Evidence map›Paper›PMID 38374043›Full record

ArticleNature communications2024

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.

Elvira Mennillo, Yang Joon Kim, Gyehyun Lee, Iulia Rusu, Ravi K Patel, Leah C Dorman, Emily Flynn, Stephanie Li, Jared L Bain, Christopher Andersen and 21 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
51citing papers in PubMed, 1 pooled it
10.5field-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

51 citing papers in PubMed, 1 synthesis or guideline pooled it, 46 citations in OpenAlex.

  1. Pooled it
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  7. Emerging technologies in the spatial proteomics landscape.Analytical and bioanalytical chemistry · 2026
    Review
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

31 authors at 2 institutions in 1 country.

Elvira MennilloDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.ORCID 0000-0002-3210-1004
Yang Joon KimChan Zuckerberg Biohub, San Francisco, CA, USA.
Gyehyun LeeDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Iulia RusuDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Ravi K PatelDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.ORCID 0000-0001-5203-899X
Leah C DormanChan Zuckerberg Biohub, San Francisco, CA, USA.
Emily FlynnCoLabs, University of California San Francisco, San Francisco, CA, USA.
Stephanie LiDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Jared L BainDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Christopher AndersenDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Arjun RaoDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Stanley TamakiCoLabs, University of California San Francisco, San Francisco, CA, USA.
Jessica TsuiDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Alan ShenDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Madison L LotsteinDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Maha RahimHelen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94143, USA.
Mohammad NaserBiological Imaging Development CoLab, University of California San Francisco, San Francisco, CA, USA.ORCID 0000-0002-9025-2759
Faviola Bernard-VazquezDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Walter EckalbarCoLabs, University of California San Francisco, San Francisco, CA, USA.
Soo-Jin ChoDepartment of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA.ORCID 0000-0001-6324-6858
Kendall BeckDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Najwa El-NachefDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Sara LewinDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Daniel R SelvigDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Jonathan P TerdimanDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Uma MahadevanDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
David Y OhDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Gabriela K FragiadakisDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.ORCID 0000-0001-9703-2591
Angela PiscoChan Zuckerberg Biohub, San Francisco, CA, USA.ORCID 0000-0003-0142-2355
Alexis J CombesDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.ORCID 0000-0002-9110-6542
Michael G KattahDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA. michael.kattah@ucsf.edu.ORCID 0000-0002-6067-6585
University of California, San Francisco · USChan Zuckerberg Initiative (United States) · US

Funding

Research BaseP30DK063720 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KRUMMEL, MATTHEW F · 2003 to 2019
$21.8M
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 · 2020 to 2026
$4.5M
A shared resource for multiplexed ion beam imaging microscopyS10OD025187 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI VANDENBERG, SCOTT RUSSEL · 2018 to 2018
$1.2M
Mechanisms of intestinal epithelial injury in intestinal inflammationK08DK123202 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KATTAH, MICHAEL GEORGE · 2020 to 2024
$860k
UCSF DVS CyTOF Mass CytometerS10OD018040 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LANIER, LEWIS LEE · 2014 to 2014
$600k
NIAMS NIH HHS P30 AR070155NIDDK NIH HHS K08 DK123202NIDDK NIH HHS P30 DK063720NIGMS NIH HHS T32 GM136547NIH HHS S10 OD018040NIH HHS S10 OD025187
6 · The paper itself

Abstract

Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we perform single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.

Indexed as

Colitis, UlcerativeGastrointestinal AgentsHumansIntegrinsMultiomicsProteomicsRetrospective StudiesTreatment OutcomeGastrointestinal AgentsIntegrins

Identifiers

PMID38374043
PMCPMC10876948
OpenAlexW4391926902

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.