Mitophagy coordinates organelle crosstalk in health and diseases

Abstract

Eukaryotic cells contain various membrane- and non-membrane-bound organelles, whose spatial and functional organization underpins intracellular homeostasis. Organelle coordination is governed by complex signaling and metabolic networks, often facilitated by direct physical contacts and molecular exchange. Mitochondria, as central hubs of bioenergetic and metabolic activity, are essential to functional coordination among cellular organelles. They engage in diverse cellular processes, encompassing ATP production, biosynthesis of key metabolites, calcium ion buffering, redox balance, and cellular turnover. To preserve their integrity and functionality, dysfunctional mitochondria undergo selective elimination via mitophagy, a specialized form of macroautophagy. Mitophagy plays dual roles in maintaining mitochondrial fidelity and actively shapes interorganelle communication. Through bidirectional signaling, mitophagy influences the activity of multiple organelles, including the endoplasmic reticulum, nucleus, lysosomes, peroxisomes, and lipid droplets. This interorganelle crosstalk is essential for adapting to metabolic stress, maintaining redox balance, and coordinating cell fate decisions. In this review, we explore the intricate signaling networks connecting mitophagy with various organelles and discuss how these interactions influence organ function and overall cellular health. We also highlight emerging small-molecule modulators of mitophagy, providing insight into potential therapeutic strategies aimed at restoring or enhancing organelle communication in pathological conditions.

Introduction

Organelles are essential for sustaining cellular vitality. Eukaryotic cells contain various membrane- and nonmembrane-bound organelles that enable the spatial segregation of incompatible biochemical reactions.^1–3 These organelles engage in highly orchestrated and dynamic regulatory interactions that form a functional network of interdependence.² This coordination, facilitated by division of labor, physical contacts, and molecular exchange, enables efficient communication and material transfer, thereby sustaining essential cellular functions and maintaining homeostasis under diverse physiological conditions.^4,5 Dysregulation of interorganelle crosstalk contributes to the development of multiple pathological conditions.^6,7

Over the past decades, the interactions among cellular organelles have drawn significant attention regarding the exact mechanisms by which they preserve cellular homeostasis through signal transduction and material transfer.^8,9 Among these organelles, mitochondria function as primary coordinators of bioenergetics by generating adenosine triphosphate (ATP) and are crucial for regulating both metabolism and cellular fate.¹⁰ Mitochondria maintain bidirectional communication with other organelles via feedback signaling mechanisms to preserve their functional integrity and support cell survival.¹¹ Mitochondrial dysfunction perturbs organelle crosstalk and disrupts cellular homeostasis.^12,13

Autophagy represents a highly conserved intracellular degradation process that eliminates dispensable or damaged cellular components in response to environmental stimuli.^14–16 By orchestrating substance exchange, signaling dynamics, and organelle turnover efficiency, it functions as a nodal integrator for preserving intracellular homeostasis. Three evolutionarily conserved autophagy modalities are recognized: microautophagy, chaperone-mediated autophagy (CMA), and macroautophagy.^14–18 Microautophagy directly internalizes cargo for hydrolytic processing, although its degradation capacity is inherently limited.¹⁶ CMA is a process that targets the degradation of cytosolic proteins with a lysine-phenylalanine-glutamate-arginine-glutamine (KFERQ) motif, which are delivered to lysosomes by molecular chaperones and bind with lysosomal-associated membrane protein 2A (LAMP2A) on the lysosomal membrane, followed by lysosomal degradation.^17,18 Macroautophagy initiates cytoplasmic cargo sequestration through de novo formation of double-membrane autophagosomes at phagophore assembly sites.^14,15,19 This process culminates in lysosomal degradation, thereby conferring cellular adaptation to environmental stress.^14,15,19 Notably, both macroautophagy and microautophagy exhibit either nonselective or selective modalities.^14–16 Selective autophagy enables targeted degradation of organelles or specific cargo, allowing for more precise quality control of organelles and emerging as a pivotal mechanism coordinating interorganellar functional homeostasis.^20–22

Mitochondrial selective autophagy primarily includes micromitophagy and mitophagy.^16,23 Micromitophagy operates independently of autophagosome-dependent lysosomal degradation. It is characterized by the formation of mitochondria-derived vesicles (MDVs) and subsequent lysosomal internalization for cargo degradation.^16,23,24 Current studies position micromitophagy as a complementary pathway to mitophagy by further coordinating mitochondrial turnover beyond bulk degradation mechanisms to maintain mitochondrial health.^23,24 However, it is less effective in addressing severe damage.²⁴ Mitophagy, a conserved subtype of macroautophagy, orchestrates mitochondrial quality surveillance. This process is activated under conditions such as decreased mitochondrial membrane potential, nutrient deprivation, redox imbalance, and hypoxia. By eliminating damaged or excess mitochondria, mitophagy limits reactive oxygen species (ROS) accumulation and prevents mitochondria-induced cellular dysfunction and death.^12,25 It has become a central focus in mitochondria-related research, prompting the development of various experimental methods and model organisms^26–36 (mainstream experimental methods for studying mitophagy are briefly described in Fig. 1).

Fig. 1.

Methods for assessing mitochondrial function. a Mitochondrial isolation. This section focuses primarily on differential centrifugation (initial separation) and density gradient centrifugation (high-purity isolation) techniques. b Detection of mitochondrial morphology and structure. Major imaging techniques, including TEM, LSCM, and STED, with their respective applications in morphological analysis specified. c Detection of mitochondrial function. Functional assessment methodologies are detailed, encompassing oxygen consumption rate measurement to evaluate respiratory chain activity, mitochondrial membrane potential detection, mtDNA quantification, mtROS level monitoring, and assessment of mitophagy capacity through various biochemical and imaging approaches. d Model organisms for mitochondrial function research. Key model organisms with established experimental advantages are presented: Caenorhabditis elegans for rapid genetic screening, Drosophila melanogaster in neuromuscular and metabolic studies, zebrafish enabling real-time in vivo imaging of mitochondrial dynamics, and mice providing critical insights into mammalian pathophysiology and therapeutic development. BNIP3 B-cell leukemia/lymphoma 2/adenovirus E1B 19 kDa protein-interacting protein 3, Cre-loxP Cyclization recombination enzyme/locus of x-over P1 system, CRISPR/Cas9 clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9, GAL4/UAS GAL4/upstream activating sequence system, JC-1 5,5’,6,6’-Tetrachloro-1,1’,3,3’-tetraethylbenzimidazolylcarbocyanine iodide, JC-10 5,6’-Dichloro-1,1’,3,3’-tetraethylbenzimidazolylcarbocyanine iodide, LC3 microtubule associated protein 1 light chain 3, LSCM laser scanning confocal microscopy, mtDNA mitochondrial DNA, mtROS mitochondrial reactive oxygen species, PINK1 PTEN induced putative kinase 1, PRKN E3 ubiquitin-protein ligase parkin, qPCR quantitative real-time polymerase chain reaction, STED stimulated emission depletion microscopy, TEM transmission electron microscopy, TMRM tetramethylrhodamine methyl ester, TOMM20 translocase of outer mitochondrial membrane 20 homolog, WB western blotting. This figure was created using Adobe Illustrator (Adobe Inc., San Jose, CA, USA)

As a guardian of mitochondrial health, mitophagy interacts with various organelles, including the endoplasmic reticulum (ER), nucleus, lysosomes, peroxisomes, lipid droplets (LDs), and proteasomes, through signaling pathways, vesicular trafficking, and membrane contact sites. These interactions orchestrate bioenergetic flux, anabolic processes, cell death, and cellular turnover.^37–40 Consequently, the interorganelle regulatory network centered on mitophagy is crucial for maintaining cellular homeostasis.

This review synthesizes current knowledge on mitophagy pathways and mechanisms, emphasizing crosstalk with organelles. We summarize current evidence on how these interactions preserve cellular integrity and examine their relevance to multiorgan dysfunction and disease pathogenesis. Additionally, we highlight emerging small-molecule modulators of mitophagy that offer promising avenues for targeted therapeutic intervention. Collectively, this review aims to shed light on the mitophagy-centered organelle network and its potential as a therapeutic target in disease contexts.

Overview of mitophagy

Approximately 60 years ago, Belgian scientist Christian de Duve and his colleagues first described the phenomenon of “mitophagy” after observing mitochondrial degradation within lysosomes of rat hepatocytes.⁴¹ This marked an early indication of selective autophagy, wherein specific organelles are targeted for degradation. Subsequent advancements in microscopy and molecular biology identified additional forms of organelle-selective autophagy, revealing the presence of key molecular regulators that mediate organelle-specific turnover. These discoveries laid the foundation for novel strategies in organelle quality control.^20,42

Mitophagy functions as a cytoprotective mechanism of selective macroautophagy, empowering cells to eliminate dysfunctional or excess mitochondria triggered by metabolic stress, redox imbalance, and inflammation.^43,44 By preserving mitochondrial health and limiting the accumulation of ROS, mitophagy plays a central role in maintaining cellular homeostasis.^45,46 This process is evolutionarily conserved and is critical for embryonic development, cell differentiation, metabolic adaptation, and apoptosis modulation.^27,47,48

Mechanistically, mitophagy is controlled through both ubiquitin (Ub)-dependent and Ub-independent pathways, involving a complex interplay of autophagy receptors, adaptors, and signaling cascades (Fig. 2, Table 1).³⁷ The canonical model of mitophagy posits that mitophagy receptors or adaptor proteins eliminate target mitochondria by recruiting preformed autophagosomes to damaged mitochondria. However, emerging evidence proposes a mechanistic model of autophagosome de novo formation at the mitochondrial surface.^20,49–51 The process can be divided into five sequential stages.^20,49,50 At the priming stage, mitochondrial damage triggers autophagic protein recruitment to the mitochondria and/or the ubiquitination of the outer mitochondrial membrane (OMM).^20,52 During the cargo recognition phase, in ubiquitin-dependent mitophagy, proteins such as optineurin (OPTN) recognize ubiquitin chains through their ubiquitin-binding domain, effectively anchoring damaged mitochondria. In contrast, mitophagy receptors can directly bind to WD repeat domain phosphoinositide-interacting protein (WIPI) family members in ubiquitin-independent mitophagy, preparing for the initiation/nucleation phase.^53,54 The initiation/nucleation stage involves recruiting the unc-51-like kinase 1 (ULK1) complex and the phosphatidylinositol-3-kinase (PI3K) complex to initiate phagophore formation.^50,55,56 At the elongation stage, the autophagy-related protein 12 (ATG12)-autophagy-related protein 5 (ATG5)-autophagy-related protein 16-L1 (ATG16L1) complex mediates the lipidation of microtubule-associated protein 1 light chain 3 (MAP1LC3/LC3) to extend the membrane structure and encircle the target mitochondria. Finally, in the fusion and degradation stage, autophagosome-lysosome fusion facilitates mitochondrial degradation.²⁰

Fig. 2.

Ubiquitin-dependent and ubiquitin-independent mitophagy pathways. a Ubiquitin-dependent mitophagy pathways. In the ubiquitin-dependent mitophagy section, the sequence from left to right describes the molecular mechanisms mediated by PINK1-PRKN, mitophagy adaptor proteins, AMFR, MUL1, and SMURF1. b Ubiquitin-independent mitophagy pathways. The ubiquitin-independent mitophagy section briefly outlines the independent processes mediated by NLRX1, CL, PHB2, ceramide, SPATA33, BNIP3, BNIP3L, BCL2L13, FKBP8, and FUNDC1 in mitophagy. AMBRA1 activating molecule in BECN1-regulated autophagy protein 1, AMFR E3 ubiquitin-protein ligase AMFR, MAM mitochondria-associated endoplasmic reticulum membrane, ATG5 autophagy-related protein 5, ATG12 autophagy-related protein 12, ATG16L1 autophagy-related protein 16-like 1, BCL2L13 B-cell leukemia/lymphoma 2-like protein 13, BNIP3 B-cell leukemia/lymphoma 2/adenovirus E1B 19 kDa protein-interacting protein 3, CERS1 ceramide synthase 1, CRL cullin-RING ubiquitin ligase complex, CL cardiolipin, DNM1L dynamin-1-like protein, FKBP8 38 kDa FK506-binding protein, FUNDC1 FUN14 domain-containing protein 1, FIP200 RB1 inducible coiled-coil 1, HIF1-α hypoxia-inducible factor-1α, HUWE1 the E3 ubiquitin-protein ligase HUWE1, IKK-α IκB kinase α, KEAP1 Kelch-like ECH-associated protein 1, LC3 microtubule associated protein 1 light chain 3, LIR LC3-interacting region, LLO listeriolysin O, MFNs mitofusins, MUL1 mitochondrial ubiquitin ligase activator of NFKB 1, NBR1 neighbor of BRCA1 gene 1, NDP52 calcium-binding and coiled-coil domain-containing protein 2, NIX B-cell leukemia/lymphoma 2/adenovirus E1B 19 kDa interacting protein 3-like, NLRX1 NOD-like receptor family X1, OMM outer mitochondrial membrane, OPTN optineurin, P phosphorylation, p62 sequestosome 1, PGAM5 mitochondrial phosphatase phosphoglycerate mutase 5, PHB2 prohibitin-2, PI3K phosphatidylinositol-3-kinase, PINK1 PTEN induced putative kinase 1, PRKN E3 ubiquitin-protein ligase parkin, RBX1 RING-box protein 1, ROS reactive oxygen species, SMURF1 Smad-ubiquitin regulatory factor 1, SPATA33 spermatogenesis-associated protein 33, SUMO small ubiquitin-related modifier, TBK1 TANK-binding kinase 1, Ub ubiquitination, TAX1BP1 tax1-binding protein 1, ULK1 Unc-51-like kinase 1, VDAC2 voltage-dependent anion channel 2, XBP1s X-box-binding protein 1 spliced, ΔΨm mitochondrial membrane potential. This figure was created using Adobe Illustrator (Adobe Inc., San Jose, CA, USA)

Table 1.

Mitophagy regulators and receptors in mammals

Mitophagy types	Regulator or receptor names	Discovery time	Initiating factors	Mitochondrial localization	Related proteins	Mechanisms of action	References
Ubiquitin -dependent mitophagy	PRKN	2008	Mitochondrial stress; Mitochondrial membrane depolarization; PINK1 stabilization at the OMM	OMM	PINK1, PRKN, TBK1, OPTN, CALCOCO2, p62, MAP1LC3B/LC3B	PRKN is phosphorylated by PINK1 to exert its E3 ubiquitin ligase function, ubiquitinating the OMM of damaged mitochondria and recruiting adapter proteins that can interact with MAP1LC3B/LC3B. These adapter proteins bind to ubiquitinated OMM proteins and are ultimately transported to autophagosomes for degradation.	61,62
	MUL1	2015	Oxidative stress; Mitochondrial membrane depolarization	OMM	MFN2, DNM1L/DRP1, ULK1, MAP1LC3B/LC3B	1. Promote the SUMOylation of DNM1L/DRP1 and ubiquitination of MFN2, inducing mitochondrial fragmentation and facilitating the biogenesis of mitophagy. 2. Augment the translocation of ULK1 to mitochondria and mediate its ubiquitination, leading to mitophagy	97,98
	AMFR/gp78	2013	Ubiquitination of MFNs; Excessive fragmentation of mitochondria	MAMs	MGRN1, MFN1, MFN2, MAP1LC3B/LC3B	1. Ubiquitination of MFNs enhances proteasome dependent degradation, resulting in excessive mitochondrial fragmentation and membrane potential collapse, thereby promoting mitophagy. 2. Mediate the destruction of OMM and the formation of mitoplasts, triggering RETREG1/FAM134B mediated OPA1 dependent mitophagy.	101,103,104
	SMURF1	2011	–	OMM	SMURF1 and its C2 membrane-targeting domain	By interacting with the newly formed autophagosome membrane through its C2 domain, mitophagy is mediated.	105,107
Ubiquitin-independent mitophagy	FUNDC1	2012	Hypoxia; Mitochondrial membrane depolarization	OMM	PGAM5, ULK1, MAP1LC3B/LC3B	PGAM5 induces the dephosphorylation of FUNDC1 (Tyr18 and Ser13), while ULK1 mediates the phosphorylation (Ser17) of FUNDC1, enhancing FUNDC1-MAP1LC3B/LC3B interaction, promoting mitophagic flux.	120,123,124
	BNIP3L/NIX	2008	Hypoxia; Physiological conditions	OMM	MAP1LC3/LC3	Interaction with MAP1LC3/LC3 family proteins mediates mitophagy.	127,128
	BNIP3	2012	Oxidative stress; Hypoxia	OMM	MAP1LC3/LC3, PINK1, PRKN	1. Interaction with MAP1LC3/LC3 family proteins mediates mitophagy. 2. Inhibit PINK1 degradation and promote its accumulation in the OMM, activating PINK1-PRKN mediated mitophagy.	68,128,130,132
	BCL2L13	2015	Mitochondrial membrane depolarization	OMM	MAP1LC3B/LC3B	Interaction with MAP1LC3B/LC3B mediates mitophagy.	134,135
	FKBP8	2017	Stress; Hypoxia	OMM	MAP1LC3/LC3	Interaction with MAP1LC3/LC3 family proteins mediates mitophagy, but FKBP8 itself is not degraded during the mitophagy process.	117,137,139
	NLRX1	2019	Bacterial infection	OMM	MAP1LC3/LC3	NLRX1 undergoes oligomerization and mediates mitophagy through interaction with MAP1LC3/LC3 family proteins.	140,145
	SPATA33	2021	Starvation	OMM	VDAC2, ATG16L1, ATG5, ATG12	Its carboxyl end binds to VDAC2 and is located on the OMM. Its amino end interacts with ATG16L1, initiating mitophagy through the binding of ATG16L1-ATG5-ATG12 complex to MAP1LC3B/LC3B.	115,147
	PHB2	2017	CCCP; Oligomycin and antimycin	IMM	PRKN, MAP1LC3B/LC3B	1. PRKN first initiates a ubiquitin‒proteasome cascade targeting, leading to OMM rupture and exposure of PHB2. Subsequently, PHB2 binds to MAP1LC3B/LC3B to initiate mitophagy. 2. As a ubiquitination substrate of PRKN, PHB2 is ubiquitinated by PRKN and initiates mitophagy through the PINK1-PRKN pathway.	116,156,158
	CL	2013	Mitochondrial damage	IMM	AMBRA1, BECN1, WIPI1	CL translocates to the OMM upon mitochondrial impairment, and interacts with MAP1LC3/LC3 family proteins to mediate mitophagy.	118,162
	CERAMIDE	2012	Stress	OMM	DNM1L/DRP1, p17/PERMIT, CerS1	p17/PERMIT dissociates from DNM1L/DRP1 and interacts with newly translated CerS1 on MAMs, jointly translocating to mitochondria. At this time, CerS1 produces C18-ceramide, which accumulates on the OMM and mediates mitophagy by binding to MAP1LC3B/LC3B-II hydrophobic regions on autophagosomes.	150,152,154,155

AMBRA1 activating molecule in BECN1-regulated autophagy protein 1, AMFR/gp78 E3 ubiquitin-protein ligase AMFR, ATG5 autophagy-related protein 5, ATG12 autophagy-related protein 12, ATG16L1 autophagy-related protein 16-1, BCL2L13 B-cell leukemia/lymphoma 2-like protein 13, BECN1 Beclin1, BNIP3 B-cell leukemia/lymphoma 2/adenovirus E1B 19 kDa protein-interacting protein 3, BNIP3L/NIX B-cell leukemia/lymphoma 2/adenovirus E1B 19 kDa interacting protein 3-like, CALCOCO2 calcium-binding and coiled-coil domain-containing protein 2, CCCP carbonyl cyanide 3-chlorophenylhydrazone, CerS1 ceramide synthase 1, CL cardiolipin, DNM1L/DRP1 dynamin-1-like protein, FKBP8 38 kDa FK506-binding protein, FUNDC1 Tyr18 tyrosine 18 FUN14 domain-containing protein 1, IMM inner mitochondrial membrane, MAM mitochondria-associated endoplasmic reticulum membrane, MAP1LC3B/LC3B microtubule associated protein 1 light chain 3 beta, MFN1 mitofusin1, MFN2 mitofusin2, MGRN1 E3 ubiquitin-protein ligase MGRN1, MUL1 mitochondrial ubiquitin ligase activator of NFκB 1, NLRX1 NOD-like receptor family X1, OMM outer mitochondrial membrane, OPA1 dynamin-like GTPase OPA1, OPTN optineurin, p17/PERMIT the protein that mediates ER-mitochondria trafficking, p62 sequestosome 1, PGAM5 mitochondrial phosphatase phosphoglycerate mutase 5, PHB2 prohibitin-2, PINK1 PTEN induced putative kinase 1, PRKN E3 ubiquitin-protein ligase parkin, RETREG1/FAM134B reticulophagy regulator 1, Ser13 serine 13, Ser17 serine 17, SMURF1 Smad-ubiquitin regulatory factor 1, SPATA33 spermatogenesis-associated protein 33, SUMO small ubiquitin-related modifier, TBK1 TANK-binding kinase 1, Tyr18 tyrosine 18, ULK1 Unc-51-like kinase 1, VDAC2 voltage-dependent anion channel 2, WIPI1 WD repeat domain phosphoinositide-interacting protein 1

Functioning as a pivotal quality control pathway, mitophagy represents a critical therapeutic target for disorders involving mitochondrial impairment and tissue damage. Elucidating the molecular mechanisms of mitophagy will further advance our understanding of its functional coordination with other organelles and its role in the pathogenesis of diverse diseases.

Ub-dependent mitophagy

Ub-dependent pathways refer to the use of Ub as a degradation signal on impaired mitochondria.^57,58 This signal recruits mitophagy-related molecules to initiate the autophagic pathway. Ub-tagged mitochondria are selectively transported to autolysosomes for degradation⁵⁹ (Fig. 2a).

