Focusing on microglial mitochondria-lysosome crosstalk and neuroinflammation underlying depression: from molecular pathways to potential therapeutic interventions

The immune and nervous systems exhibit bidirectional crosstalk via neural and humoral pathways (23, 30). Peripheral inflammatory signals can affect the CNS through the signal transduction or transport mechanisms of blood-brain barrier (BBB)-related structures (5, 31, 32). Many studies have shown that chronic immune-mediated inflammation plays an important role in the development and progression of depression (24, 33, 34). Proposed mechanisms include altered monoamine neurotransmission (35), changes in neurotrophic factor expression, impaired synaptic plasticity, and induction of neuroinflammation associated with depressive-like behaviors (36–38). Studies by Haapakoski et al. (39) and Su et al. (40) reported associations between depression and elevated inflammatory cytokines in cerebrospinal fluid. In the CNS, cytokines are mainly produced by microglia, astrocytes, neurons, and other immune cells (12, 41). Peripheral inflammatory mediators cross the BBB and influence the CNS, activating glial cells and triggering local cytokine release. This process, facilitated through MLCs, thereby forming a positive feedback loop and exacerbating neuroinflammation (12, 31, 42). Cytokines may further promote depressive symptoms by shunting tryptophan metabolism toward the kynurenine pathway and disrupting hypothalamic–pituitary–adrenal (HPA) axis feedback (5, 23, 43–45).

Beyond immune activation, oxidative stress is a key driver of neuroinflammation, a core pathological process implicated in depression (46, 47). Oxidative stress arises when ROS generation exceeds cellular antioxidant capacity, resulting in redox imbalance and downstream molecular injury (48). Many studies have shown that depression is linked to reduced antioxidant activity (49, 50). Oxidative stress damages lipids, proteins, and DNA and can amplify ROS production by activating NADPH oxidase 2 (NOX2) (51, 52). Increased ROS can elevate intracellular Ca²⁺ levels through pathways such as ROS-sensitive ion channels or abnormal calcium handling in organelles, thereby enhancing inflammatory signal transduction (53). Excess ROS may also compromise BBB integrity and facilitate peripheral-to-central immune signaling, thereby sustaining neuroinflammation and synaptic dysfunction (23, 54). In microglia, chronic oxidative stress can impair mitochondrial bioenergetics and disrupt endolysosomal and lysosomal degradation, amplifying a feed-forward ROS–inflammation loop (55, 56). This coupling favors the persistence of neuroinflammation. In chronic social defeat stress models, elevated microglial ROS is associated with neuroinflammatory activation and has been proven to be involved in driving depressive-like behavioral phenotypes (57, 58).

Autophagy is a physiological cellular stress response that removes damaged organelles and misfolded proteins via lysosomal pathways to keep cellular homeostasis (59–61). Clinical and experimental studies indicate that autophagy dysregulation contributes to depression pathogenesis, in part by shaping neuroinflammatory signaling (62, 63). Altered autophagy markers have been reported in patients with depression and in animal models, including within microglia (62, 64). Disruption of the autophagy–lysosome pathway raises the inflammatory set point. When autophagic flux is impaired, damaged mitochondria and pro-inflammatory substrates accumulate, increasing ROS and danger-associated signaling, and promoting the initiation and amplification of inflammatory cascades (65–67). Notably, autophagy plays a crucial role in suppressing NLRP3 inflammasome activation and limiting the release of IL-1 family cytokines (65, 68–70). Recent studies have shown that during depression, microglial autophagic flux is specifically regulated at MLCs, with key proteins like PINK1 and LC3 being persistently dysregulated in depression models (71–73). This dysregulation leads to defective mitophagy, which further exacerbates neuroinflammation. Accordingly, reduced autophagy can permit sustained activation of inflammatory pathways and accumulation of pro-inflammatory cytokines, thereby exacerbating neuroinflammation and promoting depression-relevant pathology (74). Autophagy also intersects with Ca²⁺ signaling. Impaired autophagy can perturb Ca²⁺ homeostasis, heighten microglial inflammatory reactivity, and ultimately affect emotional and cognitive functions (75).

