Evidence map›Paper›PMID 26194095›Full record

ArticleNature communications2015

Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst.

Daniel B Graham, Christine E Becker, Aivi Doan, Gautam Goel, Eduardo J Villablanca, Dan Knights, Amanda Mok, Aylwin C Y Ng, John G Doench, David E Root and 2 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.

0numbers the graph read from it
0cells of the map it votes in
24citing papers in PubMed
1.7field-weighted citation impact, top 17% 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

24 citing papers in PubMed, 37 citations in OpenAlex.

  1. Review
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  4. Article
  5. Article
  6. Article
  7. Review
  8. Review
  9. Article
  10. Friend or Foe: The Relativity of (Anti)oxidative Agents and Pathways.International journal of molecular sciences · 2022
    Review
  11. Review
  12. Article
  13. Article
  14. Article
  15. Review
  16. Jersey steer ruminal papillae histology and nutrigenomics with diet changes.Journal of animal physiology and animal nutrition · 2019
    Article
  17. Article
  18. Article
  19. Article
  20. CPT1A methylation is associated with plasma adiponectin.Nutrition, metabolism, and cardiovascular diseases : NMCD · 2017
    Article
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

12 authors at 4 institutions in 1 country.

Daniel B GrahamBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Christine E BeckerCenter for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.
Aivi DoanBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Gautam GoelCenter for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.
Eduardo J VillablancaBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Dan KnightsDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA.
Amanda MokBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Aylwin C Y NgBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
John G DoenchBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
David E RootBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Clary B ClishBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Ramnik J XavierBroad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Broad Institute · USHarvard University · USCenter for Systems Biology · USUniversity of Minnesota · US

Funding

Pilot & Feasibility ProgramP30DK043351 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI RAYMOND T CHUNG · 1991 to 2026
$35.3M
Universite de Montreal IBD Genetics Research CenterU01DK062432 · NIDDK · WHITEHEAD INSTITUTE FOR BIOMEDICAL RES · PI John D. Rioux · 2002 to 2026
$9.6M
NIDDK NIH HHS DK043351NIDDK NIH HHS P30 DK043351NIDDK NIH HHS U01 DK062432
6 · The paper itself

Abstract

The phagocyte oxidative burst, mediated by Nox2 NADPH oxidase-derived reactive oxygen species, confers host defense against a broad spectrum of bacterial and fungal pathogens. Loss-of-function mutations that impair function of the Nox2 complex result in a life-threatening immunodeficiency, and genetic variants of Nox2 subunits have been implicated in pathogenesis of inflammatory bowel disease (IBD). Thus, alterations in the oxidative burst can profoundly impact host defense, yet little is known about regulatory mechanisms that fine-tune this response. Here we report the discovery of regulatory nodes controlling oxidative burst by functional screening of genes within loci linked to human inflammatory disease. Implementing a multi-omics approach, we define transcriptional, metabolic and ubiquitin-cycling nodes controlled by Rbpj, Pfkl and Rnf145, respectively. Furthermore, we implicate Rnf145 in proteostasis of the Nox2 complex by endoplasmic reticulum-associated degradation. Consequently, ablation of Rnf145 in murine macrophages enhances bacterial clearance, and rescues the oxidative burst defects associated with Ncf4 haploinsufficiency.

Indexed as

Respiratory BurstAnimalsBase SequenceCell LineGenomicsImmunoglobulin J Recombination Signal Sequence-Binding ProteinMembrane GlycoproteinsMembrane ProteinsMiceMolecular Sequence DataNADPH Oxidase 2NADPH OxidasesPhagocytesPhosphofructokinase-1Staphylococcus aureusCybb protein, mouseImmunoglobulin J Recombination Signal Sequence-Binding ProteinMembrane GlycoproteinsMembrane ProteinsNADPH Oxidase 2NADPH OxidasesPhosphofructokinase-1Rbpj protein, mouseRNF145 protein, mouse

Identifiers

PMID26194095
PMCPMC4518307
OpenAlexW1045432066

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.