PINK1- and PRKN-mediated mitophagy

The PTEN-induced putative kinase 1 (PINK1) and E3 ubiquitin-protein ligase parkin (PRKN) pathways currently represent the most comprehensively characterized molecular pathways for mitophagy regulation.⁵⁹ This pathway, a depolarization-dependent stress response promoting mitochondrial ubiquitination, is essential for mitochondrial homeostasis.⁶⁰ PINK1, anchored to the OMM, serves as the key regulator of mitophagy. Under physiological conditions, PINK1 undergoes rapid degradation and does not accumulate extensively on the OMM.^61,62 Its mitochondrial targeting sequence is typically translocated into the mitochondria, where it undergoes proteolytic cleavage by mitochondrial processing peptidases; the transmembrane domain of PINK1 undergoes proteolytic processing mediated by the presenilin-associated rhomboid-like protein (PARL); and the remaining fragments are degraded via the ubiquitin‒proteasome system (UPS).⁶³ During this state, PRKN resides in the cytoplasm, and its E3 ubiquitin ligase activity is suppressed. However, under cellular stress or inflammatory conditions, PINK1 degradation is inhibited, allowing PINK1 to accumulate and stably associate with the OMM.^64,65

PINK1 recruits PRKN from the cytoplasm to the OMM and induces phosphorylation at serine 65 of PRKN, consequently triggering the E3 ubiquitin ligase functional activity of this protein. This E3 ligase activity ubiquitinates various OMM proteins, which subsequently interact with adaptor proteins, including OPTN, calcium-binding and coiled-coil domain-containing protein 2 (CALCOCO2/NDP52), and sequestosome 1 (SQSTM1/p62).^46,55,66 These adaptor proteins possess ubiquitin-binding sites and the MAP1LC3/LC3 interacting region (LIR). PINK1 can be transcriptionally regulated by the endoplasmic reticulum stress (ERS)-related protein X-box-binding protein 1 spliced (XBP1s). Overexpression of XBP1s enhances the transcriptional activation of PINK1, leading to increased PINK1 expression in cells.⁶⁷ In addition, it promotes the stabilization and subsequent retention of PINK1 on the OMM.⁶⁷ The stable binding of PINK1 on the OMM functionally interacts with B-cell leukemia/lymphoma 2/adenovirus E1B 19 kDa protein-interacting protein 3 (BNIP3), a critical receptor of mitophagy. The N-terminal mitochondrial targeting sequence of PINK1 can interact with the C-terminal transmembrane region of BNIP3, which inhibits PINK1 proteolysis and promotes PINK1 accumulation on the OMM, thereby activating PINK1-PRKN-dependent mitophagy activation.⁶⁸

Indeed, as a crucial regulator, PRKN orchestrates the dynamic balance between mitophagy and mitochondrial biogenesis. PRKN mediates proteasomal degradation of its interacting substrate PARIS (ZNF746) through ubiquitination, thereby relieving PARIS-induced transcriptional suppression of peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1α) and ultimately promoting mitochondrial biogenesis.⁶⁹

Collectively, these results demonstrate the intricate and multilayered regulation governing the PINK1-PRKN signaling axis during mitochondrial stress.

Ub-dependent mitophagy adaptor proteins

The recognition and targeting of ubiquitin-labeled mitochondria by autophagosomes represent an essential mechanistic phase in the mitophagy process, with autophagy adaptor proteins playing a central role in mediating this interaction.⁷⁰ In mammalian cells, five key ubiquitin-dependent mitophagy adaptors have been identified that facilitate this essential function: SQSTM1/p62, activating molecule in beclin1 (BECN1)-regulated autophagy protein 1 (AMBRA1), CALCOCO2/NDP52, OPTN, and tax1-binding protein 1 (TAX1BP1).^71–75

SQSTM1/p62

SQSTM1/p62 is a classic mitophagy adaptor protein that binds to various ubiquitinated mitochondrial proteins and MAP1LC3B/LC3B, facilitating the transport of Ub-tagged mitochondria to autophagosomes for degradation in autolysosomes.⁷⁶ Additionally, this protein promotes the ubiquitination of damaged mitochondria. Its mechanism primarily involves the interaction of Kelch-like ECH-associated protein 1 (KEAP1) and its associated cullin 1-RING ubiquitin ligase complex (CRL1) with the E3 ubiquitin-protein ligase RBX1 to ubiquitinate proteins on the OMM, independent of the PINK1-PRKN pathway.^76,77

Nuclear receptor subfamily 4 group A member 1 (NR4A1, also known as Nur77, TR3, or NGFI-B) undergoes subcellular redistribution from the nuclear compartment to the mitochondria. It coordinates phase separation through “head-to-head” and “tail-to-tail” oligomerization with SQSTM1/p62, consequently assembling membrane-less NR4A1-SQSTM1/p62 condensates that drive triptolide-induced mitophagy.⁷⁸ The “tail-to-tail” interaction involves the interaction of ubiquitinated NR4A1 with the UBA domain of SQSTM1/p62 on mitochondria, which promotes phase separation and isolates dysfunctional mitochondria.⁷⁸ The “head-to-head” interaction involves the N-terminal inherent disordered zone of NR4A1 and the N-terminal PB1 domain of SQSTM1/p62.⁷⁸ This interaction provides mobility to the NR4A1-SQSTM1/p62 condensates. The mobility enables ubiquitinated mitochondria to be delivered to autophagosomes via the autophagic machinery, resulting in their degradation in autolysosomes.⁷⁸ These findings highlight the critical role of phase separation of SQSTM1/p62 in the regulation of mitophagy.

CALCOCO2/NDP52

CALCOCO2/NDP52 functions by simultaneously binding to ubiquitinated substrates on the OMM and to autophagy-related proteins, thereby serving as a molecular tether that facilitates the delivery of ubiquitin-tagged mitochondria to autophagosomes.⁵⁶ Through its scaffolding activity, CALCOCO2/NDP52 ensures the spatial and temporal coordination of mitophagy initiation.

Notably, CALCOCO2/NDP52 undergoes targeted translocation to the OMM upon oxidative stress or mitochondrial injury. Upon ROS stimulation, CALCOCO2/NDP52 undergoes disulfide bond formation and oligomerization, which enhances its ability to attract autophagy initiation factors, including ULK1 and RB1 inducible coiled-coil 1 (RB1CC1/FIP200), to sites of mitochondrial damage.^79,80 This promotes the assembly of the autophagy initiation complex, accelerating autophagosome formation and mitochondrial degradation.⁷⁹ This redox-sensitive oligomerization of CALCOCO2/NDP52 highlights its dual function to simultaneously detect mitochondrial redox imbalance and initiate mitophagy.

OPTN

OPTN assists in directing the ULK1 complex to sites of autophagy initiation during the early stages of PINK1-PRKN-mediated mitophagy. OPTN can directly bind to class III PI3K complex I through TANK-binding kinase 1 (TBK1) and initiate mitophagy.^51,81,82 This process occurs independently of binding to RB1CC1/FIP200 or the involvement of ULK1/2.⁸¹ OPTN also forms complexes with WIPI2 and ATG12-ATG5 conjugates.⁸³ This promotes the transport of the ATG12-ATG5-ATG16L1 complex to autophagosomes containing WIPI2.⁸³

The ATG12-ATG5-ATG16L1 complex is involved in the covalent modification of MAP1LC3B/LC3B with phosphatidylethanolamine on autophagosome membranes, suggesting that OPTN may also be involved in the lipidation of MAP1LC3B/LC3B.⁸⁴ OPTN binds to autophagy-related protein 8 (ATG8)-family proteins through its LIR domain, with TBK1-dependent phosphorylation at Ser177 significantly augmenting this binding affinity.⁵⁶ A recent study using the Fluoppi assay revealed that OPTN is a critical upstream regulator in the formation of autophagosome membranes.⁵⁴ This protein specifically recruits vesicles containing autophagy-related protein 9 A (ATG9A), forming a complex through its leucine zipper domain with ATG9A.⁵⁴ Furthermore, it recruits TBK1 and ATG8 family proteins through its curling coil 1 and LIR domains to initiate the local formation of autophagosome membranes.⁵⁴ This indicates that OPTN not only acts as an adaptor linking autophagosomes and ubiquitinated substrates but also serves as a “scaffold” connecting various autophagic mechanisms near ubiquitinated substrates.

TAX1BP1

TAX1BP1 is a crucial bridge linking ubiquitinated substrates with autophagosomes in mitophagy.⁸⁵ Although SQSTM1/p62, NBR1 (next to BRCA1 gene 1 protein), and TAX1BP1 all interact with the autophagy-initiating protein RB1CC1/FIP200, TAX1BP1 primarily drives the recruitment of RB1CC1/FIP200, whereas SQSTM1/p62 is the driver for the aggregation of ubiquitin conjugates.^85,86 NBR1 scaffolds TAX1BP1 onto SQSTM1/p62-encapsulated ubiquitin condensates, and TAX1BP1 further recruits RB1CC1/FIP200 to these aggregates.⁸⁵ More importantly, TAX1BP1 acts as a regulator of the clearance of copper oxide nanoparticle-induced mitochondrial damage⁷⁵: TAX1BP1 knockout increases mitochondrial ROS (mtROS) production, decreases mitochondrial clearance, and exacerbates cell death in vascular endothelial cells. Similarly, CALCOCO2/NDP52 or OPTN knockout exacerbates cell death induced by copper oxide nanoparticles, although their protective effects are significantly less pronounced than those of TAX1BP1.⁷⁵

TAX1BP1 also mediates the autophagic degradation of key regulatory proteins, including glutathione peroxidase 4 (GPX4) and stimulator of interferon genes (STING). This degradation accelerates ferroptosis and compromises the antitumor immune response by enhancing oxidative stress and suppressing immune surveillance.^87,88 These findings highlight a broader functional repertoire for TAX1BP1 beyond mitochondrial clearance, implicating it in redox regulation, immunometabolism, and tumor immunity. Thus, TAX1BP1 acts as a central node linking mitochondrial damage, oxidative stress responses, and immune regulation through selective autophagy.

AMBRA1

AMBRA1 is a multifunctional autophagy regulator that participates in multiple mitophagy pathways.^89,90 In PINK1-PRKN-dependent mitophagy, AMBRA1 translocates to perinuclear aggregates of depolarized mitochondria via a PRKN-dependent mechanism.⁹¹ Once localized, it licenses class III PI3K complex activation near depolarized organelles, driving phagophore nucleation and enabling mitophagic degradation.⁸⁹ This recruitment is essential for the spatial organization of mitophagy initiation and highlights AMBRA1’s scaffolding role in coupling mitochondrial damage recognition to autophagosome biogenesis.

In PINK1-PRKN-independent mitophagy, AMBRA1 also functions through distinct regulatory mechanisms. Specifically, upon mitochondrial membrane depolarization, AMBRA1 undergoes phosphorylation at serine 1014, a posttranslational modification facilitated by its interactions with the E3 ubiquitin-protein ligase HUWE1 and the inhibitor of nuclear factor kappa-B kinase subunit α (IKKα).⁹⁰ This phosphorylation triggers a conformational shift in AMBRA1, facilitating its complex assembly with MAP1LC3B or GABARAP subfamily members to mediate the biogenesis of mitophagy.⁹⁰

Mitochondrial ubiquitin ligase activator of NFκB 1 (MUL1)-mediated mitophagy

MUL1, a multifunctional protein located on the OMM, triggers mitophagy primarily in response to oxidative stress and mitochondrial depolarization. MUL1 functions as an active E3 ubiquitin ligase that targets multiple substrates for polyubiquitination and proteasomal degradation, including mitofusin 2 (MFN2), RAC serine/threonine-protein kinase (AKT), cellular tumor antigen TP53 (p53), and ULK1.^92–95 In addition, it promotes the SUMOylation (small ubiquitin-related modifier, SUMO) of dynamin-1-like protein (DNM1L/DRP1); it stabilizes this process and accelerates mitochondrial fission.^96,97 Simultaneously, the MUL1-mediated proteasomal clearance of MFN2 further accelerates mitochondrial fission, reduces mitochondrial fusion, and promotes mitochondrial fragmentation. This fosters a microenvironment that promotes mitophagy.⁹⁸ Additionally, MUL1 induces mitophagy triggered by selenite via ULK1- and ATG5-dependent pathways, bypassing PRKN.⁹⁷

However, MUL1 exhibits context-dependent complexity in mitochondrial quality control.^97,99 Under physiological conditions or mild oxidative stress, it maintains mitochondrial homeostasis through multimodal regulation: monitoring the quality of the OMM to mediate degradation of mitochondrial-associated proteins via SUMOylation/ubiquitination while simultaneously suppressing ULK1-initiated mitophagy to preserve mitochondrial fusion-fission homeostasis.⁹⁹ Significantly, this homeostatic function exerts a marked phenotypic switch upon selenite exposure or severe oxidative stress, where MUL1 bolsters its pro-autophagic activity. Functional plasticity reflects the adaptive response of MUL1 in response to differential stress conditions—converting its role to promote mitochondrial degradation during chronic loss of membrane potential or acute cellular insults, thereby safeguarding cellular integrity.⁹⁷

E3 ubiquitin-protein ligase AMFR (AMFR/gp78)-mediated mitophagy

AMFR/gp78, an ER-resident E3 ubiquitin ligase, drives ER-associated degradation (ERAD) through substrate polyubiquitylation.¹⁰⁰ It participates in the ubiquitination and degradation of various substrates.^101,102 AMFR/gp78 is situated within mitochondria-associated ER membranes (MAMs)¹⁰³ and mediates mitophagy under mitochondrial depolarization conditions through two primary steps: first, it ubiquitinates mitofusins and promotes their proteasome-dependent degradation, thereby facilitating mitochondrial fission; second, the resulting fragmented mitochondria undergo excessive fragmentation and loss of membrane potential, which triggers mitophagy. AMFR/gp78, along with its mediated OMM ubiquitination and mitophagy, is a crucial mechanism in both mitochondria and ER turnover processes induced by reticulophagy regulator 1 (RETREG1/FAM134B).¹⁰⁴

Smad-ubiquitin regulatory factor 1 (SMURF1)-mediated mitophagy

SMURF1 is an E3 ubiquitin ligase with a HECT domain. It mediates the K48-linked polyubiquitylation and degradation of mothers against decapentaplegic homolog (SMAD) 1 and SMAD5.^105,106 SMURF1 can mediate mitophagy.^107,108 However, this process does not rely on its own E3 ubiquitin ligase activity and SQSTM1/p62. Instead, it involves the C2 membrane-targeting domain of SMURF1. This C2 domain can target anionic phospholipids on plasma or intracellular membranes.^105,109 The Smurf1 mutant lacking the C2 membrane-targeting domain exhibits a complete loss of mitophagic function in carbonyl cyanide 3-chlorophenylhydrazone (CCCP)-treated Smurf1^−/− murine embryonic fibroblasts. These findings suggest that SMURF1-mediated mitophagy may function through interactions between its C2 membrane-targeting domain and the membrane of nascent autophagosomes, thereby promoting the recruitment and delivery of selective autophagy substrates for subsequent degradation.¹⁰⁷

Ub-independent mitophagy

Ub-independent mitophagy primarily refers to receptor-mediated mitophagy, where mitophagy-related receptors do not rely on Ub tagging but interact directly with MAP1LC3B/LC3B via their LIR domains.^110,111 Mammalian cells employ distinct classes of mitophagy receptors to license mitochondrial selective clearance, including B-cell leukemia/lymphoma 2/adenovirus E1B 19 kDa interacting protein 3-like (BNIP3L/NIX), BNIP3, FUN14 domain-containing protein 1 (FUNDC1), 38 kDa FK506-binding protein (FKBP8), B-cell leukemia/lymphoma 2-like protein 13 (BCL2L13), prohibitin-2 (PHB2), cardiolipin (CL), NOD-like receptor (NLR) family X1 (NLRX1), spermatogenesis-associated protein 33 (SPATA33), and ceramide^112–119 (Fig. 2b).

Mitophagy-related receptors on the OMM

FUNDC1-mediated mitophagy

FUNDC1 is an OMM-localized transmembrane protein. It comprises three transmembrane domains, which interact directly with MAP1LC3B/LC3B to modulate mitophagy under hypoxia or various mitochondrial stresses.^120,121 Posttranslational modifications (PTMs) serve as the principal mechanism controlling FUNDC1-mediated mitophagy. Under basal conditions, serine 13 and tyrosine 18 of FUNDC1 are phosphorylated by casein kinase 2 (CK2) and proto-oncogene tyrosine-protein kinase Src (SRC), respectively. Phosphorylations reduce the binding affinity between FUNDC1 and MAP1LC3B/LC3B, causing downregulation of the associated mitophagic process.¹²⁰ The activity of mitochondrial phosphatase phosphoglycerate mutase 5 (PGAM5) increases during hypoxia or mitochondrial depolarization. This induces the dephosphorylation of serine 13 and tyrosine 18 on FUNDC1.¹²² Concurrently, the expression and mitochondrial translocation of ULK1 increase, consequently mediating FUNDC1 phosphorylation at serine 17. Through this phosphorylation event, enhanced FUNDC1/LC3B association occurs, which actively stimulates mitophagy.^123,124 The bidirectional regulatory function of FUNDC1 in mitophagy maintains mitochondrial quality and homeostasis under varying environmental conditions.

BNIP3- and BNIP3L/NIX-mediated mitophagy

BNIP3 and BNIP3L/NIX are classified as BH3-only family proteins.^125,126 They share 56% homology, and both contain a BH3 domain.^126–128 BNIP3L/NIX serves as the key regulator of mitochondrial degradation in erythrocyte differentiation. Moreover, BNIP3L/NIX dysfunction emerges as an important determinant in anemia progression.¹²⁷ Recent research¹²⁹ has demonstrated that BNIP3L/NIX interacts with WIPI2, thereby recruiting the ATG16L1 and RB1CC1/FIP200 complexes to initiate autophagosome biogenesis. In contrast, BNIP3 is often associated with hypoxia-induced mitophagy and regulates mitophagy through multiple pathways. The LIR domain of BNIP3 enables its interaction with MAP1LC3B/LC3B following OMM homodimerization, promoting mitophagy activation under hypoxic or oxidative stress.^130,131

ULK1-dependent phosphorylation of BNIP3 at Ser17 and Ser24 can enhance its interaction with MAP1LC3B/LC3B.¹³² However, the specific regulatory mechanism warrants further exploration. BNIP3 can interact with PINK1,^68,133 prevent its degradation, and promote its OMM accumulation, subsequently activating PINK1-PRKN-mediated mitophagy. In a study on hepatocellular carcinoma (HCC),⁶⁸ BNIP3 knockout or pharmacological inhibition via the cyclin-dependent kinase 9 (CDK9) inhibitor LDC067 to reduce the exogenous level of BNIP3 led to decreased expression of both PINK1 and PRKN. BNIP3 overexpression reversed these outcomes, consistent with its established function in the stabilization of PINK1.

BCL2L13-mediated mitophagy

Sharing homology with the yeast autophagy-related protein 32 (ATG32) protein in mammals, BCL2L13 exhibits expression patterns and functions akin to those of ATG32. BCL2L13-mediated mitophagy is primarily triggered by mitochondrial depolarization.^134,135 Phosphorylation at serine 272 of BCL2L13 elicits mitophagic activity, in turn enhancing the interaction between its LIR domain and MAP1LC3B/LC3B. However, the precise kinase mediating this phosphorylation event remains to be determined.^135,136

FKBP8-mediated mitophagy

As an OMM anchored member of the FKBP protein family, FKBP8 interacts with BCL2 to suppress apoptotic processes.^117,137,138 Similar to other mitophagy receptors, FKBP8’s N-terminal region harbors an LIR motif that allows it to directly interact with MAP1LC3B/LC3B to regulate mitophagy. However, this OMM protein is not degraded during autophagy. Thus, it does not trigger unnecessary apoptosis through an escape mechanism.^117,137 FKBP8-mediated mitophagy is inducible by cellular energy deprivation and hypoxia, independent of mitochondrial depolarization. Furthermore, the LIR motif-like sequence of FKBP8 can mediate mitochondrial fission under hypoxic conditions.¹³⁹ FKBP8 overexpression simultaneously promotes mitochondrial fragmentation and TOMM20 (translocase of outer mitochondrial membrane 20 homolog) degradation, indicating that both canonical LIR motifs and LIR-like sequences are essential for stress-induced mitophagy mediated by FKBP8.

NLRX1-mediated mitophagy

As a multifunctional immune regulator, NLRX1 represents one of the most structurally intricate and distinctive NLR family members.^140,141 It suppresses type I interferon and inhibits the NF-κB (the pro-inflammatory factor)-mediated inflammatory signaling pathways.^142–144 These anti-inflammatory roles highlight its importance in sustaining immunological stability and restraining hyperinflammatory reactions during infection or stress.

What sets NLRX1 apart from other NLR family members is the presence of a sequence directing mitochondrial localization, which facilitates its specific accumulation on the OMM. Importantly, NLRX1 also contains a functional LIR motif, allowing it to directly bind to MAP1LC3B/LC3B and initiate mitophagy.^145,146 This position positions NLRX1 at the intersection of innate immunity and mitochondrial quality control, providing a unique mechanism by which mitochondrial stress is coupled to immune regulation.

NLRX1 triggers mitophagy upon detection of bacterial infection. For example, Listeria monocytogenes can induce the oligomerization of NLRX1 in macrophages through its secreted virulence factor listeriolysin O, consequently promoting the interaction of its LIR motif with MAP1LC3B/LC3B to regulate NLRX1-mediated mitophagy.¹⁴⁵ Through this pathway, NLRX1 assists in clearing impaired mitochondria under infectious conditions, thereby decreasing mtROS generation and modulating inflammatory responses.

SPATA33-mediated mitophagy

SPATA33 is a protein closely associated with sperm vitality and reproductive defects; it can target the transport of calcineurin to mitochondria in sperm.^147,148 SPATA33 is a receptor for mitophagy in the testes.^115,149 Its C-terminal domain mediates mitochondrial association through direct interaction with the OMM-resident protein voltage-dependent anion-selective channel protein 2 (VDAC2). Upon starvation, the N-terminus of this protein mediates binding to the ATG12-ATG5-ATG16L1 complex, thereby promoting autophagosome formation.¹⁴⁹ It connects damaged mitochondria directly to autophagosomes through direct binding between ATG5 and MAP1LC3B/LC3B to facilitate the selective degradation of mitochondria.¹¹⁵ SPATA33 overexpression increases autophagosome formation and promotes mitophagy in male germ cells.¹¹⁵ However, autophagosome-lysosome fusion remains unaffected by this process.

Ceramide-mediated mitophagy

Ceramide is an apoptosis-promoting sphingolipid formed by amide bond conjugation between sphingosine and fatty acids with C14-C26 hydrocarbon chains.^150,151 The accumulation of C18-ceramide, synthesized by ceramide synthase, on the OMM enables its binding to autophagosome-associated LC3B through hydrophobic interactions, thereby facilitating the occurrence of mitophagy.^152,153 This process is triggered by diverse cellular stress signals. Studies in head/neck squamous cell carcinoma and acute myeloid leukemia (AML)^154,155 revealed that cellular stress triggers DNM1L/DRP1 release from the protein that mediates ER-mitochondria trafficking (p17/PERMIT), leading to its cytoplasmic activation and subsequent induction of mitochondrial fission. p17/PERMIT interacts with newly translated ceramide synthase 1 at MAMs and translocates to mitochondria, where ceramide synthase 1 generates C18-ceramide on the OMM, thereby inducing mitophagy. These findings reveal novel therapeutic opportunities for cancer treatment development.

