bims-micgli Biomed News
on Microglia
Issue of 2026–06–21
29 papers selected by
Matheus Garcia Fragas, Universidade de São Paulo



  1. Sci Rep. 2026 06 15. pii: 18516. [Epub ahead of print]16(1):
      Microglia are the brain's resident immune cells, essential for homeostasis and implicated in common neurodegenerative diseases like Alzheimer's and Parkinson's disease (PD), where their early activation and sustained inflammatory mediator release contribute to neuronal loss. However, their role in rare disorders is unclear. β-propeller protein-associated neurodegeneration (BPAN), caused by WDR45 mutations, shares key features with PD, including iron accumulation and dopaminergic neuron loss, but the impact of microglia and mutant WDR45 in BPAN pathophysiology remains unexplored. To address this, we established the first induced pluripotent stem stell (iPSC)-derived microglia model from BPAN patients. Parallel targeted transcriptomic and secretomic profiling revealed a shift from a homeostatic microglial toward a stress-adapted and transcriptionally reprogrammed state characterized by selective remodeling of immune signaling pathways and dysregulation of autophagy and cellular stress responses. Complementary secretomic analysis identified reduced secretion of lysosomal enzymes alongside increased shedding of immune-associated surface proteins, indicating altered lysosomal trafficking and remodeling of microglial immune signaling. These findings identify a distinct microglial phenotype in BPAN and implicate microglial dysfunction as a potential contributor to disease mechanisms, highlighting new avenues for therapeutic strategies targeting neuroimmune pathways.
    DOI:  https://doi.org/10.1038/s41598-026-55648-w
  2. Acta Neuropathol. 2026 Jun 15. pii: 66. [Epub ahead of print]151(1):
      Microglia are the resident immune cells of the human central nervous system and play key roles in development, homeostasis, and disease. These functions are mediated by a broad repertoire of cell-surface receptors, including G protein-coupled receptors such as the ADP receptor P2Y12 and GPR34, a receptor for lysophosphatidylserine. While GPR34 deficiency has been linked to impaired microglial phagocytosis, its regulation in relation to amyloid-β (Aβ) and tau pathology in Alzheimer's disease (AD) remains unclear. We performed a quantitative analysis of microglial density, morphology, and GPR34 expression in the medial temporal lobe cortex (MTLC) of elderly human body and tissue donors across the AD spectrum. Using fluorescence in situ hybridization and immunolabeling, we analyzed 187,670 microglial cells and correlated microglial parameters with the severity and spatial proximity of Aβ plaques and tau inclusions. In parallel, we analyzed human single-nucleus RNA sequencing data from 236,002 cells to assess GPR34 expression across microglial subtypes, brain regions, and neuropathological stages. Microglial density and overall morphology in the MTLC were largely preserved, independent of local Aβ or hyperphosphorylated tau burdens. Apart from a moderate shortening of microglial processes in the immediate vicinity of Aβ plaques, no consistent pathology-associated morphological changes were detected. GPR34 expression showed pronounced cell-to-cell variability and differed across microglial subtypes and brain regions, but neither expression intensity nor the proportion of GPR34-positive microglia correlated consistently with Braak stage or Thal phase. These findings suggest that GPR34 regulation in human microglia is highly context-dependent and shaped by regional and cellular heterogeneity rather than AD-associated pathology alone.
    Keywords:  Amyloid beta plaques; Glia; Neurodegenerative disease; Neurofibrillary tangles; Neuropathology
