Evidence map›Paper›PMID 36480602›Full record

ArticleScience (New York, N.Y.)2022

Decoding CAR T cell phenotype using combinatorial signaling motif libraries and machine learning.

Kyle G Daniels, Shangying Wang, Milos S Simic, Hersh K Bhargava, Sara Capponi, Yurie Tonai, Wei Yu, Simone Bianco, Wendell A Lim

Open access · greenFull text read
In one paragraph

Article in Science (New York, N.Y.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.

0numbers the graph read from it
0cells of the map it votes in
77citing papers in PubMed
11.1field-weighted citation impact, top 1% of its field
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

77 citing papers in PubMed, 116 citations in OpenAlex.

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  18. A unified genetic perturbation language for human cellular programming.bioRxiv : the preprint server for biology · 2025
    Article
  19. Review
  20. Harnessing chimeric antigen receptor macrophages against solid tumors.Cancer communications (London, England) · 2025
    Review

17 more citing papers are in PubMed but not listed here.

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

9 authors at 2 institutions in 1 country.

Kyle G DanielsCell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0001-9992-1210
Shangying WangDepartment of Functional Genomics and Cellular Engineering, IBM Almaden Research Center, San Jose, CA 95120, USA.ORCID 0000-0003-3876-7680
Milos S SimicCell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0002-1167-0857
Hersh K BhargavaCell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0003-4675-9293
Sara CapponiDepartment of Functional Genomics and Cellular Engineering, IBM Almaden Research Center, San Jose, CA 95120, USA.ORCID 0000-0001-8117-7526
Yurie TonaiCell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0001-9610-6667
Wei YuCell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0002-3154-5084
Simone BiancoDepartment of Functional Genomics and Cellular Engineering, IBM Almaden Research Center, San Jose, CA 95120, USA.ORCID 0000-0003-3367-2084
Wendell A LimCell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0003-4052-8056
San Francisco Art Institute · USIBM Research - Almaden · US

Funding

STRUCTURAL BIOLOGY TRAINING PROGRAMT32GM008284 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KORTEMME, TANJA · 1988 to 2022
$10.1M
User-control and safetyU54CA244438 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LIM, WENDELL A · 2019 to 2022
$7.8M
Recognizing the tumor ecosystem: Integrating stromal and cancer antigen signals to achieve precision recognition of solid tumors by CAR T cellsR01CA249018 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI WENDELL A LIM · 2021 to 2026
$2.8M
Protein Recognition in Signal TransductionR01CA220257 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LIM, WENDELL A · 2018 to 2022
$1.7M
NCI NIH HHS R01 CA220257NCI NIH HHS R01 CA249018NCI NIH HHS U54 CA244438NIGMS NIH HHS T32 GM008284
6 · The paper itself

Abstract

Chimeric antigen receptor (CAR) costimulatory domains derived from native immune receptors steer the phenotypic output of therapeutic T cells. We constructed a library of CARs containing ~2300 synthetic costimulatory domains, built from combinations of 13 signaling motifs. These CARs promoted diverse human T cell fates, which were sensitive to motif combinations and configurations. Neural networks trained to decode the combinatorial grammar of CAR signaling motifs allowed extraction of key design rules. For example, non-native combinations of motifs that bind tumor necrosis factor receptor-associated factors (TRAFs) and phospholipase C gamma 1 (PLCγ1) enhanced cytotoxicity and stemness associated with effective tumor killing. Thus, libraries built from minimal building blocks of signaling, combined with machine learning, can efficiently guide engineering of receptors with desired phenotypes.

Indexed as

Machine LearningPeptide LibraryReceptors, Chimeric AntigenT-Lymphocytes, CytotoxicHumansPhenotypeProtein DomainsSignal TransductionPeptide LibraryReceptors, Chimeric Antigen

Identifiers

PMID36480602
PMCPMC10026561
OpenAlexW4311887602

What OpenQuestion holds

Textfull text, public
LicenceCC BY
measurements read4
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 OpenQuestion graph.