Microglial mitochondrial dysfunction is widely recognized as a key molecular correlate of neuroinflammation in depression (82, 83). In depressed states, microglial mitochondria undergo alterations in number, morphology, and electron transport chain activity, accompanied by mutations and deletions in mitochondrial DNA (84). Collectively, these abnormalities reduce mitochondrial membrane potential and ATP output while promoting excessive ROS generation (85, 86). Excess mitochondrial ROS acts as a pro-inflammatory signal by engaging redox-sensitive pathways, thereby activating microglia and increasing pro-inflammatory cytokine release, which aggravates neuroinflammation (24, 76). Neuroinflammation can then impair synaptic transmission and further disrupt mitochondrial function, creating a feed-forward loop that amplifies oxidative stress and inflammatory signaling and ultimately worsens depressive phenotypes (24, 76). Furthermore, chronic stress can hinder the clearance of dysfunctional mitochondria by mitophagy by inhibiting the stability of PTEN-induced kinase 1 (PINK1) and its accumulation on damaged mitochondria, a process that leads to the continuous accumulation of damaged mitochondria, further amplifying oxidative stress and chronic neuroinflammation (87). These pathological disturbances (oxidative stress, neuroinflammation, and mitochondrial dysfunction) significantly impair neurotransmission (88), thereby exacerbating depression-related symptoms (89, 90).

In addition to mitochondrial impairment, microglial lysosomal dysfunction is a critical contributor to neuroinflammation underlying depression (80). Lysosomes degrade intracellular macromolecules and serve as signaling hubs that couple nutrient sensing to mTORC1 activity. Through mTORC1-dependent control of TFEB nuclear localization, lysosomes also regulate lysosomal biogenesis and downstream homeostatic programs (91–93). Under depressive conditions, lysosomal activity is often markedly impaired. Studies report that key microglial lysosomal proteins—including lysosomal-associated membrane protein 1 (LAMP1), cathepsin D, and TFEB—are downregulated (94–96). These alterations can impair lysosomal acidification and hydrolase activity, thereby weakening the degradation of damaged cellular components (97–99). This, in turn, compromises autophagic flux. Specifically, defects in lysosome–autophagosome fusion can occur alongside reduced acidification and lysosomal protein expression, leading to the accumulation of dysfunctional organelles and proteins. This buildup impairs microglial clearance capacity (including phagocytic processing) and can promote neuroinflammatory signaling (100, 101). Additionally, lysosomal dysfunction prevents the efficient degradation of defective organelles and misfolded proteins. The resulting accumulation of danger-associated molecular patterns (DAMPs) can promote NLRP3 inflammasome assembly and activation, thereby sustaining IL-1 family cytokine signaling (102). Impaired autophagy and reduced lysosomal activity in microglia disrupt neuronal homeostasis and worsen neuroinflammation, exacerbating depressive symptoms.4 Microglial MLCs.

It has been clarified in the previous text that mitochondrial and lysosomal dysfunction in microglia is an important pathological feature in neuroinflammation-associated depression. The functional synergy and signal transmission between the two organelles depend on the specific MLCs formed between them. As a non-fusogenic inter-organelle communication hub, MLCs affect the maintenance of homeostasis and inflammatory responses of microglia. Their functional abnormalities can exacerbate neuroinflammation through multiple mechanisms and promote the occurrence of depression.