    DOI:  https://doi.org/10.1007/s00401-026-03035-0
  3. Alzheimers Res Ther. 2026 Jun 18.
      Aging is the strongest risk factor for Alzheimer's disease (AD), a multifactorial neurodegenerative disorder characterized by amyloid-β (Aβ) accumulation, tau pathology (hyperphosphorylated tau and neurofibrillary tangles [NFTs]), and associated neuroinflammatory processes. Age-related cellular and molecular stressors, including mitochondrial dysfunction, genomic instability, and chronic low-grade inflammation, progressively increase vulnerability to neurodegeneration. In parallel, sex is increasingly recognized as a biological variable that shapes AD risk, clinical course, and neuropathological burden. Women account for roughly two-thirds of AD cases, a disparity not fully explained by longevity. Multiple factors likely contribute, including hormonal transitions across the lifespan (particularly menopausal estrogen decline), sex chromosome-linked immune regulation, sex-dependent interactions between genetic risk factors (e.g., APOE4 and TREM2) and brain aging, and differences in vascular risk, cognitive reserve, and sociocultural exposures that influence disease expression and detection. Microglia, the brain's resident immune cells, are sexually dimorphic, and respond to Aβ and tau pathology, modulating inflammatory signaling, synaptic remodeling, and neurovascular dysfunction implicated in AD. Emerging human and experimental evidence indicate that microglial activation states, immunometabolism, and functional responses differ between males and females and may contribute to sex-specific AD trajectories. Here, we synthesize current evidence supporting microglial sexual dimorphism across aging and AD, highlight possible candidates (hormonal signaling, immuno-aging, disease-associated microglial states, and immunometabolic remodeling), and discuss key knowledge gaps toward sex-informed precision approaches for prevention and treatment.
    DOI:  https://doi.org/10.1186/s13195-026-02099-0
  4. J Neuroinflammation. 2026 Jun 13.
      Myeloid cells, including infiltrating macrophages and resident microglia, are critical regulators of retinal homeostasis and respond rapidly to photoreceptor stress. Dysregulated myeloid responses, however, can exacerbate retinal degeneration. Triggering receptor expressed on myeloid cells 2 (TREM2) modulates phagocytosis, metabolism, and inflammatory signaling, yet its role in retinal degeneration remains incompletely understood. Here, we investigated TREM2 function in the retinal degeneration 10 (rd10) mouse model of inherited retinal degeneration, characterized by progressive photoreceptor loss and robust myeloid cell activation. TREM2 expression was upregulated in degenerating retinas, and global TREM2-deficiency in rd10 mice exhibited accelerated photoreceptor cell death, reduced outer nuclear layer thickness, disrupted retinal pigment epithelium integrity, and altered microglial spatial dynamics. Single-cell transcriptomics revealed that TREM2-positive microglia express APOE-associated and interferon-primed programs. Global TREM2 deficiency was associated with increased inflammasome-related signaling in retinal myeloid cells, including elevated cleaved caspase-1, cleaved gasdermin D, and mature interleukin-1β, linking amplified immune priming to pyroptotic signaling. Genetic or pharmacological inhibition of gasdermin D significantly mitigated photoreceptor loss in global TREM2-deficient rd10 retinas, demonstrating a functional contribution of inflammasome-associated responses to disease exacerbation. Together, these findings support a protective role for TREM2-associated immune regulation in the degenerating retina and identify downstream inflammasome pathways as potential therapeutic targets in retinal degenerative diseases.
    Keywords:  Gasdermin D; Inflammasome Activation; Myeloid Cells; Myeloid Pyroptosis; Photoreceptors; Retinal Degeneration; TREM2
    DOI:  https://doi.org/10.1186/s12974-026-03903-2
  5. Front Immunol. 2026 ;17 1783786
      Alzheimer's disease (AD) remains a major therapeutic challenge despite the availability of amyloid-targeting disease-modifying therapies for selected patients with early symptomatic disease. These therapies have shown that disease modification is possible, but their benefits are modest and constrained by amyloid confirmation, safety monitoring, infusion delivery, access, and eligibility requirements. Neuroinflammation is increasingly viewed as a context-dependent modifying process that interacts with β-amyloid (Aβ), tau pathology, metabolic stress, and vascular dysfunction, rather than as an unequivocally established primary initiating driver. This review provides a selective, glia-centered synthesis of AD neuroinflammation focused on microglia, astrocytes, and their reciprocal crosstalk. We examine how microglial and astrocytic responses can support Aβ handling, plaque containment, tissue homeostasis, and synaptic protection, while chronic or poorly resolved glial signaling can amplify cytokine and complement responses, metabolic and oxidative stress, and neuronal vulnerability. Representative signaling nodes, including NF-κB, AMPK/mTOR, and PI3K/Akt, are discussed as organizing mechanisms linking inflammatory transcription, proteostatic stress, glial metabolism, and neuronal injury, rather than as equivalently validated therapeutic targets. Therapeutic implications are interpreted across three evidence tiers: approved anti-amyloid antibodies with indirect inflammatory relevance, clinically tested anti-inflammatory or immunomodulatory strategies that have not established disease-modifying efficacy, and experimental precision approaches aimed at glial-state modulation. Overall, the translational challenge is not broad suppression of neuroinflammation, but stage-specific identification and modulation of maladaptive glial states while preserving protective microglial and astrocytic functions.
