Evidence map›Paper›PMID 26282792›Full record

ArticleThe EMBO journal2015

KIM-1-/TIM-1-mediated phagocytosis links ATG5-/ULK1-dependent clearance of apoptotic cells to antigen presentation.

Craig R Brooks, Melissa Y Yeung, Yang S Brooks, Hui Chen, Takaharu Ichimura, Joel M Henderson, Joseph V Bonventre

Open access · bronzeAbstract read
In one paragraph

Article in The EMBO journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.

0numbers the graph read from it
0cells of the map it votes in
60citing papers in PubMed
3.9field-weighted citation impact, top 6% 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

60 citing papers in PubMed, 90 citations in OpenAlex.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors at 3 institutions in 1 country.

Craig R BrooksDepartment of Medicine, Renal Division, Brigham and Women's Hospital Harvard Medical School, Boston, MA, USA crbrooks@partners.org joseph_bonventre@hms.harvard.edu.
Melissa Y YeungDepartment of Medicine, Renal Division, Brigham and Women's Hospital Harvard Medical School, Boston, MA, USA Transplantation Research Center, Brigham and Women's Hospital Harvard Medical School, Boston, MA, USA.
Yang S BrooksCutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, MA, USA Department of Dermatology, Harvard Medical School, Boston, MA, USA.
Hui ChenDepartment of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA.
Takaharu IchimuraDepartment of Medicine, Renal Division, Brigham and Women's Hospital Harvard Medical School, Boston, MA, USA.
Joel M HendersonDepartment of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA.
Joseph V BonventreDepartment of Medicine, Renal Division, Brigham and Women's Hospital Harvard Medical School, Boston, MA, USA Harvard Stem Cell Institute, Cambridge, MA, USA crbrooks@partners.org joseph_bonventre@hms.harvard.edu.
Brigham and Women's Hospital · USBoston University · USHarvard University · US

Funding

KIDNEY INJURY MOLECULE-1 IN EPITHELIAL REPAIRR01DK072381 · NIDDK · BRIGHAM AND WOMEN'S HOSPITAL · PI BONVENTRE, JOSEPH VINCENT · 2005 to 2025
$8.6M
Mechanisms of Ischemic Kidney Injury and RepairR01DK039773 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI JOSEPH VINCENT BONVENTRE · 1987 to 2026
$6.2M
Mechanisms of Ischemic Kidney Injury and RepairR37DK039773 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI BONVENTRE, JOSEPH VINCENT · 1993 to 2021
$5.2M
Proximal tubule Kim-1 expression modulates acute and chronic kidney injuryK01DK099473 · NIDDK · VANDERBILT UNIVERSITY MEDICAL CENTER · PI BROOKS, CRAIG ROBERT · 2013 to 2017
$787k
Kim-1 regulation of autophagy and MHC presentation in kidney injuryF32DK088418 · NIDDK · BRIGHAM AND WOMEN'S HOSPITAL · PI BROOKS, CRAIG ROBERT · 2010 to 2012
$153k
NIDDK NIH HHS DK088418NIDDK NIH HHS DK099473NIDDK NIH HHS DK39773NIDDK NIH HHS DK72381NIDDK NIH HHS K01 DK099473NIDDK NIH HHS R01 DK072381NIDDK NIH HHS R37 DK039773
6 · The paper itself

Abstract

Phagocytosis of apoptotic cells by both professional and semi-professional phagocytes is required for resolution of organ damage and maintenance of immune tolerance. KIM-1/TIM-1 is a phosphatidylserine receptor that is expressed on epithelial cells and can transform the cells into phagocytes. Here, we demonstrate that KIM-1 phosphorylation and association with p85 results in encapsulation of phagosomes by lipidated LC3 in multi-membrane organelles. KIM-1-mediated phagocytosis is not associated with increased ROS production, and NOX inhibition does not block LC3 lipidation. Autophagy gene expression is required for efficient clearance of apoptotic cells and phagosome maturation. KIM-1-mediated phagocytosis leads to pro-tolerogenic antigen presentation, which suppresses CD4 T-cell proliferation and increases the percentage of regulatory T cells in an autophagy gene-dependent manner. Taken together, these data reveal a novel mechanism of epithelial biology linking phagocytosis, autophagy and antigen presentation to regulation of the inflammatory response.

Indexed as

Antigen PresentationApoptosisAutophagy-Related Protein-1 HomologAutophagy-Related Protein 5CD4-Positive T-LymphocytesCell ProliferationHEK293 CellsHepatitis A Virus Cellular Receptor 1HumansIntracellular Signaling Peptides and ProteinsLipoylationMembrane GlycoproteinsMicrotubule-Associated ProteinsPhagocytosisProtein Serine-Threonine KinasesReactive Oxygen SpeciesATG5 protein, humanAutophagy-Related Protein-1 HomologAutophagy-Related Protein 5HAVCR1 protein, humanHepatitis A Virus Cellular Receptor 1Intracellular Signaling Peptides and ProteinsMAP1LC3A protein, humanMembrane GlycoproteinsMicrotubule-Associated ProteinsProtein Serine-Threonine KinasesReactive Oxygen SpeciesReceptors, VirusULK1 protein, humanacute kidney injurybiomarkerheterophagyMHCT regs

Identifiers

PMID26282792
PMCPMC4601664
OpenAlexW2122008192

What OpenQuestion holds

Textmetadata
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.