MLCs in microglia are increasingly recognized as important platforms for maintaining cellular homeostasis and shaping neuroinflammatory signaling (18, 80, 103, 104). These non-fusogenic membrane contact sites form between the outer mitochondrial membrane and the lysosomal membrane; as with other contact sites, the intermembrane gap is typically ~10–30 nm, whereas MLCs average ~10 nm (103). The formation and dissolution of MLCs are governed by protein-based tethering/untethering machineries composed of proteins on both organelle membranes (105). Table 1 summarizes the functional roles of MLCs-related proteins (Table 1). As a key environmental trigger for depression (106), chronic stress may influence the number and dynamics of MLCs primarily by perturbing mitochondrial and lysosomal function, rather than by directly damaging the contact structures (80, 104, 107, 108). Specifically, chronic stress can be accompanied by changes such as a decrease in mitochondrial membrane potential, restricted ATP production, increased ROS, and a decline in lysosomal acidification and degradation capacity (80, 108). At the molecular level, these stress-induced organelle disturbances can converge on key regulators of MLCs dynamics (103). These stress-associated alterations may shift Rab7 nucleotide cycling (18, 109, 110), reduce lysosomal Ca²⁺ release (e.g., TRPML1), and blunt TFEB-driven lysosome biogenesis (111–113). Collectively, these changes may reduce the number and stability of MLCs, weaken inter-organelle coordination, and contribute to early microglial phenotypes characterized by metabolic imbalance, impaired autophagic flux, and inflammatory priming (103, 104, 107). Beyond stress-related regulation, another unresolved issue concerns whether MLCs exhibit regional heterogeneity across different brain regions. Although direct evidence for brain region-specific differences in microglial MLCs is currently lacking, microglia are known to exhibit marked regional heterogeneity in their developmental trajectories and maturation, transcriptional identity, metabolic state, and inflammatory responsiveness (114–116). Brain regions such as the prefrontal cortex and hippocampus differ substantially in neuronal activity patterns, synaptic remodeling, and vulnerability to stress, all of which may influence microglial metabolic demands and organelle dynamics (117–120). Given that MLCs are highly sensitive to cellular metabolic and inflammatory states, it is plausible that microglial MLCs may exhibit brain region-dependent heterogeneity in composition or function (18, 81, 103). Elucidating such heterogeneity will require future brain region-specific analyses integrating microglia-specific purification techniques with ultrastructural analysis and proteomic profiling ultrastructural and proteomic approaches (18, 121).

Microglial MLCs are crucial sites for Ca²⁺ inter-organelle transport and signal transduction, and their dysfunction can lead to Ca²⁺ signaling dysregulation, thereby exacerbating neuroinflammation and depressive pathology. Under physiological conditions, lysosomes release Ca²⁺ through the TRPML1 channels located on MLCs, and Ca²⁺ is quickly absorbed by mitochondria to promote ATP synthesis and autophagy activation. Furthermore, Ca²⁺ release mediated by TRPML1 promotes the nuclear translocation of TFEB, supporting lysosome formation and the expression of autophagy-related genes, thereby maintaining microglial homeostasis (122–125). However, under chronic stress, excessive ROS production damages the TRPML1 channels, reducing lysosomal Ca²⁺ release (123, 124, 126–128), which not only disrupts mitochondrial Ca²⁺ uptake, decreasing ATP production and impairing microglial metabolism but also inhibits TFEB nuclear translocation and lysosome regeneration (129). This dysregulation of Ca²⁺ signaling not only impairs the maintenance of microglial homeostasis but also disrupts neuronal synaptic plasticity, thereby further promoting neuroinflammation and ultimately exacerbating the development of depressive symptoms (130).

Microglial MLCs are critical regulatory sites for mitochondrial quality control and autophagic pathways. Their dysfunction can exacerbate neuroinflammation-induced depression by blocking autophagic flux (131). Under physiological conditions, stable MLCs regulate lysosomal acidification, enzymatic activity, and autophagosome maturation (132), ensuring effective recognition and clearance of damaged mitochondria to prevent inflammation caused by organelle accumulation. Meanwhile, MLCs maintain autophagic flux stability through the Ca²⁺–TFEB axis and AMPK/mTORC1 pathways (133–135). Chronic stress, which reduces MLCs number and stability, weakens the interaction between mitochondria and lysosomes (19, 124, 136). On the other hand, it blocks the fusion of autophagosomes and lysosomes, slowing autophagic flux and causing the accumulation of damaged organelles, protein aggregates, and lipids, which further exacerbates microglial stress (137–139). A decline in autophagic function further impairs mitochondrial quality control, exacerbates oxidative stress and neuroinflammation, and reduces synaptic plasticity (95), ultimately accelerating the progression of depression.