Mitophagy-related receptors on the inner mitochondrial membrane (IMM)

PHB2-mediated mitophagy

PHB2 is one of the few IMM proteins that functions as a mitophagy receptor, and its mediation of mitophagy requires the assistance of PRKN.^156,157 PHB2 bound to MAP1LC3B/LC3B via its LIR and initiated mitophagy only after PRKN-directed ubiquitination and proteasome-mediated OMM protein clearance. This process is triggered by mitochondrial depolarization induced by CCCP or antimycin A and oligomycin.^156,158 In contrast, PRKN knockout mice exhibited impaired PHB2-MAP1LC3B/LC3B binding. Additionally, PRKN can bind directly to PHB2 through its RING1 domain to strengthen PHB2-MAP1LC3B/LC3B binding, facilitating mitophagy.¹¹⁶ This dual regulatory mechanism, through both structural remodeling of mitochondrial membranes and direct protein‒protein interactions, positions PHB2 as a unique IMM receptor that bridges mitochondrial damage signals with autophagosome formation.

CL-mediated mitophagy

CL is a lipid mitophagy receptor that exists as a dimer on the IMM.^118,159,160 In neuronal cells,¹¹⁸ CL can be triggered by a specific mechanism to translocate to the OMM when the mitochondria are damaged.¹⁶¹ It subsequently interacts with MAP1LC3B/LC3B to enable the selective clearance of dysfunctional mitochondria. Disruption of CL biosynthesis or impaired OMM targeting attenuates mitophagy in neuronal cells. However, the mechanism underlying the translocation of CL and its interaction with MAP1LC3B/LC3B remains unclear. A recent study¹⁶² identified CL in MAM components, revealing its interaction with the AMBRA1-BECN1-WIPI1 multiprotein complex after the initiation of autophagy. This complex is a significant regulatory factor formed during the early stages of autophagy in MAMs. Therefore, CL facilitates autophagosome generation by engaging the AMBRA1-BECN1-WIPI1 complex, thereby revealing its indispensable function in mitophagy induction and maintenance.

Cooperation among mitophagy-related receptors and regulators

Mitophagy-related receptors and regulators do not function in isolation within the intracellular environment. Instead, they are integrated into a dynamic and interconnected regulatory network that ensures mitochondrial quality control while stabilizing their functional integrity. Crosstalk among these receptors and regulators enables the cell to respond flexibly to various forms of mitochondrial damage and stress, tailoring mitophagic responses to the nature and severity of the insult.

For example, a study on intestinal ischemia‒reperfusion injury demonstrated that hypoxia-reoxygenation downregulates NLRX1 expression, consequently impairing mitophagy processes regulated by NLRX1.¹¹⁹ This downregulation enhances the phosphorylation of FUNDC1, which subsequently disrupts its interaction with the OMM repair proteins NipSnap1 and NipSnap2. As a result, mitophagy flux is inhibited, damaged mitochondria accumulate, and epithelial apoptosis is exacerbated. This highlights how the functional interplay between mitophagy receptors can influence downstream events, such as mitochondrial repair or cell death.

Further evidence of receptor crosstalk is provided by the interactions between BNIP3, PHB2, and the PINK1-PRKN pathway.^133,163 BNIP3 effectively stimulates PINK1-PRKN-dependent mitophagic activity by blocking PINK1 turnover and increasing mitochondrial membrane retention.¹³³ The binding of BNIP3 to PINK1 is mediated by BNIP3’s C-terminal transmembrane region and PINK1’s N-terminal mitochondrial localization sequence, occurring independently of mitochondrial membrane potential loss. PHB2 enhances PINK1-PRKN-mediated mitophagy by modulating the PARL-PGAM5-PINK1 pathway. Specifically, PHB2 maintains PINK1 stability via PARL-PGAM5 signaling, induces ubiquitin-mediated degradation of OMM proteins, and ultimately promotes OMM disruption upon mitochondrial damage.¹⁶³ Subsequently, MAP1LC3B/LC3B crosses the OMM, where it engages PHB2, triggering the PHB2-dependent mitophagy pathway. This suggests that mitophagy receptor proteins on the IMM and OMM can synergistically promote mitophagy.¹⁶³

Collectively, these findings suggest that mitochondrial membrane-localized mitophagy receptors present on both the IMM and OMM can function in a coordinated and synergistic manner. Their cooperative interactions ensure efficient recognition and elimination of impaired mitochondria, particularly during metabolic or oxidative stress.

Crosstalk between mitophagy and multiple organelles

Mitophagy and mitochondria

As highly dynamic and plastic organelles, mitochondria are essential for diverse cellular activities, such as programmed cell death control, autophagy modulation, redox signal transduction, and calcium ion (Ca²⁺) homeostasis maintenance.^25,164,165 The proper execution of these core functions is largely reliant on a sequence of regulatory networks, such as mitochondrial fusion and fission, mitophagic clearance, and the biogenesis of new mitochondria.¹⁶⁶ These networks synergistically maintain mitochondrial stability and enable the organelle to respond to different stressors and metabolic demands.^167,168 Thus, mitochondria function as key hubs in cellular metabolism and signaling.^167,169

Mitophagy works in concert with mitochondrial vesicular transport and the Ub-proteasome-dependent degradation of damaged mitochondrial proteins, collectively forming the mitochondrial clearance system.^170,171 This system, in synergy with other regulatory mechanisms such as mitochondrial dynamics, establishes a mitochondrial quality control network that monitors and ensures optimal mitochondrial performance. Therefore, it regulates various physiological processes and maintains both mitochondrial and cellular homeostasis.^52,172 Imbalances or disruptions in the crosstalk between mitophagy and other regulatory pathways can impair mitochondrial function, mediate abnormal cell fate, and lead to numerous diseases (Fig. 3).

Fig. 3.

Interactions between mitophagy and mitochondria. a The interaction between mitochondrial dynamics and mitophagy. The process of mitochondrial fusion and fission is intimately associated with mitophagy. On the one hand, stimulating mitochondrial fission or suppressing mitochondrial fusion serves as an essential triggering factor for mitophagy. On the other hand, mitophagy itself is necessary for the remodeling of the mitochondrial network. b The impact of mitochondrial damage-associated molecular patterns on mitophagy. The mitophagy mechanism effectively eliminates multiple mtDAMPs, such as mtDNA and accumulated mtROS, thereby limiting the detrimental effects of mtDAMPs on cellular functions. Conversely, certain mtDAMPs can act as agonists for mitophagy under appropriate conditions, promoting cellular survival during stress. c The synergistic effect between the mitochondrial unfolded protein response and mitophagy. Mitophagy and the mtUPR work in concert to alleviate disease-induced mitochondrial dysfunction, thereby jointly maintaining mitochondrial homeostasis. ATAD3B ATPase family AAA domain-containing protein 3B, ATF4 activating transcription factor 4, BAX Bcl-2-associated X protein, BNIP3L B-cell leukemia/lymphoma 2/adenovirus E1B 19 kDa interacting protein 3-like, cGAS cyclic GMP-AMP synthase, CL cardiolipin, DRP1 dynamin-1-like protein, eIF2α eukaryotic translation initiation factor 2 subunit 1, FUNDC1 FUN14 domain-containing protein 1, FIS1 mitochondrial fission 1 protein, MFF mitochondrial fission factor, MFN1 mitofusin-1, mtDAMPs mitochondrial damage-associated molecular patterns, mtDNA mitochondrial DNA, mtROS mitochondrial ROS, mtUPR mitochondrial unfolded protein response, NLRP3 NACHT, LRR and PYD domains-containing protein 3, p62 sequestosome 1, PGAM5 mitochondrial phosphatase phosphoglycerate mutase 5, PINK1 PTEN induced putative kinase 1, PRKN E3 ubiquitin-protein ligase parkin, RIPK3 receptor-interacting protein kinase 3, SIRT1 NAD-dependent protein deacetylase sirtuin 1, STING stimulator of interferon genes. This figure was created using Adobe Illustrator (Adobe Inc., San Jose, CA, USA)

The close relationship between mitochondrial dynamics and mitophagy

The balance between mitochondrial fusion and fission constitutes the core of mitochondrial dynamics, serving as a vital process for ensuring proper mitochondrial function and maintaining cellular homeostasis.¹⁷³ Mitochondrial fission facilitates the isolation of impaired mitochondrial components, enabling their selective elimination through mitophagy.¹⁷⁴ In contrast, mitochondrial fusion promotes the exchange of mitochondrial contents, facilitating the dilution of partially damaged components into healthier mitochondria, thereby mitigating cellular stress and preventing the accumulation of dysfunctional organelles.¹⁷⁵ However, both mechanisms are closely intertwined with mitophagy, as they mutually regulate and balance each other to maintain a healthy mitochondrial network. Changes in mitochondrial dynamics, including the activation of fission or inhibition of fusion, are essential triggers of mitophagy. Mitochondrial fission, in particular, is considered a hallmark of both mitophagic degradation and mitochondrial biogenesis.^173,176 Peripherally localized mitochondrial fission,¹⁷⁷ mediated by DNM1L/DRP1 and modulated through mitochondrial fission 1 protein (FIS1)-dependent lysosome recruitment, represents a key trigger for mitophagy.^176,178 This process fragments damaged mitochondria into smaller, discrete units to initiate autophagosome formation and subsequent lysosome-dependent degradation.¹⁷⁷ In contrast, the mitochondrial fission factor (MFF)-dependent mitochondrial fission occurring in the midzone generally promotes mitochondrial biogenesis rather than turnover.¹⁷⁷

A recent study designated the novel mitochondrial fission factor Atg44 and its orthologs as mitofissin, which is essential for yeast mitophagy.¹⁷⁹ Mitofissin directly interacts with lipid membranes, consequently driving mitochondrial fission by affecting membrane fragility. In its absence, damaged mitochondria fail to separate from the mother mitochondria. This prevents autophagosomes from fully encapsulating the impaired mitochondria, thereby suppressing mitophagy.¹⁷⁹

The mitochondrial fusion-related protein mitofusin 1 (MFN1), a critical mediator of mitochondrial fusion, is deeply involved in mitochondrial dysfunction as well as mitophagy.¹⁸⁰ miRNA-142a-5p suppresses its expression, triggering excessive mitochondrial fragmentation and functional impairment in denervated skeletal muscle cells. This dysregulation abnormally stimulates mitophagic activity and ultimately induces mitochondria-mediated apoptosis.¹⁸¹ These specialized molecular pathways elucidate cellular control over mitochondrial destiny through fission regulation.

Mitophagy is vital for remodeling the mitochondrial network. BNIP3L/NIX- and FUNDC1-mediated mitophagy facilitates mitochondrial network expansion and functional maturation during cardiac progenitor cell differentiation,¹⁸² a process critical for mitochondrial network restructuring. The absence of these proteins triggers mitochondrial depolarization and the appearance of donut-shaped damage, which subsequently elevates ROS levels and persistently stimulates fission activity.¹⁸² This makes cells more prone to programmed cell death triggered by oxidative damage. Similarly, BNIP3L/NIX-mediated mitophagy was significantly upregulated during oligodendrocyte differentiation and played a crucial role in mitochondrial network remodeling in a study on retinal demyelinating diseases¹⁸³ (Fig. 3a).

The mutual influence between mitochondrial damage-associated molecular patterns (mtDAMPs) and mitophagy

mtDAMPs are a class of endogenous molecules released by mitochondria during cellular damage or stress.¹⁸⁴ Owing to the evolutionary homology between mitochondrial and bacterial structures, these components are identified by immune receptors as “pathogen-like signals”,¹⁸⁵ thereby activating immune responses such as inflammatory reactions and subsequently mediating tissue damage.^186,187 mtDAMPs include proteins, lipids, metabolites, and DNA, with mitochondrial DNA (mtDNA), mtROS, and CL as the most common.^185,188 Mitophagy is the optimal strategy for clearing mtDAMPs. Its ability to target and remove damaged mitochondria effectively controls the levels of various mtDAMPs. Moreover, mitophagy cooperates with complementary mitochondrial quality control events, including fusion-fission dynamics, to minimize the detrimental impact of mtDAMPs on cellular function.^189,190

As the DNA encoding mitochondrial respiratory chain complexes, mtDNA maintains mitochondrial homeostasis and integrity.¹⁹¹ However, it is highly susceptible to damage or leakage under various physiological stresses, particularly oxidative stress. Damaged or leaked mtDNA is one of the most common mtDAMPs released by mitochondria and can serve as a broad activator of inflammatory pathways. It binds to sensors, including TLRs, NLRs, and the cyclic GMP-AMP synthase (cGAS)-STING pathway, to initiate abnormal inflammatory cascades.^192–194 The mitophagic pathway plays an essential role in clearing impaired mtDNA and preventing aberrant activation of inflammatory signal transduction.^195,196

In aged mice, specific mitophagy activation significantly reduced mtDNA escape and cGAS-STING pathway hyperactivation, thereby restoring mitochondrial homeostasis and extending lifespan.¹⁹⁵ Impaired mitophagy in hepatic macrophages induces mtDNA-cGAS-STING axis activation, thereby driving hepatocyte pyroptosis in acute liver injury.¹⁹⁷ ATPase family AAA domain-containing protein 3 (ATAD3) B, a mitochondria-associated protein specifically expressed in primates, plays a key role under oxidative stress. Oxidative stress disrupts the hetero-oligomerization between this protein and ATAD3A, causing the C-terminal region of ATAD3B, which normally resides in the intermembrane, to become exposed at the OMM.¹⁹⁸ This process triggers PINK1-independent mitophagy, promoting the degradation of impaired mitochondria and mtDNA that has been damaged or leaked.¹⁹⁸ These results highlight the specialized function of mitophagy in eliminating impaired or leaked mtDNA.

As the primary generators of cellular ROS, mitochondria produce mtROS primarily through mitochondrial electron transport chain (ETC) activity, which is tightly linked to ATP production.^199,200 In addition, these organelles are involved in heme and Fe-S cluster biosynthesis, which further induces ROS generation.²⁰⁰ Thus, the production of physiological levels of mtROS is a normal consequence of mitochondrial participation in cellular functions. Physiologically or mildly elevated levels of mtROS can act as positive signaling molecules that stimulate mitophagic activity and enhance cellular adaptation and survival in response to environmental changes.²⁰¹ However, lethal levels of mtROS are significant and dangerous mtDAMPs that can mediate cellular damage through oxidative stress or by inducing mtDNA mutations or leakage.²⁰² This necessitates their clearance via mitophagy to maintain appropriate ROS levels within the cell, thereby limiting ROS-induced damage to cellular function. Abnormal CL levels can promote mitochondrial apoptosis by facilitating the formation of BAX (Bcl-2-associated X protein) pores. Moreover, the mitophagy receptor can induce NLRP3 inflammasome activation to mediate cell death.^203,204 CL can be activated to mediate mitophagy under oxidative stress, thereby enabling cell survival under various stress-induced damages^118,203 (Fig. 3b).

The coordinated role of the mitochondrial unfolded protein response (mtUPR) and mitophagy

mtUPR represents a stress adaptation pathway activated by cells to address proteostasis imbalance within mitochondria.²⁰⁵ In the setting of mitochondrial dysfunction or stress, unfolded protein signals in the mitochondrial matrix are transmitted to the nucleus via specific pathways.^205,206 These signals stimulate chaperone and protease expression to restore protein folding competence within mitochondria and maintain mitochondrial function. The mtUPR restores proteostasis by activating specialized transcriptional responses in the nucleus, thereby protecting mitochondria from proteotoxic damage and regulating organismal homeostasis.^199,206,207 In eukaryotic cells, mtUPR serves as a primary stress adaptation system and protective strategy for mitochondrial restoration. Mitophagy and mtUPR synergistically maintain mitochondrial homeostasis to preserve mitochondrial integrity and function.²⁰⁸

Mitophagy and mtUPR can synergistically improve mitochondrial dysfunction caused by various diseases, mitigate mitochondrial damage, and prevent or reverse disease progression to maintain overall health.^209–212 For example, lycopene prevents di(2-ethylhexyl) phthalate-induced liver mitochondrial quality control disorders by modulating the NAD-dependent protein deacetylase sirtuin-1 (SIRT1)-PINK1-mitophagy axis and mtUPR.²¹⁰ Traditional Chinese medicine, such as the Xinyang tablet, prevents cardiac pressure overload by regulating the receptor-interacting serine/threonine-protein kinase 3 (RIPK3)-FUNDC1-dependent mtUPR and mitophagy pathways.²¹¹ Additionally, PGAM5-mediated dephosphorylation of PHB2 inhibits mitophagy and mtUPR, resulting in endotoxemia-induced cardiac dysfunction.²¹² These findings underscore the pivotal roles of mitophagy and mtUPR as essential components of mitochondrial quality control that synergistically maintain mitochondrial homeostasis.^209–212

Mitophagy and mtUPR are interrelated mitochondrial quality control mechanisms that can influence and regulate each other. Evidence from a study on septic cardiomyopathy²¹³ indicates that these pathways act in concert to preserve mitochondrial function and cardiac performance under septic stress. When mitophagy is suppressed, mtUPR signaling is rapidly activated as a compensatory response to maintain mitochondrial homeostasis. Conversely, inhibition of mtUPR impairs the cardioprotective effects of mitophagy, indicating that mtUPR may function downstream of mitophagic processes and is essential for cellular adaptation to cardiac stress.

In addition to acting as a compensatory mechanism, mtUPR can actively induce mitophagy to eliminate mitochondria burdened by misfolded or unfolded proteins. For instance, in a study exploring therapeutic strategies for intervertebral disc degeneration,²¹⁴ mtUPR activation was shown to promote mitophagy through the upregulation of the stress-inducible protein Sestrin2. This process is mediated by eukaryotic translation initiation factor 2 subunit 1 (eIF2α), which facilitates the translocation of PRKN and SQSTM1/p62 to mitochondria, thereby enhancing mitochondrial clearance. These findings highlight a bidirectional regulatory relationship between mtUPR and mitophagy and reveal novel therapeutic targets for mitochondrial dysfunction-related diseases, including cardiac injury and intervertebral disc degeneration (Fig. 3c).

Mitophagy and ER

In eukaryotic cells, the ER represents one of the most voluminous organelles, comprising approximately 35% of the total cytoplasmic space.^215,216 It mediates polypeptide chain production, folding dynamics, covalent modifications, and proteolytic processing, serving as the central hub for lipid metabolism and calcium storage.²¹⁷ The smooth ER also has detoxification functions; it contains enzymes that mediate oxidation, reduction, and hydrolysis reactions, consequently transforming lipophilic toxins into hydrophilic substances that can be excreted from the body.²¹⁷

Mitochondrial-ER communication is vital for normal mitochondrial function. These two organelles are interconnected, and their contact sites are known as MAMs. The regions contain various complementary membrane proteins that facilitate interorganelle signaling.^218,219 MAMs are central to the crosstalk of these organelles, as they regulate various cellular functions, such as lipid transport, Ca²⁺ transfer, mitochondrial remodeling, and mitophagic clearance. Thus, they sustain cellular homeostatic balance²²⁰ (Fig. 4).

Fig. 4.

Interactions between mitophagy and the endoplasmic reticulum. a The impact of endoplasmic reticulum stress on mitophagy. ERS can activate the PINK1-PRKN-mediated mitophagy pathway by facilitating the mitochondrial localization of PRKN or enhancing PINK1 expression. b The influence of endoplasmic reticulum-regulated calcium on mitophagy. Excessive accumulation or efflux of Ca²⁺ within mitochondria can trigger mitophagy. Conversely, mitophagy-related proteins PINK1 and PRKN also regulate the activity of the ER Ca²⁺ channel IP3R by ubiquitinating CISD1, thereby modulating intracellular Ca²⁺ homeostasis. c The interactions between mitochondria-associated endoplasmic reticulum membranes and mitophagy. MAMs function as the primary site for the formation of mitophagosomes and the main source of their membranes. Moreover, mitophagy-related receptors and regulatory proteins such as FUNDC1 and MFN2 are localized at MAMs, where they regulate Ca²⁺ transport and mitochondria-ER tethering within MAMs. d The interrelationships between ER quality control and mitophagy. Excessive ER-associated protein AMFR mediates the generation of mitoplasts. Within these structures, the OPA1 protein interacts with RETREG1, which subsequently recruits LC3 to sequester both mitoplasts and AMFR into autophagosomes, thereby achieving dual turnover of mitochondria and ER. Furthermore, AMFR cooperates with HRD1 to catalyze the ubiquitination of PINK1, critically regulating mitophagy efficiency. The mitochondria-associated protein PINK1, through ubiquitinating Rtnl1 and activating PRKN, respectively orchestrates the induction of ER-phagy and mitophagy. AMFR E3 ubiquitin-protein ligase AMFR, ATF6 activating transcription factor 6, BECN1 Beclin1, CAMK1 calcium/calmodulin-dependent serine/threonine-protein kinase 1, CISD1 CDGSH iron-sulfur domain-containing protein 1, CREB cyclic AMP-responsive element-binding protein, ERS endoplasmic reticulum stress, FIS1 mitochondrial fission 1 protein, FUNDC1 FUN14 domain-containing protein 1, HRD1 ER-associated degradation-associated E3 ubiquitin-protein ligase synoviolin, IP3R inositol 1,4,5-trisphosphate receptors, IRE1α inositol-requiring protein-1α, KEAP1 Kelch-like ECH-associated protein 1, LC3 microtubule associated protein 1 light chain 3, MAM mitochondria-associated endoplasmic reticulum membrane, MFN1 mitofusin-1, MFN2 mitofusin-2, MGRN1 E3 ubiquitin-protein ligase MGRN1, OPA1 dynamin-like GTPase OPA1, P phosphorylation, PERK eukaryotic translation initiation factor 2-alpha kinase 3, PINK1 PTEN induced putative kinase 1, PRKN E3 ubiquitin-protein ligase parkin, RETREG1 reticulophagy regulator 1, RHOT1 mitochondrial Rho GTPase 1, RHOT2 mitochondrial Rho GTPase 2, Rtnl1 reticulon-like protein, RYR ryanodine receptors, TM tunicamycin, TG thapsigargin, Ub ubiquitination, XBP1s X-box-binding protein 1 spliced. This figure was created using Adobe Illustrator (Adobe Inc., San Jose, CA, USA)

The effect of ERS on mitophagy

ERS is a stress response activated when the ER becomes dysfunctional due to factors such as excessive protein folding load, dysregulated Ca²⁺ signaling, or excessive oxidative damage.^221,222 When unfolded or misfolded proteins accumulate in the ER, ERS coordinates repair mechanisms through the unfolded protein response (UPR) signaling pathway to restore proteostasis or trigger apoptosis.^223–225 ERS is closely related to mitophagy: 1) The ER appears to provide essential membrane material during autophagosome assembly²²⁶ and provides Ca²⁺ signaling for the induction of autophagy²²⁷; 2) ERS and mitophagy each contribute crucially to organelle quality control systems. Their interdependence is strengthened through both structural connections and biochemical crosstalk between ER and mitochondrial networks. Furthermore, ERS can trigger mitophagy.^67,228 For example, ERS promotes PRKN translocation to the OMM, subsequently activating PRKN-dependent mitophagy.²²⁸ In another study, low doses of the ERS inducers tunicamycin and thapsigargin led to ERS-induced PRKN-dependent mitophagy in mice, significantly alleviating brain damage caused by ischemia‒reperfusion. The protective effects were markedly diminished when the ERS sensor eukaryotic translation initiation factor 2-alpha kinase 3 (eIF2αK3/PERK), its downstream effector cyclic AMP-dependent transcription factor ATF4 (ATF4), or PRKN were knocked out.²²⁸ Moreover, ERS can activate mitophagy via XBP1.⁶⁷ This transcription factor is activated through aberrant splicing by inositol-requiring protein-1α (IRE1α) under ERS, resulting in the production of XBP1s. Subsequently, XBP1s forms a functional loop with PINK1 (XBP1s-PINK1), where PINK1 induces its phosphorylation and subsequently regulates its nuclear localization. Phosphorylated XBP1s acts as a transcriptional regulator that directly upregulates PINK1 expression, thereby regulating mitophagy⁶⁷ (Fig. 4a).

