Harnessing Mitophagy for Therapeutic Advances in Aging and Chronic Neurodegenerative Diseases

Abstract

Introduction: Mitophagy, the selective degradation of damaged mitochondria, is essential for maintaining cellular health and function, particularly in high-energy demanding post-mitotic cells like neurons and in microglial cells. Aging results in impaired mitophagy, leading to mitochondrial dysfunction, oxidative stress, the release of damage-associated proteins (DAMPs), and neuroinflammation, which contribute to neurodegenerative diseases such as Alzheimer’s and Parkinson’s. Mitochondrial dysfunction also contributes to the pathophysiology of depression by affecting synaptic plasticity, increasing neuroinflammation, and heightening oxidative stress. Aim: In this review, we summarize the recent developments on mechanisms of mitophagy, its therapeutic role in neuroprotection, and its implications in aging and neuroinflammation, complemented by future research requirements and implications. Result/Discussion: Therapeutic strategies that promote mitochondrial health, including enhancing mitophagy and mitochondrial biogenesis, show promise in treating neurodegenerative diseases and depression. Recent findings have emphasized therapeutic strategies to modulate mitophagy, such as pharmacological agents like urolithin A and rapamycin, genetic interventions such as PINK1/Parkin gene therapy, mitochondrial transplantation, and lifestyle and dietary interventions such as caloric restriction, exercise, and dietary supplements such as resveratrol and CoQ10. Key regulators of mitophagy, including the PINK1/Parkin pathway and various proteins like BNIP3, NIX, and FUNDC1, which facilitate the removal of damaged mitochondria, play a crucial role. Conclusions: These results highlight the importance of understanding the interplay between mitophagy and neuroinflammation and show that modulation of mitophagy can reduce oxidative stress and improve neuroinflammatory outcomes and depression in age-related neurodegenerative diseases. However, despite significant progress, challenges remain in understanding the underlying molecular mechanisms of mitophagy and its therapeutic regulation in aging disorders.

1. Introduction

Mitophagy, the process by which cells selectively degrade damaged or superfluous mitochondria through autophagy, is essential for maintaining mitochondrial quality control. It plays a crucial role in preserving cellular health by eliminating dysfunctional mitochondria, which helps sustain cellular metabolism, reduce oxidative stress, and prevent apoptosis. This is especially important in post-mitotic cells like neurons [1,2].

As organisms age, they experience a gradual decline in cellular function and an increased susceptibility to stress and inflammation. Mitochondrial dysfunction is both a cause and an effect of aging, and it contributes to various age-related diseases, including neurodegenerative disorders like Alzheimer’s, Parkinson’s, and Huntington’s disease, and multiple sclerosis [3]. In neurons, impaired mitophagy leads to the accumulation of damaged mitochondria, causing cellular dysfunction and toxicity. This is particularly problematic due to neurons’ high energy demands and inability to divide, making them more vulnerable to mitochondrial abnormalities [4]. As mitophagy becomes impaired through ageing, there occurs a release of mitochondria-derived DAMPs such as DNA (mtDNA), cardiolipin, N-formyl peptides, and cytochrome c, which act as potent pro-inflammatory agents.

Mitochondrial dysfunction is also implicated in the pathophysiology of depression. It affects synaptic plasticity, increases neuroinflammation, and heightens oxidative stress, contributing to the development of major depressive disorder (MDD). Therapeutic strategies that promote mitochondrial health, including mitophagy and mitochondrial biogenesis, hold promise for alleviating depressive symptoms and improving neural health [5]. For instance, chronic stress can induce Drp1-dependent mitochondrial fission in the medial prefrontal cortex, leading to mitochondrial dysfunction and depressive-like behaviors. Inhibiting Drp1 has been shown to improve synaptic transmission and stress responses, while enhancing Drp1 worsens stress effects, which can be mitigated by CoQ10 [6].

Neuroinflammation, a common feature of neurodegenerative diseases, is closely associated with mitochondrial health. Deficient mitophagy can lead to cellular aging and sustained neuroinflammation, potentially resulting in neuronal death and impaired brain function [7]. The interplay between mitophagy and neuroinflammation suggests that enhancing mitophagy might be a therapeutic approach to improve microglial function, reduce neuroinflammation, and decrease Alzheimer’s pathology, such as β-amyloid plaques and phosphorylated tau tangles [8]. Recent studies have shown promise in therapies aimed at boosting mitophagy as a treatment for age-related neurodegenerative diseases. Pharmacological agents like urolithin A, rapamycin, spermidine, and NAD+ precursors have been found to stimulate mitophagy and reverse cognitive deficits in neurodegenerative disorder models [9,10,11,12]. Additionally, lifestyle interventions like caloric restriction and exercise have been demonstrated to enhance mitophagy and improve mitochondrial function [13].

This review seeks to examine the mechanisms and neuroprotective effects of mitophagy, how it influences the outcome of aging and neuroinflammation when impaired, and the therapeutic potential of modulating mitophagy to treat age-related neurodegenerative diseases. By summarizing recent findings and suggesting future research directions, we aim to underscore the importance of mitophagy in maintaining neuronal health and mitigating neurodegeneration.

