Evidence map›Paper›PMID 40880129›Full record

ArticleThe Journal of cell biology2025

ATG conjugation-dependent/independent mechanisms underlie lysosomal stress-induced TFEB regulation.

Shiori Akayama, Takayuki Shima, Tatsuya Kaminishi, Mengying Cui, Jlenia Monfregola, Kohei Nishino, Andrea Ballabio, Hidetaka Kosako, Tamotsu Yoshimori, Shuhei Nakamura

Abstract read
In one paragraph

Article in The Journal of cell biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
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

2 citing papers in PubMed.

  1. Review
  2. Review
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

10 authors.

Shiori Akayama *Graduate School of Frontier Biosciences, Osaka University , Suita, Japan.ORCID 0009-0000-0553-2530
Takayuki Shima *Department of Biochemistry, Nara Medical University, Kashihara, Japan.ORCID 0000-0003-4480-3959
Tatsuya KaminishiGraduate School of Medicine, Osaka University , Suita, Japan.ORCID 0000-0001-5056-1074
Mengying CuiGraduate School of Medicine, Osaka University , Suita, Japan.ORCID 0009-0006-1086-9932
Jlenia MonfregolaTelethon Institute of Genetics and Medicine (TIGEM) , Naples, Italy.ORCID 0000-0001-7408-4428
Kohei NishinoFujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University , Tokushima, Japan.ORCID 0000-0002-1573-3173
Andrea BallabioTelethon Institute of Genetics and Medicine (TIGEM) , Naples, Italy.ORCID 0000-0003-1381-4604
Hidetaka KosakoFujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University , Tokushima, Japan.ORCID 0000-0003-3228-6368
Tamotsu YoshimoriDepartment of Beyond Cell Reborn Research, Graduate School of Medicine, The University of Osaka, Suita, Japan.ORCID 0000-0001-9787-3788
Shuhei NakamuraDepartment of Biochemistry, Nara Medical University, Kashihara, Japan.ORCID 0000-0002-1488-8317

Funding

Associazione Italiana per la Ricerca sul CancroAstellas Foundation for Research on Metabolic DisordersCell Science Research FoundationChugai FoundationEuropean Research CouncilJapan Agency for Medical Research and Development JP22gm1410014Japan Agency for Medical Research and Development JP24gm1910008Japan Society for the Promotion of Science 19K22429Japan Society for the Promotion of Science 21H02428Japan Society for the Promotion of Science 22H04982Japan Society for the Promotion of Science 22J11895Japan Society for the Promotion of Science 23K18140Japan Society for the Promotion of Science 24H01910Japan Society for the Promotion of Science 24K01979Japan Society for the Promotion of Science 24K18072Ministero dell'Università e della RicercaMinistry of Education, Culture, Sports, Science and Technology 21H05145Mitsubishi FoundationMochida Memorial Foundation for Medical and Pharmaceutical ResearchNara Medical UniversityNOVARTIS Foundation (Japan) for the Promotion of ScienceTakeda Science FoundationTelethon FoundationThe Uehara Memorial FoundationTokushima UniversityToray Science Foundation 23-6408
6 · The paper itself

Abstract

TFEB, a master regulator of autophagy and lysosomal biogenesis, is activated by several cellular stresses including lysosomal damage, but its underlying mechanism is unclear. TFEB activation during lysosomal damage depends on the ATG conjugation system, which mediates lipidation of ATG8 proteins. Here, we newly identify ATG conjugation-independent TFEB regulation that precedes ATG conjugation-dependent regulation, designated Modes I and II, respectively. We reveal unique regulators of TFEB in each mode: APEX1 in Mode I and CCT7 and/or TRIP6 in Mode II. APEX1 interacts with TFEB independently of the ATG conjugation system, and is required for TFEB stability, while both CCT7 and TRIP6 accumulate on lysosomes during lysosomal damage, and interact with TFEB mainly in ATG conjugation system-deficient cells, presumably blocking TFEB activation. TFEB activation by several other stresses also involves either Mode I or Mode II. Our results pave the way for a unified understanding of TFEB regulatory mechanisms from the perspective of the ATG conjugation system under a variety of cellular stresses.

Indexed as

AutophagyAutophagy-Related Protein 8 FamilyBasic Helix-Loop-Helix Leucine Zipper Transcription FactorsLysosomesStress, PhysiologicalAnimalsHEK293 CellsHeLa CellsHumansMiceAutophagy-Related Protein 8 FamilyBasic Helix-Loop-Helix Leucine Zipper Transcription FactorsTFEB protein, human

Identifiers

PMID40880129
PMCPMC12396377

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.