    Keywords:  Alzheimer’s disease; astrocytes; evidence hierarchy; glial crosstalk; microglia; neuroinflammation; therapeutic implications
    DOI:  https://doi.org/10.3389/fimmu.2026.1783786
  6. J Clin Invest. 2026 06 15. pii: e207022. [Epub ahead of print]136(12):
      Traumatic brain injury (TBI) disproportionately kills and disables older adults, yet the biology driving this vulnerability remains unresolved. In this issue of the JCI, Lu et al. combined single-cell transcriptomics, metabolomics, and chromatin profiling in mice, validated in human TBI tissue, to define an age-dependent microglial dichotomy. They report that an NLRP3+/IL-1β-linked state dominates the aged brain, while a Lysozyme+/Lyz2+ state predominates in the young. Microglia-targeted perturbation of NLRP3 and ELF1 each shifted the balance and improved survival in mouse models of TBI, and the repurposed drug Imeglimin improved outcomes in these models, confirming that this pathway is druggable. By connecting NLRP3 inflammasome dominance, ELF1-driven transcription, and glycolytic reprogramming to the loss of a protective Lyz2+ response, this work converts age from a clinical risk factor to a set of druggable microglial targets.
    DOI:  https://doi.org/10.1172/JCI207022
  7. Elife. 2026 Jun 17. pii: RP107276. [Epub ahead of print]14
      In presynaptic nerve terminals, the endocytic apparatus rapidly restores synaptic vesicles after neurotransmitter release. Many endocytic proteins localize to the periactive zone, a loosely defined area adjacent to active zones. A prevailing model posits that recruitment of these endocytic proteins to the periactive zone is activity-dependent. We show that periactive zone targeting of endocytic proteins is largely independent of active zone machinery and synaptic activity. At mouse hippocampal synapses and Drosophila neuromuscular junctions, pharmacological or genetic silencing resulted in unchanged or increased levels of endocytic proteins including Dynamin, Amphiphysin, Nervous Wreck, Endophilin A, Dap160/Intersectin, PIPK1γ, and AP-180. Similarly, disruption of active zone assembly via genetic ablation of active zone scaffolds at each synapse did not impair the localization of endocytic proteins. Overall, our work indicates that endocytic proteins are constitutively deployed to the periactive zone and supports the existence of independent assembly pathways for active zones and periactive zones.
    Keywords:  D. melanogaster; cell biology; endocytosis; exocytosis; exo–endocytic coupling; mouse; neuroscience; synaptic terminals
    DOI:  https://doi.org/10.7554/eLife.107276
  8. Neuroreport. 2026 Jun 23.
       BACKGROUND: Microglial repopulation after depletion via colony-stimulating factor 1 receptor (CSF1R) inhibition holds therapeutic potential for neurological disorders, but the cellular sources remain debated. We investigated whether repopulation arises solely from surviving microglia or also from nonmicroglial progenitors.
    METHODS: Using Cx3cr1CreER:Ai14 (tdTomato) reporter mice, we labeled microglia before PLX3397-induced depletion and assessed repopulation. Next, in Cx3cr1CreER+/-:Csf1rfl/fl mice, we combined tamoxifen-induced genetic CSF1R deletion with PLX3397 to ablate microglia completely and evaluated recovery.
    RESULTS: We found that repopulated microglia were predominantly tdTomato+, indicating derivation from surviving Cx3cr1+ microglia. Combined tamoxifen and PLX3397 achieved near-complete ablation, yet microglia repopulated and were re-depletable by PLX3397, confirming potential nonmicroglial origins.
