Evidence map›Paper›PMID 39910194›Full record

ArticleNature biotechnology2025

SEED-Selection enables high-efficiency enrichment of primary T cells edited at multiple loci.

Christopher R Chang, Vivasvan S Vykunta, Jae Hyun J Lee, Ke Li, Clara Kochendoerfer, Joseph J Muldoon, Charlotte H Wang, Thomas Mazumder, Yang Sun, Daniel B Goodman and 8 more

Abstract read
In one paragraph

Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing 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

13 citing papers in PubMed.

  1. Review
  2. Article
  3. Dual CD8 and TCR editing in regulatory T cells mediates HLA-A2-restricted tissue-specific homing.Molecular therapy : the journal of the American Society of Gene Therapy · 2026
    Article
  4. Ultra-large targeted DNA integrations in primary human cells.bioRxiv : the preprint server for biology · 2026
    Article
  5. Engineering Immune Cell to Counteract Aging and Aging-Associated Diseases.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Review
  6. Article
  7. Review
  8. Article
  9. Review
  10. Article
  11. A unified genetic perturbation language for human cellular programming.bioRxiv : the preprint server for biology · 2025
    Article
  12. Article
  13. Article
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

18 authors.

Christopher R ChangGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-3124-8773
Vivasvan S VykuntaGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-5409-8635
Jae Hyun J LeeGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.ORCID http://orcid.org/0009-0009-2998-5249
Ke LiGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
Clara KochendoerferGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
Joseph J MuldoonGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-3784-3565
Charlotte H WangGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
Thomas MazumderDivision of Rheumatology, University of California, San Francisco, San Francisco, CA, USA.
Yang SunDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-9344-8060
Daniel B GoodmanGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-3759-6883
William A NybergGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-9982-1305
Chang LiuGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.ORCID http://orcid.org/0009-0003-1294-9686
Vincent AllainGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
Allison RothrockGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.ORCID http://orcid.org/0009-0002-6734-6180
Chun J YeGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-6560-3783
Alexander MarsonGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-2734-5776
Brian R ShyGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. Brian.Shy@ucsf.edu.ORCID http://orcid.org/0000-0001-9569-3708
Justin EyquemGladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. Justin.Eyquem@ucsf.edu.ORCID http://orcid.org/0000-0001-8262-1190

Funding

Research BaseP30DK063720 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GERMAN, MICHAEL S · 2003 to 2019
$21.8M
Single-cell Mapping Center for Human Regulatory Elements and Gene ActivityUM1HG012076 · NHGRI · STANFORD UNIVERSITY · PI Michael Ryan Corces, Ansuman Satpathy · 2021 to 2026
$13.8M
Project 2: Assessing Brain Dysfunction in Clinically Quiescent SLEP01AI172523 · NIAID · FEINSTEIN INSTITUTE FOR MEDICAL RESEARCH · PI Betty Diamond · 2024 to 2026
$11.4M
Medical Scientist Training Program (T32 NRSA Training Grant)T32GM141323 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Aimee Kao · 2021 to 2026
$10.5M
Sjögren’s Team for Accelerating Medicines Partnership (STAMP)UC2DE032254 · NIDCR · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ALAN N BAER, A Darise Farris · 2022 to 2026
$8.8M
RESOURCE-BASED CENTER FOR THE ADVANCEMENT OF PRECISION MEDICINE IN RHEUMATOLOGYP30AR070155 · NIAMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Mary C Nakamura · 2016 to 2026
$8.2M
Restorative practice in repairing harm and promoting safe and inclusive practices in the laboratory.T32GM136547 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Adrian Erlebacher, Anita Sil · 2020 to 2026
$4.5M
Sjögren's International Collaborative Clinical Alliance Next Generation Studies (SICCA-NextGen)U01DE028891 · NIDCR · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SHIBOSKI, CAROLINE HELENE · 2020 to 2024
$4.0M
Mapping the cell-type-specific molecular and genetic basis of lupus using single cell multiomicsR01AI171184 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Chun Jimmie Ye · 2024 to 2026
$2.4M
Non-viral genome, epigenome, and transcriptome engineering for clinical CAR-T cell manufacturingK08CA273529 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Brian R Shy · 2022 to 2026
$1.2M
Cancer Research Institute (CRI) Irvington postdoctoral fellowshipNCATS NIH HHS L30 TR002983NCI NIH HHS K08 CA273529NHGRI NIH HHS UM1 HG012076NIAID NIH HHS P01 AI172523NIAID NIH HHS R01 AI171184NIAMS NIH HHS P30 AR070155NIDCR NIH HHS U01 DE028891NIDCR NIH HHS UC2 DE032254NIDDK NIH HHS P30 DK063720NIGMS NIH HHS T32 GM136547NIGMS NIH HHS T32 GM141323U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) K08CA273529U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) L30TR002983U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) T32GM141323
6 · The paper itself

Abstract

Engineering T cell specificity and function at multiple loci can generate more effective cellular therapies, but current manufacturing methods produce heterogenous mixtures of partially engineered cells. Here we develop a one-step process to enrich unlabeled cells containing knock-ins at multiple target loci using a family of repair templates named synthetic exon expression disruptors (SEEDs). SEEDs associate transgene integration with the disruption of a paired target endogenous surface protein while preserving target expression in nonmodified and partially edited cells to enable their removal (SEED-Selection). We design SEEDs to modify three critical loci encoding T cell specificity, coreceptor expression and major histocompatibility complex expression. The results demonstrate up to 98% purity after selection for individual modifications and up to 90% purity for six simultaneous edits (three knock-ins and three knockouts). This method is compatible with existing clinical manufacturing workflows and can be readily adapted to other loci to facilitate production of complex gene-edited cell therapies.

Indexed as

Gene EditingT-LymphocytesExonsGene Knock-In TechniquesGenetic LociHumans

Identifiers

PMID39910194
PMCPMC12320447

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Registered trials

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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.