The interaction between the ER regulation of Ca²⁺ and mitophagy

Ca²⁺ serves as a key secondary messenger, participating in diverse and dynamic biological processes.^229,230 As the primary cellular Ca²⁺ reservoir, the ER primarily discharges these ions through membrane-localized inositol 1,4,5-trisphosphate receptors (IP3Rs) and ryanodine receptors (RyRs), while the SERCA proton pump recycles them.^231,232 In contrast, mitochondria act as an important buffering system for intracellular Ca²⁺.²³³ Physiological concentrations of Ca²⁺ can activate key metabolic enzymes, including tricarboxylic acid (TCA) cycle dehydrogenases and FAD-glycerophosphate dehydrogenases, thereby maintaining mitochondrial ATP and protein production. Therefore, Ca²⁺ flux from the ER to mitochondria represents a critical mechanism for controlling cellular viability and maintaining mitochondrial homeostasis.²³⁴ This Ca²⁺ flux is principally governed by ion-conducting channels embedded in mitochondria-ER contacts, such as the IP3R-GRP75 (75 kDa glucose-regulated protein)-VDAC-MCU (mitochondrial calcium uniporter protein) and vesicle-associated membrane protein-associated protein B/C (VAPB)-regulator of microtubule dynamics protein 3 (PTPIP51/RMDN3) complexes.^235,236 However, if these transfer mechanisms become uncontrolled, abnormal mitochondrial Ca²⁺ concentrations can disrupt mitochondrial quality control. Excessive Ca²⁺ accumulation in mitochondria can increase mitochondrial fission and subsequently induce mitophagy to remove damaged organelles.^237,238 Additionally, excessive release of mitochondrial Ca²⁺ due to mitochondrial depolarization and abnormal surface Ca²⁺ accumulation on impaired mitochondria can promote mitophagy. The main pathway entails calcium/calmodulin-dependent protein kinase type 1 (CAMK1) stimulation, which subsequently targets the activation of PINK1, PRKN, and DJ-1 to regulate mitophagy.^239,240

The VAPB-PTPIP51/RMDN3 complex regulates Ca²⁺ transfer flux by modulating contact with the mito-ER, thereby affecting the formation of autophagosomes.²⁴¹ The overexpression of any component in the VAPB-PTPIP51/RMDN3 complex enhances Mito-ER contact and increases Ca²⁺ transfer flux. Conversely, VAPB or PTPIP51/RMDN3 knockdown weakens the link between the mito-ER, reduces Ca²⁺ transfer flux, and subsequently stimulates the biogenesis of mitophagy.²⁴¹ Mitochondrial Rho GTPases 1 (RHOT1) and 2 (RHOT2), Ca²⁺ sensors, are essential for Ca²⁺-dependent mitophagy.²⁴² During mitochondrial depolarization, Ca²⁺ binds to both RHOT1 and RHOT2, each of which can promote the mitochondrial translocation of PRKN, consequently enabling subsequent PINK1-PRKN-mediated mitophagy.²⁴²

The important mitophagy receptors PINK1 and PRKN participate in the conserved maintenance of intracellular calcium balance.²⁴³ A study²⁴³ proposed that physiological PINK1 activation enhances PRKN-mediated ubiquitination and degradation of CDGSH iron-sulfur domain-containing protein 1 (CISD1) on the OMM. This ubiquitination of CISD1 decreases the activity of the ER calcium channel IP3R and the cytoplasmic Ca²⁺ levels.²⁴³ Calcium-mediated intracellular signaling plays a pivotal role in modulating mitophagy.²⁴⁴ Another study indicated that the absence of Cisd1 could increase mitophagy in the thoraces and neurons of Drosophila and that the levels of mitophagy in Pink1- or Prkn-knockout Drosophila could be restored to normal after crossing with Cisd knockout or knockdown Drosophila. This suggests that decreased cytosolic Ca²⁺ concentrations in CISD1-deficient cells may trigger mitophagic activation, elucidating how CISD1 modulates mitophagy and its interaction with ER Ca²⁺ signaling in cells (Fig. 4b).

The interrelationship between MAMs and mitophagy

The dynamic crosstalk between organelles substantially impacts cell viability and physiological functions, particularly at ER-mitochondria membrane contact sites and the MAMs formed by these interactions.²⁴⁵ MAMs have become a complex hub that is central to the transport of phospholipid membranes and crucial in maintaining Ca²⁺ balance, lipid metabolism, apoptosis, autophagy, and mitochondrial biological functions.^246,247 MAMs are key sites for the formation of autophagosomes and primary sources of their membranes.²⁴⁸ During classic autophagy induced by starvation, BECN1 translocates to MAMs and assembles autophagic machinery components to initiate autophagosome biogenesis. Similar to classic autophagy, the formation of autophagosomes in mitophagy occurs at MAMs.

The ER-mitochondria encounter structure complexes,²⁴⁹ which connect the ER and mitochondria and colocalize with the sites of mitochondrial autophagosome formation in yeast, thereby regulating membrane formation for autophagosomes.²⁵⁰ In mammalian cells, endogenous PINK1 relocates to MAMs and recruits BECN1 after CCCP-induced mitophagy, thereby promoting the formation of autophagosomes within MAMs.²⁴⁸ The molecular interplay between PINK1 and BECN1 strengthens the Mito-ER contact sites within MAMs, an effect that does not depend on PRKN.²⁴⁸

Mitophagy receptors or associated proteins are closely linked to the formation and regulation of MAMs. The mitophagy receptor FUNDC1 is localized to MAMs and can interact with IP3R, thereby regulating Ca²⁺ transport associated with MAMs.²⁵¹ Importantly, a reduction in FUNDC1 expression at the MAMs prevents Mito-ER contact, reduces mitochondrial and cytoplasmic Ca²⁺ flux, and further inhibits the activity of cyclic AMP-responsive element-binding protein 1 (CREB).²⁵¹ It results in decreased FIS1 transcription, subsequently inducing abnormal elongation and functional impairment of mitochondria.²⁵¹ The OMM protein MFN2 (mitofusin-2), acting as a tether in MAMs, reduces its ubiquitination, thereby weakening the Mito-ER contact and promoting mitophagy via the PINK1-PRKN-VCP/p97 (transitional endoplasmic reticulum ATPase) axis.²⁵² The Ub-dependent mitophagy receptor Mul1 is a negative regulator of Mito-ER tethering at MAMs. Its absence increases MFN2 activity and upregulates the Mito-ER tethering protein PTPIP51/RMDN3, consequently maintaining Mito-ER contact at MAMs and inhibiting PRKN-mediated mitophagy²⁵³ (Fig. 4c).

The interrelationships between ER quality control and mitophagy

Reciprocal regulation has been identified between mitophagy and ER quality control. For example, the ER E3 ligase AMFR/gp78 can induce mitophagy by facilitating the UPS-mediated clearance of OMM proteins.¹⁰⁴ The interaction between the E3 ubiquitin-protein ligase MGRN1 and AMFR/gp78 is disrupted under acute stress or elevated Ca²⁺ levels, in turn contributing to increased levels of AMFR/gp78.¹⁰⁴ Excess AMFR/gp78 promotes ubiquitin-dependent proteolysis of MFN1 and MFN2 on the OMM, resulting in OMM disruption, exposure of the IMM, and the formation of mitoplasts that migrate toward the ER.¹⁰⁴ At this stage, RETREG1/FAM134B interacts with the dynamin-like GTPase OPA1 on the inner membrane of mitoplasts and connects with MAP1LC3B/LC3B to drag mitoplasts into autophagosomes, leading to lysosomal fusion and degradation.¹⁰⁴ During this process, excess AMFR/gp78 is degraded along with the “Mito-ER-autophagy” process, consequently achieving Mito-ER turnover and alleviating ERS and the disruption of mitochondrial homeostasis.¹⁰⁴

AMFR/gp78 can interact with the ER-associated degradation-associated E3 ubiquitin-protein ligase synoviolin (HRD1), synergistically promoting PINK1 ubiquitination and its subsequent proteasomal degradation.²⁵⁴ HRD1 initiates the formation of polyubiquitin chains on PINK1, whereas AMFR/gp78 extends these chains. Given the importance of PINK1 in mitophagy, the regulatory mechanisms of AMFR/gp78 and HRD1 on PINK1 are crucial in mitochondrial quality control.²⁵⁴ Similarly, another study revealed the significant role of cross-organelle remodeling mediated by mitophagy in cellular and organismal health.²⁵⁵ The study revealed that PINK1-mediated regulation of KEAP1- and PRKN-dependent substrate ubiquitination pathways can influence targeted degradation of ER and mitochondria.²⁵⁵ PINK1 regulates KEAP1-Cullin3-mediated ubiquitination of reticulon-like protein (Rtnl1) to activate ER-phagy. In addition, PINK1 can activate PRKN-mediated mitophagy. Therefore, the ability of PINK1 to coordinate both mitophagy and ER-phagy through substrate-specific ubiquitination pathways suggests a broader function in regulating organelle homeostasis (Fig. 4d).

Mitophagy and nucleus

The nucleus, composed of the nuclear membrane, chromatin, nucleolus and nuclear matrix, serves as the genetic information repository and metabolic regulation center of eukaryotic cells.²⁵⁶ It maintains cellular life activities and the complexity of multicellular organisms through DNA storage, gene expression regulation, material exchange and control of cell division and differentiation.²⁵⁷

The nucleus and mitochondria maintain cellular homeostasis through complex and dynamic interactions.²⁵⁸ 1) Genomic synergy. During evolution, mitochondria experienced substantial gene transfer to the nuclear genome, preserving only 13 genes essential for oxidative phosphorylation. The two can ensure the precise matching of respiratory chain complex subunits through coevolution.²⁵⁹ 2) Metabolic signal feedback. Metabolites such as acetyl-CoA produced by mitochondria regulate histone acetylation and DNA methylation in the nucleus, reshaping the open state of chromatin, while nuclear-encoded transcription factors (such as nuclear respiratory factor 1 [NRF1] and forkhead box protein O1 [FOXO1]) can in turn regulate mitochondrial biosynthesis.^260–263 3) Stress synergy. Mitochondrial damage activates nuclear repair pathways through mitochondrial retrograde signaling pathways such as mtROS and mtDNA release, while nuclear repair proteins can also translocate to mitochondria to repair mtDNA oxidative damage.²⁶⁴ Thus, the multidimensional regulatory network formed by the two jointly determines cell fate and functional homeostasis²⁶⁵ (Fig. 5).

Fig. 5.

Interactions between mitophagy and the nucleus. a The regulatory role of mitochondrial retrograde signaling in mitophagy. Upon mitochondrial dysfunction, mitochondria orchestrate retrograde signaling to the nucleus via the integrated stress response, ROS, and Ca²⁺ fluxes. This activates adaptive changes in the expression of specific genes (e.g., NFAT, ATF4, NRF2), which subsequently induce mitophagy to preserve cellular functional homeostasis. b The regulation of mitophagy by nuclear transcription factors. Multiple transcription factors, such as TFEB, SMAD3, FOXO3, and FOXD1, regulate mitophagy progression by dynamically modulating their subcellular localization, stability, and transcriptional activity through posttranslational modifications. c The influence of nucleus-localized proteins on mitophagy. Specific nucleus-localized proteins, including LC3, OGG1, and DNA-PKcs, regulate mitophagy through both direct and indirect mechanisms. ATF4 activating transcription factor 4, BECN1 Beclin1, DELE1 DAP3-binding cell death enhancer 1, DNA-PKcs DNA-dependent protein kinase catalytic subunit, eIF2α eukaryotic translation initiation factor 2 subunit 1, FOXD1 forkhead box protein D1, FOXO3 forkhead box protein O3, FUNDC1 FUN14 domain-containing protein 1, G glycosylation, GCN2 general control nonderepressible 2, HRI heme-regulated inhibitor, IP3R inositol 1,4,5-trisphosphate receptor, ISR^mt mitochondrial integrated stress response, LC3 microtubule associated protein 1 light chain 3, NFAT nuclear factor of activated T cells, NRF2 nuclear factor erythroid 2-related factor 2, OGG1 8-oxoguanine DNA glycosylase, OMA1 metalloendopeptidase OMA1, P phosphorylation, PERK eukaryotic translation initiation factor 2-alpha kinase 3, PINK1 PTEN induced putative kinase 1, PKR double-stranded RNA-dependent protein kinase, PRKN E3 ubiquitin-protein ligase parkin, ROS reactive oxygen species, S-DELE1 DAP3-binding cell death enhancer 1 short form, SMAD3 mothers against decapentaplegic homolog 3, TFEB transcription factor EB. This figure was created using Adobe Illustrator (Adobe Inc., San Jose, CA, USA)

Mitochondrial retrograde signaling regulates mitophagy

Mitochondrial retrograde signaling refers to the reverse signaling mechanism in which mitochondria send signals to the nucleus when they are damaged or functionally impaired, requesting adaptive changes in nuclear gene expression to respond to alterations in mitochondrial function and regulate cellular functional homeostasis.^266,267 These retrograde signals mainly include some molecules with signaling functions emitted by mitochondria that can penetrate or act on the nuclear membrane, such as ROS, Ca²⁺, metabolic products, mtUPR, and integrated stress response (ISR).^267,268 Abnormal mitochondrial conditions and cellular metabolic changes are presented to the nucleus, which then mobilizes multiple nuclear transcription factors, activating important signaling networks and regulating the state of the cell.^266,269

ISR is a signaling network capable of recognizing various cellular stresses, including mitochondrial dysfunction.^267,270 Its core mechanism is to coordinate protein synthesis and stress adaptation by regulating the activity of eIF2α, thereby helping cells restore homeostasis.^267,271 ISR is composed of four distinct branches: heme-regulated inhibitor (HRI), eIF2αK3/PERK, double-stranded RNA-dependent protein kinase (PKR), and general control nonderepressible 2 (GCN2), each responding to different types of cellular stress.^267,272 Upon sensing stress, each branch inhibits the activity of eIF2α through phosphorylation by its central kinase. Among them, the HRI branch mainly senses stress types such as heme deficiency and mitochondrial dysfunction.^273,274 Studies²⁷³ have indicated that the HRI signaling pathway critically governs mitochondrial quality surveillance and can selectively drive mitophagy. When mitochondria are damaged (such as by iron chelation or depolarization), the mitochondrial metalloproteinase OMA1 processes DAP3-binding cell death enhancer 1 (DELE1) to produce its truncated isoform (S-DELE1), which stimulates HRI kinase activity together with the phosphorylation of eIF2α.²⁷³ Phosphorylated eIF2α (p-eIF2α) specifically accumulates on the mitochondrial surface, forming a signal “tag” that recruits autophagy-related proteins (such as MAP1LC3/LC3), directly inducing mitophagy. Experiments show that artificially anchoring p-eIF2α to mitochondria can trigger autophagy, while other organelles (such as peroxisomes) do not have this effect.²⁷³ Additionally, researchers²⁷³ have found that HRI-mediated mitophagy operates independently yet concurrently with the PINK1-PRKN signaling axis. Even if the PINK1-PRKN pathway is inhibited, HRI activation can still promote autophagosome formation through the mitochondrial localization of p-eIF2α. This indicates that the ISR provides an additional layer of protection for mitochondrial quality control.

ROS and Ca²⁺ signaling are key intracellular second messengers that act as bridges to connect the regulatory signals between mitophagy and other organelles into a network, forming a complex stress response and homeostasis maintenance system.^275,276 In mitochondrial retrograde signaling, ROS and Ca²⁺ signaling can serve as driving factors for mitophagy-nucleus interactions. When PINK1 deficiency disrupts mitophagy, accumulated mitochondrial ROS trigger nuclear factor erythroid 2-related factor 2 (NRF2) activation through mitochondrial-nuclear communication, promoting nuclear translocation and upregulating thioredoxin reductase 1 (TXNRD1) and PI3K-AKT signaling, ultimately driving epithelial–mesenchymal transition in retinal pigment cells of age-related macular degeneration patients.²⁷⁷ Targeting mitophagy or administering antioxidants to clear ROS can block mitochondrial retrograde signaling and alleviate retinal pigment epithelial heterogeneity and may become a therapeutic strategy for early age-related macular degeneration.

Ca²⁺ signaling, similar to ROS, serves as a pivotal mediator of mitochondrial retrograde communication, coordinating mitophagy and nuclear responses through multiple molecular pathways.^278,279 Elevated Ca²⁺ levels elicit dual regulatory roles. On the one hand, Ca²⁺ binds to calmodulin, promoting the nuclear translocation of transcriptional regulators such as nuclear factor of activated T cells (NFAT), NF-κB, and transcription factor EB (TFEB), thereby upregulating the expression of autophagy markers (ATGs, MAP1LC3/LC3) and lysosomal components to facilitate mitophagy.^280,281 Moreover, Ca²⁺ activates PGC-1α, which enhances mitochondrial biogenesis and antioxidant defense, contributing to the restoration of mitochondrial integrity.²⁸² The mitophagy receptor BNIP3L/NIX additionally modulates nuclear Ca²⁺ dynamics and influences muscle cell differentiation. Field et al.³⁸ reported that BNIP3L/NIX regulated mitochondrial function and ER Ca²⁺ release, maintaining nuclear calcium homeostasis and activating Ca²⁺-dependent NFAT signaling to enhance the formation of oxidative muscle fibers. In contrast, BNIP3L/NIX deficiency disrupted ER Ca²⁺ release, suppressed NFAT activation, downregulated its target gene expression, and induced a metabolic shift in muscle fiber types, ultimately impairing muscle function and promoting myopathic phenotypes.³⁸ These findings underscore BNIP3L/NIX as a promising therapeutic avenue for addressing mitochondrial myopathies, muscular atrophy, and metabolic disorders, highlighting the pathological relevance of mitochondrial-nuclear Ca²⁺ coupling³⁸ (Fig. 5a).

The eIF2αK3/PERK branch of ISR and mtUPR have been documented to engage in complex crosstalk with mitophagy. The mechanistic interplay between these signaling pathways and mitophagic regulation is discussed in the sections with regard to mitophagy-mitochondria and mitophagy-ER.

Nuclear transcription factors regulate mitophagy

Nuclear transcriptional regulators coordinate mitophagic processes through complex regulatory networks. Among them, TFEB has been extensively characterized as a principal controller of lysosome formation and autophagy-associated transcriptional programs. Recent studies have highlighted TFEB as a key regulator of mitophagy as well.^283,284 Kim et al.²⁸⁴ noticed that carbon monoxide (CO) stimulation promoted TFEB nuclear translocation, which subsequently enhanced PRKN recruitment to mitochondria and lysosomal biogenesis, thereby initiating PRKN-mediated mitophagy. In addition, TFEB activation upregulates the expression of PGC-1α and NRF1, facilitating mitochondrial biosynthesis. This dual regulatory role of TFEB coordinates mitochondrial quality control by simultaneously promoting damaged mitochondria removal through mitophagy and supporting the replenishment of functional mitochondria via biogenesis, thus preserving mitochondrial quality and preventing mitochondrial dysfunction-related tissue damage.²⁸⁴ SMAD3, a central signal transducer in the transforming growth factor (TGF)-β-SMAD cascade, has recently been identified as directly influencing the transcription of PINK1.²⁸⁵ Upon mitochondrial depolarization, SMAD3 activates PINK1 transcription independently of canonical TGF-β signaling components. In turn, PINK1 phosphorylates SMAD3 at serine positions 423 and 425, initiating a positive feedback mechanism that enhances mitophagy. This bidirectional regulation between SMAD3 and PINK1 serves a protective function in mitigating cell death caused by mitochondrial stress.²⁸⁵ Forkhead box protein O3 (FOXO3) is well established as a vital transcriptional regulator coordinating essential cellular processes such as cell cycle control, apoptosis, and the detoxification of ROS.²⁸⁶ It also serves as a transcriptional activator of multiple mitophagy-related genes.^286,287 Under stress conditions, FOXO3 undergoes nuclear translocation facilitated by dephosphorylation and deacetylation, subsequently activating downstream targets such as PINK1, BNIP3, and BECN1 and thereby initiating mitophagy.^288–290 Recently, Chen et al.²⁹¹ developed a CRISPR/Cas9-based system for editing the FOXO3 gene in chondrocytes, which was then encapsulated into injectable hydrogel microspheres (FOXO3-NETT@SMs). This approach successfully activated mitophagy via FOXO3-PINK1-PRKN signaling and reestablished mitochondrial balance in osteoarthritic chondrocytes, underscoring the therapeutic potential of targeting FOXO3-regulated mitophagy in clinical applications.²⁹¹

PTMs, such as phosphorylation, acetylation, and glycosylation, precisely regulate protein structure, localization, function, and interactions, thereby orchestrating complex cellular functions.²⁹² The PTMs of transcription factors, in particular, critically influence mitophagy by regulating their subcellular distribution, stability, and transcriptional activity.²⁹³ In a study investigating osteogenic dysfunction in type 2 diabetes mellitus (T2DM), Xian et al.²⁸⁹ reported reduced expression of the NAD-dependent deacetylase sirtuin-3 (SIRT3) in the bone tissue of diabetic mice. The reduction led to hyperacetylation of FOXO3, suppression of PRKN transcription, and consequent impairment of PINK1-PRKN-mediated mitophagy, leading to the accumulation of damaged mitochondria.²⁸⁹ Conversely, overexpression of SIRT3 or its pharmacological activation restored FOXO3 deacetylation, reactivated mitophagy, and ameliorated T2DM-induced osteogenic defects.²⁸⁹ It is likely that in human endometrial cancer cells,²⁸⁸ overexpression of the deacetylase SIRT1 enhances FOXO3 deacetylation and nuclear translocation, thereby activating BNIP3 transcription and initiating mitophagy. Inhibition of the SIRT1-FOXO3 axis, either alone or in combination with mitophagy inhibitors, could offer a new therapeutic approach for endometrial carcinoma.²⁸⁸ In nasopharyngeal carcinoma, Wang et al.²⁹⁴ identified that asparagine-linked glycosylation protein 3 homolog (ALG3) facilitated the glycosylation of forkhead box protein D1 (FOXD1), which improved its stability and promoted its localization in the nucleus. This modification activates BNIP3 transcription and promotes mitophagy, contributing to cell survival, proliferation, invasion, and gemcitabine resistance. These findings indicate that targeting the ALG3-FOXD1-BNIP3 pathway may provide a novel strategy for treating nasopharyngeal carcinoma.²⁹⁴

Conversely, mitophagy can also influence disease progression by modulating the PTMs of transcription factors. In hepatocellular carcinoma (HCC), Liu et al.²⁹⁵ noted that enhanced mitophagy suppressed p53 activity and promoted cancer stemness. Under conditions of elevated mitophagy, p53 colocalized with mitochondria and underwent PINK1-mediated phosphorylation. The modification targets p53 for mitophagic degradation along with damaged mitochondria, resulting in decreased nuclear p53 levels. Consequently, the expression of the pluripotency-associated transcription factor NANOG is maintained, supporting the self-renewing capacity of hepatic cancer stem cells.²⁹⁵ In contrast, mitophagy inhibition results in increased nuclear p53, which binds to the NANOG promoter, inhibiting its transcription. This reduces the stem cell pool and hampers tumor progression. This study reveals a key mechanism by which mitophagy facilitates HCC malignancy via modulation of p53 PTMs and nuclear translocation²⁹⁵ (Fig. 5b).

