Evidence map›Paper›PMID 27301863›Full record

ArticleBlood2016

Modeling altered T-cell development with induced pluripotent stem cells from patients with RAG1-dependent immune deficiencies.

Patrick M Brauer, Itai M Pessach, Erik Clarke, Jared H Rowe, Lisa Ott de Bruin, Yu Nee Lee, Carmen Dominguez-Brauer, Anne M Comeau, Geneve Awong, Kerstin Felgentreff and 13 more

Open access · bronzeAbstract read
In one paragraph

Article in Blood, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.

0numbers the graph read from it
0cells of the map it votes in
29citing papers in PubMed
2.0field-weighted citation impact, top 14% 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

29 citing papers in PubMed, 47 citations in OpenAlex.

  1. Trial
  2. Article
  3. HEB collaborates with TCR signaling to upregulatebioRxiv : the preprint server for biology · 2025
    Article
  4. Adoptive Cell Therapy from the Dish: Potentiating Induced Pluripotent Stem Cells.Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie · 2025
    Review
  5. Article
  6. Review
  7. Article
  8. Review
  9. Frontiers in immunology · 2022
    Review
  10. Article
  11. NovelFrontiers in pediatrics · 2022
    Article
  12. Review
  13. Review
  14. Article
  15. Cutting Edge: TCR-β Selection Is Required at the CD4Journal of immunology (Baltimore, Md. : 1950) · 2021
    Article
  16. Review
  17. Article
  18. Review
  19. Review
  20. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

23 authors at 11 institutions in 5 countries.

Patrick M BrauerSunnybrook Research Institute, and Department of Immunology, University of Toronto, Toronto, ON, Canada;ORCID 0000-0001-7788-5204
Itai M PessachDivision of Immunology, Boston Children's Hospital, Boston, MA; Department of Pediatric Critical Care, Sheba Medical Center, Tel-Aviv University, Tel-Aviv, Israel;
Erik ClarkeDepartment of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA;
Jared H RoweDivision of Immunology, Boston Children's Hospital, Boston, MA;
Lisa Ott de BruinDivision of Immunology, Boston Children's Hospital, Boston, MA;
Yu Nee LeeDivision of Immunology, Boston Children's Hospital, Boston, MA;
Carmen Dominguez-BrauerOntario Cancer Institute, University Health Network, Toronto, ON, Canada;
Anne M ComeauDepartment of Pediatrics, University of Massachusetts Medical School, Worcester, MA;
Geneve AwongSunnybrook Research Institute, and Department of Immunology, University of Toronto, Toronto, ON, Canada; McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON, Canada;
Kerstin FelgentreffDivision of Immunology, Boston Children's Hospital, Boston, MA;
Yuhang H ZhangDepartments of Immunobiology and Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT;
Andrea BredemeyerDepartment of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO;
Waleed Al-HerzDepartment of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait;
Likun DuDivision of Immunology, Boston Children's Hospital, Boston, MA;
Francesca VerversDivision of Immunology, Boston Children's Hospital, Boston, MA;
Marion KennedyMcEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON, Canada;
Silvia Giliani"Angelo Nocivelli" Institute for Molecular Medicine, University of Brescia, Brescia, Italy;
Gordon KellerMcEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON, Canada;
Barry P SleckmanDepartment of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO;
David G SchatzDepartments of Immunobiology and Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT; Howard Hughes Medical Institute, New Haven, CT; and.
Frederic D BushmanDepartment of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA;
Luigi D NotarangeloDivision of Immunology, Boston Children's Hospital, Boston, MA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA.ORCID 0000-0002-8335-0262
Juan Carlos Zúñiga-PflückerSunnybrook Research Institute, and Department of Immunology, University of Toronto, Toronto, ON, Canada;
Boston Children's Hospital · USSunnybrook Health Science Centre · CAUniversity Health Network · CAUniversity of Pennsylvania · USWashington University in St. Louis · USHoward Hughes Medical Institute · USKuwait University · KWOntario Institute for Cancer Research · CAUniversity of Brescia · ITUniversity of Massachusetts Chan Medical School · USYale University · US