2. Mitophagy: Mechanism and Neuroprotection

Under conditions of stress, such as exposure to reactive oxygen species (ROS), nutrient deprivation, or aging, mitochondria can become depolarized and damaged. Mitophagy, a specialized type of autophagy, is an essential cellular process that targets damaged or redundant mitochondria for degradation, thereby preserving mitochondrial quality and cellular homeostasis. During mitophagy, dysfunctional mitochondria are encapsulated into double-membrane vesicles called autophagosomes, which then fuse with lysosomes to degrade and recycle mitochondrial components. This selective autophagy process is crucial for removing damaged mitochondria, preventing the accumulation of mitochondrial defects that could lead to oxidative stress, cellular dysfunction, and apoptosis. Mitophagy reduces the number of mitochondria, which in turn decreases the energy supply to the body. Meanwhile, an increase in the AMP/ATP and NAD+/NADH ratios triggers a timely activation of mitochondrial biogenesis [3,14,15].

Several key regulators and signaling pathways, such as the PINK1/Parkin pathway, BNIP3, NIX, FUNDC1, and AMPK, orchestrate mitophagy (

Table 1. Key regulators of mitophagy. The table lists the key regulators of mitophagy, their key function, the pathway they follow, and diseases they play an important role in.

Regulator	Function	Pathway	Relevance to Disease	References
PINK1	Accumulates on the outer mitochondrial membrane upon depolarization, recruits Parkin	PINK1/Parkin Pathway	Impaired function linked to Parkinson’s Disease	[4,16,17,18,19]
Parkin	Ubiquitinates mitochondrial surface proteins, marking them for degradation	PINK1/Parkin Pathway	Mutations associated with familial Parkinson’s Disease	[4,16,17,18,19,20]
BNIP3	Interacts with LC3 to promote mitophagy under hypoxia	BNIP3 Pathway	Involved in hypoxia-induced mitophagy in cancer and cardiac tissues	[21,22]
NIX	Similar to BNIP3, interacts with LC3 during hypoxia	BNIP3 Pathway	Important for erythrocyte maturation and heart function	[21,22]
FUNDC1	Mediates hypoxia-induced mitophagy through interaction with LC3	FUNDC1 Pathway	Plays a role in ischemic heart diseases	[23,24]
AMPK	Initiates mitophagy by phosphorylating ULK1(vital for neuroprotection). Also inhibits mTORC1.	AMPK-ULK1 pathway	Reduces neuroinflammation and protects neuronal cells.	[25,26,27]

).

PINK1/Parkin Pathway: The PINK1/Parkin pathway is a well-known mechanism of mitophagy. PINK1 (PTEN-induced kinase 1) is a mitochondrial kinase that accumulates on the outer membrane of depolarized mitochondria. Normally, PINK1 is quickly degraded, but when mitochondria are damaged and lose membrane potential, PINK1 stabilizes and accumulates on the outer mitochondrial membrane. This accumulation recruits and activates Parkin, an E3 ubiquitin ligase, which ubiquitinates various outer mitochondrial membrane proteins, marking the mitochondria for degradation. Ubiquitination of these proteins signals the recruitment of autophagic machinery, leading to the encapsulation of damaged mitochondria into autophagosomes for degradation [4,16,17].

BNIP3 and NIX: BNIP3 (BCL2 interacting protein 3) and NIX (BNIP3L) are members of the BCL2 family that play significant roles in hypoxia-induced mitophagy. Both proteins contain LC3-interacting regions (LIRs), enabling them to bind to LC3 on the autophagosome membrane and facilitate the engulfment of damaged mitochondria. BNIP3 and NIX are upregulated in response to hypoxia and help clear mitochondria during cellular stress, especially in tissues with high metabolic demands, such as the heart and skeletal muscles [21,22].

FUNDC1: FUNDC1 (FUN14 domain containing 1) is another receptor that mediates hypoxia-induced mitophagy. Under hypoxic conditions, FUNDC1 interacts with LC3 through its LIR motif, promoting the sequestration of damaged mitochondria into autophagosomes. The phosphorylation state of FUNDC1 regulates its activity; for example, dephosphorylation at serine 13 enhances its interaction with LC3, thus promoting mitophagy. This pathway is critical for maintaining mitochondrial quality under stress and preventing cellular damage [23,24].

AMPK (AMP-activated protein kinase): AMPK initiates mitophagy by phosphorylating ULK1, a critical autophagy-initiating kinase vital for neuroprotection. This process is especially important under metabolic stress conditions. In addition to phosphorylating ULK1, AMPK also inhibits mTORC1, further promoting autophagy. This dual mechanism helps reduce neuroinflammation and protects neuronal cells [25]. Morin, a natural compound, has demonstrated neuroprotective effects in Parkinson’s disease models via the AMPK-ULK1 pathway [26]. Additionally, certain flavonoids have been found to influence the AMPK/PGC-1α pathway, enhancing mitochondrial biogenesis and mitophagy, which is beneficial for neuroprotection in neurodegenerative disorders [27].

Mitochondrial dynamics, including fusion and fission, are crucial for regulating mitophagy and maintaining mitochondrial health.

Mitochondrial Fusion: Mitochondrial fusion involves the merging of two mitochondria, allowing the exchange of mitochondrial contents such as DNA, proteins, and lipids. This process, mediated by mitofusins (Mfn1 and Mfn2) and optic atrophy 1 (OPA1), helps dilute damaged components by mixing them with healthier mitochondria, thus preserving mitochondrial function and integrity. Fusion is vital for preventing the accumulation of mitochondrial damage and supporting biogenesis [28,29].

Mitochondrial Fission: Mitochondrial fission involves the division of a mitochondria into smaller ones, a process facilitated by the dynamin-related protein 1 (Drp1). Fission helps segregate damaged mitochondrial sections, which are then selectively degraded through mitophagy. This process is essential not only for removing damaged mitochondria but also for ensuring proper mitochondrial distribution during cell division [6,30,31].