Nucleus-localized proteins influence mitophagy

Certain nucleus-localized proteins regulate mitophagy through both direct and indirect mechanisms. One such example is MAP1LC3/LC3, a core component of autophagosome formation.²⁹⁶ The dynamic nucleocytoplasmic distribution of MAP1LC3/LC3 is a critical step in the onset of macroautophagy.^296,297 Under nutrient-abundant environments, MAP1LC3/LC3 is predominantly localized in the nucleus, where it acts as a sensor of cellular stress and helps coordinate responses to metabolic challenges.²⁹⁶ Upon nutrient deprivation, nuclear MAP1LC3/LC3 undergoes deacetylation, becomes activated, and translocates to the cytoplasm to initiate autophagosome biogenesis.^296,297 In mitophagy, MAP1LC3/LC3 exhibits a similar regulatory dynamic.²⁹⁸ In hepatocytes, glucagon stimulation has been shown to upregulate BNIP3 expression, facilitating the nuclear-to-mitochondrial relocalization of MAP1LC3/LC3. This nuclear-to-mitochondrial trafficking of MAP1LC3/LC3 augments BNIP3-mediated mitophagy in response to nutrient starvation, subsequently contributing to the restoration of hepatic metabolic homeostasis.²⁹⁸

8-Oxoguanine DNA glycosylase (OGG1) is an essential enzyme in DNA repair that identifies and excises oxidatively damaged 8-oxoguanine (8-oxoG) lesions from DNA, thereby triggering the base excision repair (BER) pathway.²⁹⁹ In addition to its canonical DNA repair role, OGG1 can assemble transcriptional complexes at proinflammatory gene promoters, boosting their expression in response to oxidative stress.^299,300 Recent evidence suggests that OGG1 participates in mitophagy regulation. Zhao et al.³⁰¹ reported that OGG1 exhibited increased cytoplasmic localization in renal tubular epithelial cells from a mouse model of ischemic kidney injury. Under these conditions, OGG1 interacted directly with PINK1 and inhibited its translocation to the mitochondria, in turn suppressing mitophagy. This suppression leads to exacerbated mitochondrial dysfunction and worsened ischemic renal injury.³⁰¹ Notably, genetic deletion or pharmacological inhibition of OGG1 partially restored PINK1-mediated mitophagy and mitigated mitochondrial damage, suggesting a reciprocal regulatory loop between OGG1 activity and mitophagy regulation.³⁰¹

The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) serves as the core enzymatic element in the classical nonhomologous end joining (c-NHEJ) pathway and is essential for repairing DNA double-strand breaks, immune diversity, and disease pathogenesis.^302,303 Emerging studies demonstrate a strong connection between DNA-PKcs and mitochondrial homeostasis.^304–306 Multiple studies^304–306 have demonstrated that DNA-PKcs can promote mitochondrial injury through specific regulatory mechanisms, contributing to dysfunction in multiple organ systems, including the cardiovascular and hepatic systems. Zhou and colleagues³⁰⁶ uncovered that DNA-PKcs controls mitochondrial homeostasis in alcoholic liver disease by coordinating fission dynamics and mitophagic flux. In a chronic ethanol-induced liver injury mouse model,³⁰⁶ DNA-PKcs was found to enhance p53 activation in hepatocytes, which in turn upregulated DNM1L/DRP1-mediated mitochondrial fission while concurrently inhibiting FUNDC1-dependent mitophagy. Thus, the imbalance induces excessive mitochondrial fragmentation, elevates oxidative stress, and aggravates hepatic injury (Fig. 5c).

Mitophagy and lysosomes

Lysosomes are membrane-enclosed organelles containing an acidic lumen and serve two primary functions³⁰⁷: 1) degradation and secretion and 2) cellular signal transduction. Lysosomes contain numerous hydrolytic enzymes capable of degrading specific intracellular substrates. Additionally, they participate in the degradation and recycling of both intracellular and extracellular materials via autophagy or endocytosis. For example, extracellular materials can be transported to these organelles for degradation via endocytosis, or lysosomal contents can be extracellularly secreted through Ca²⁺-dependent exocytosis to facilitate the repair of damaged plasma membranes and regulation of cellular clearance.^308,309 In cellular signal transduction, lysosomes establish a unique lysosome-to-nucleus feedback pathway to sense nutrient levels and regulate cellular energy metabolism.^307,310 Furthermore, they serve as storage sites for various amino acids, metabolites, and ions. Their involvement in numerous biological processes implies deep connections with other organelles.

Mitophagy constitutes the most intimate and direct interaction between mitochondria and lysosomes,³¹¹ primarily because lysosomes are the final site for autophagic degradation. These organelles directly interact to regulate mitochondrial dynamics and function, support the maintenance of cellular metabolic balance, and facilitate the transmission of cellular signaling pathways, including Ca²⁺ signaling^178,312,313 (Fig. 6).

Fig. 6.

Interactions between mitophagy and lysosomes. a The effects between mitophagy impairment and lysosomal function. Impaired mitophagy significantly contributes to lysosomal dysfunction, while compromised lysosomal quantity or pathological accumulation reciprocally exacerbates mitophagy defects. b The correlation between lysosome repair/degradation and mitophagy. The ESCRT machinery serves as a critical lysosomal repair system that safeguards the membrane integrity and functional homeostasis of lysosomes. By regulating the sealing of phagophores, ESCRT mediates mitophagy initiation. Furthermore, the ESCRT complex recognizes and sequesters depolarized mitochondria, which are encapsulated into single-membrane RAB5-positive endosomes. These cargo-laden endosomes subsequently mature into RAB7-positive compartments, eventually delivering depolarized mitochondria to lysosomes for degradation. c The relationship between lysosomal regulation of Ca²⁺ and mitophagy. Lysosomal Ca²⁺ release triggered by mitochondrial or metabolic stress activates TFEB to induce mitophagy. ER-mediated lysosomal Ca²⁺ refilling further amplifies TFEB activation, establishing a positive feedback loop termed the “ER-Lysosome Ca²⁺-Mitophagy Axis”. TRPML1 acts as a mitochondrial stress sensor: it promotes autophagy by releasing Ca²⁺ in response to mitochondrial ROS bursts and mediates lysosomal Ca²⁺ overload upon impaired ETC activity. ADP adenosine diphosphate, AMPK AMP-activated protein kinase, ATP adenosine triphosphate, ROS reactive oxygen species, BNIP3 B-cell leukemia/lymphoma 2/adenovirus E1B 19 kDa protein-interacting protein 3, CLDM clindamycin, ERM erythromycin, ESCRT endosomal sorting complex required for transport, ETC mitochondrial electron transport chain, FLCN folliculin, mtDNA mitochondrial DNA, MYH10 myosin-10, NDP52 calcium-binding and coiled-coil domain-containing protein 2, NLRP3 NACHT, LRR and PYD domains-containing protein 3, NRF2 nuclear factor erythroid 2-related factor 2, OPTN optineurin, PGC1 peroxisome proliferator-activated receptor gamma coactivator 1, PINK1 PTEN induced putative kinase 1, PRKN E3 ubiquitin-protein ligase parkin, RAB5 Ras-related proteins Rab-5A, RAB7 Ras-related proteins Rab-7A, TFEB transcription factor EB, TRPML1 mucolipin-1, TSG101 tumor susceptibility gene 101 protein. This figure was created using Adobe Illustrator (Adobe Inc., San Jose, CA, USA)

Mitophagy impairment leads to lysosomal dysfunction

Impaired mitophagy substantially contributes to lysosomal dysfunction^314,315; however, the specific reasons remain unclear. This could be associated with mitochondrial dysfunction resulting from impaired mitophagy. To sustain optimal activity, most lysosomal enzymes depend on an acidic environment, which is preserved by V-ATPase. V-ATPase harnesses the energy from ATP hydrolysis to transport protons across the lysosomal membrane into the lumen, thereby maintaining the acidic environment.³¹⁶ Dysfunctional mitochondria are not efficiently removed when mitophagy is impaired, leading to disruption in mitochondrial quality control and mitochondrial dysfunction. It further disrupts ATP production.^310,317

Irazoki et al.³¹⁸ discovered that the lack of the mitophagy receptor BNIP3 not only affected mitophagy flux but also induced lysosomal dysfunction, resulting in pathological accumulation of impaired lysosomes in muscle cells. This may be due to the impairment of mitophagy and lysosomal function owing to reduced BNIP3 levels, which release mtDAMPs. Consequently, it activates various inflammatory signaling pathways, including Toll-like receptor (TLR) 9-mediated signaling activation and NLRP3 inflammasome assembly.³¹⁸ Furthermore, the involvement of BNIP3 in lysosomal function regulation extends beyond its canonical mitophagy function, which is crucial for inflammation activation.³¹⁸ Therefore, further exploration of the mechanisms by which BNIP3 mediates lysosomal dysfunction is important for understanding the inflammatory responses in patients with muscle atrophy and identifying potential therapeutic targets.

In macroautophagy, the final step in autophagy requires autophagosome-lysosome fusion to form autolysosomes, where the degradation of substrates is completed. Lysosomal dysfunction can lead to the failure of autophagosomes to fuse with lysosomes, thereby disrupting autophagic flux.³¹¹ In another study,³¹⁹ treatment with erythromycin (ERM) and clindamycin (CLDM) reduced lysosomal populations across multiple human cell lines and resulted in impaired mitophagy flux as well as the subsequent buildup of damaged mitochondria that triggered apoptosis. However, the overexpression of TFEB can promote lysosome biogenesis, restore mitophagy flux, and improve mitochondrial function.³¹⁹

The pathological accumulation of lysosomes inhibited PINK1-PRKN-mediated mitochondrial clearance in the neural cells of type II Gaucher disease (a lysosomal dysfunction disease) mice.³²⁰ The potential mechanism involves decreased activity of mitochondrial membrane complexes I-III in neuronal cells, consequently leading to impaired ETC function.³²⁰ Meanwhile, the compensatory upregulation of complex V activity helps maintain a certain degree of mitochondrial membrane potential. However, this process consequently inhibits PINK1 stabilization on the OMM and subsequent PRKN translocation³²⁰ (Fig. 6a).

The relationship between lysosome regulation of Ca²⁺ and mitophagy

Changes in lysosomal Ca²⁺ also affect mitophagy. For instance, in pancreatic β-cells, mitochondrial or metabolic stress-induced Ca²⁺ efflux from lysosomes triggers TFEB activation.³²¹ TFEB promotes mitophagic clearance in pancreatic β-cells by activating mitophagy receptor proteins, including CALCOCO2/NDP52 and OPTN.³²¹ During this process, the ER further activates TFEB by refilling lysosomal Ca²⁺, thereby forming a positive feedback loop of “ER-lysosomal Ca²⁺-mitophagy.” This loop enables pancreatic β-cells to physiologically adjust to metabolic stress conditions.³²¹

TRPML1 (also known as MCOLN1, mucolipin 1) functions as an endolysosomal transmembrane cation channel, serves as the main Ca²⁺ release channel on the lysosomal membrane,³²² and functions as a sensor for mitochondrial dysfunction. When mitochondrial damage induces an excessive increase in ROS levels, TRPML1 is activated and facilitates Ca²⁺ release from the lysosome, which stimulates PPP3/calcineurin-dependent TFEB nuclear import to enhance autophagic activity.³²² In contrast, TRPML1 can sense lesions to the ETC, with a critical influence on lysosomal function.³²³ In turn, the impaired ETC can result in the secretion of a significant amount of the AMPK-inhibitory protein FLCN (folliculin), leading to AMPK inactivation, which is essential for basic lysosomal function.³²³ Subsequently, inactivated AMPK inhibits TRPML1 activity via the phosphoinositide kinase FYVE-type zinc finger-containing (PIKFYVE)-phosphatidylinositol-3,5-bisphosphate (PtdIns[3,5]P2) pathway, causing Ca²⁺ overload within lysosomes and ultimately leading to lysosomal hydrolytic metabolic dysfunction.³²³ The AMPK-TRPML1 regulatory axis reveals how TRPML1 senses mitochondrial damage through the AMPK signaling cascade, thereby influencing lysosomal function and cellular metabolic homeostasis.³²³ These mechanisms provide a new perspective on mitochondrial-lysosomal crosstalk and potential therapeutic strategies for associated disorders.³²³ TRPML1 has recently been identified as a promising molecular target for anticancer therapy.³²⁴ For example, TRPML1 demonstrates therapeutic potential for HCC through its regulatory effects on mitochondrial homeostasis, but its activity needs to be precisely controlled. Under physiological conditions, TRPML1 can maintain mitochondrial function by preserving mitophagic flux and mitochondrial Ca²⁺ homeostasis.³²⁴ However, both deficiency and overactivation of TRPML1 disrupt this homeostasis.³²⁴ Siow et al.³²⁴ demonstrated that TRPML1 knockout impairs mitophagy, whereas TRPML1 overactivation induces mitochondrial Ca²⁺ overload, both of which suppress tumor progression by interfering with mitochondrial function in HCC cell lines.

Similar regulatory roles have been observed with ras-related proteins involved in the endolysosomal system, including RAB5A (RAB5) and RAB7A (RAB7).³²⁵ RAB5 primarily mediates PRKN-dependent mitophagy,³²⁶ whereas RAB7 regulates lysosomal dynamics by modulating lysosomal transport and fusion. The combined inhibition of the RAB5 and RAB7 signaling pathways induces colorectal cancer cell eradication and tumor lesion regression.³²⁵

Collectively, these results highlight the essential functions of TRPML1 and related lysosomal trafficking proteins in regulating mitochondrial quality control, autophagy, and cell viability that can be exploited for cancer therapy (Fig. 6c).

The correlation between lysosomal repair degradation and mitophagy

The endosomal sorting complex required for transport (ESCRT) is a specialized mechanism that regulates membrane dynamics processes such as membrane rupture and sealing.³²⁷ Thus, it significantly contributes to maintaining protein stability, facilitating endosomal maturation, preserving lysosomal function, and regulating cell signaling pathways. The impact of ESCRT on lysosomes primarily involves the repair of damaged lysosomes to preserve lysosomal membrane integrity and restore pH levels and hydrolytic function within the lysosomal compartment.³²⁸ In addition, the irreplaceable function of ESCRT machinery has been demonstrated in modulating mitochondrial flux and the regulation of cell death. The ESCRT mechanism can modulate mitophagy, primarily through its ability to mediate mitophagy by regulating phagophore closure in the formation of mitophagosomes.

The absence of ESCRT-III subunits inhibits the initiation of mitophagosome formation, impairing both PRKN-mediated mitophagic mechanisms and PRKN-independent pathways.^329,330 This conclusion is supported by research on frontotemporal dementia, where myosin-10 interacted with ESCRT-III in neuronal cells. The interaction helps recruit ESCRT-III to damaged mitochondria, consequently facilitating the closure of phagophores and mediating mitophagy to maintain neuronal homeostasis.³³¹ Furthermore, the ESCRT pathway mediates mitochondrial clearance and flux regulation independent of mitophagy. The ESCRT machinery can recognize and capture depolarized mitochondria, isolating them in single-membraned RAB5-positive endosomes through the regulation of membrane invagination and scission.³²⁶ This process involves the maturation of the captured RAB5-positive endosomes into RAB7-positive endosomes, ultimately culminating in lysosomal breakdown of depolarized mitochondria. Moreover, the signaling pathway relies on the activation of RAB5 by the autophagy protein BECN1.³²⁶ Although the stressors that activate this pathway subsequently induce mitophagy, the degradation process occurs before mitophagy. Thus, the ESCRT-mediated internalization of impaired mitochondria into endosomal compartments represents an immediate protective response for removing defective mitochondria.³²⁶

Tumor susceptibility gene 101 protein (TSG101), an essential subunit of the ESCRT machinery, is closely related to mitochondrial flux.³³² However, this relationship is independent of mitophagy and macroautophagy. Rather, it mechanistically connects to stimulation of PGC-1α and NRF2-dependent mitochondrial generation, underscoring its importance in maintaining the number and size of mitochondria in axonal compartments.³³² The unique and essential function of the ESCRT system in regulating lysosomal and mitochondrial clearance indicates its potential as a critical bridge coordinating these two degradation pathways, thus serving an essential function in preserving fundamental cellular homeostasis (Fig. 6b).

Mitophagy and peroxisomes

Peroxisomes, dynamic and multifunctional oxidative metabolic organelles, are key players in various metabolic pathways.³³³ They play critical roles in fatty acid catabolism and anabolism, ether lipid and bile acid production, and ROS metabolic regulation.³³⁴ Given their central fundamental metabolic functions, peroxisomes establish essential communication with multiple membrane-bound organelles engaged in cellular lipid homeostasis, particularly the ER and mitochondrial networks.^333,335 Beyond their established metabolic roles, peroxisomes function as vital intracellular signaling hubs that coordinate essential biological processes, including innate immunity, inflammation, and cell survival. This position positions them as key determinants of human physiology and disease³³⁶ (Fig. 7a).

Fig. 7.

Interactions between mitophagy and proteasomes, peroxisomes, and lipid droplets. a The interaction between peroxisomes and mitophagy. Peroxisomes and mitochondria exhibit interdependent coordination, manifested in three key aspects: (1) metabolic synergy in fatty acid β-oxidation and ROS metabolism; (2) shared fission machinery (FIS1, MFF, DRP1) regulating the division of both organelles through distinct pathways; and (3) material transfer via mitochondria-derived vesicles (MDVs). Additionally, under DFP treatment, BNIP3L coenriches peroxisomes and mitochondria to independently induce mitophagy and pexophagy. b The interaction between lipid droplets and mitophagy. Excessive LD deposition suppresses mitophagy initiation. Conversely, downregulating LD-associated Plin4 reduces LD accumulation and reactivates mitophagy. Impaired LD biogenesis also inhibits mitophagy: DGAT1 deficiency prevents FFA esterification into TAG, disrupting LD synthesis. Concurrent FFA accumulation induces lysosomal dysfunction through lipotoxicity, reduces mitophagic flux, and ultimately triggers cell death. c Interaction between proteasomes and mitophagy. Impact of proteasome function on mitophagy (left): early-stage 26S proteasome dysfunction promotes PRKN-mediated mitophagy, whereas sustained dysfunction suppresses mitophagy initiation. Impact of mitophagy on the proteasome (right): PRKN-mediated mitophagy activates proteasomes and the UPS. Conversely, defective mitophagy leads to pathological mitochondrial retention and oxidative stress, which impair NFE2L1 and its transcriptional activation of proteasome subunits. ABCA1 ATP-binding cassette transporter A1, ATG9A autophagy-related protein 9A, ATP adenosine triphosphate, BNIP3L B-cell leukemia/lymphoma 2/adenovirus E1B 19 kDa interacting protein 3-like, DFP deferiprone, DGAT1 diacylglycerol O-acyltransferase 1, DRP1 dynamin-1-like protein, FFA free fatty acids, FIS1 mitochondrial fission 1 protein, LC3 microtubule associated protein 1 light chain 3, LD lipid droplet, MFF mitochondrial fission factor, MFN2 mitofusin-2, NFE2L1 endoplasmic reticulum membrane sensor NFE2L1, OPTN optineurin, P phosphorylation, p62 sequestosome 1, PGC1 peroxisome proliferator-activated receptor gamma coactivator 1, PLIN1 perilipin-1, PLIN4 perilipin-4, PLIN5 perilipin-5, PPARα peroxisome proliferator-activated receptor alpha, PRKN E3 ubiquitin-protein ligase parkin, ROS reactive oxygen species, TAG triacylglycerol, Ub ubiquitination. This figure was created using Adobe Illustrator (Adobe Inc., San Jose, CA, USA)

The relationship between mitochondria and peroxisomes is intimate and multifaceted: 1) Mitochondria and peroxisomes functionally collaborate to coordinate fatty acid β-oxidation and ROS metabolic regulation. They collectively accomplish related metabolic reactions, ensuring efficient processing of these critical molecules.^337–339 2) Mitochondria and peroxisomes share several proteins, including the fission-related factor FIS1, mitochondrial fission factor (MFF), and DNM1L/DRP1. These proteins are localized to both organelles and regulate their fission through independent signaling pathways, maintaining the dynamic balance of both organelles.^335,340 3) Mitochondria can transport substances to peroxisomes via MDVs. These DNM1L/DRP1-dependent vesicles bud off from both sides of the mitochondria and merge with peroxisomes, consequently promoting the transport of metabolites, lipids, or proteins to peroxisomal subpopulations. Additionally, MDVs may retrieve mislocalized peroxisomal (membrane) proteins from mitochondria.^341–343 4) Peroxisome proliferator-activated receptor alpha (PPARα) activation stimulates both peroxisomal biogenesis and mitochondrial proliferation via its downstream activator PGC-1. Mitochondrial dysfunction can lead to impaired peroxisomal activity. Conversely, impaired peroxisomal biogenesis or activity induces both ultrastructural and functional changes in mitochondria.^344,345 These interactions underscore the interdependent and coordinated relationship between peroxisomes and mitochondria in both function and signal transduction. These observations suggest that mitochondria and peroxisomes are closely connected, relying on each other to maintain cellular homeostasis and effectively execute their metabolic functions.

The crosstalk between mitophagy and peroxisomes primarily manifests in their synergistic relationship. Wilhelm et al.³³⁹ found that BNIP3L/NIX was predominantly localized to mitochondria under basal conditions. However, upon exposure to hypoxic conditions or treatment with the iron chelator deferiprone, BNIP3L/NIX was enriched in both mitochondria and peroxisomes. The redistribution promotes the initiation of mitophagy and pexophagy as independent yet potentially coordinated processes. These findings indicate that BNIP3L/NIX operates as a dual organelle receptor capable of regulating the selective clearance of both mitochondria and peroxisomes.

Although current research on mitophagy-peroxisome interactions is limited, emerging studies suggest^346,347 that mitochondrial dysfunction can impact peroxisomal function. As mitophagy is a primary pathological mechanism for mitochondrial dysfunction, it suggests a connection between mitophagy and peroxisomes. However, further investigation concerning the interactions and regulatory mechanisms between mitophagy and peroxisomes is needed to elucidate the cellular regulatory networks of metabolism and redox homeostasis. This study provides novel molecular targets and intervention approaches for treating associated diseases.

