bims-tofagi 2025-06-08 papers

Issue of 2025–06–08
five papers selected by
Michele Frison, University of Cambridge

J Mol Biol. 2025 Jun 03. pii: S0022-2836(25)00329-8. [Epub ahead of print] 169263

The developing retina undergoes mitochondrial remodeling via PINK1/PRKN-dependent mitophagy.

Juan Zapata-Muñoz, Juan Ignacio Jiménez-Loygorri, Michael Stumpe, Beatriz Villarejo-Zori, Sandra Alonso-Gil, Petra Terešak, Benan J Mathai, Ian G Ganley, Anne Simonsen, Jörn Dengjel, Patricia Boya.

Mitophagy, the selective degradation of mitochondria, is essential for retinal ganglion cell (RGC) differentiation and retinal homeostasis. However, the specific mitophagy pathways involved and their temporal dynamics during retinal development and maturation remain poorly understood. Using proteomics analysis of isolated mouse retinas across developmental stages and the mitophagy reporter mouse line, mito-QC, we characterized mitophagy throughout retinogenesis. While mitolysosomes were more prevalent in the mature retina, we observed two distinct mitophagy peaks during embryonic development. The first, independent of PTEN-induced kinase 1 (PINK1) activation, was associated with RGCs. The second, PINK1-dependent peak was triggered after an increase in retinal oxidative stress. This PINK1-dependent, oxidative stress-induced mitophagy pathway is conserved in mice and zebrafish, providing the first evidence of programmed, PINK1-dependent mitophagy during development.

Keywords: PINK1; autophagy; development; mitophagy; retina

DOI: https://doi.org/10.1016/j.jmb.2025.169263

Nat Commun. 2025 Jun 04. 16(1): 5179

An AI-assisted fluorescence microscopic system for screening mitophagy inducers by simultaneous analysis of mitophagic intermediates.

Yicheng Wang, Pengfei Song, Heqing Zhou, Pengwei Wang, Yan Li, Zhiyong Shao, Lu Wang, Yan You, Zuhai Lei, Jinhua Yu, Cong Li.

Mitophagy, the selective autophagic elimination of mitochondria, is essential for maintaining mitochondrial quality and cell homeostasis. Impairment of mitophagy flux, a process involving multiple sequential intermediates, is implicated in the onset of numerous neurodegenerative diseases. Screening mitophagy inducers, particularly understanding their impact on mitophagic intermediates, is crucial for neurodegenerative disease treatment. However, existing techniques do not allow simultaneous visualization of distinct mitophagic intermediates in live cells. Here, we introduce an artificial intelligence-assisted fluorescence microscopic system (AI-FM) that enables the uninterrupted recognition and quantification of key mitophagic intermediates by extracting mitochondrial pH and morphological features. Using AI-FM, we identify a potential mitophagy modulator, Y040-7904, which enhances mitophagy by promoting mitochondria transport to autophagosomes and the fusion of autophagosomes with autolysosomes. Y040-7904 also reduces amyloid-β pathologies in both in vitro and in vivo models of Alzheimer's disease. This work offers an approach for visualizing the entire mitophagy flux, advancing the understanding of mitophagy-related mechanisms and enabling the discovery of mitophagy inducers for neurodegenerative diseases.

DOI: https://doi.org/10.1038/s41467-025-60315-1

J Biol Chem. 2025 Jun 03. pii: S0021-9258(25)02184-2. [Epub ahead of print] 110334

Mitochondrial tRNA processing defects reprogram mitochondrial and cellular homeostasis.

Gao Zhu, Yunfan He, Xincheng Li, Yun Xiao, Huisen Zhan, Maoli Duan, Min-Xin Guan.

Mitochondrial tRNA processing defects have been associated with some clinical presentations including deafness. Especially, a deafness-linked m.7516delA mutation impaired the 5' end processing of RNA precursors and mitochondrial translation. In this study, we investigated the mechanism by m.7516delA mutation induced-deficiencies mitigate organellular and cellular integrity. The m.7516delA mutation downregulated the expression of nucleus encoding subunits and upregulated assemble factors of complex IV and altered the assembly and activities of oxidative phosphorylation (OXPHOS) complexes. The impairment of OXPHOS alleviated mitochondrial quality control processes, including the imbalanced mitochondrial dynamics via increasing fission with abnormal mitochondrial morphology. The m.7516delA mutation upregulated both ubiquitin-dependent and independent mitophagy pathways, evidenced by increasing levels of Parkin, BNIP3, NIX and MFN2-ubiquitination and altering interaction between MFN2 and MUL1 or Parkin, to facilitate the degradation of severely damaged mitochondria. Strikingly, the m.7516delA mutation activated integrated stress response (ISR) pathway, evidenced by upregulation of GCN2, P-GCN2, p-eIF2α, CHOP, ATF4 and elevating the nucleus-location of ATF5 to minimizes the damages in defective mitochondria. Both activation of ISR and PINK1/Parkin mitophagy pathways ameliorate the cell homeostasis via elevating the autophagy process and upregulating apoptotic pathways. Our findings provide new insights into underlying aberrant RNA processing-induced dysfunctions reprogrammed organelles and cellular integrity.

