Microglia are resident immune cells of the CNS (24–27). In physiological states, microglia exhibit a highly dynamic dendritic morphology, performing functions such as immune surveillance, waste clearance, and maintenance of synaptic homeostasis, thereby supporting brain development and regulating learning and memory capabilities (28, 29). Microglia express a vibrant array of receptors, including pattern recognition receptors (Toll-like receptors (TLRs)), etc.), phagocytic receptors (TAM (Tyro3, Axl, Mer) receptors, etc.), immunoregulatory receptors (Triggering Receptor Expressed on Myeloid cells 2 (TREM2), CD33, etc.), and multiple neurotransmitter receptors, which respond sensitively to signals ranging from neuronal activity to tissue injury (30–33). Once pathological stimuli are detected, microglia rapidly transition from a ramified to an amoeboid activated state, shifting from sentinels to executors of phagocytosis and inflammatory responses (34, 35).

In the pathological progression of PD, the immune response within the CNS serves as a core driver of neurodegeneration (36). Microglia play a dual role, and the dynamic equilibrium of their functions determines the direction of neuroinflammation in PD. In 1988, the presence of HLA-DR-positive reactive microglia in postmortem tissues of PD patients first linked neuroinflammation to the pathology of PD (37). On one hand, microglia exhibit neuroprotective functions. Through mechanisms such as Toll-like receptor (TLR) 2, TLR4-NF-κB, and L-cystine-associated endocytosis (LANDO), microglia phagocytose and degrade misfolded and aggregated α-synuclein, leading to the clearance of pathogenic aggregates (38). Research has revealed that microglia actively clear accumulated α-syn and tau pathological proteins within neurons by establishing tunnel nanotubes (TNTs). They share healthy mitochondria with neurons, reversing oxidative stress and functional impairment, which performs a crucial neuroprotective function (39). On the other hand, microglia also exert neurotoxic effects. Widespread microglia proliferation is observed in the SN of PD’s brain (4, 40). Misfolded α-syn excessively activates microglia by binding to specific surface receptors (e.g., TLR) or intracellular receptors (e.g., NLRP3), leading to the release of large amounts of proinflammatory cytokines such as IL-1β and IL-6, thereby exacerbating damage to dopaminergic neurons (41). Microglia phagocytose excessively aggregated α-syn, converting it into PD-like lesions, presenting α-syn-associated antigens, recruiting peripheral immune cells to form immune crosstalk, which promotes the malignant progression of PD (42, 43). Activated microglia secrete cytokines (e.g., IFN-γ) that impair lysosomal function in dopaminergic neurons (44). Since microglia are not a homogeneous population, the molecular mechanisms underlying their distinct states and their functional differences in development, aging, and disease are worthy of further investigation.

The functional heterogeneity of microglia is closely associated with their highly dynamic morphology and plasticity (Figure 1C). During the pathological progression of PD, microglia respond to pathological stimuli through specific activation phenotypes and functional adjustments, with the classic activation phenotype characterized by a dynamic equilibrium between M1 and M2 states, a terminology that has been widely used in early studies (45). However, current research favors state - based classification systems for microglia. The activation of the M1 phenotype leads to the massive secretion of proinflammatory cytokines such as IL-1β and TNF-α, which not only prevents further damage to the central nervous system but may also exert neurotoxic effects on neurons (36, 46). M2 phenotype activation releases anti-inflammatory factors, like IL-10 and TGF-β, along with neurotrophic factors, suppressing excessive inflammatory responses and promoting tissue repair and regeneration, providing neuroprotection for dopaminergic neurons (47). The microglial phenotype exhibits high heterogeneity and dynamism, with activation states forming a continuum rather than discrete polarized states (48). Research has systematically revealed the functional heterogeneity of microglia, defining 12 functionally specialized subpopulations (49, 50). DAM, the microglial neurodegenerative phenotype (MGnD), and proliferative area-associated microglia (PAM), etc., are important microglial subpopulations in PD (51–53). DAM represents one of the most distinct reactive subpopulations, characterized by genes such as ApoE, LPL, and TREM2 that are significantly associated with the progression of neurodegenerative diseases (54, 55).