Mitophagy and LDs

LDs are primarily composed of a hydrophobic core rich in neutral lipids, such as triacylglycerol (TAG) and sterol esters, and surrounded by a phospholipid monolayer embedded with or attached to various proteins.³⁴⁸ LD formation demonstrates intimate connections with the ER. Their biosynthesis begins with lipid accumulation and the emergence of oil lenses within the ER bilayer, marking the initial state of LD development. Subsequently, the asymmetric distribution of membrane proteins and phospholipids across the ER bilayer generates surface tension gradients, ultimately causing the release of nascent LDs from the ER membrane into the cytoplasmic compartment.^348,349 Following membrane detachment, LDs expand through cell death-inducing DNA fragmentation factor-α-like effector (CIDE)-mediated coalescence and local TAG production catalyzed by diacylglycerol O-acyltransferase (DGAT) 2 on their surface. They are regulated by lipolytic enzymes, including adipose triglyceride lipase (ATGL), perilipin (PLIN) family proteins, and LD autophagy-related proteins that hydrolyze or degrade LDs to maintain cellular metabolic homeostasis.³⁴⁸ As lipid storage organelles, LDs are widely distributed throughout the cytoplasm, utilizing cytoskeletal networks for motility while establishing functional contacts with various membrane-bound organelles. Thus, as multifunctional organelles, LDs centrally regulate lipid homeostasis, membrane trafficking pathways, proteostatic mechanisms, and intracellular signaling networks.

Lipid catabolism through sequential hydrolysis provides cells with an efficient energy-generating pathway to compensate for metabolic deficiencies during stress conditions. During this process, the liberated fatty acids are transported to mitochondria through LD-mitochondria contact sites. They are then efficiently utilized to support continuous ATP production. Mitochondria cannot receive the necessary energy support if lipid degradation is impaired, leading to disrupted mitochondrial homeostasis and dysfunction.³⁵⁰ PLIN1 and the OMM protein MFN2 are crucial mediators of LD-mitochondria communication in brown adipose tissue.^350,351 Similarly, PLIN5 has a relationship with mitochondria, with its overexpression inducing the recruitment of mitochondria to the periphery of LDs. However, it remains elusive whether this protein directly mediates LD-mitochondria tethering through binding to specific mitochondrial proteins or the mitochondrial membrane³⁵² (Fig. 7b).

The effect of excessive accumulation of LDs on mitophagy

Excessive deposition of LDs can inhibit the biogenesis of mitophagy.³⁵³ In Parkinson’s disease (PD),³⁵³ the downregulation of the LD-associated protein PLIN4 and inhibition of LD accumulation can promote the restoration of mitophagy and mitigate mitochondrial damage. PLIN4 localizes to LD surfaces and is essential for LD biogenesis, classical lipolysis regulation, and autophagy.³⁵⁴ PLIN4 expression was upregulated in a PD model induced via MPTP/p (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine/probenecid), leading to increased intracellular LD accumulation.³⁵³ In vitro experiments demonstrated that the downregulation of PLIN4 expression inhibited LD storage, restored mitophagy, reduced mitochondrial damage, and consequently promoted the survival of SH-SY5Y cells.³⁵³ Thus, this research demonstrates the involvement of the defective PLIN4-LD-mitophagy pathway as a key contributor to PD pathogenesis, suggesting that PLIN4-LDs could serve as promising diagnostic markers and intervention targets.³⁵³

The effect of impaired LD synthesis on mitophagy

Impaired LD biogenesis can inhibit mitophagy.^355,356 Mitochondria serve as the cellular iron ion reservoir, containing 20–50% of cellular iron ions. Iron ion depletion triggers pathological cascades characterized by mitochondrial respiratory chain impairment and lipid deposition.³⁵⁷ Deferiprone-induced iron ion depletion leads to the coordinated action of DGAT1 and mitophagy under normal conditions.³⁵⁵ Iron ion depletion rapidly remodels the cellular metabolome, particularly the lipid metabolome, thereby activating DGAT1 and promoting LD biogenesis and TAG storage to maintain cellular metabolic homeostasis.³⁵⁵ In addition, deferiprone induces mitochondrial damage, thereby promoting BNIP3L/NIX-dependent mitophagy. This coordinated action protects cellular and tissue integrity.³⁵⁵

Free fatty acids in the cell cannot be esterified into TAG in the absence of DGAT1,³⁵⁵ consequently inhibiting LD synthesis. The accumulation of free fatty acids increases cytotoxicity, exacerbates lipid dysfunction, disrupts lysosomal homeostasis, reduces mitophagy efficiency, and ultimately triggers cell death.³⁵⁵ In further experiments, knockout of the Drosophila homolog of DGAT1 midway (mdy) revealed fewer mitolysosomes with altered morphology in animals lacking mdy than in the controls.³⁵⁵ Some animal models exhibited wing posture abnormalities concurrent with mitolysosomal dysfunction, similar to the defect characteristic of Plin1 and Prkn mutant Drosophila. These findings at the organismal level confirm DGAT1’s physiological role in mitophagic processes, establishing a function in coordinating DGAT1-mediated LD-mitochondria communication for organelle turnover.³⁵⁵

Based on the interactions between LDs and mitophagy, recent studies utilizing artificial intelligence platforms have identified a lipid-lowering drug called probucol as an enhancer of mitophagy.³⁵⁶ Probucol induces mitophagy through an ATP-binding cassette transporter A1 (ABCA1)-dependent mechanism that bypasses the canonical PINK1-PRKN pathway. The interaction mediates changes in LD dynamics and enhances mitochondrial turnover by increasing the contact between LDs and mitochondria.³⁵⁶ These results underscore the essential contribution of LD homeostasis to the regulation of mitophagy. Further investigation into the intricate crosstalk mechanisms between LDs and mitophagy might provide valuable insights for future research.

Mitophagy and the proteasome

Functioning as an intricate proteolytic complex, the proteasome precisely regulates protein catabolism in eukaryotic systems through its sophisticated subunit architecture. The 26S proteasome is the primary proteolytic organelle in eukaryotic cells³⁵⁸; it regulates the proteome and coordinates cellular stress adaptation, cell cycle progression, and signal transduction.³⁵⁹ As the endpoint of the UPS, this proteasome recognizes Ub-tagged substrates, employs ATP-derived energy to unfold target proteins, and translocates the linearized polypeptides to its catalytic core for proteolysis, ultimately completing substrate degradation.³⁶⁰

The interplay between mitochondria and proteasomes is evident in several ways, primarily in protein regulation. The proteasome regulates protein turnover within cells, including the transport of proteins to mitochondria. Cytoplasmic protein turnover becomes dysregulated when proteasome function is impaired. This triggers protein aggregate formation and cytotoxic effects, subsequently inducing mitochondrial dysfunction. Mitochondrial damage can stimulate ROS production, consequently inducing protein damage, misfolding, and aggregation; this results in proteasome overload.³⁶¹ Additionally, the functional crosstalk between mitochondria and proteasomes is fundamentally dependent on ATP. The proteasome exhibits high ATP dependence. Given mitochondria’s “powerhouses” role in cells, mitochondrial dysfunction and insufficient ATP production lead to decreased proteasome activity. It impairs the Ub-proteasome degradation pathway and affects intracellular protein homeostasis.^360,362

Last, a close cooperative relationship has been observed between the UPS and mitophagy. The UPS and mitophagy represent complementary degradation pathways in cells: the UPS mediates proteasomal breakdown of soluble proteins, whereas mitophagy selectively eliminates impaired or redundant mitochondria via autophagosome-lysosome fusion.³⁶³ The degradation processes of both systems are interlinked: Ub-dependent mitophagy and the initiation of UPS both rely on the ubiquitination of target substrates. Their coordinated work effectively regulates mitochondrial homeostasis³⁶⁴ (Fig. 7c).

PRKN-dependent mitophagy serves as a key regulator that stimulates both proteasomal activity and UPS function.^365,366 PRKN activates the UPS when recruited to the OMM, increasing OMM protein ubiquitination, facilitating 26S proteasome recruitment, and accelerating OMM protein turnover.³⁶⁶ Inhibition of the 26S proteasome completely abolished PRKN-mediated mitophagy in cells. In this regard, Furuya et al.³⁶⁵ discovered that defective mitophagy causes pathological mitochondrial retention and oxidative stress during denervation-induced slow-twitch muscle atrophy, which further inhibits the nuclear translocation of NFE2L1 (endoplasmic reticulum membrane sensor) and NFE2L1 signaling disruption. It suppressed proteasome activity, thereby delaying skeletal muscle atrophy.

The functional state of the proteasome has a bidirectional regulatory effect on mitophagy. Proteasome dysfunction can promote the biogenesis of mitophagy. For instance, Ugun-Klusek et al.³⁶⁷ observed that lysine 48 of PRKN and OMM proteins, including MFN2, underwent ubiquitination, resulting in mitochondrial damage, fragmentation, and accumulation near the nucleus in the neurons of the cerebral cortex in mice. It was associated with p62/SQSTM1 phosphorylation, elevated OPTN levels, and MAP1LC3B/LC3B upregulation, suggesting that early 26S proteasome impairment promotes PRKN-dependent mitophagic activation. Similarly, Tsakiri et al.³⁶⁸ reported that the knockdown of proteasome subunits in Drosophila led to severe mitochondrial dysfunction, which in turn stimulated mitophagy and alleviated the cytotoxicity caused by proteasome dysfunction. Furthermore, sustained dysfunction of the 26S proteasome inhibited mitophagy.³⁶⁷ This may be because prolonged proteasome dysfunction reduces key autophagy regulators, including autophagy-related protein 9 (ATG9) and MAP1LC3B/LC3B, ultimately impairing both macroautophagy and mitophagy. In another study investigating the mechanisms underlying mitophagy induction under hypoxic conditions, Sulkshane et al.³⁶⁹ found that damaged or dysfunctional mitochondria were heavily ubiquitinated and cleared in a manner that involved the cooperation of the UPS and BNIP3- or BNIP3L/NIX-mediated mitophagy under hypoxia. The inhibition of proteasome function also blocked CoCl₂-induced mitophagy. This suggests a synergistic effect between proteasome function and receptor-mediated mitophagy, where proteasome-mediated OMM protein clearance serves as a critical early event for initiating receptor-mediated mitophagy under hypoxic conditions.

Mitophagy-organelle crosstalk in multi-organ dysfunction

As a central mediator of mitochondrial quality control, mitophagy maintains cellular homeostasis by engaging in bidirectional regulatory interactions with various organelles. Through these interactions, mitophagy contributes to preserving functional integrity across cellular organelles, thereby enhancing both cell survival and adaptive responses. Although the structural composition and organelle distribution vary among different cell types and tissues, mitophagy exerts a conserved and pivotal regulatory influence across organ systems. This forms a mitophagy-mediated interorganelle regulatory network (MIORN), which orchestrates cellular and tissue-level homeostasis through a dynamic and self-reinforcing signaling cascade.

MIORN serves as a central hub for mitochondrial crosstalk with other organelles, including the ER, lysosomes, peroxisomes, and nucleus, to coordinate metabolic responses, redox balance, and stress adaptation. These signals are not confined to individual cells but can propagate to neighboring cells and tissues, ultimately contributing to systemic physiological homeostasis. However, when mitophagy is dysregulated, this interorganelle signaling network becomes impaired. Such dysfunction extends beyond localized mitochondrial damage and initiates a cascade of pathological events, similar to a “domino effect”, that amplifies and disseminates stress signals across multiple tissues.

Consequently, disruption of the MIORN compromises interorganelle communication, disturbs cellular and tissue integrity, and culminates in multiorgan dysfunction. This breakdown in coordinated organ function potentially destabilizes systemic homeostasis and contributes to the pathogenesis of complex diseases (Fig. 8).

Fig. 8.

The role of mitophagy-mediated interorganelle regulatory network in multiorgan dysfunction and its molecular mechanisms. The central section of the figure illustrates an intricate and tightly coupled interaction network between mitophagy and other organelles, mediated by Ca²⁺ signaling. Dysregulation of these interactions may significantly contribute to human diseases. The surrounding sections of the figure illustrate the pathological interactions between mitophagy and multiple organelles, detailing their impact on specific human organ systems—including nervous, immune, respiratory, cardiovascular, digestive and urinary systems—along with critical effects on myopathies and malignancies. It emphasizes mitophagy as a key event in the pathogenesis of multiorgan dysfunction. ALCAT1 acyl-CoA: lysocardiolipin acyltransferase-1, AML acute myeloid leukemia, APPL1 adaptor protein containing the pleckstrin homology domain, phosphotyrosine binding domain and leucine zipper motif, ATF4 activating transcription factor 4, cGAS the cyclic GMP-AMP synthase, CHOP DNA damage-inducible transcript 3 protein, DRP1 dynamin-1-like protein, DsbA-L disulfide-bond A oxidoreductase-like protein, ER endoplasmic reticulum, ERS endoplasmic reticulum stress, FIS1 mitochondrial fission 1 protein, FUNDC1 FUN14 domain-containing protein 1, GSDMD gasdermin D, HELZ2 3’-5’ exoribonuclease HELZ2, LD lipid droplet, Lp-PLA₂ lipoprotein-associated phospholipase A₂, MAM mitochondria-associated endoplasmic reticulum membrane, MFN2 mitofusin2, mtDNA mitochondrial DNA, mTORC1 the mechanistic target of rapamycin complex 1, mtROS mitochondrial ROS, NLRP3 NACHT, LRR and PYD domains-containing protein 3, NPC1 NPC intracellular cholesterol transporter 1, PACS-2 phosphofurin acidic cluster sorting protein 2, PERK eukaryotic translation initiation factor 2-alpha kinase 3, PGC1 peroxisome proliferator-activated receptor gamma coactivator 1, PHB2 prohibitin-2, PINK1 PTEN induced putative kinase 1, PLIN4 perilipin-4, RAB5 Ras-related proteins Rab-5A, RAB7 Ras-related proteins Rab-7A, RyR1 ryanodine receptor type 1, STING stimulator of interferon genes, TBC1D15 TBC1 domain family member 15, TFEB transcription factor EB, TIPE1 tumor necrosis factor alpha-induced protein 8-like 1, TRPML1 mucolipin-1, VPS35 vacuolar protein sorting-associated protein 35, XBP1 X-box-binding protein 1. This figure was created using Adobe Illustrator (Adobe Inc., San Jose, CA, USA)

Nervous system

The growth, survival, and functional activities of neurons require a substantial amount of ATP. Thus, they heavily rely on the mitochondrial energy supply. This dependence suggests that mitochondrial dysfunction may underlie many neurological disorders. Of note, neurons rely on autophagy for protein quality control, with mitophagy playing a protective role under normal conditions. Therefore, mitochondria are fundamentally required for proper nervous system physiology.

PD manifests as a progressive neurodegenerative condition marked by dopaminergic neuron degeneration and Lewy body deposition containing α-synuclein fibrils. XBP1s can activate PINK1 to regulate mitophagy and mitochondrial health in neurons.⁶⁷ However, this regulatory mechanism may be disrupted in PD, leading to mitochondrial dysfunction and disease progression. In MPTP/p-induced PD mouse brains,³⁵³ suppression of LD-associated proteins inhibited LD accumulation, restored mitophagy, reduced mitochondrial damage, and promoted the survival of SH-SY5Y cells. Additionally, α-synuclein abnormalities and mitochondrial dysfunction are linked to impairments in the autophagy‒lysosome pathway.³¹¹ Mitophagy can activate TFEB, consequently upregulating lysosomal protein expression. Concurrently, the mRNA levels of PGC-1α are also increased together with enhanced mitochondrial content. It maintains the autophagy‒lysosome pathway and mitochondrial biogenesis, thereby improving α-synuclein clearance and mitochondrial function in PD.

Alzheimer’s disease (AD) manifests as a progressive neurological deterioration characterized by β-amyloid deposition within neuronal subcellular structures.³⁷⁰ Early stages of AD show progressive mitochondrial dysfunction, which directly correlates with mitophagy deficiency. Roca et al.³⁷¹ reported that elevated levels of intracellular cholesterol promoted the stabilization of mitochondrial PINK1 and induced PRKN-independent mitophagosome formation in cholesterol-enriched neuronal models. However, this process impairs autophagosome-lysosome fusion, compromising lysosome-mediated clearance and leading to pathological mitochondrial accumulation.

Respiratory system

Respiratory diseases are among the most prevalent conditions worldwide, largely due to their close relationship with oxygen-rich environments, making the lungs more susceptible to pathological damage related to ROS. Mitochondria are the main cellular ROS producers³⁷²; therefore, their functional status significantly influences respiratory disease pathogenesis by disrupting redox homeostasis. Mitophagy acts as a fundamental driving force in multiple respiratory pathologies, ranging from chronic airway obstruction and acute pulmonary damage to ischemia‒reperfusion injury and nasopharyngeal carcinoma.^373,374 In this context, MIORN effectively modulates homeostasis and maintains interorganelle balance, in turn enhancing cellular responses to inflammation in respiratory diseases. Silicosis is a type of pneumoconiosis characterized by bilateral diffuse nodular pulmonary fibrosis.³⁷⁵ Studies have shown that the differentiation and functional state of monocyte-derived macrophages (MoMacs) in lung tissue is an important mechanistic node influencing the progression of pulmonary fibrosis.^376–378 Li et al.³⁷⁸ confirmed that under silica exposure, mouse MoMacs highly expressed lipoprotein-associated phospholipase A₂ (Lp-PLA₂), which pathological CL remodeling through activating acyl-CoA: lysocardiolipin acyltransferase-1 (ALCAT1)-mediated acylation and oxidative modification. This, in turn, impaired the mitochondrial recruitment of PINK1 and MAP1LC3B/LC3B and inhibited the initiation of mitophagy; simultaneously, due to the defect in mitophagy, damaged mitochondria accumulate, further inducing the accumulation of mtROS within MoMacs, which resulted in lysosomal dysfunction and led to cathepsin B cytosolic leakage in MoMacs. The synergistic effect of mitophagy defects and lysosomal dysfunction exacerbated the M1/M2 polarization of MoMacs, activating the cGAS-STING inflammatory pathway and TGF-β-SMAD2/3 signaling and ultimately promoting pulmonary fibrogenesis. This work elucidates the integrative significance of MIORN in regulating cellular stress and tissue fibrosis, providing a pathological mechanistic basis for targeting the Lp-PLA₂-ALCAT1-CL axis in fibrosis intervention.

Acute lung injury, characterized by a severe endothelial pro-inflammatory phenotype and heightened permeability changes, represents a leading fatal complication in systemic inflammatory response diseases, such as sepsis. Mitochondrial dysfunction has been established as a key pathological driver of ALI.^373,379 In a study regarding septic acute lung injury, Jiang et al.³⁸⁰ reported that SIRT1 physically associates with RAB7 to activate late endosome-dependent mitophagy. This interaction obviously downregulated mtROS levels, reduced mtDNA leakage, and suppressed excessive NLRP3 inflammasome activation and STING signaling pathways. It consequently led to improvements in pulmonary endothelial lesions and sepsis progression in murine models. These studies were further validated through pharmacological recovery experiments on SIRT1 activity, underscoring the translational value of SIRT1 as a viable strategy for acute lung injury clinical management.

Circulatory system

Of the various hypothesized mechanisms underlying cardiovascular pathogenesis, mitochondrial dysfunction has emerged as a predominant focus. Its priority stems from mitochondria’s dual role as both the cellular power plants and initiators of apoptotic pathways when dysfunctional. Thus, ensuring strict mitochondrial quality is crucial for regulating cellular redox balance and survival, with mitophagy serving as the primary mechanism for mitochondrial quality control.³⁸¹ Cytosolic Ca²⁺ accumulation leads to increased mitochondrial Ca²⁺ during ischemia/reperfusion, consequently activating the matrix chaperone cyclophilin D and triggering mitochondrial permeability transition pore (mPTP) opening, culminating in lethal cell injury. The reduction in ER-mitochondria tethering can prevent cytosolic Ca²⁺ accumulation, thereby blocking downstream cell death pathways.³⁸¹

A study³⁸¹ on diabetic cardiomyopathy demonstrated that the inactivation of AMPK increased the stability of FUNDC1 in a high-glucose environment and enhanced binding between FUNDC1 and the ER protein IP3R2. Thus, it augments MAM formation and facilitates pathological mitochondrial Ca²⁺ overload. Excessive mitochondrial Ca²⁺ uptake induces mitochondrial dysfunction and myocardial cell injury.

TBC1 domain family member 15 (TBC1D15), which modulates RAB7 GTPase activity, plays a regulatory role in controlling mitochondrial dynamics. In acute myocardial infarction,³⁸² TBC1D15 serves as an essential molecular link coordinating mitochondrial-lysosomal interactions and mitophagy. Overexpressed TBC1D15 levels promote mitochondrial targeting through mitochondrial FIS1 interaction, thereby stimulating RAB7 GTPase activity to facilitate the dissociation of abnormal mitochondrial-lysosome contacts. It prevents pathological lysosomal enlargement, restores lysosomal function, and enhances defective mitochondrial removal. Consequently, TBC1D15 preserves mitochondrial performance, mitochondrial integrity, and myocardial contractility during acute myocardial infarction, potentially providing a new therapeutic target for its clinical treatment.

Digestive system

Mitochondria function as the central hubs for cellular energy generation and are also pivotal in substance metabolism within metabolically dynamic organ systems. The liver, the body’s main metabolic organ, is fundamentally linked to mitochondrial dysfunction in the pathogenesis and advancement of liver disorders. Lysosome-localized TRPML1 contributes to lysosomal storage, transport, and pH homeostasis while also supporting mitochondrial function.³⁸³ For instance, TRPML1-mediated lysosomal Zn²⁺ release can induce mitochondria-mediated cell death,³⁸⁴ whereas the dysfunction of TRPML1 is related to defects in mitochondrial Ca²⁺ uptake.³¹² In addition, lysosomes undergo swelling, pH changes, and functional impairment upon TRPML1 knockout. Subsequently, mitochondrial morphology is significantly altered, and both mitophagy and mitochondrial renewal are disrupted in liver cancer cells.³²⁴

Mitochondrial phosphorylated DNM1L/DRP1 (p-DRP1) has emerged as a newly identified interorganelle bridging protein that targets mitochondrial-lysosomal interfaces via RAB7 binding, in turn increasing mitochondria-lysosome crosstalk. For example, Che and colleagues³⁸⁵ demonstrated that the direct dephosphorylation of p-DRP1 affected its interaction with RAB7. It suppressed mitophagy while promoting apoptosis through mitochondrial pathways, which might provide a new approach for targeted intervention in hepatocellular carcinoma.