    CONCLUSION: Microglial repopulation primarily involves proliferation of surviving microglia but can recruit nonmicroglial progenitors when depletion is exhaustive. These insights resolve prior inconsistencies and guide therapeutic strategies for microglial replacement treatment.
    Keywords:  CX3C motif chemokine receptor 1; PLX3397; colony-stimulating factor 1 receptor; microglia; repopulation
    DOI:  https://doi.org/10.1097/WNR.0000000000002286
  9. J Neuroinflammation. 2026 Jun 13. pii: 199. [Epub ahead of print]23(1):
      Extracellular adenosine triphosphate (ATP) and diphosphate (ADP) act as key signalling molecules in the central nervous system (CNS) and regulate neuroinflammatory responses through purinergic receptors. Although astrocytes and neurons undergo profound changes in signalling and metabolism during inflammation, the contribution of specific purinergic pathways to inflammation-induced neurodegeneration remains unclear. Here we show that the ADP/ATP-activated Gq-coupled receptor P2Y1 drives astrocyte-mediated neurotoxicity in experimental autoimmune encephalomyelitis (EAE), a model of multiple sclerosis (MS). Using plasma membrane-targeted luciferase reporter mice, we demonstrate that extracellular ATP levels are increased during acute EAE. This was accompanied by elevated astrocytic P2ry1 expression, which is also observed in inflammatory MS lesions. In vivo, pharmacological inhibition or astrocyte-specific deletion of P2Y1 reduced disease severity, astrocytosis, and neuronal loss, whereas neuron-specific deletion exerted only modest effects. Mechanistically, astrocytic P2Y1 signalling promoted cytokine-induced ERK activation, inflammatory gene expression, and metabolic reprogramming in vitro. In contrast to supernatants from stimulated P2Y1-deficient astrocyte culture, supernatants derived from stimulated P2Y1-proficient astrocytes reduced neuronal viability, demonstrating neurotoxic effects mediated by astrocyte-derived factors. In contrast, neuronal P2Y1 signalling primarily contributed to oxidative stress and mitochondrial dysfunction. Together, these findings identify astrocytic P2Y1 as a key regulator of neuroinflammatory damage and a potential therapeutic target.
    Keywords:  Adenine nucleotides; EAE; Neuroinflammation; Neuron-glial crosstalk; Purine receptors
    DOI:  https://doi.org/10.1186/s12974-026-03904-1
  10. J Neuroinflammation. 2026 Jun 17.
      Lipid droplet (LD) accumulation in microglia results in a dysfunctional and proinflammatory state after ischemic stroke and worsens neurological outcomes; yet how this accumulation is regulated remains unclear. Interferon regulatory factor 7 (IRF7) is an immune regulatory factor whose role in lipid metabolism and autophagy has been increasingly studied in peripheral tissues. However, the role of IRF7 in microglial lipophagy (a selective autophagic process that targets LDs) and poststroke functional recovery remains unexplored. In this study, using a mouse photothrombotic ischemia (PTI) model, we observed that microglia in the peri-infarct region displayed persistent lipophagy impairment and LD accumulation for up to 21 days. Reanalysis of the single-cell RNA sequencing (scRNA-seq) dataset revealed that an Irf7high microglial MG1 subcluster (disease-associated microglia) was significantly associated with autophagy and lipid metabolism poststroke. Furthermore, microglial Irf7 conditional knockout (Irf7 cKO) mice exhibited a significant rescue of lipophagy impairment and an alleviation of the ensuing LD accumulation in microglia, accompanied by enhanced synaptic plasticity and motor functional recovery during the subacute phase poststroke. Consistently, in the 15-month-old distal middle cerebral artery occlusion (dMCAO) model, Irf7 cKO mice also displayed similar improvements. Similar results were also observed in vitro. Mechanistically, Gnai2 was identified as a positively regulated transcriptional target of IRF7. In BV2 cells and primary microglia, Gnai2 knockdown mitigated lipopolysaccharide (LPS)-induced lipophagy impairment, thereby reducing LD accumulation. This treatment also increased the level of phosphatidylcholine (PC), a key lipid for stabilizing small LDs as well as promoting autophagosome formation and autophagic flux. Consistently, microglial Irf7 deletion or knockdown attenuated stroke- or LPS-induced PC reduction both in vivo and in vitro. Furthermore, exogenous supplementation with CDP-choline, an intermediate in PC synthesis, alleviated LD accumulation and lipophagy impairment, thereby improving motor function. Additionally, delayed administration of an inhibitor of stimulator of interferon genes (STING, an upstream target of IRF7) replicated the beneficial effects observed in Irf7 cKO mice, and its effects were not further enhanced by microglial Irf7 deletion. Taken together, these novel findings reveal that persistent impairment of microglial lipophagy is a key contributor to poststroke LD accumulation, and that IRF7 is involved in this process through direct transcriptional activation of Gnai2, which reduces the PC levels. Suppressing IRF7 with a STING inhibitor is a potential strategy for modulating microglial lipid metabolism and promoting functional recovery following stroke.