Microglial MLCs serve as crucial hubs for ROS transmission, signaling amplification, and inflammatory activation. Dysfunction in these sites exacerbates neuroinflammation and depression through ROS-mediated signaling pathways. When MLCs become structurally unstable or reduced in number due to chronic stress, mitochondrial quality control is compromised, and the accumulation of defective mitochondria leads to excessive ROS (140, 141). As inter-organelle contact sites, MLCs amplify ROS signaling and act as crucial platforms for its transmission. On one hand, excessive ROS directly damages the TRPML1 channel (125) and the TFEB–mTORC1 pathway. On the other hand, mitochondrial ROS (mtROS) and mitochondrial DNA (mtDNA) act as danger signals, promoting NLRP3 inflammasome activation, which can accumulate at mitochondrial-associated membrane platforms (142). This cascade of reactions continuously impairs neuronal function and synaptic plasticity, ultimately driving the onset and progression of depression mediated by neuroinflammation.

In this context, a key unresolved issue is whether MLCs dysfunction in microglia is an initiating factor in the pathogenesis of depression or a secondary consequence of neuroinflammation. Current evidence supports a bidirectional and stage-dependent relationship rather than a strictly upstream or downstream causal model (143, 144). In the early stages of the disease or prior to symptom onset, mitochondrial stress, impaired lysosomal degradation capacity, and compromised organelle quality control may precede or occur concomitantly with neuroinflammatory escalation, thereby predisposing microglia toward a pro-inflammatory phenotype (145, 146). During this phase, destabilization of MLCs may promote mitochondrial ROS accumulation, impaired mitophagy, and calcium signaling imbalance, ultimately increasing the sensitivity of microglia to inflammatory stimuli and enhancing the pro-inflammatory signaling pathways (147, 148). Conversely, once neuroinflammation is initiated, persistent inflammatory cytokines, oxidative stress, and neuroendocrine stress responses can further disrupt mitochondrial dynamics and lysosomal function, leading to secondary damage to MLCs integrity and reinforcing the inflammatory cascades (149, 150). It is important to note that current temporally resolved studies in depression models are limited in definitively delineating the chronological sequence between MLCs disruption, microglial activation, and depressive-like symptoms (18, 81, 151). Synthesizing existing findings, it can be hypothesized that MLCs dysfunction in microglia contributes to a feed-forward pathogenic cycle, organelle stress and inflammatory responses mutually reinforce each other, sustaining neuroinflammation and increasing vulnerability to depression-related neuropathology (152, 153). Accordingly, MLCs impairment may exacerbate neuroinflammation through multiple mechanisms, and may promote the persistence and exacerbation of depression-related pathological processes.