XBP1 is a key component of ERS that regulates ERS signaling in both immunity and inflammation. In a study on acute liver injury,¹⁹⁷ its deletion led to impaired mitophagy in mouse hepatocytes, resulting in excessive production of mtROS, which significantly activated the NLRP3-caspase-1-Gasdermin D pathway, consequently triggering hepatocyte pyroptosis and facilitating the release of mtDNA into the extracellular space. It further enhanced mtDNA-triggered cGAS-STING signaling in macrophages, which might reveal a promising intervention point for acute liver injury. Zhang et al.³⁸⁶ found that excessive mitophagy and ERS were critically involved in cytotoxicity induced by Tripterygium wilfordii Hook. f. (TwHF), and ERS regulated mitophagy via the eIF2αK3/PERK-ATF4 pathway. Inhibition of eIF2αK3/PERK by GSK2656157 attenuated the excessive mitophagy mediated by triptolide, the main active and toxic component of TwHF, in HepaRG cells, showing the mitigation of hepatotoxicity resulting from TwHF.

Urinary system

Abnormal changes and damage to renal tubules are observed in various kidney diseases. Renal tubular epithelial cells (RTECs) are among the cell types with the highest mitochondrial content. They rely on mitochondrial oxidative phosphorylation to generate the substantial ATP required for sustained renal reabsorption, making them susceptible to mitochondrial dysregulation.³⁸⁷ In several rare tubular kidney diseases, such as nephropathic cystinosis, Lowe syndrome, and methylmalonic acidemia, disrupted mitophagy in RTECs can be constantly observed and represents a core pathophysiological feature, all of which involve lysosomal and mitochondrial dysfunction.^388,389 For example, in nephropathic cystinosis, aberrant accumulation of cystine within lysosomes compromises lysosomal degradation function. This subsequently compromises mitophagy flux, leading to the buildup of dysfunctional mitochondria within renal proximal tubules. These defective mitochondria generate excessive ROS, ultimately triggering RTEC injury. This corroborates the important mechanism of lysosomal-mitochondrial cooperation in maintaining RTEC viability. Additionally, RTECs in diabetic nephropathy (DN) exhibit excessive mitochondrial fragmentation and defects in mitophagy, contributing to dysfunctional mitochondria and continuous accumulation of mitochondrial ROS, ultimately activating mitochondria-dependent apoptosis.³⁹⁰

MAMs regulate mitophagic processes and play a pivotal role in DN pathogenesis.³⁹¹ Disulfide-bond An oxidoreductase-like protein (DsbA-L), a key protein located in MAMs, contributes to renal protection.³⁹² Yang and colleagues³⁹¹ reported that DsbA-L deficiency in diabetic mice resulted in exacerbated renal tubular damage compared to diabetic wild-type mice. Renal tubular lesions correlated with MAM structural destabilization and impaired mitophagy. Further studies revealed that DsbA-L activated mitophagy by preserving MAM stability through the HELZ2 (3’-5’ exoribonuclease HELZ2)-MFN2 pathway, thereby alleviating diabetes-induced renal tubular damage. The loss of phosphofurin acidic cluster sorting protein 2 (PACS-2), a critical MAM-organizing protein, disrupts the integrity of these membranes.³⁹³ Li et al.³⁹³ demonstrated that reduced PACS-2 levels showed positive associations with renal functional preservation and inverse relationships with the degree of tubular interstitial lesions in the RTECs of patients with DN. In DN mice, PACS-2 deficiency inhibited mitophagy, accompanied by tubular damage and increased proteinuria. Further reports have documented that PACS-2 interacts with BECN1, facilitating its translocation to MAMs and thus promoting the biogenesis of mitophagosomes.

The aforementioned evidence emphasizes the importance of MAM formation and integrity in regulating mitophagy while also highlighting the potential of mitophagy in alleviating DN-induced tubular damage. Moreover, the interaction between the UPS and mitophagy appears to contribute to DN development. Liu et al.³⁹⁴ reported that tumor necrosis factor alpha-induced protein 8-like 1 (TNFAIP8L1/TIPE1) interacted with the mitophagy receptor PHB2, consequently promoting its ubiquitination and proteasomal degradation. It destabilizes the protein and affects PHB2-dependent and PINK1-PRKN-regulated mitophagy, ultimately disrupting mitochondrial homeostasis and exacerbating tubular damage.

Immune system

The immune network consists of specialized cell populations that perform various functions in maintaining immunological balance and managing inflammation according to tissue requirements.³⁹⁵ Mitochondria are essential for both innate and adaptive immune functions.^396,397 Innate immunity acts as the essential defense against pathogenic microbes or harmful stimuli, with pathogen-associated molecular patterns (PAMPs) and DAMPs as major inflammatory stimuli.³⁹⁸ mtDNA damage and abnormalities are common types of DAMPs.³⁹⁹ mtDNA activates the cGAS-STING axis, further enhancing inflammasome activation and subsequently affecting the host innate immune response.⁴⁰⁰ Endosome-dependent mitophagy effectively clears damaged mitochondria to inhibit mtDNA leakage.⁴⁰¹ This process mainly depends on lysosomal activity potentiation and the capture of mtDNA by vacuolar protein sorting-associated protein 35 (VPS35) endosomes.

The endosomal adaptor protein containing the pleckstrin homology domain, phosphotyrosine binding domain and leucine zipper motif (APPL1) regulates the activity of the NLRP3 inflammasome in macrophages by enhancing mitophagy through the APPL1-RAB5 axis.⁴⁰² Mitochondria in macrophages became damaged upon treatment with an NLRP3 agonist.⁴⁰² APPL1 then translocated from early endosome compartments to mitochondria, where its interaction with RAB5 potentiated mitophagic flux and inhibited NLRP3 inflammasome activation in macrophages. Conversely, APPL1 deficiency disrupts mitophagic clearance, resulting in the buildup of dysfunctional mitochondria, redox imbalance with ROS overproduction, mtDNA oxidation, and overactivation of the NLRP3 inflammasome in macrophages. Thus, it exacerbated IL-1β secretion in obese and endotoxin-induced septic models.⁴⁰²

Myopathies

Mitochondrial dysfunction represents the primary pathological feature of most myopathies in mammals^403–406 and is characterized by a gradual impairment of the ETC and pathogenic mtDNA mutation accumulation.^404,405 Related studies have shown that in aged mice and human myopathic skeletal muscle, defects in mitophagy are essentially responsible for the dysregulation of the ETC and the progression of pathology.^404–406 During the initial phases of the disease, mitophagy is enhanced, forming perinuclear degradation zones in cooperation with lysosomes to eliminate damaged mitochondria^404,406; however, in the late disease stages, there is a significant defect in intracellular mitophagy, accompanied by lysosomal homeostasis disruption, leading to pathological mitochondrial retention and the progression of mitochondria-related myopathy.^404,406 This pathogenic process may involve the interplay between mitophagy and lysosomal function.

Inclusion body myopathy (IBM) represents an adult-onset, nonfamilial muscle disorder featuring asymmetric weakness in the finger flexor and knee extensor muscle groups,^405,407,408 with its etiology and effective treatments yet to be clearly defined.^405,408 The pathogenic mechanism of IBM is closely related to lysosomal defects and halted mitophagy; lysosomal dysfunction and mitochondrial damage have been observed in muscle fibers of IBM patients.^405,407 Mitochondrial damage creates a demand for mitophagy, while lysosomal dysfunction induces the cessation of mitophagy, leading to pathological mitochondrial accumulation that drives IBM.⁴⁰⁵ Recently, Vidal et al.⁴⁰⁴ reported that ER-mitophagy crosstalk might be a potential factor in the etiology of various myopathies. They observed that in several myopathies, such as necrotizing myopathy, IBM, and polymyositis, the transcription level and protein content of RyR1 were significantly reduced.⁴⁰⁴ This systemic deficiency disrupted ER-mitochondria contacts within muscle tissue, decreasing Ca²⁺ flux to mitochondria and resulting in impaired mitochondrial function.⁴⁰⁴ Conversely, it inhibited the occurrence of mitophagy, which correlated with pathological retention of damaged mitochondria.⁴⁰⁴ Thus, the interplay between mitophagy and ERS leads to functional impairment of muscle fibers, forming the important pathological mechanism of these myopathies. These studies indicate that mitophagy, through dynamic interactions with organelles, including the ER and lysosomes, creates a specific organelle interaction network in myopathies, and the degree of its dysregulation is a critical feature of the pathological progression of myopathy, providing new insights for targeted interventions.^403–407

Malignancies

Tumor cells undergo alterations in mitochondrial function, such as the Warburg effect and abnormal mitochondrial quality control, to survive in the tumor microenvironment.^409,410 Mitophagy exhibits dual tumor-modulatory functions through MIORN homeostasis regulation, either promoting or suppressing malignant transformation depending on the cellular context.^{409,411–415} Liu et al.⁴¹⁵ utilized patient-derived organoid models of colorectal cancer and found that in tumor cells with intact mitophagy function, lipid peroxidation triggers ERS, which upregulates the expression of PRKN protein through ATF4-mediated transcription, thereby activating mitophagy. This process effectively inhibited the accumulation of mtROS by clearing damaged mitochondria, thus limiting the generation of lipid peroxidation products and resisting ferroptosis. In contrast, tumors with defective mitophagy lack such a protective mechanism, leading to uncontrolled lipid peroxidation that significantly enhances ferroptosis induced by agents such as erastin, as well as by radiotherapy and immunotherapy. Ferroptosis-inducing treatments can selectively inhibit the growth and metastasis of mitophagy-deficient tumors in vivo. This study provides a mechanistic foundation for developing new strategies targeting such tumors.⁴¹⁵

Davis et al.⁴¹⁶ highlighted the significance of the dysfunction of lysosomes and mitochondria in the development of nasopharyngeal carcinoma (NPC). NPC intracellular cholesterol transporter 1 (NPC1), a lysosomal membrane-embedded cholesterol transporter with multiple transmembrane domains, can restore cholesterol export pathways from lysosomes. It downregulates cholesterol—the mechanistic target of rapamycin complex 1 (mTORC1) signaling, improves lysosomal membrane integrity and proteolytic function, and augments the recovery of mitophagic flux, consequently maintaining the balanced interorganelle network within NPC cells.

In a study on AML,⁴¹³ the combined use of the ceramide transfer protein inhibitor HPA-12 and the FMS-like tyrosine kinase 3 (FLT3) inhibitor crenolanib⁴¹⁷ was found to disrupt ER-to-Golgi ceramide trafficking while enhancing ceramide synthesis, causing pathological ceramide accumulation in AML cells. This accumulation triggers ERS, which, via the activation of the ER chaperone BiP (GRP78)-cyclic AMP-dependent transcription factor ATF6 (ATF6)-DNA damage-inducible transcript 3 protein (CHOP) signaling axis, upregulates pro-apoptotic CHOP expression, driving apoptosis.⁴¹³ Meanwhile, ceramide accumulation induces mitochondrial dysfunction and activates mitophagy. The interplay between ERS and mitophagy, mediated through CHOP-dependent apoptosis and autophagy-dependent clearance mechanisms, significantly suppresses FLT3-mutant AML cell growth while triggering apoptosis, revealing that the interorganelle interaction network between ER and mitophagy is a critical mechanism of lethality in AML.

Therapeutic strategies targeting mitophagy

In recent years, growing interest has emerged in the development of innovative therapeutic approaches targeting the modulation of mitophagy. Approaches such as small-molecule compounds, nanotechnology-based delivery systems, and mitochondrial transplantation therapy (MTT) have shown promise in achieving clinically meaningful outcomes. These mitophagy-targeting interventions hold the potential to remodel the intricate network of interactions between mitochondria and other organelles, thereby preserving the homeostasis of MIORN. By restoring MIORN balance, these strategies enable precise modulation of disease-associated microenvironments. In the sections below, we highlight representative mitophagy modulators and emerging mitochondrial transplantation technologies with therapeutic potential.

Mitophagy modulators

Mitophagy inducers

Urolithin A

Urolithin A (UA), a naturally occurring metabolite, is generated via the gut microbiota through the biotransformation of ellagitannins in terms of polyphenolic compounds abundant in pomegranates, berries, and nuts. Beyond its recognized antioxidative and anti-inflammatory effects, UA has recently gained attention for its ability to modulate key cellular processes, including immune function, neuroprotection, and cancer suppression.^418–420 Specifically, UA exhibits a multisystem capacity to regulate neuronal amyloidosis, promote memory T-cell proliferation and longevity, and inhibit tumor cell growth, indicating its pleiotropic therapeutic potential.

At the mitochondrial level, UA exerts a profound influence on mitochondrial quality control by promoting mitophagy, restoring mitochondrial membrane potential, and maintaining calcium and ROS homeostasis.^{418,419,421,422} A recent study⁴²⁰ revealed that UA induced mitophagy through activation of TFEB. Mechanistically, UA promotes the partial nuclear translocation of TFEB in an mTOR-dependent manner while simultaneously preventing its ubiquitin-mediated degradation. The stabilization and activation of TFEB augments the removal of dysfunctional mitochondria in macrophages exposed to tumor-derived supernatants. By restoring mitochondrial homeostasis, UA reduces proinflammatory signaling and suppresses both the initiation and advancement of mammary tumors in preclinical models.

Overall, its ability to bridge gut microbiota-derived metabolites with mitochondrial quality control and immune modulation offers a novel framework for the development of nutraceutical-based or combinatory cancer therapies.

Artesunate

The mitophagy-promoting activity of artesunate, a semisynthetic derivative of artemisinin, enhances mitophagy through FUNDC1 modulation, establishing this mitochondrial receptor as a key mediator of its pharmacological effects.⁴²³ In sorafenib-resistant HCC cells, artesunate downregulates actin filament-associated protein 1-like 2 (AFAP1L2) expression, a negative regulator of signaling cascades associated with drug resistance. The downregulation inhibits the phosphorylation of both SRC kinase and FUNDC1 and enhances the interaction between FUNDC1 and MAP1LC3B/LC3B. By stabilizing the interaction, artesunate facilitates autophagic machinery recruitment to impaired mitochondria and activates FUNDC1-dependent mitophagy. Thus, it significantly restores sorafenib responsiveness in previously resistant HCC cells and enhances its antitumor efficacy.⁴²³

Beyond liver cancer, artesunate demonstrates mitophagy-inducing impacts on other tumors. In breast cancer cells, artesunate upregulates the levels of key mitophagy regulators, such as PINK1 and PHB2. The elevation of PINK1 enhances PRKN recruitment and outer mitochondrial membrane ubiquitination, while increased PHB2 expression promotes mitophagy at the inner mitochondrial membrane. These effects collectively lead to impaired mitochondrial function, reduced cellular proliferation, and increased cell death in breast cancer models.⁴²⁴

Taken together, these findings highlight artesunate as a potent mitophagy modulator with broad-spectrum anticancer potential. Its ability to target multiple mitophagy pathways, both PRKN-dependent and receptor-mediated, suggests that it could be repurposed or combined with other therapeutics to counteract drug resistance and inhibit tumor progression across various cancer types.

Bergapten (BeG)

BeG, a naturally occurring furanocoumarin, is a plant-derived compound widely distributed in various herbs, citrus fruits, and vegetables. BeG exhibits diverse therapeutic properties encompassing antioxidant, anticancer, and anti-inflammatory effects. Notably, it significantly reduces key inflammatory mediators, including interleukin (IL)-6, IL-1β, and tumor necrosis factor (TNF)-alpha,^425,426 indicating its therapeutic potential for infectious and inflammatory pathologies.

In addition to its anti-inflammatory properties, recent evidence suggests that BeG modulates mitochondrial quality control. Luo et al.’s study⁴²⁷ investigating the underlying mechanisms with regard to inhibition of the NLRP3 inflammasome revealed that BeG significantly promoted mitophagy. Specifically, BeG upregulates the expression of MAP1LC3B/LC3B and enhances its colocalization with mitochondria, thereby facilitating the autophagic removal of impaired mitochondria. Mitophagy induction reduces mtROS production, a key trigger of NLRP3 stimulation, and consequently inhibits pyroptosis in lipopolysaccharide (LPS)-stimulated J774A.1 macrophages and bone marrow-differentiated macrophages.

These results indicate that BeG exerts its anti-inflammatory effect not only through inhibiting cytokine formation but also by modulating the innate immune response via mitophagy activation.

Empagliflozin

Empagliflozin, a sodium-glucose cotransporter 2 (SGLT2) inhibitor, functions as a first-line therapeutic agent for the intervention of type 2 diabetes mellitus. Beyond its glucose-lowering effects, empagliflozin has been demonstrated to confer significant cardioprotective benefits, notably reducing cardiovascular-related mortality in diabetic patients with preexisting cardiovascular diseases.^428,429 Recent evidence has expanded our understanding of its mechanism of action, revealing empagliflozin’s essential function in maintaining mitochondrial homeostasis through mitophagy.

A study regarding cardiac microvascular ischemia‒reperfusion injury⁴³⁰ identified empagliflozin as an endothelium-specific protective agent that preserved cardiac microvascular function by promoting mitophagy. Mechanistically, empagliflozin enhances the expression of AMPKα1, which in turn activates ULK1. This cascade leads to the phosphorylation of the mitophagy receptor FUNDC1 at serine 17, triggering FUNDC1-mediated mitophagy and facilitating the efficient removal of impaired mitochondria. Mitochondrial integrity restoration through this pathway contributes to mitigating ischemia-induced oxidative stress and endothelial injury.

Interestingly, empagliflozin has been found to influence the Wnt/β-catenin signaling pathway to reinforce FUNDC1-mediated mitophagy in cardiomyocytes associated with type 3 cardiorenal syndrome.⁴³¹ This dual modulation of both the AMPK-ULK1 and Wnt/β-catenin axes converging on FUNDC1-mediated mitophagy underscores the multifaceted impacts of empagliflozin on cardiac function.

Delta opioid (D-Ala[2], D-Leu[5])enkephalin (DADLE)

DADLE, a chemically synthesized compound exhibiting selective δ-opioid receptor activation, has been shown to effectively improve the survival of neurons and brain microvascular endothelial cells (BMECs) upon pathological insults.⁴³² Previous studies have established a strong link between DADLE and autophagy, indicating that treatment with DADLE promotes neuronal autophagy through activation of the AMPK-mTOR-ULK1 pathway and exerts neuroprotective effects in models of cerebral ischemia.⁴³³

More recently, a direct connection between DADLE and mitophagy has been identified. In a study with cerebral ischemia‒reperfusion injury, Deng et al.⁴³⁴ demonstrated that DADLE treatment upregulated the expression of transient receptor potential vanilloid 4 (TRPV4), an ion channel facilitating Ca²⁺ transmembrane transport, in BMECs under ischemic stress. The resulting influx of Ca²⁺ triggers the upregulation of proteins associated with mitophagy, such as BECN1, MAP1LC3/LC3-II/I, PINK1, and PRKN, thereby enhancing mitophagy and restoring mitochondrial function. The mitophagic response contributes to improved mitochondrial clearance and cellular survival under oxidative and metabolic stress conditions induced by ischemia‒reperfusion injury.⁴³⁴

Strikingly, pharmacological inhibition or RNA interference-mediated knockdown of TRPV4 can abrogate the protective effects of DADLE, underscoring the essential role of TRPV4 in mediating DADLE-induced mitophagy.⁴³⁴ These findings suggest that DADLE exerts its protective action, at least in part, through the TRPV4-Ca²⁺ signaling pathway, which activates mitophagy to preserve mitochondrial integrity and endothelial cell viability.

UMI-77

UMI-77 is a well-characterized BH3 mimetic designed to inhibit the antiapoptotic protein MCL-1 (induced myeloid leukemia cell differentiation protein Mcl-1), a key regulator of mitochondrial outer membrane integrity.⁴³⁵ Originally designed as a pro-apoptotic agent in cancer cells, UMI-77 functions by interrupting MCL-1 binding to BAX/BAK apoptotic proteins, thereby facilitating OMM permeabilization and apoptotic signaling.⁴³⁵

Cen et al.⁴³⁶ noted that UMI-77, as a strong inducer of mitophagy, was capable of promoting selective mitochondrial removal independent of nonselective macroautophagy, overt mitochondrial damage, or classical apoptotic pathways. This suggests that UMI-77 may act through a distinct signaling axis that directly regulates mitophagy machinery, potentially by modulating MCL-1 interactions with mitophagy-related proteins.

Further evidence supporting the noncanonical function, a study with lupus nephritis,⁴³⁷ confirmed that UMI-77 improved mitochondrial quality maintenance by enhancing mitophagy. This mitophagic response led to upregulated mitochondrial function and suppressed the proinflammatory phenotype of dendritic cells. Consequently, UMI-77 mitigated immune dysregulation and inhibited the progression of systemic lupus erythematosus and nephritis in preclinical models.

These findings collectively implicate UMI-77 as a dual-function compound with the ability to regulate both apoptosis and mitophagy. Its capacity to selectively promote mitophagy without inducing cell death broadens its therapeutic potential beyond oncology, offering a promising strategy for treating autoimmune and inflammatory diseases characterized by mitochondrial dysfunction.

Spautin-1

Spautin-1, a derivative of 4-([3,4-(methylenedioxy)benzyl]amino)-6-chloroquinazoline, is primarily considered a specific inhibitor of macroautophagy.⁴³⁸ It exerts its effect by inhibiting the deubiquitinases USP10 and USP13 to accelerate the degradation of VPS34 (the catalytic subunit of class III PI3K) and BECN1, which suppress the occurrence of macroautophagy.⁴³⁹ In addition to its autophagy-inhibiting properties, spautin-1 exhibits pro-apoptotic activity, further implying it functions in pathways that regulate cellular stress responses and homeostasis.^438,439

Intriguingly, recent evidence⁴⁴⁰ has identified spautin-1 as a novel and unexpected mitophagy inducer. Contrary to its role in inhibiting macroautophagy, spautin-1 appears to selectively activate PINK1-PRKN-dependent mitophagy by targeting the OMM transport complex. This action stabilizes PINK1 on the OMM and promotes PRKN mitochondrial localization, initiating mitophagy. The mitophagy-promoting impact occurs independently of macroautophagy inhibition, suggesting a unique dual-function profile for spautin-1.

The differential regulatory capacity of spautin-1 toward distinct types of autophagy highlights its mechanistic complexity and multifaceted therapeutic potential. Future studies will require further exploration of precise molecular targets in regulating diverse autophagic pathways, as well as the context-dependent applicability in complex clinical conditions.

Mitophagy inhibitors

Triptolide

Triptolide, a diterpenoid triepoxide extracted from TwHF, has garnered substantial research interest owing to its significant pharmacological activities, including anti-inflammatory, immunosuppressive, and antitumor effects.^441,442 Several studies^443–445 have demonstrated that the antitumor effects of triptolide are mainly mediated by triggering the mitochondria-dependent apoptotic cascade. Specifically, triptolide triggers OMM permeabilization, promotes cytochrome c efflux, and activates caspase-dependent signaling, thereby linking its cytotoxic effects to mitochondrial regulatory pathways.