Funding

Yale Pathology Tissue Services Shared ResourceP30CA016359 · NCI · YALE UNIVERSITY · PI DAVID L RIMM · 1985 to 2026
$85.0M
Training of Clinical Investigators in Primary Immune DeficienciesU54AI082973 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI TORGERSON, TROY R · 2009 to 2023
$23.3M
ATM FUNCTION DURING V(D)J RECOMBINATIONR01AI074953 · NIAID · WEILL MEDICAL COLL OF CORNELL UNIV · PI SLECKMAN, BARRY P · 2009 to 2023
$5.9M
Modeling and correcting human SCID using patient-derived iPS cellsR01AI100887 · NIAID · BOSTON CHILDREN'S HOSPITAL · PI MANIS, JOHN P · 2012 to 2020
$4.5M
Massively Parallel Analysis of Integration in Therapeutic Gene TransferR01AI082020 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI BUSHMAN, FREDERIC D · 2009 to 2018
$3.5M
Immunoglobulin and T Cell Receptor Gene AssemblyR37AI032524 · NIAID · YALE UNIVERSITY · PI SCHATZ, DAVID G. · 2007 to 2016
$3.5M
CIHRNCI NIH HHS P30 CA016359NIAID NIH HHS R01 AI074953NIAID NIH HHS R01 AI082020NIAID NIH HHS R01 AI100887NIAID NIH HHS R37 AI032524NIAID NIH HHS U54 AI082973
6 · The paper itself

Abstract

Primary immunodeficiency diseases comprise a group of heterogeneous genetic defects that affect immune system development and/or function. Here we use in vitro differentiation of human induced pluripotent stem cells (iPSCs) generated from patients with different recombination-activating gene 1 (RAG1) mutations to assess T-cell development and T-cell receptor (TCR) V(D)J recombination. RAG1-mutants from severe combined immunodeficient (SCID) patient cells showed a failure to sustain progression beyond the CD3(--)CD4(-)CD8(-)CD7(+)CD5(+)CD38(-)CD31(-/lo)CD45RA(+) stage of T-cell development to reach the CD3(-/+)CD4(+)CD8(+)CD7(+)CD5(+)CD38(+)CD31(+)CD45RA(-) stage. Despite residual mutant RAG1 recombination activity from an Omenn syndrome (OS) patient, similar impaired T-cell differentiation was observed, due to increased single-strand DNA breaks that likely occur due to heterodimers consisting of both an N-terminal truncated and a catalytically dead RAG1. Furthermore, deep-sequencing analysis of TCR-β (TRB) and TCR-α (TRA) rearrangements of CD3(-)CD4(+)CD8(-) immature single-positive and CD3(+)CD4(+)CD8(+) double-positive cells showed severe restriction of repertoire diversity with preferential usage of few Variable, Diversity, and Joining genes, and skewed length distribution of the TRB and TRA complementary determining region 3 sequences from SCID and OS iPSC-derived cells, whereas control iPSCs yielded T-cell progenitors with a broadly diversified repertoire. Finally, no TRA/δ excision circles (TRECs), a marker of TRA/δ locus rearrangements, were detected in SCID and OS-derived T-lineage cells, consistent with a pre-TCR block in T-cell development. This study compares human T-cell development of SCID vs OS patients, and elucidates important differences that help to explain the wide range of immunologic phenotypes that result from different mutations within the same gene of various patients.

Indexed as

Cells, CulturedDNA BreaksGenes, RAG-1Homeodomain ProteinsHumansInduced Pluripotent Stem CellsInfantMutationReceptors, Antigen, T-Cell, alpha-betaSevere Combined ImmunodeficiencyT-LymphocytesV(D)J RecombinationHomeodomain ProteinsRAG-1 proteinReceptors, Antigen, T-Cell, alpha-beta

Identifiers

PMID27301863
PMCPMC4982452
OpenAlexW2435859559

What OpenQuestion holds

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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.