The balance between fusion and fission is critical for efficient mitophagy. An imbalance, such as excessive fission or impaired fusion, can lead to the accumulation of damaged mitochondria, resulting in increased oxidative stress and neuroinflammation. This imbalance is associated with various age-related diseases and neurodegenerative disorders [12,32].

3. Mitophagy and Aging

Aging involves a deterioration of cellular functions, heightened sensitivity to stress, and the build-up of damaged cellular components. Mitochondria, which are responsible for producing energy, are especially vulnerable to damage because they ROS. Furthermore, mitophagy decreases with age, leading to the accumulation of dysfunctional mitochondria and contributing to cellular senescence [4]. It has been reported that MFN2 expression reduces with age in the skeletal muscle of mice. A deficiency in MFN2 results in reduced mitophagy and the accumulation of damaged mitochondria, leading to sarcopenia and atrophy [33]. There is an accumulation of PINK1 and Parkin in the mitochondria and a decrease in mitochondrial ubiquitination during cellular aging. These changes result in decreased mitophagy and increased cell damage and aging [34].

Various age-related cellular dysfunctions, including impaired energy metabolism, increased oxidative stress, and heightened susceptibility to cell death, have been linked to reduced mitophagy. In skeletal muscle, aging is associated with a decreased ratio of healthy to damaged mitochondria, indicating impaired mitochondrial quality control. This impairment can result in reduced muscle function and increased muscle loss (sarcopenia) [20,35]. A decline in copy number, which serves as a proxy for mitochondrial content, has been observed with age in peripheral blood cells. This decline has been associated with poorer cognitive performance, decreased physical strength, and higher all-cause mortality in elderly individuals, emphasizing the importance of mitophagy in maintaining mitochondrial health and overall cellular function [36]. Research on human right atrial tissue from young (≤50 years) and aged (≥70 years) patients undergoing coronary artery bypass surgery showed reduced mitochondrial content and decreased markers of mitophagy, such as Parkin, in aged tissues, suggesting a decline in mitophagic signaling with age. This decline may lead to increased apoptosis and mitochondrial dysfunction [37]. Additionally, elevated levels of mitokines (mitochondrial stress response molecules), such as FGF21 and GDF15, have been observed in aged individuals. These elevated levels are correlated with markers of cellular stress and metabolic dysfunction, possibly reflecting the body’s response to cope with mitochondrial dysfunction, which becomes more pronounced with age [38].

When mitophagy is compromised, damaged mitochondria accumulate within cells, leading to the release of mitochondrial-derived damage-associated molecular patterns (mtDAMPs). These mtDAMPs, including mtDNA, cardiolipin, N-formyl peptides, and cytochrome c, act as potent pro-inflammatory agents. They can activate innate immune receptors such as Toll-like receptors (TLRs) and NOD-like receptors (NLRs), notably the NLRP3 inflammasome. For example, studies have shown that mtDNA released into the cytosol can activate TLR9 and the cGAS-STING pathway, triggering type I interferon production and inflammatory responses [39]. Cardiolipin, normally confined to the inner mitochondrial membrane, can be externalized during mitochondrial stress and serve as a signal for mitophagy initiation or act as a DAMP when released, further stimulating the NLRP3 inflammasome [40,41]. Similarly, N-formyl peptides and cytochrome c can induce immune cell activation, contributing to chronic inflammation [42]. The accumulation of these mtDAMPs not only exacerbates inflammatory pathways but also promotes apoptotic and pyroptotic cell death. The resultant inflammation and cell death are implicated in the progression of neurodegenerative diseases, cardiovascular disorders, and age-related pathologies. The critical role of mitophagy in mitigating these harmful effects highlights the therapeutic potential of targeting this pathway to restore cellular homeostasis and reduce inflammation in disease states.

Research involving mice has shown that enhancing mitophagy can reduce age-related cellular damage and extend lifespan. Mice with genetically enhanced mitophagy displayed lower levels of damaged mitochondria accumulation and demonstrated better metabolic health than control mice [43]. In humans, aging has been associated with a reduction in the expression of autophagy-related genes in skeletal muscle, which correlates with a decline in physical performance and muscle mass. A study involving older adults revealed that levels of mitophagy markers such as BNIP3 and Parkin were lower compared to those in younger individuals. This decline in mitophagy was linked to decreased mitochondrial function and increased muscle dysfunction [44]. Studies examining the effects of hyperglycemia on mitophagy in individuals with prediabetes and type 2 diabetes mellitus (T2DM) found that mitophagy was initially upregulated in prediabetic individuals to manage mild hyperglycemia. However, it became significantly impaired in patients with advanced T2DM, leading to increased oxidative stress and mitochondrial damage. These findings highlight the importance of maintaining mitophagy for cellular health [45,46].

4. Mitophagy and Neuroinflammation

Mitophagy, the selective removal of damaged mitochondria via autophagy, is essential for maintaining mitochondrial quality control and cellular homeostasis, especially in the central nervous system (CNS). Neurons rely heavily on mitochondrial function due to their high energy demands and limited ability to regenerate. Therefore, the clearance of dysfunctional mitochondria through mitophagy is vital for neuronal survival and proper function. Impaired mitophagy is associated with various neurodegenerative diseases, as the accumulation of damaged mitochondria can lead to increased oxidative stress and cellular dysfunction [4,47].

Neuroinflammation is a hallmark of many neurodegenerative diseases and involves the activation of glial cells and the release of pro-inflammatory cytokines. Mitophagy influences neuroinflammation through several mechanisms:

Regulation of Mitochondrial ROS: Damaged mitochondria are significant sources of ROS, which can activate inflammatory pathways. Mitophagy helps lower ROS production and oxidative stress by removing these dysfunctional mitochondria, thereby reducing inflammation [48].