More recently, an increasing number of studies have demonstrated that triptolide also modulates mitochondrial homeostasis through the inhibition of mitophagy. In a study evaluating its impact on pathological cardiac remodeling,⁴⁴⁶ triptolide was found to enhance remodeling capacity in mice by modulating mitophagy-related signaling in cardiomyocytes. Mechanistically, triptolide upregulated the expression of FOXP3, which in turn suppressed activating ATF4 activity. It induced the downregulation of PRKN expression together with the inhibition of PRKN-mediated mitophagy.

These results indicate that the regulation of mitophagy by triptolide may contribute to its broader impacts on mitochondrial function and disease progression.

Liensinine

Liensinine, a bisbenzylisoquinoline alkaloid isolated from lotus (Nelumbo nucifera) seeds, exhibits potent antioxidant and antitumor properties. It suppresses cancer cell proliferation and metastasis while promoting ROS-mediated apoptosis. Liensinine has been recognized as a new inhibitor of mitophagy, functioning by the suppression of DNM1L/DRP1-dependent mitochondrial fission, an essential step in mitophagy initiation.⁴⁴⁷ By disrupting mitochondrial fragmentation, liensinine impedes the recruitment of mitophagy machinery and blocks the clearance of dysfunctional mitochondria.

In a report on azithromycin-induced cardiotoxicity, Liang et al.⁴⁴⁸ confirmed that liensinine mitigated cardiac dysfunction and apoptosis in cardiomyocytes by inhibiting DNM1L/DRP1 phosphorylation. This inhibition prevents mitochondrial fission and subsequent mitophagy activation, thus preserving mitochondrial integrity and cellular viability under drug-induced stress.

Beyond cardioprotection, liensinine has shown efficacy in metabolic disease models. In obesity-related studies,⁴⁴⁹ liensinine reduced weight gain and increased energy expenditure by disrupting mitophagy flux in adipose tissue. Mechanistically, it inhibits lysosomal protease activity by causing the buildup of precursor forms of cathepsins (B, D, L), in turn resulting in impaired lysosomal degradation and suppression of mitophagy. The preservation of mitochondrial content can contribute to the maintenance of beige adipocyte identity, a main component in thermogenesis and metabolic health.

In summary, its ability to selectively inhibit mitophagy through both mitochondrial fission and lysosomal degradation pathways positions it as a therapeutic potential candidate for conditions linked to aberrant mitochondrial turnover, such as cardiomyopathies, cancer, and metabolic disorders.

N-acetyl-cysteine (NAC)

NAC was initially developed as a mucus-dissolving medication owing to its strong ability to reduce disulfide bonds in mucoproteins, thereby decreasing sputum viscosity and facilitating clearance in respiratory diseases characterized by excessive mucus production.^450,451 Beyond its classical use, NAC has gained significant attention for its potent antioxidant properties, functioning as a ROS scavenger and a precursor to intracellular glutathione (GSH). By replenishing GSH levels, NAC neutralizes mtROS, stabilizes mitochondrial membrane potential, and prevents the accumulation of PINK1 on the OMM, a key early step in PINK1-PRKN-dependent mitophagy.^452,453

In a study with regard to the reproductive toxicity of di (2-ethylhexyl) phthalate (DEHP) and its metabolite monoethylhexyl phthalate (MEHP), NAC was shown to significantly reduce MEHP-induced ROS/mtROS levels, alleviate ERS, and prevent the translocation of XBP1s into the nucleus.⁴⁵⁴ These effects restored the viability of mouse spermatogonia and spermatocytes impaired by MEHP exposure, implying the protective potential of NAC in mitigating DEHP-associated reproductive toxicity through inhibition of ERS and mitophagy.

In the context of DN, combined treatment with NAC and insulin was found to suppress FUNDC1-mediated excessive mitophagy in renal cells, thereby leading to reduced mitochondrial degradation and attenuation of kidney tissue injury.⁴⁵⁵ This underscores the therapeutic promise of NAC in preserving renal function in diabetic models.

Mitoquinone (MitoQ)

MitoQ is a potent antioxidant specifically targeting mitochondria, consisting of a ubiquinone (coenzyme Q10) moiety covalently attached to a lipophilic triphenylphosphonium (TPP⁺) cation.³⁸⁷ This design allows MitoQ to preferentially accumulate within the mitochondrial matrices by harnessing the mitochondrial membrane potential, achieving concentrations several hundred-fold higher than in the cytosol. Once localized to the mitochondria, MitoQ is continuously reduced by complex II of the ETC to its active antioxidant form, enabling sustained neutralization of mitochondrial reactive oxygen species (mtROS). Studies have reported that MitoQ is ~1000 times more effective than conventional antioxidants in protecting mitochondria against oxidative injury.^456,457 Recent findings by Sang et al.⁴⁵⁷ indicated that MitoQ suppressed mitophagy by preventing mitochondrial depolarization and reducing ROS accumulation, thus stabilizing mitochondrial membrane potential and inhibiting the initiation of mitophagy signaling pathways. This suggests that MitoQ not only preserves mitochondrial integrity but also functions in regulating mitochondrial turnover under conditions marked by redox imbalance.

Moreover, in a study concerning the pathological impact of particulate matter 2.5 (PM2.5) exposure, MitoQ was revealed to reverse excessive mitophagy in vascular smooth muscle cells derived from human and mouse aorta.⁴⁵⁸ Chronic exposure to PM2.5 triggered mitochondrial impairment and vascular injury through ROS-dependent mitophagy activation. Treatment with MitoQ significantly restored mitophagy to physiological levels by scavenging mtROS, which in turn ameliorated mitochondrial damage and diminished vascular fibrosis.⁴⁵⁸ Its ability to fine-tune mitophagy in response to environmental or pathological stressors implicates its therapeutic potential in diseases associated with mitochondrial dysfunction.

KCKT

Self-assembling nanoparticles have emerged as powerful delivery platforms in precision medicine due to their tunable size distribution, excellent biocompatibility, and high efficiency in intracellular targeting and cargo release.^459,460 These properties allow for selective interaction with specific cellular environments, making them ideal for organelle-targeted therapy. Recently, an innovative nanosystem referred to as KCKT was developed with in situ transformable capabilities designed to overcome intracellular delivery barriers and precisely regulate mitochondrial function.⁴⁶¹

Lv et al.⁴⁶¹ reported that KCKT nanoparticles underwent conformational transformation in the acidic tumor microenvironment, forming nanofiber structures within lysosomes. Activated by sonodynamic therapy, this nanofiber system induces a burst of ROS generation, synergistically destabilizing lysosomal membranes and enabling the fibers to breach lysosomal sequestration barriers. Postescape, the nanofibers specifically anchor near mitochondria through charge interactions, where ultrasound irradiation triggers sustained ROS production to inflict mitochondrial damage. Concurrently, lysosomal abnormalities prevent the autophagic degradation of impaired mitochondria, effectively inhibiting mitophagy.⁴⁶¹ This breakthrough addresses critical technical bottlenecks in organelle-targeted therapy, such as spatiotemporal precision, and holds immense potential for advancing mitophagy-targeted therapeutic strategies.⁴⁶⁰

In addition to the aforementioned representative compounds, many other promising mitophagy modulators have been reported. We have provided a brief summary of their action targets and related pathways, with further details available in Table 2^{420,430,462–484} (Fig. 9, Table 2).

Table 2.

Mitophagy modulators

Classification		Names	Mechanisms	NCT number	References
Mitophagy inducers	Furanocoumarin Plant Hormone	Bergapten	By increasing MAP1LC3/LC3-II levels and enhancing the mitochondrial-MAP1LC3B/LC3B colocalization, mitophagy is promoted	NCT00533195	425–427
	Bioactive compounds isolated from ligusticum chuanxiong hort and angelica sinensis (Oliv.) diels	Ligustilide	By upregulating PINK1-PRKN expression, promoting the aggregation of PRKN on OMM, and activating PINK1-PRKN mediated mitophagy	–	477,478
	Naturally occurring compound natural flavanol	Kaempferol and Kaempferol nanoparticle	By promoting PINK1 expression, stimulating PINK1-PRKN-dependent mitophagy	NCT06060691; NCT02191241	462,469
	Naturally occurring compound stilbenoid/Phytoalexin	Rhapontigenin	Promoting mitophagy	–	462
	Natural compound-flavonoid	Morin	Inducing mitophagy by facilitating TFEB nuclear translocation and activating the AMPK-ULK1 signaling without affecting mitochondrial membrane potential	–	465
	Natural compound extracted from Forsythia suspensa (Thunb.)	Forsythiaside A	Activation of PINK1-PRKN mediated mitophagy by upregulating the expression levels of PINK1 and PRKN proteins	–	467
	The triacetyl derivative of andrographolide	3,14,19-Triacetylandrographolide (ADA)	By increasing the expression of BNIP3 and its recruitment to mitochondria, BNIP3 mediated mitophagy is activated	–	466
	Naturally occurring compound converted from ellagitannin-like precursors in pomegranates and nuts by intestinal flora	Urolithin A	Inducing the TFEB, a key regulator of autophagy, into the nucleus in a partially mTOR dependent manner and inhibiting the ubiquitination degradation of TFEB, thereby promoting mitophagy	NCT04783207; NCT06556706; NCT05735886	418–422
	A galactoglucan from Panax notoginseng flower	RN0D	By selectively inhibiting galectin-3 and activating the PINK1-PRKN pathway, mitophagy is promoted	–	471
	Water-soluble hemisuccinate derivative of artemisinin	Artesunate	1. By reducing the expression of AFAP1L2 protein, inhibiting the phosphorylation levels of SRC and FUNDC1 proteins, enhancing the interaction between FUNDC1 and MAP1LC3B/LC3B, and promoting mitophagy; 2. Promoting mitophagy by upregulating the expression of PHB2 and PINK1	NCT01523002; NCT04921930; NCT00292942	423,424
	Benzocoumarin compound	Mitophagy-inducing coumarin	By inhibiting ligand induced activation of nuclear hormone receptor FXR, upregulating TFEB and BNIP3 expression, and enhancing mitophagy	–	476
	Selective PARP1/2 inhibitor	Olaparib	Promoting mitophagy	NCT02677038; NCT03782818	475
	The established BH3-mimetic for MCL-1	UMI-77	Augmenting the binding of MCL-1 to MAP1LC3B/LC3B and inducing mitophagy by blocking the interaction between MCL-1 and BAX/BAK	–	435–437
	A derivative of 4-[[3,4-(methylenedioxy)benzyl]amino]-6-chloroquinazoline	Spautin-1	Targeting the OMM transport complex, promoting the stability of PINK1 on the OMM and the mitochondrial translocation of PRKN, thereby inducing PINK1-PRKN dependent mitophagy	–	438–440
	Polyamine-related compounds	VL-004	Mediating mitophagy through PINK1 dependence	–	463
	Autophagy-tethering compounds	mT1	Simultaneously, binding to OMM protein TSPO and MAP1LC3B/LC3B, promoting mitophagy	–	464
	The peptide agonist of the δ opioid receptor	DADLE	By upregulating TRPV4, the influx of Ca2+ into the cell is promoted, thereby increasing the level of mitophagy	–	432–434
	Anti-diabetes drug; Inhibitor of Sodium/glucose cotransporter 2	Empagliflozin	1. Promoting the phosphorylation of FUNDC1 at the Serine 17 site through the AMPK/ULK1 pathway, thereby activating FUNDC1-mediated mitophagy; 2. Promoting FUNDC1-mediated mitophagy by activating the Wnt/β - catenin signaling axis	NCT02471963; NCT05584319	428–431
Mitophagy Inhibitors	Natural compound extracted from TwHF	Triptolide	Upregulating FOXP3 expression, disrupting ATF4 activity, and reducing PRKN protein levels, thereby suppressing PRKN-mediated mitophagy	–	441–446
	Natural compound extracted from lotus seeds	Liensinine	1. Blocking the phosphorylation of DNM1L/DRP1, inhibiting mitochondrial fission, thereby suppressing the initiation of mitophagy; 2. Impairing lysosomal cathepsin activity, thereby inhibiting mitophagy flux	NCT00664703	447–449
	Natural flavonoid compound	Isovitexin	By promoting the expression of SIRT3, thereby suppressing BNIP3-mediated mitophagy	–	483
	Glutathione precursor	N-acetyl-cysteine (NAC)	1. By significantly increasing intracellular GSH levels, neutralizing mtROS, stabilizing mitochondrial membrane potential, and preventing PINK1 accumulation on the OMM, thereby inhibiting the initiation of mitophagy; 2. By reducing ROS/mtROS levels, alleviating ERS, and inhibiting the nuclear translocation of XBP1s, thereby suppressing mitophagy; 3. Inhibiting FUNDC1-mediated excessive mitophagy	NCT01394497; NCT00332605	450–455
	TPP-based mitochondrial-targeted antioxidants	Mitoquinone (MitoQ)	Inhibiting mitochondrial damage and ROS generation, maintaining mitochondrial membrane potential, thereby suppressing mitophagy	NCT05410873; NCT05686967	387,456–458
	The OMM protein	FBXL4	By promoting the ubiquitination and degradation of BNIP3 and BNIP3L, thereby inhibiting mitophagy	–	484
	Immunosuppressive agent	Cyclosporine A	By modulating the mPTP, thereby inhibiting mitophagy	NCT05745701; NCT04705584; NCT05996393	480–482
	self-assembled nanoparticles	KCKT	Mediating lysosomal dysfunction, thereby inhibiting mitophagy	–	459–461

AFAP1L2 actin filament-associated protein 1-like 2, AMPK AMP-activated protein kinase, ATF4 cyclic AMP-dependent transcription factor ATF-4, BAK Bcl-2 homologous antagonist/killer, BAX apoptosis regulator BAX, BNIP3 B-cell leukemia/lymphoma 2/adenovirus E1B 19 kDa protein-interacting protein 3, BNIP3L B-cell leukemia/lymphoma 2/adenovirus E1B 19 kDa interacting protein 3-like, DADLE delta opioid [D-Ala(2),D-Leu(5)] enkephalin, DNM1L/DRP1 dynamin-1-like protein, ERS endoplasmic reticulum stress, FBXL4 F-box and leucine-rich repeat protein 4, FOXP3 forkhead box P3, FUNDC1 FUN14 domain-containing protein 1, FXR farnesoid X receptor, GSH glutathione, MAP1LC3B/LC3B microtubule associated protein 1 light chain 3 beta, MCL-1 induced myeloid leukemia cell differentiation protein Mcl-1, mPTP mitochondrial permeability transition pore, mTOR the mechanistic target of rapamycin, mtROS mitochondrial ROS, OMM outer mitochondrial membrane, PHB2 prohibitin-2, PINK1 PTEN induced putative kinase 1, PRKN E3 ubiquitin-protein ligase parkin, ROS reactive oxygen species, SIRT3 NAD-dependent protein deacetylase sirtuin-3, SRC proto-oncogene tyrosine-protein kinase Src, TFEB transcription factor EB, TSPO translocator protein, TRPV4 transient receptor potential vanilloid 4, ULK1 Unc-51-like kinase 1, XBP1s X-box-binding protein 1 spliced

Fig. 9.

Targets and molecular mechanisms of mitophagy modulators. The figure illustrates the targets and associated pathways of mitophagy modulators, including inducers and inhibitors, acting on mitophagy mechanisms. ADA 3,14,19-triacetylandrographolide, AFAP1L2 actin filament-associated protein 1-like 2, AMPK AMP-activated protein kinase, BNIP3 B-cell leukemia/lymphoma 2/adenovirus E1B 19 kDa protein-interacting protein 3, CsA cyclosporine A, DADLE delta opioid [D-Ala(2),D-Leu(5)] enkephalin, DRP1 dynamin-1-like protein, FBXL4 F-box and leucine-rich repeat protein 4, FUNDC1 FUN14 domain-containing protein 1, FXR farnesoid X receptor, LC3B microtubule associated protein 1 light chain 3 beta, MCL-1 induced myeloid leukemia cell differentiation protein Mcl-1, MIC mitophagy-inducing coumarin, MitoQ mitoquinone, mPTP mitochondrial permeability transition pore, NAC N-acetyl-cysteine, P phosphorylation, PHB2 prohibitin-2, PINK1 PTEN induced putative kinase 1, PRKN E3 ubiquitin-protein ligase parkin, ROS reactive oxygen species, TFEB transcription factor EB, TRPV4 transient receptor potential vanilloid 4, ULK1 Unc-51-like kinase 1. This figure was created using Adobe Illustrator (Adobe Inc., San Jose, CA, USA)

Mitochondrial transplantation therapy

Mitochondrial transplantation therapy (MTT), inspired by the physiological processes of mitophagy and spontaneous mitochondrial transfer, has recently attracted considerable interest as a novel approach to restore mitochondrial quality control. These therapies enable the rapid, precise, and efficient turnover or replacement of dysfunctional mitochondria within cells, thereby re-establishing mitochondrial homeostasis and reactivating suppressed mitophagy.⁴⁸⁵ By enhancing mitochondrial function, MTT has shown considerable therapeutic promise across a wide spectrum of diseases, including mitochondrial disorders, immune dissonance, and various cancers.⁴⁸⁶

A recent study targeting spontaneous mitochondrial transfer offers a potential therapeutic avenue. This process, frequently exploited by cancer cells, augments proliferation and chemotherapeutic resistance. Inhibiting mitochondrial transfer, particularly through blocking tunneling nanotubes (TNTs), the primary conduits for intercellular organelle exchange, may reverse tumor-promoting interactions between malignant cells and their microenvironment.⁴⁸⁶ For instance, selective inhibition of TNT formation prevents tumor cells from acquiring mitochondria from T cells, thereby preserving immune cell function and preventing T-cell exhaustion.⁴⁸⁶

Clinically, autologous mitochondrial transplantation has entered trials for treating ischemia‒reperfusion-related myocardial injury, showing encouraging results.^487,488 However, traditional exogenous mitochondrial transplantation faces two major challenges: maintaining mitochondrial viability postisolation and ensuring efficient intracellular delivery. A recent study⁴⁸⁹ suggests that transplanted mitochondria, even if nonfunctional or transiently active, can act as mitophagy triggers. Mitophagy activation increases endogenous mitochondrial biogenesis, enhances mitochondrial dynamics, and stimulates spontaneous mitochondrial transfer via TNTs.⁴⁸⁹ As a result, cellular bioenergetics are markedly improved, even when donor mitochondria are short-lived. Such a response, validated in endothelial cells, suggests that minimal mitochondrial uptake may be enough to reboot mitophagy and initiate broader systemic benefits.⁴⁸⁹ Nevertheless, additional investigations are warranted to establish whether this phenomenon underlies the observed therapeutic effects across other cell types and tissues.

In parallel, advances in material science have revolutionized the delivery of mitochondrial therapeutics. Wu et al.⁴⁹⁰ recently developed a noninvasive, orally administered mitochondrial therapy using nitric oxide-releasing nanomotors encapsulated in pH-responsive enteric capsules. This system enabled targeted mitochondrial delivery to ischemic cardiac tissue, where it successfully reprogrammed cardiomyocytes by reducing oxidative stress, improving ejection fraction, and limiting infarct size. Notably, the therapy outperformed conventional β-blockers and demonstrated dynamic microenvironmental modulation and enhanced cellular uptake and preservation of mitochondrial function in damaged tissue, representing a major breakthrough in the clinical translation of mitochondrial therapies.⁴⁹⁰

Collectively, these advancements illustrate that therapeutic strategies targeting mitophagy provide a powerful means to address dysfunction within the MIORN. By replacing dysfunctional mitochondria and restoring energy metabolism while concurrently normalizing aberrant mitophagy, MTT can repair local network dysregulation and restore the hierarchical homeostatic balance of the MIORN.

Conclusion and perspective

Mitophagy is essential for safeguarding mitochondrial quality and orchestrating organelle communication, thereby maintaining cellular and systemic functional balance. Through its interaction with the ER, lysosomes, proteasomes, lipid droplets, and other organelles, mitophagy forms a highly coordinated regulatory network in terms of MIORN. This network is pivotal not only in routine mitochondrial turnover but also in modulating organelle crosstalk under metabolic, oxidative, and inflammatory stress conditions. Dysregulation of mitophagy disrupts MIORN integrity, leading to uncontrolled ROS accumulation, inflammatory signaling, and ultimately, multiorgan dysfunction.

Notably, Ca²⁺ serves as a pivotal intracellular messenger, participating in diverse physiological processes by regulating proliferation, signal transduction, autophagy, and cell death. As elucidated in earlier sections of this review, many studies have demonstrated significant correlations between Ca²⁺ dynamics across organelles and mitophagic activity. This evidence confirms that Ca²⁺, through its storage and release across multiple organelles and coordinated interorganelle communication, plays an indispensable role in constructing and regulating MIORN and acts beyond a signal transmitter at the single-organelle level. Collectively, Ca²⁺ appears to be a key component coordinating mitophagy with the dynamic equilibrium of multiorganelle functions, encompassing host stress response integration, metabolic signal synergy, and multiorganelle quality control.

Despite remarkable advances in the mechanistic understanding of mitophagy and its cross-organelle roles, several key challenges remain. First, the precise molecular determinants governing the selectivity and hierarchy of mitophagy-related receptors under different stress contexts require further clarification. Second, our knowledge of tissue- and cell type-specific mitophagy programs is limited, hindering the development of organ-targeted therapies. Third, although recent progress in mitophagy-targeting pharmacological agents, such as urolithin A, MitoQ, or TRPML1 modulators, has shown therapeutic promise, translating these findings into clinical applications faces barriers, including bioavailability, specificity, and safety concerns.^458,491

Moreover, emerging research suggests that mitophagy is not a unidirectional degradative process but rather a dynamic and adaptable mechanism that coordinates with other quality control systems, including the UPR, mitochondrial biogenesis, and intercellular mitochondrial transfer.^267,273,492 Understanding how mitophagy integrates with these systems in real time and across different subcellular compartments remains a critical area for exploration.

Looking forward, advances in live-cell imaging, organelle-specific proteomics, and spatial transcriptomics will accelerate the mapping of mitophagy-centered crosstalk at unprecedented resolution.^80,493,494 Within this framework, organelle-specific multiomics will constitute a fundamental methodological system, uncovering the key mechanisms governing mitochondrial homeostasis, signal transduction, and functional regulation.^495,496 Additionally, novel nanotechnologies and mitochondrial transplantation platforms offer exciting opportunities to rewire dysfunctional MIORN nodes and restore homeostasis in mitochondrial and degenerative diseases. Ultimately, a deeper understanding of mitophagy as a central regulator of organelle coordination may unlock new therapeutic avenues to combat aging, metabolic disorders, cancer, and multiorgan dysfunction syndrome.

Author contributions

M.W. wrote the manuscript and designed the figures and tables, P.H., Y.L., and Y.W. organized the figures and tables, T.Z. contributed to manuscript revision and supplementary figure design, L.W. reviewed the literature, and D.T., Y.Y., and R.Y. conceived, designed, and edited the manuscript. All authors have read and approved the manuscript.

Competing interests

The authors declare no competing interests.

Consent for publication

All authors have agreed on the contents of the manuscript.