Evidence map›Paper›PMID 40667223›Full record

ArticlebioRxiv : the preprint server for biology2025

Cell cycle-coupled transcriptional network orchestrates human B cell fate bifurcation.

Nicholas A Pease, Jingyu Fan, Swapnil Keshari, Jered Stratton, Peter Gerges, Betsy Ann Varghese, Narayanan Vp Nampoothiri, Christopher S McGinnis, Wenxi Zhang, Steven B Gierlack and 13 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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

23 authors.

Nicholas A PeaseCenter for Systems Immunology and Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.ORCID 0000-0001-6140-1949
Jingyu FanCenter for Systems Immunology and Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.ORCID 0000-0003-2440-2015
Swapnil KeshariCenter for Systems Immunology and Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.ORCID 0000-0001-6451-9432
Jered StrattonCenter for Systems Immunology and Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.
Peter GergesCenter for Systems Immunology and Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.
Betsy Ann VargheseDeparment of Computational and Systems Biology, UPMC Hillman Cancer Center, University of Pittsburgh, PA.
Narayanan Vp NampoothiriDeparment of Computational and Systems Biology, UPMC Hillman Cancer Center, University of Pittsburgh, PA.
Christopher S McGinnisDeparment of Pathology, Stanford University, Stanford, CA.
Wenxi ZhangDeparment of Pathology, Stanford University, Stanford, CA.
Steven B GierlackCenter for Systems Immunology and Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.
Tanush SwaminathanCenter for Systems Immunology and Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.
Akanksha SachanCenter for Systems Immunology and Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.
Godhev Manakkat VijayCenter for Systems Immunology and Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.
Luis Mena HernandezCenter for Systems Immunology and Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.
Zarifeh Heidari RaraniCenter for Systems Immunology and Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.
Camila MacedoDepartment of Surgery, University of Pittsburgh, Pittsburgh, PA.
Diana MetesDepartment of Surgery, University of Pittsburgh, Pittsburgh, PA.
Ansuman T SatpathyDeparment of Pathology, Stanford University, Stanford, CA.
Abhinav K JainDepartment of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX.
Nidhi SahniDepartment of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX.
Wayne StallaertDeparment of Computational and Systems Biology, UPMC Hillman Cancer Center, University of Pittsburgh, PA.
Jishnu DasCenter for Systems Immunology and Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.ORCID 0000-0002-5747-064X
Harinder SinghCenter for Systems Immunology and Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.ORCID 0000-0002-6330-8526

Funding

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
Autoimmunity and Immunopathology Training ProgramT32AI089443 · NIAID · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI SHLOMCHIK, MARK J · 2010 to 2024
$6.6M
Linking genome variation to transcriptional network dynamics in human B cellsU01HG012041 · NHGRI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Jishnu Das, HARINDER SINGH · 2021 to 2026
$6.1M
Uncovering latent factors underlying weak and robust responses to influenza vaccine in healthy and obese older adultsR01AI170108 · NIAID · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI John F Alcorn, Jishnu Das · 2022 to 2026
$3.9M
Diversity of TFH cells and DSA generation after kidney transplantationR01AI130010 · NIAID · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI METES, DIANA M · 2017 to 2021
$3.4M
B and Tfh cell dynamics underlying durable antibody responses to flu vaccine in childrenU01AI179514 · NIAID · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI John F Alcorn, Jishnu Das · 2024 to 2026
$2.0M
High-Throughput Computing for Genomics and Bioinformatics ResearchS10OD028483 · OD · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI LEE, ADRIAN V · 2021 to 2021
$574k
NHGRI NIH HHS U01 HG012041NHGRI NIH HHS UM1 HG012076NIAID NIH HHS R01 AI130010NIAID NIH HHS R01 AI170108NIAID NIH HHS T32 AI089443NIAID NIH HHS U01 AI179514NIH HHS S10 OD028483
6 · The paper itself

Abstract

Antibody responses are determined by activated B cells bifurcating into plasmablasts (PBs) and germinal center B cells (GCBCs). Gene regulatory networks (GRNs) underlying human B cell fate choice remain uncharted. Temporally resolved single-cell multi-omics, computational modeling and CRISPR-based perturbations were used to assemble, simulate and test high-resolution GRNs underlying PB and GC fates. The results converged with orthogonal predictions of transcription factor (TF) action at single-nucleotide resolution, revealing dominant and reciprocal actions of IRF4 and its binding partners at simple and composite IRF motifs. Single-cell perturbation analysis of these TFs demonstrated multiple reciprocal negative feedback loops controlling the bifurcation. Additionally, IRF4 and BLIMP1, co-repressed the cell cycle regulators

Indexed as

cell cycle-coupled cell fatesGene regulatory networkshuman B cell differentiationMap-Predict-Perturbsingle-cell multi-omics

Identifiers

PMID40667223
PMCPMC12262194

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.