Evidence map›Paper›PMID 36571819›Full record

ArticleJournal of Crohn's & colitis2023

Mass-Cytometry-Based Quantification of Global Histone Post-Translational Modifications at Single-Cell Resolution Across Peripheral Immune Cells in IBD.

Lawrence Bai, Denis Dermadi, Laurynas Kalesinskas, Mai Dvorak, Sarah E Chang, Ananthakrishnan Ganesan, Samuel J S Rubin, Alex Kuo, Peggie Cheung, Michele Donato and 3 more

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

Article in Journal of Crohn's & colitis, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
0.7field-weighted citation impact, top 32% 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

8 citing papers in PubMed, 8 citations in OpenAlex.

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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

13 authors at 1 institution in 1 country.

Lawrence BaiImmunology Program, Stanford University School of Medicine, 1215 Welch Road, Modular B, Stanford, CA 94305, USA.
Denis DermadiInstitute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.
Laurynas KalesinskasBiomedical Informatics Training Program, Stanford University School of Medicine, 1265 Welch Road, MSOB X-343, Stanford, CA 94305, USA.ORCID 0000-0002-2903-2378
Mai DvorakInstitute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.
Sarah E ChangInstitute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.
Ananthakrishnan GanesanComputational and Mathematical Engineering, Stanford University, 475 Via Ortega, Suite B060, Stanford, CA 94305, USA.ORCID 0000-0001-6242-4261
Samuel J S RubinDivision of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
Alex KuoInstitute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.
Peggie CheungInstitute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.
Michele DonatoInstitute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.
Paul J UtzImmunology Program, Stanford University School of Medicine, 1215 Welch Road, Modular B, Stanford, CA 94305, USA.
Aida HabtezionImmunology Program, Stanford University School of Medicine, 1215 Welch Road, Modular B, Stanford, CA 94305, USA.
Purvesh KhatriImmunology Program, Stanford University School of Medicine, 1215 Welch Road, Modular B, Stanford, CA 94305, USA.ORCID 0000-0002-4143-4708
Stanford University · US

Funding

Using a tonsil organoid system to probe conditions for the induction of protective antibody and T cell responses to influenza.U19AI057229 · NIAID · STANFORD UNIVERSITY · PI Mark Morris Davis · 2003 to 2026
$88.5M
Translational Incubator CoreU19AI109662 · NIAID · STANFORD UNIVERSITY · PI GLENN, JEFFREY S · 2014 to 2019
$28.6M
NIAID NIH HHS U19 AI057229NIAID NIH HHS U19 AI109662
6 · The paper itself

Abstract

BACKGROUND AND

aimsCurrent understanding of histone post-translational modifications [histone modifications] across immune cell types in patients with inflammatory bowel disease [IBD] during remission and flare is limited. The present study aimed to quantify histone modifications at a single-cell resolution in IBD patients during remission and flare and how they differ compared to healthy controls.

methodsWe performed a case-control study of 94 subjects [83 IBD patients and 11 healthy controls]. IBD patients had either ulcerative colitis [n = 38] or Crohn's disease [n = 45] in clinical remission or flare. We used epigenetic profiling by time-of-flight [EpiTOF] to investigate changes in histone modifications within peripheral blood mononuclear cells from IBD patients.

resultsWe discovered substantial heterogeneity in histone modifications across multiple immune cell types in IBD patients. They had a higher proportion of less differentiated CD34+ haematopoietic progenitors, and a subset of CD56bright natural killer [NK] cells and γδ T cells characterized by distinct histone modifications associated with gene transcription. The subset of CD56bright NK cells had increases in several histone acetylations. An epigenetically defined subset of NK cells was associated with higher levels of C-reactive protein in peripheral blood. CD34+ monocytes from IBD patients had significantly decreased cleaved H3T22, suggesting they were epigenetically primed for macrophage differentiation.

conclusionWe describe the first systems-level quantification of histone modifications across immune cells from IBD patients at a single-cell resolution, revealing the increased epigenetic heterogeneity that is not possible with traditional ChIP-seq profiling. Our data open new directions in investigating the association between histone modifications and IBD pathology using other epigenomic tools.

Indexed as

Colitis, UlcerativeInflammatory Bowel DiseasesCase-Control StudiesHistonesHumansLeukocytes, MononuclearProtein Processing, Post-TranslationalHistonescrohn's diseasehistone modificationsinflammatory bowel diseaseSingle-cell epigeneticulcerative colitis

Identifiers

PMID36571819
PMCPMC10155749
OpenAlexW4312211040

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.