DOI: https://doi.org/10.1016/j.jbc.2025.110334

Aging Cell. 2025 Jun 06. e70125

Type-Specific Single-Neuron Analysis Reveals Mitochondrial DNA Maintenance Failure Affecting Atrophying Pontine Neurons Differentially in Lewy Body Dementia Syndromes.

Eloise J Stephenson, Laura J Bailey, Stephen Gentleman, Helen Tuppen, Istvan Bodi, Claire Troakes, Christopher M Morris, Tony M Carr, Sarah Guthrie, Joanna L Elson, Ilse S Pienaar.

The age-associated neurodegenerative disorder, Lewy body dementia (LBD), encompasses neuropsychiatric symptom-overlapping Dementia with Lewy bodies (DLB) and Parkinson's Disease with Dementia (PDD). We characterised how differential mitochondrial DNA (mtDNA) profiles contribute to neurotype-specific neurodegeneration and thereby clinicopathological heterogeneity, between LBD's syndromes. We further characterised key nuclear-encoding genes' recalibrations in response to such mtDNA changes. In post-mortem 'single-cell' acetylcholine- and noradrenaline-producing neurons, respectively of the pedunculopontine nucleus (PPN) and locus coeruleus (LC) from DLB, PDD and neurological-control brains, we quantified 'major arc'-locating mtDNA deletions (mtDels) and -copy number (mtCN), and measured mRNA levels of nuclear-encoding genes regulating mtDNA maintenance, -biogenesis and mitophagy. DLB cases' OXPHOS defect instigating mtDel burden was higher in both neurotypes than PDD. In DLB, mtCN was reduced for both neurotypes, but PDD cases revealed mtDNA depletion in LC-noradrenergic neurons only. DLB patients' shorter survival correlated with PPN-cholinergic neurons' mtDel levels, inversely with wild-type mtCN, implying that such neurons' inability to maintain sufficient wild-type mtDNA content drive DLBs' rapid psycho-cognitive manifestations. Contrastingly, PDD's longer disease duration allowed compensation against mtDels' clonal expansion in PPN-cholinergic neurons. Moreover, PDD induced mRNA depletion of a mitochondrial genome maintenance gene in PPN-cholinergic neurons, whilst LC-noradrenergic neurons displayed reduced expression of a mitophagy regulating gene. Here we identify mitochondrial genome maintenance and mitophagy pathway enrichment as therapeutic targets to offset defective mtDNA within pontine cholinergic and noradrenergic neurons of PDD patients. The pronounced LBD subtype-related mitochondria-nuclear genetic differences question the consensus that pathology converges at disease end-stage, calling for LBD subtype and neurotype-specific therapeutics.

Keywords: Lewy body dementia; brainstem; cholinergic neurons; mitochondrial DNA; noradrenergic neurons; nuclear gene transcriptomic responses

DOI: https://doi.org/10.1111/acel.70125

FEBS J. 2025 Jun 01.

PINK1/Parkin-based live-cell quantitative FRET imaging for mitophagy drug screening.

Beini Sun, Kangrong Deng, Qialing Huang, Lin Cheng, Wei Yao, Zhirui Wu, Xiaoping Wang, Ming Dong, Tongsheng Chen.

PINK1 (PTEN-induced kinase 1) and Parkin (parkin RBR E3 ubiquitin protein) ligase are important regulators for cells to maintain mitochondrial number and functional homeostasis. Here, we established a PINK1/Parkin-based mitophagy drug evaluation method using quantitative Förster resonance energy transfer (FRET) imaging in living cells. A stable model of carbonyl cyanide 3-chlorophenylhydrazone (CCCP)-induced mitophagy was established, verified by increased colocalization of mitochondria with LC3 aggregates, decreased mitochondrial membrane potential (MMP), and increased intracellular reactive oxygen species (ROS) level. Next, by silencing PINK1 and overexpressing LC3 proteins in MCF-7 cells, it was verified that PINK1 and Parkin significantly promoted CCCP-induced mitophagy, in which CCCP promoted the direct interaction of PINK1 and Parkin. Quantitative FRET imaging analysis for the cells coexpressing CFP-PINK1 and YFP-Parkin was used to assess the action of five drugs [3-methyladenine (3-MA), CCCP, doxorubicin hydrochloride (DOX), metformin (Met), resveratrol (RSV)] on the interaction between PINK1 and Parkin. After 6 h of treatment with these drugs, the CCCP, DOX, Met, and RSV groups showed significantly higher maximum donor-centric FRET efficiency (EDmax) than the control group, suggesting that these four drugs promoted the direct interaction between PINK1 and Parkin. While the 3-MA group showed similar EDmax to the control group, suggesting that 3-MA did not promote direct interaction between PINK1 and Parkin. We also performed these experiments in HeLa cells and obtained the same results, further demonstrating that the PINK1/Parkin-based quantitative FRET drug screening method is a potential tool for mitophagy drug screening in living cells.

Keywords: PINK1; Parkin; drug screening; mitophagy; quantitative FRET

DOI: https://doi.org/10.1111/febs.70146