROWN UNIVERSITY · PI BORYS, SAMANTHA · 2023 to 2025
$136k
Understanding Prostate Resident Memory T CellsF31AI176705 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI TAKEHARA, KENNIDY · 2024 to 2025
$64k
NCI NIH HHS K00 CA222711NIAID NIH HHS F31 AI176705NIAID NIH HHS R01 AI072117NIAID NIH HHS R01 AI150282NIAID NIH HHS R01 AI172905NIAID NIH HHS R01 AI179952NIAID NIH HHS R01 AI192333NIAID NIH HHS R37 AI067545NIDCR NIH HHS F31 DE032593
6 · The paper itself

Abstract

Mouse CD8 T cell differentiation has been studied extensively in models of infections and cancer, yet no unified framework spans the full spectrum of immunological contexts. We present the CD8 immgenT framework, integrating >200,000 single-cell transcriptomes and 128-plex surface proteomes from 734 samples spanning multiple perturbations, tissues, and timepoints. Unbiased analysis identifies 21 states encompassing naive, effector, circulating memory, tissue-resident memory, progenitor-exhausted, and terminally-exhausted compartments, among others. These states re-emerge with striking molecular convergence across acute/chronic infections, cancer, autoimmunity, aging, and homeostasis, showing that near-identical transcriptional programs support protective or dysfunctional outcomes depending on developmental history and microenvironment. Classic archetypes map to discrete clusters but exhibit unappreciated heterogeneity and overlap, cautioning against rigid nomenclature. We provide validated combinatorial markers, flow cytometry gating strategies, and immgenT reference-based integration for reproducible annotation of new datasets. This universal coordinate system harmonizes fragmented CD8 T cell literature and clarifies relationships across diverse immune challenges.

Identifiers

PMID41676596
PMCPMC12889609

What Socratic holds

Textmetadata
LicenceCC BY-ND
Read underepoch 390

Registered trials

None linked

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 Socratic graph.