Evidence map›Paper›PMID 38173717›Full record

ArticleFrontiers in immunology2023

Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization.

Yubo Zhang, Wenbo Yang, Yutaro Kumagai, Martin Loza, Weihang Zhang, Sung-Joon Park, Kenta Nakai

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

Article in Frontiers in immunology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.8field-weighted citation impact, top 26% 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

4 citing papers in PubMed, 5 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

7 authors at 2 institutions in 1 country.

Yubo ZhangDepartment of Computational Biology and Medical Science, the University of Tokyo, Tokyo, Japan.
Wenbo YangDepartment of Computational Biology and Medical Science, the University of Tokyo, Tokyo, Japan.
Yutaro KumagaiDepartment of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
Martin LozaHuman Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan.
Weihang ZhangDepartment of Computational Biology and Medical Science, the University of Tokyo, Tokyo, Japan.
Sung-Joon ParkHuman Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan.
Kenta NakaiDepartment of Computational Biology and Medical Science, the University of Tokyo, Tokyo, Japan.
The University of Tokyo · JPNational Institute of Advanced Industrial Science and Technology · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Macrophages display extreme plasticity, and the mechanisms and applications of polarization and de-/repolarization of macrophages have been extensively investigated. However, the regulation of macrophage hysteresis after de-/repolarization remains unclear. In this study, by using a large-scale computational analysis of macrophage multi-omics data, we report a list of hysteresis genes that maintain their expression patterns after polarization and de-/repolarization. While the polarization in M1 macrophages leads to a higher level of hysteresis in genes associated with cell cycle progression, cell migration, and enhancement of the immune response, we found weak levels of hysteresis after M2 polarization. During the polarization process from M0 to M1 and back to M0, the factors IRFs/STAT, AP-1, and CTCF regulate hysteresis by altering their binding sites to the chromatin. Overall, our results show that a history of polarization can lead to hysteresis in gene expression and chromatin accessibility over a given period. This study contributes to the understanding of de-/repolarization memory in macrophages.

Indexed as

ChromatinTranscription Factor AP-1MacrophagesMultiomicsChromatinTranscription Factor AP-1graph embeddingM1 macrophageM2 macrophagemacrophage hysteresismacrophagesmulti omics analysispolarization memoryrepolarization

Identifiers

PMID38173717
PMCPMC10761412
OpenAlexW4390009140

What OpenQuestion holds

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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.