Regulation of NLRP3 Inflammasome Activation: The NLRP3 inflammasome is a key regulator of inflammation in the CNS. Studies have shown that mitophagy can inhibit NLRP3 inflammasome activation by preventing the accumulation of damaged mitochondria and mitochondrial DNA, which are potent activators of this inflammasome [49,50]. Recent research underscores the vital role of mitophagy and autophagy in maintaining cellular health and regulating inflammation. Inhibition of these processes can lead to the accumulation of dysfunctional, ROS-producing mitochondria. This mitochondrial dysfunction can trigger the activation of the NLRP3 inflammasome, a key component of the innate immune response [32,51].

Clearance of Inflammasome Activators: Mitophagy aids in the clearance of inflammasome activators, such as oxidized mitochondrial components and misfolded proteins, which can trigger inflammatory responses. This clearance is vital for maintaining cellular homeostasis and preventing chronic inflammation [52,53].

cGAS-STING Pathway: This pathway is a key sensor of cytosolic DNA, including mtDNA that escapes from damaged mitochondria. When mitophagy is impaired, such as in aging or neurodegenerative diseases, damaged mitochondria accumulate, leading to the release of mtDNA into the cytoplasm. This release can activate the cGAS-STING pathway, subsequently triggering an inflammatory response [7,54]. The activation of cGAS-STING signaling by cytosolic mtDNA can promote the production of type I interferons and other pro-inflammatory cytokines, exacerbating neuroinflammation. This has been observed in various models of neurodegenerative diseases, where defective mitophagy correlates with increased inflammation [55]. Conversely, enhancing mitophagy can reduce the cytosolic accumulation of mtDNA, thereby mitigating the activation of the cGAS-STING pathway and the associated inflammatory responses [56]. Further research suggests that pharmacological interventions targeting mitophagy could be an effective strategy to modulate the cGAS-STING pathway. For example, drugs that promote mitophagy have shown potential in reducing neuroinflammation by decreasing the levels of cytosolic mtDNA, thus preventing excessive cGAS-STING activation [57,58]. These findings underscore the therapeutic potential of targeting mitophagy to control neuroinflammation and neurodegeneration.

HMGB1: HMGB1 translocates from the nucleus to the cytoplasm in response to cellular stress and acts as a pro-inflammatory mediator [59]. It can interact with Beclin-1, a key protein in autophagy, promoting autophagosome formation and facilitating mitophagy, which helps reduce ROS production. Conversely, impaired mitophagy can lead to the release of HMGB1, exacerbating inflammation [60,61].

Mitophagy is increasingly recognized as a key factor in the pathology and potential treatment of neurodegenerative diseases (

Table 2. Mitophagy in neurodegenerative diseases. This table highlights how mitophagy impairment, marked by specific molecular changes, contributes to neurodegenerative diseases like Alzheimer’s, Parkinson’s, Huntington’s, and multiple sclerosis, and outlines potential therapeutic strategies, including pharmacological agents, gene therapy, and lifestyle interventions.

Disease	Mitophagy Impairment	Molecular Markers	Therapeutic Approaches	References
Alzheimer’s Disease	Reduced PINK1/Parkin activity, accumulation of damaged mitochondria	Decreased PINK1, Parkin levels	Urolithin A, Rapamycin, lifestyle interventions (exercise, caloric restriction)	[8,12,18]
Parkinson’s Disease	Mutations in PINK1, Parkin lead to impaired mitophagy	Reduced Parkin-mediated ubiquitination	Gene therapy (PINK1/Parkin), mitochondrial transplantation	[2,9,19,60]
Huntington’s Disease	Accumulation of damaged mitochondria due to impaired mitophagy	Altered mitochondrial dynamics proteins (e.g., Drp1)	Pharmacological agents, lifestyle interventions	[12]
Multiple Sclerosis	Accumulation of damaged mitochondria due to impaired mitophagy	Altered mitochondrial dynamics proteins (e.g., Drp1)	Pharmacological agents, lifestyle interventions	[62]

).

Alzheimer’s Disease (AD): Alzheimer’s disease is characterized by the accumulation of amyloid-beta plaques and neurofibrillary tangles, leading to neuronal death and cognitive decline. Impaired mitophagy has been observed in AD, contributing to mitochondrial dysfunction and increased oxidative stress. Studies have reported reduced levels of mitophagy markers such as PINK1 and Parkin in AD patients, correlating with increased mitochondrial damage and neuroinflammation [18].

Parkinson’s Disease (PD): Parkinson’s disease is associated with the loss of dopaminergic neurons in the substantia nigra, leading to motor symptoms such as tremors and rigidity. Mutations in PINK1 and Parkin, key regulators of mitophagy, are linked to familial forms of PD. These mutations impair mitophagy, resulting in the accumulation of dysfunctional mitochondria and increased oxidative stress, which contribute to neuronal death and neuroinflammation [19].

Huntington’s Disease (HD): Huntington’s disease is a genetic disorder characterized by the progressive degeneration of neurons in the brain, leading to motor dysfunction, cognitive decline, and psychiatric symptoms. Research indicates that impaired mitophagy plays a significant role in HD pathogenesis. The accumulation of damaged mitochondria and increased oxidative stress have been observed in HD models, highlighting the importance of mitophagy in maintaining neuronal health [12].