Behind the functional continuum lies a complex molecular regulatory network. In PD patients, TLRs are activated by pathological α-syn (56). Dectin-1 and TLR4 exhibit synergistic signaling crosstalk that amplifies neuroinflammatory responses. Laminin inhibits Dectin-1, promotes the phenotypic shift of microglia from a pro-inflammatory functional state to an anti-inflammatory and suppresses their neurotoxic effects (57). Neuroinflammation driven by NLRP3 inflammasome activation constitutes a critical component of PD pathological progression, and α-syn induces NLRP3 inflammasome-mediated IL-1β secretion in primary human microglia (58, 59). Reduced nicotinamide adenine dinucleotide phosphate (NADPH) can act as an endogenous inhibitor of P2X7R, alleviating NLRP3 inflammasome activation in microglia to exert neuroprotective effects (60). Different forms of α-syn exhibit distinct properties in activating microglial NLRP3 inflammasomes. Even when polarized toward a proinflammatory phenotype, they may retain protective functions, suggesting that targeting NLRP3 holds potential as a therapeutic strategy for PD (61). At specific stages of PD pathology, microglia exert protective functions. Anti-inflammatory cytokines such as IL-10 can restore microglial homeostasis, enhance phagocytic and clearance activities, and mitigate PD neuropathology (62). The drawback of conventional methods using agonists like capsaicin to stimulate TRPV1 is uncontrolled activation, which can easily lead to excessive Ca²⁺ influx. Instead of protecting microglia, this damages them and triggers harmful inflammatory responses. Research utilizing photothermal nanotechnology enables CS-AT nanoparticles to transiently and controllably activate TRPV1 ion channels on the surface of microglia. This induces moderate Ca²⁺ influx, enhancing the microglia’s autophagy and degradation of α-syn, avoiding the side effects associated with excessive microglial activation (63).

Microglia differentiate into a spectrum of functional states ranging from neurotoxicity to neuroprotection in response to microenvironmental signals. Understanding and targeting the complex neuroinflammatory network mediated by microglia and exacerbated by peripheral immunity, while suppressing immune crosstalk, represents a promising therapeutic strategy for PD.

Microglia perform distinct functions at different developmental and adult stages or within specific brain regions. Multiple independent studies confirm that microglia exhibit spatial heterogeneity, displaying distinct gene expression profiles in a region-specific manner (Figure 1D). Different microglial transcript clusters are enriched in distinct brain areas of mice, potentially predetermining unique immune responses to pathological irritations in different brain regions (64). Different regions of the human brain harbor distinct microglia subpopulations. Microglia subclusters enriched in the subventricular zone and thalamus exhibit heightened activity, while cerebellar microglia possess unique protein expression profiles (65). Additional studies have confirmed that in the striatum of PD patients, microglia exhibit distinct regional differences compared to other brain regions (66). Furthermore, microglia in white matter express higher levels of antigen-presenting molecules (e.g., HLA-DR) than those in gray matter (67). During the PD process, specific microglia subpopulations may exhibit distinct distributions or responses across different brain regions. Areas with severe α-syn pathology deposition (e.g., SN, striatum) show a higher proportion of DAM, whereas relatively unaffected regions predominantly harbor homeostatic microglia (67). The SN exhibits the highest microglia density in the entire brain, presenting a unique microglia microenvironment where microglia maintain a state of heightened immune vigilance (68). Widespread activation of microglia in the substantia nigra leads to sustained release of cytotoxic factors such as ROS, inducing higher levels of α-syn production and thereby accelerating the progression of PD (68, 69). Microglia exhibit region-specific transcriptional profiles throughout the adult lifespan. The loss of specific immune phenotypes in forebrain regions such as the hippocampus during aging provides a potential cellular basis for explaining the spatially specific pathogenesis of PD pathology (34). Transcriptional heterogeneity in human microglia varies across brain regions and during aging (70). The regional diversity of microglia may also influence regional immune responses. Midbrain microglia located in the lesion core exhibit a distinct anti-inflammatory and phagocytic phenotype, whereas striatal microglia display a pro-inflammatory state, suggesting that potential immunomodulatory targets for microglia may vary across brain regions (71).