Microglial MLCs serve as critical hubs for interorganellar Ca²⁺ crosstalk. MLCs provide nanoscale proximity, spatially coupling lysosomal Ca²⁺ release (such as TRPML1) with mitochondrial uptake mechanisms, thereby promoting Ca²⁺ transfer and shaping metabolic and inflammatory phenotypes (81). Ca²⁺ disorder can be accompanied by a decrease in mitochondrial bioenergetics, and occurs concurrently with impaired lysosomal acidification and hydrolase activity (21, 154). These microglial dysfunctions further induce excessive ROS production and inflammatory activation, thereby exacerbating neuroinflammation and promoting depression-like phenotypes. TRPML1 is a key regulator of Ca²⁺ crosstalk at microglial MLCs. When TRPML1 is activated, it causes Ca²⁺ release from lysosomes and allows Ca²⁺ to enter mitochondria through MLCs. Jia-Wen Mo et al. reported that the lysosomal TFEB–TRPML1 axis in astrocytes modulates depressive-like behaviors, supporting a broader role of glial lysosomal Ca²⁺ signaling in affective regulation (111). In microglia, MCOLN1/TRPML1 deficiency is associated with a pro-inflammatory molecular signature and neuroinflammatory responses, indicating that impaired TRPML1-dependent lysosomal Ca²⁺ signaling can bias microglia toward inflammatory activation (155–157), which contributes to the progression of neuroinflammation-associated depression. Recent studies have shown that in depression models, certain drugs and molecules, such as ML-SA1 and MK6-83, have been tested in preclinical settings and shown to activate TRPML1, increasing Ca²⁺ transfer from lysosomes to mitochondria, potentially restoring the MLCs function and reducing inflammation (158–160). However, TRPML1 agonists such as ML-SA1 are not inherently microglia-specific and can also influence lysosomal Ca²⁺ signaling in neurons and other glial cell types (111, 161–163). In this context, current evidence suggests that microglia-specific modulation of MLCs is more likely to depend on targeted delivery strategies, rather than on the intrinsic pharmacological selectivity of available compounds. Possible approaches include exploiting microglia-enriched uptake pathways, e.g., through CSF1R-, TREM2-, CX3CR1-, or P2RY12-associated mechanisms (164–170), as well as cell- specific gene expression strategies employing microglia-specific promoters such as TMEM119 or P2RY12 for experimental validation and prospective gene therapy applications (171–180). Together, these targeted delivery and cell-specific gene expression strategies outline a conceptual framework for improving therapeutic precision while potentially limiting off-target effects. Nevertheless, rigorous safety assessment and in vivo validation remain essential, given the conserved and indispensable roles of lysosomal Ca²⁺ signaling and organelle contact sites across multiple CNS cell populations (162, 181, 182).

Autophagy is a basic cellular process for maintaining cellular homeostasis and physiological balance (183). In microglia, efficient autophagy/lysosomal clearance supports mitochondrial quality control and limits the accumulation of mitochondrial-derived danger signals, thereby restraining ROS production and pro-inflammatory cytokine release and mitigating neuroinflammation-induced neuronal injury (184). Under chronic stress–related conditions, mitochondrial and lysosomal dysfunction may remodel MLCs dynamics and compromise lysosomal degradative capacity, contributing to impaired autophagic flux and the accumulation of damaged mitochondria and other toxic substrates, which in turn biases microglia toward inflammatory activation and neuroinflammation amplification (104, 185). However, translating these MLCs-related therapies into clinical practice faces several challenges. Li et al. summarized that VPS39, as a HOPS/tethering-related factor, regulates autophagosome–lysosome fusion and may influence mitochondria–lysosome functional coupling, providing a plausible molecular link between MLCs-associated organelle coordination and autophagic flux control (186). Persistent microglial autophagy dysregulation (including flux impairment and/or maladaptive activation depending on context) can further reinforce oxidative stress and pro-inflammatory signaling cascades such as NLRP3 inflammasome pathways, thereby supporting neuroinflammation-driven depressive pathophysiology (187).

Besides regulating Ca²⁺ signaling and autophagy, emerging evidence shows that microglial MLCs dysfunction may influence redox homeostasis and neuroinflammation. Under stress-related conditions, mitochondrial dysfunction and lysosomal impairment in microglia are frequently accompanied by increased oxidative stress and inflammatory signaling, including activation of the TXNIP–NLRP3 inflammasome axis. TXNIP can translocate to mitochondria under cellular stress and has been implicated in promoting NLRP3 inflammasome activation (188), while NOX4-derived ROS may further enhance TXNIP induction, thereby amplifying inflammatory signaling (189–191). Importantly, TSPO is closely associated with microglial inflammatory states, and TSPO ligands have been reported to suppress NLRP3-related inflammation in microglial models, potentially through improving mitochondrial quality control (192, 193). Although direct nanoscale localization of NOX4/TXNIP/NLRP3 specifically at MLCs microdomains remains limited in the depression context, these pathways converge on mitochondria- and lysosome-dependent stress responses—processes that are functionally coupled to MLCs dynamics. Therefore, targeting MLCs-regulated organelle coordination may indirectly attenuate oxidative stress–inflammasome amplification and alleviate neuroinflammation-driven depressive phenotypes (194–196).