Multiple Sclerosis (MS): Multiple sclerosis is an autoimmune disease characterized by demyelination and neurodegeneration in the CNS. Recent studies have suggested a role for mitophagy in MS, where impaired mitophagy may contribute to mitochondrial dysfunction and neuroinflammation. Elevated levels of mitophagy markers such as Parkin and PINK1 have been detected in the cerebrospinal fluid of MS patients, particularly during active disease phases [62].

5. Therapeutic Interventions to Modulate Mitophagy

Pharmacological agents that target mitophagy show considerable potential in advancing treatments for neurodegenerative diseases and aging. Several compounds, including urolithin A, rapamycin, spermidine, and NAD+ precursors have been explored for their effects on modulating mitophagy and enhancing mitochondrial function (

Table 3. Therapeutic interventions to modulate mitophagy. This table showcases various therapeutic aspects that modulate mitophagy and improve mitochondrial function.

Agent	Mechanism of Action	Evidence from Studies	Potential Therapeutic Use	References
Urolithin A	Induces mitophagy, promotes mitochondrial health, stimulates mitochondrial biogenesis.	Improves mitochondrial function, muscle function, and lifespan; enhances cognitive functions, synaptic plasticity; reduces neuroinflammation and neuron loss in neurodegenerative models.	Neurodegenerative diseases (e.g., Alzheimer’s, Parkinson’s), Aging.	[9,63,64]
Rapamycin	Inhibits mTOR, enhances autophagy and mitophagy, aids in clearance of damaged mitochondria.	Improves learning, memory, synaptic plasticity, and mitochondrial function; reduces oxidative stress, apoptosis, and neuronal loss in neurodegenerative models.	Alzheimer’s Disease, longevity	[10,65,66,67]
Spermidine	Stimulates autophagy and mitophagy (markers, including Beclin-1, LC3-II, PINK1, PARKIN, ULK1, Atg, AMPK, and inhibiting mTOR), aids in the removal of dysfunctional mitochondria.	Enhances cognitive function, decreases oxidative stress, extends lifespan; improves memory performance in older adults	Improves cognitive decline, promotes neuroprotection.	[11,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86]
NAD+ Precursors	Increases intracellular NAD+ levels, activates sirtuins (e.g., SIRT1, SIRT3) involved in mitochondrial biogenesis and quality control.	Restores mitochondrial function, reduces oxidative stress in astrocytes and microglia.	Neurodegenerative diseases, mitochondrial dysfunction.	[57,87]
PINK1 and Parkin Gene Therapy	Restores mitophagy by introducing functional copies of PINK1 or Parkin genes.	Corrects mitochondrial defects, reduces neuroinflammation, enhances motor function in Parkinson’s disease models.	Parkinson’s disease, other neurodegenerative diseases.	[88,89]
Mitochondrial Transplantation	Transplants healthy mitochondria into cells with dysfunctional ones.	Enhances cellular function and alleviates symptoms of neurodegenerative diseases.	Neurodegenerative diseases characterized by mitochondrial dysfunction.	[90,91,92,93,94,95,96]
CRISPR/Cas9-Based Therapies	Edits genes to correct mutations disrupting mitophagy, restores normal mitochondrial function.	Ongoing research focused on mitochondrial myopathies and neurodegenerative diseases.	Mitochondrial myopathies, neurodegenerative diseases.	[97,98,99]
Caloric Restriction (CR)	Enhances mitophagy, improves mitochondrial function, reduces oxidative stress and reduces inflammatory markers	Extends lifespan, delays age-related diseases, improves metabolic health and cognitive function. Decreases fasting insulin levels, body temperature, resting energy expenditure and thyroid axis activity	Aging, cardiometabolic risk, metabolic health, cognitive function.	[100,101]
Exercise	Promotes elimination of damaged mitochondria, stimulates mitochondrial biogenesis.	Improves cognitive function, therapeutic strategy for dementia patients, delays neurodegenerative diseases, increases angiogenesis, neurogenesis, reducing age-related brain atrophy and supports healthy aging.	Neurodegenerative diseases, healthy aging.	[102,103,104,105,106,107,108,109,110,111,112,113,114]
Dietary Polyphenols	Enhances mitophagy, reduces oxidative stress, improves mitochondrial function.	Improves cognitive function, reduces inflammation and oxidative stress in neurodegenerative models.	Aging, neurodegenerative diseases.	[80,100,115,116]

).

Urolithin A: Urolithin A (UA), a metabolite produced from the consumption of ellagitannins found in pomegranates and other fruits, has been found to induce mitophagy and promote mitochondrial health. Research conducted on animal models and humans has demonstrated that urolithin A can stimulate mitochondrial biogenesis, enhance muscle function, and extend lifespan. Recent studies have highlighted various health benefits of UA. One clinical trial confirmed that UA is safe and bioavailable in elderly individuals, improving mitochondrial and cellular health by modulating mitochondrial biomarkers [63]. Another study indicated that UA enhances cognitive functions and synaptic plasticity, thereby improving learning and memory in Alzheimer’s disease models [64]. Additionally, research on Parkinson’s disease revealed that UA reduces dopaminergic neuron loss and neuroinflammation by promoting mitophagy and inhibiting the activation of the NLRP3 inflammasome in microglia [9]. These findings collectively underscore the therapeutic potential of urolithin A in mitigating neurodegenerative conditions.