The spatial heterogeneity of microglia is a key factor shaping region-specific pathology and neuronal susceptibility in PD. Microglia may perform specific functions adapted to the microenvironment of their brain region. Understanding the regional specificity and temporal dynamics of microglial responses is crucial for elucidating selective susceptibility and disease progression in PD.

Microglia begin migrating into the brain from embryonic day 8.5 and continue until the blood-brain barrier forms. Self-renewal becomes the sole source of new microglia in the healthy brain throughout subsequent life (26). Microglia in embryonic, juvenile, and adult stages exhibit distinct transcriptional profiles, clustering into separate cell groups, indicating that microglia dynamically adapt to the brain’s developmental state (64). The functional state of microglia exhibits temporal heterogeneity in regulating α-syn propagation. Microglia in a resting state limit pathological protein diffusion, whereas their excessive activation or significant loss markedly accelerates α-syn propagation (72). Disturbances in the microglia environment during development may disrupt developmental timing, leading to misregulated expression of inflammatory and other gene pathways and impairing neuronal development (73). Early-onset PD-associated α-syn is more susceptible to triggering microglia polarization toward a proinflammatory phenotype (74). Epigenetic factors Hdac1/2 impair microglia maturation when lost during development but enhance protective functions in disease when lost in adulthood.

The heterogeneity of microglia exhibits age-dependent characteristics, with the functional state of microglia in the brain deteriorating with age (Figure 1E) (75). Most adult microglia expressing steady-state genes exhibit high transcriptional similarity, while early postnatal microglia show greater heterogeneity (76). In human microglia, gene expression associated with motility and cell migration decreases with age, consistent with the reduced motility observed in microglia from aged mice (77). The most significant non-genetic risk factor for PD is aging (78, 79). All microglia are affected by aging, and microglia exhibit further transcriptional alterations in PD (80). Age-related inflammatory changes exert a dual impact on the pathogenesis of PD. An ongoing low-grade neuroinflammatory environment creates conditions conducive to pathological aggregation of α-syn. Age-related inflammatory changes exert a dual impact on the pathogenesis of PD. An ongoing low-grade neuroinflammatory environment creates conditions conducive to pathological aggregation of α-syn (81). Concurrently, aging microglia exhibit impaired clearance functions, rendering them incapable of effectively degrading abnormal proteins. These two mechanisms collectively heighten the vulnerability of dopaminergic neurons, contributing significantly to the initiation and progression of PD. A distinct subpopulation of pro-inflammatory and interferon-responsive microglia emerges in the aging brain (82). Stress-induced aging microglia are rich in DAM features (83). Research has found that the proportion of DAM-like microglia expressing SPP1 increases with age, with this subtype being more prominent in the aged brain compared to the young brain (64). Following a stroke in juvenile mice, DAM-like microglia enter an irreversible state and are ultimately cleared from the brain. However, in newborn stroke models, the same DAM-like cells exhibit high plasticity, capable of reverting to a steady-state phenotype during recovery and reintegrating into the microglia network. This demonstrates that microglia possess stronger remodeling and repair capabilities during early development (84).

The specific heterogeneity of the microglia response shapes its unique disease trajectory. Therapeutic strategies targeting microglia in PD require precise intervention at specific microglial states during critical disease stages and within affected brain regions. Enhancing their protective phagocytic function may be beneficial in the early disease phase, whereas potent suppression of their harmful inflammatory responses may be necessary in the middle to late stages.

PD patients exhibit a highly diverse genetic background, which directly influences microglia reactivity and the efficacy of therapeutic strategies. Genome-wide association studies (GWAS) have confirmed that variants at approximately ninety loci increase the risk of PD onset and progression (79). Over twenty distinct rare genetic variants constitute the familial PD genetic risk factors, leading to early-onset or atypical symptoms (85, 87). The discovery of genes associated with the progression and etiology of genetic PD, such as α-syn (88), Parkin (89), PINK1 (90), DJ-1 (91, 92), PARK82 (93), LRRK2, and FCGR2A (87), has advanced PD modeling and targeted therapeutic research. Genetic studies confirm that microglia significantly enrich risk variants for PD (Figure 1F) (94).