Rapamycin: Rapamycin, an mTOR inhibitor, is known for promoting longevity and alleviating neurodegenerative diseases. By inhibiting mTOR, rapamycin enhances autophagy, including mitophagy, aiding in the clearance of damaged mitochondria. In TNF-α stimulated preosteoblasts, rapamycin upregulates Parkin-mediated mitophagy, reducing mitochondrial impairment and mitigating osteoporosis in AIA mice when combined with a TNF-α neutralizing antibody [10]. In APP/PS1 mice, it enhances mitophagy, improving learning, memory, synaptic plasticity, and mitochondrial function, while reducing oxidative stress and apoptosis, thus mitigating Alzheimer’s disease [65]. Rapamycin also increases PINK1-Parkin signaling, improving mitochondrial quality control and function [66]. In 5×FAD mice, it alleviates neuronal loss and enhances cognitive function by promoting amyloid-β and damaged mitochondria clearance [67].

Spermidine: Spermidine, a naturally occurring polyamine, has attracted interest for its capacity to stimulate autophagy and mitophagy [11,68,69,70]. It is found in Mediterranean and Okinawan diets, present in foods like red wine, fresh vegetables, fruits, soy products, nuts, and mushrooms. While studies on spermidine are limited, spermidine supplementation was found to exert protective effects against age-induced memory impairment in Drosophila melanogaster via the recuperation of autophagy [71] and to improve memory performance in a phase IIa trial with 30 older adults with subjective cognitive decline [72]. Further detailed studies have shown that spermidine induces mitophagy in animal and cell models by upregulating mitophagy-related markers, including Beclin-1, LC3-II, PINK1, PARKIN, ULK1, Atg, and AMPK, and inhibiting mTOR [73,74,75,76,77,78,79,80,81,82,83]. It has been shown to induce mitophagy in mouse neuroblastoma cells [84] and in the brains of aging mouse models [81]. Multiple studies indicate that spermidine consumption not only mitigates aging effects in yeast, flies, worms, human cells, and mice, but also extends the lifespan of various model organisms and reduces oxidative stress in aging mice via autophagy [85]. Furthermore, Sharma et al. support this notion, asserting that spermidine combats age-associated cell death by activating autophagy-related pathways and decreasing reactive oxygen species formation [86].

NAD+ Precursors (e.g., Nicotinamide Riboside, Nicotinamide Mononucleotide):

NAD+ precursors, such as nicotinamide riboside and nicotinamide mononucleotide (NMN), enhance mitophagy in neuroglial cells by increasing intracellular NAD+ levels. This boost in NAD+ activates sirtuin enzymes like SIRT1 and SIRT3. These sirtuins activate pathways involved in mitochondrial biogenesis and quality control, including the deacetylation of key mitophagy regulators. Recent research demonstrates that NR and NMN can restore mitochondrial function and reduce oxidative stress in astrocytes and microglia, highlighting their potential as therapeutic agents [57,87].

Gene therapy presents a promising strategy for directly modulating mitophagy to address neurodegenerative diseases and reduce aging-related mitochondrial dysfunction. Recent advancements in genetic engineering and delivery systems have paved the way for targeted therapies that enhance mitophagy.

PINK1 and Parkin Gene Therapy: Mutations in the PINK1 and Parkin genes are associated with impaired mitophagy and mitochondrial dysfunction, particularly in neurodegenerative diseases like Parkinson’s disease. Gene therapy approaches that introduce functional copies of these genes have shown promise in restoring mitophagy and improving mitochondrial health. Animal studies have demonstrated that delivering PINK1 or Parkin genes can correct mitochondrial defects, reduce neuroinflammation, and enhance motor function in Parkinson’s disease models [88,89].

Mitochondrial Transplantation: Mitochondrial transplantation involves the transfer of healthy mitochondria from donor to recipient cells with dysfunctional mitochondria, showing potential in repairing tissue damage in neurological and other diseases, and also influencing neuroinflammation regulation [90]. Despite promising results, the mechanisms behind mitochondrial uptake in neurons remain unclear. Mitochondrial dysfunction, a hallmark of neurodegenerative diseases like Parkinson’s, Alzheimer’s, and ALS, leads to cellular energy deficits, making mitochondrial transplantation a promising therapeutic approach to restore cellular function in these conditions. Successful mitochondrial transplantation depends on several key factors: the quality of the isolated mitochondria, the protocol used for their delivery, and the ability of recipient cells to take up and integrate these mitochondria [91]. The quality and source of the mitochondria are paramount, as only intact, functional mitochondria can restore bioenergetic balance in recipient cells. Equally important is the method of delivery, which must ensure that the mitochondria reach the target cells without degradation. Lastly, the recipient cells must successfully internalize the transplanted mitochondria and incorporate them into their endogenous mitochondrial network to achieve therapeutic benefit.

However, there are still challenges that must be overcome before mitochondrial transplantation can be applied clinically. These include optimizing mitochondrial yield and purity, developing protocols for long-term mitochondrial storage, and preventing transplant rejection [92]. Mitochondrial rejection, in particular, poses a risk, as the immune system may recognize foreign mitochondria as non-self and initiate an inflammatory response. Strategies such as autologous mitochondrial transplantation—where mitochondria are sourced from the same patient—may help mitigate this issue [93]. However, for patients with congenital mitochondrial disorders, alternative solutions such as using mitochondria from close maternal relatives or gene-editing approaches may be required [92]. In conclusion, mitochondrial transplantation offers a novel therapeutic strategy for treating diseases driven by mitochondrial dysfunction. While much progress has been made in understanding the mechanisms of mitochondrial transfer, further research is needed to refine the techniques and address the remaining challenges. With continued advancements, mitochondrial transplantation could become a viable treatment option for a wide range of mitochondrial diseases, potentially offering significant clinical benefits in the near future [94,95,96].

CRISPR/Cas9-Based Therapies: The CRISPR/Cas9 gene-editing technology offers a precise way to correct genetic mutations that disrupt mitophagy. By targeting specific mutations in genes crucial for mitophagy, CRISPR/Cas9 can potentially restore normal mitochondrial function and improve cellular health. Ongoing research is focused on developing CRISPR-based therapies for conditions like mitochondrial myopathies and neurodegenerative diseases, where defective mitophagy is a key factor [97,98,99].

Lifestyle and dietary interventions have been found to influence mitophagy and enhance mitochondrial health, providing a non-pharmacological strategy to address aging and neurodegenerative diseases.

Caloric Restriction: Caloric restriction (CR), which entails reducing caloric intake without causing malnutrition, has been widely studied for its positive effects on longevity and metabolic health. CR has been observed to boost mitophagy, enhance mitochondrial function, and lower oxidative stress. Animal research has shown that CR can extend lifespan and delay the onset of age-related diseases. In humans, CR is linked to improved metabolic health, decreased inflammation, and better cognitive function [100,117].

Recent studies demonstrated that mitogenesis depends on genes from both the mitochondrial and nuclear genomes, regulated by the proliferator-activated receptor-γ coactivator 1-alpha (PGC1-α), a key mediator of mitochondrial biogenesis activated by CR and polyphenols [118,119]. However, long-term CR is difficult to maintain, prompting interest in CR-mimicking approaches. The Okinawan diet, low in calories but rich in polyphenols, is linked to high longevity rates. Short-term human CR studies have shown benefits similar to animal models. The Comprehensive Assessment of the Long-Term Effects of Reducing Intake of Energy (CALERIE) trial found that 24 months of moderate CR (15–25%) in non-obese individuals reduced inflammatory markers, cardiometabolic risks, and oxidative stress. Moreover, fasting insulin levels, body temperature, resting energy expenditure and thyroid axis activity were also found decreased, indicating CR’s feasibility and health benefits in humans [101].

Exercise: Regular physical activity is another effective modulator of mitophagy and mitochondrial well-being. Skeletal muscle serves as a valuable model tissue for studying mitochondrial adaptations due to its significant mass and its critical role in overall body metabolism. Mitochondria, known for their remarkable plasticity, can modify their volume, structure, and capacity in response to stimuli such as exercise. This adaptability is crucial for enhancing metabolic health, particularly in individuals dealing with diseases or the effects of aging. Mitochondria maintain the balance of energy production and consumption within cells. Recent studies have identified specific isoforms of the cellular energy sensor 5′ AMP-activated protein kinase (AMPKα1/α2/β2/γ1) that are located on the outer mitochondrial membrane called mitoAMPK, plays a crucial role in regulating mitochondrial quality and initiating exercise-induced mitophagy, particularly in skeletal muscle [102,103]. Beyond skeletal muscle, exercise also has a profound impact on the brain, which consumes about 20% of the body’s oxygen. Due to the limited glycolytic activity of neurons, brain relies heavily on mitochondrial energy production. Mitochondrial energy is essential for maintaining neuronal function, including establishing membrane potentials, managing neurotransmitter synthesis and recycling, and maintaining calcium homeostasis. However, mitochondria are also the primary source of reactive oxygen species (ROS) in the brain, which can lead to oxidative damage and contribute to neurodegenerative diseases like Alzheimer’s disease (AD), Parkinson’s disease (PD), and multiple sclerosis (MS) [104]. As people age, deficits in cellular energy production and an oxidized cellular environment are key factors in declining neuronal health, as seen in the post-mortem brains of AD patients [105]. Exercise has long been recognized for its benefits to brain health and is frequently recommended as both a preventive and therapeutic strategy for patients with dementia. Studies have shown that exercise induces positive changes in brain structure, such as increased angiogenesis, neurogenesis in the hippocampus, and synaptic plasticity, while also reducing age-related brain atrophy [106]. These effects are closely tied to improvements in mitochondrial function. Voluntary exercise has been shown to increase the expression of uncoupling protein (UCP) 2, boost mitochondrial oxygen consumption in the hippocampus, and enhance dendritic spine density and mitochondrial numbers in mice [107]. Moreover, exercise promotes better mitochondrial function through enhanced activity of the electron transport chain (ETC) and increased levels of mitochondrial enzymes in aged brain [108].

Exercise-induced mitochondrial adaptations in the brain may be partly mediated by myokines, signaling molecules released by contracting skeletal muscle [109]. These myokines, including members of the interleukin family, brain-derived neurotrophic factor (BDNF), and vascular endothelial growth factor (VEGF), can be transported to distant tissues, such as the brain, where they may contribute to the benefits of exercise on mitochondrial health [110,111,112,113,114]. Further research into the role of myokines in promoting mitochondrial function across tissues could provide valuable insights into their potential for combating neurodegenerative diseases.

Dietary Polyphenols: Polyphenols, which are natural compounds found in fruits, vegetables, and other plant-based foods, have been shown to enhance mitophagy and protect against mitochondrial dysfunction. Compounds like resveratrol, quercetin, and curcumin have demonstrated the capacity to induce mitophagy, reduce oxidative stress, and improve cognitive function in animal studies [100,115,116]. For instance, quercetin, a natural flavonoid with anti-inflammatory and antioxidant properties, significantly mitigates inflammation in microglia by promoting mitophagy. It reduces the production of inflammatory factors, suppresses microglial proliferation, and inhibits the activation of the NF-κB pathway and NLRP3 inflammasome. By enhancing the clearance of damaged mitochondria through mitophagy, quercetin decreases mitochondrial ROS (mtROS) accumulation, thereby reducing NLRP3 inflammasome activation [120]. These dietary polyphenols are being explored in animal studies for their potential to counteract aging and neurodegenerative diseases; however, their clinical efficacy in humans remains unclear [80]. Bioavailability is a key challenge, as the absorption and metabolism of polyphenols depend on their chemical structure and interaction with gut microbiota. In vivo data are limited, and in vitro studies use concentrations unlikely to be achieved in humans. Synergistic effects with other plant compounds are also not well understood, and the safety of high-dose polyphenol intake needs further investigation. Clinical trials are essential to assess the therapeutic potential of polyphenols in addressing mitochondrial dysfunction and age-related diseases.