Genetic differences in microglial function between individuals are key determinants of PD susceptibility. LRRK2 is one of the most common mutation genes in both familial and sporadic PD (95, 96). Pathogenic mutations in the LRRK2 gene induce microglial-specific lysosomal dysfunction, impairing their clearance function and driving the progression of PD (97). Homozygous mutations in Glucocerebrosidase (GBA) are significant genetic risk factors for PD, with over 350 GBA1 variants accounting for 5–10% of PD cases (98, 99). The R47H mutation in TREM2 is a significant risk factor for PD (100). Genetic variants in TREM2-APOE directly impair the normal differentiation and function of microglia, weakening their phagocytic capacity and increasing susceptibility to PD (100–102). The genetic heterogeneity of microglia is also reflected in common risk genes across neurodegenerative diseases (103). Loss-of-function mutations in PARK2 and PARK6 encoding the E3 ubiquitin ligase Parkin and mitochondrial serine/threonine kinase PINK1 account for the majority of autosomal recessive early-onset PD cases. PARK2/PINK1 deficiency specifically exacerbates NLRP3 inflammasome overactivation and proinflammatory factor release in microglia (104). Major histocompatibility complex class II (MHC II)-associated gene SNPs constitute risk factors for PD (105). The genetic heterogeneity of PD influences the functional phenotype of microglia. Studies have constructed a subtype-centered microglial genomic atlas, isoMiGA, revealing through genetic analysis that PD genetic risk loci are significantly associated with the expression and splicing regulation of specific subtypes (106).

Genetic variations in PD patients carrying different gene mutations drive disease progression by impairing the phagocytic, degradative, and immunoregulatory functions of microglia. Given that the pathways and states of activated microglia in patients may exhibit fundamental differences, universal therapies may only be effective for specific genetic subpopulations. Therefore, therapeutic strategies targeting microglia must incorporate genetic biomarkers for patient stratification to achieve precision medicine for PD.

Gender is one of the risk factors for PD. Microglia respond to environmental challenges in a gender and time-dependent manner starting from the prenatal stage, exhibiting significant developmental and gender-dependent differences (Figure 1G) (19, 107). Gender exerts a significant influence on the gene expression, function, and inflammatory response of microglia, affecting multiple aspects, including their density, morphology, and phagocytic capacity (82). The relative risk of PD in male patients is twice that of women across all age groups (86). Compared with male patients, female patients have a higher risk of motor impairment in the early stages of the disease, slower decline in activities of daily living, and lower risk of cognitive impairment (108). Compared to female PD patients, male PD patients exhibit more severe cortical thinning in the central posterior and central anterior regions, along with smaller volumes in the thalamus, caudate nucleus, putamen, globus pallidus, hippocampus, and brainstem (109). The phagocytic capacity and intensity of inflammatory responses in male and female microglia may exhibit sex-dependent characteristics when responding to pathological stimuli (86). In PD animal models, male individuals exhibit stronger pro-inflammatory responses in microglia, leading to more severe dopaminergic neuron loss (86). Adult female mouse microglia exhibit a unique neuroprotective transcriptional phenotype. This protective phenotype persists when female microglia are transplanted into male brains, where they provide enhanced neuroprotection. Mechanistically, this reveals intrinsic gender heterogeneity in microglia, providing a crucial cellular immunological basis for gender differences in PD prevalence and clinical manifestations (110). Estrogen modulates the reactivity of microglia, inducing a protective phenotype in females, which is one of the key mechanisms underlying the reduced risk of PD onset in females (86). Genetic studies have also revealed no significant autosomal genetic differences across the entire genome between male and female PD patients, suggesting that sex chromosomes and environmental factors may be the primary drivers of PD’s gender heterogeneity (111).

The gender heterogeneity of microglia constitutes a key cellular basis for mediating sex differences in PD susceptibility, pathological progression, and clinical manifestations. Shaped by sex hormones, sex chromosome genes, and early developmental processes, male microglia tend to exhibit stronger pro-inflammatory properties in the context of PD, while female microglia retain greater neuroprotective potential. This suggests that interventions targeting PD should account for patient gender factors.