6. Challenges and Future Directions

Despite considerable progress in our understanding of mitophagy, several challenges and limitations persist. A significant hurdle is the incomplete understanding of the molecular mechanisms that govern mitophagy. While critical proteins like PINK1 and Parkin have been identified, the interactions among various signaling pathways and their modulation in different tissues under various stress conditions have not been fully delineated [37]. Furthermore, the specific role of mitophagy in various diseases, especially neurodegenerative disorders, remains inadequately understood.

Another issue is the variability in mitophagy activity across different cell types and tissues. Neurons and cardiomyocytes, which have high metabolic demands, depend heavily on mitophagy for cellular homeostasis. However, the regulation of mitophagy in these cells can differ significantly from other cell types [1]. This variability complicates the development of universal therapies that modulate mitophagy. Technological constraints also limit advancements. Current methods for assessing mitophagy are limited. While traditional techniques like electron microscopy can occasionally identify mitochondrial remnants in autophagosomes, they only sample a small portion of cells or tissues, making quantification challenging. Mitochondrial protein turnover rates provide indirect measurements, but these methods cannot assess tissue architecture or differentiate between proteins degraded by mitochondrial proteases and those degraded after lysosomal delivery [114]. Fluorescent-based strategies, particularly dual labeling of mitochondria and autophagic markers like LC3, offer a more robust approach, but are prone to false positives due to the transient nature of mitophagy and LC3’s limitations [121]. A notable advancement in mitophagy monitoring involves the use of pH-sensitive fluorescent proteins, which offer significant advantages due to their ability to resist lysosomal degradation [122,123]. This resistance enables these proteins to provide a more comprehensive and qualitative assessment of mitophagic flux over time, as the fluorescent signal remains stable during the degradation process [124,125]. These proteins exhibit pH-dependent fluorescence, allowing researchers to accurately pinpoint the location of the protein within the cell by distinguishing between different cellular compartments: they fluoresce at a higher pH (around 8.0) when in mitochondria and at a lower pH (around 4.5) when in lysosomes. This ability to differentiate between mitochondria and lysosomes offers a precise tool for tracking the progression of mitophagy. Consequently, pH-sensitive fluorescent proteins, particularly mitochondrial-targeted variants like ‘mt-Keima’, are becoming increasingly popular for measuring mitophagy in vitro, as they provide both temporal and spatial resolution of the process [124,126,127,128].

Next, therapeutically modulating mitophagy carries potential risks and side effects. Indiscriminate enhancement of mitophagy could lead to excessive degradation of mitochondria, resulting in mitochondrial depletion and energy deficits, especially in tissues with high energy demands like the brain and heart [18]. There is also a concern about off-target effects. Pharmacological agents that target mitophagy, such as urolithin A and rapamycin, might impact other cellular processes and pathways, leading to unintended outcomes. For example, rapamycin, an mTOR inhibitor, can impair immune function and increase the risk of infections [38]. Additionally, the long-term modulation of mitophagy could result in cumulative effects that are not yet fully understood. Chronic enhancement or inhibition of mitophagy might induce adaptive changes in cells and tissues, potentially causing harmful effects over time [12]. Therefore, a careful assessment of the long-term safety and efficacy of therapies that modulate mitophagy is crucial before their widespread clinical application.

Recent developments in biotechnology and molecular biology are creating new opportunities for research into mitophagy. One promising method involves using high-throughput screening techniques to identify new mitophagy modulators. These techniques enable the rapid evaluation of thousands of compounds to determine which ones can specifically enhance or inhibit mitophagy [129]. Gene editing technologies, such as CRISPR/Cas9, provide powerful tools for exploring the genetic basis of mitophagy and for developing gene therapies to address defects related to this process. By precisely modifying genes involved in mitophagy, researchers can gain a better understanding of their roles and develop targeted therapies for conditions like Parkinson’s disease and mitochondrial myopathies [98,130]. Several critical areas require further research to deepen our understanding of mitophagy and its therapeutic potential. One significant area is the detailed elucidation of the molecular mechanisms that regulate mitophagy. Comprehensive studies are necessary to identify all the signaling pathways and regulatory proteins involved in mitophagy and to understand how these components interact under various conditions [54]. In addition, the development of reliable biomarkers is crucial for assessing mitophagy levels in clinical settings and monitoring the impact of therapeutic interventions. Identifying such biomarkers will be a key step in translating mitophagy research into practical clinical applications.

7. Conclusions

The interplay between aging, mitophagy, and neuroinflammation forms a vicious cycle where declining mitophagy leads to mitochondrial dysfunction, which in turn exacerbates oxidative stress and inflammation. This process is particularly detrimental in the brain, where chronic neuroinflammation can contribute to the onset and progression of neurodegenerative diseases like Alzheimer’s and Parkinson’s [131]. Harnessing mitophagy for therapeutic advances in aging and neuroinflammation may enhance cognitive function, thereby promoting neuronal health [7,47] as shown in Figure 1.