    Keywords:  IRF7; Lipid droplet; Lipophagy impairment; Microglia; STING; Stroke
    DOI:  https://doi.org/10.1186/s12974-026-03902-3
  11. J Clin Invest. 2026 Jun 16. pii: e190035. [Epub ahead of print]
      Dominant mutations in Progranulin (GRN) gene cause frontotemporal lobar degeneration (FTLD-GRN), whereas homozygous GRN mutations lead to neuronal ceroid lipofuscinosis, a childhood neurodegenerative disorder. While recent transcriptomic studies reveal profound glial and neuronal pathology in FTLD-GRN at the disease end stage, the mechanism that disrupts glia-neuron homeostasis remains unclear. Using induced pluripotent stem cell (iPSC)-derived cortical organoids, we showed that GRN-/- and GRNR493X mutations lead to precocious astrogliosis that promotes neuronal stress and synaptic loss. Single-cell transcriptomics and histopathology analyses revealed a robust activation in TGFb signaling pathway in GRN-/- and GRNR493X/R493X astrocytes, which was accompanied by features of immune activation, loss of synaptic support, and abundant pTDP-43+ fibrils in astroglial cytoplasm, a feature characteristic of FTLD-GRN. Intriguingly, blocking TGFb signaling mitigated astroglial activation and pTDP-43 proteinopathy in GRN-/- organoids. Together, these results provide new insights into the cell-autonomous role of astroglial activation in neurodegeneration caused by Progranulin deficiency.
    Keywords:  Aging; Dementia; Neurodegeneration; Neuroscience; iPS cells
    DOI:  https://doi.org/10.1172/JCI190035
  12. J Neuroinflammation. 2026 Jun 15.
      Stroke induces a transient period of heightened plasticity during which functional recovery is most pronounced. Experimental models have identified repair-associated processes in both the ipsilesional and contralesional cortex, indicating that stroke recovery involves regions both remote and near the lesion. However, most transcriptional studies have focused on the infarct core and peri-lesional cortex (PLC), leaving it unclear whether comparable molecular responses occur in the contralesional cortex (CLC), a region that undergoes substantial remodeling in the absence of direct tissue injury, necrosis, or widespread cellular infiltration. In addition, potential sex-dependent differences in these responses remain incompletely defined, despite known influences of biological sex on post-stroke inflammation and vascular remodeling. To address these gaps, we performed bulk RNA-sequencing of the PLC and CLC at 7 days after photothrombotic stroke, a subacute time point associated with the initiation of repair, in male and female mice. Despite distinct positions relative to the lesion, both regions exhibited robust upregulation of inflammatory signaling, including cytokine-, astrocyte-, and myeloid-lineage-associated pathways. The CLC did not demonstrate a distinct region-specific transcriptional profile; instead, shared signatures between PLC and CLC included genes strongly associated with reactive microglial phenotypes. This shared neuroinflammatory response was largely conserved across sexes. Consistent with these findings, male and female mice exhibited comparable corticospinal tract axonal sprouting originating from the CLC at 6 weeks post-stroke. Together, these findings support a shared neuroinflammatory transcriptional response as a prominent early feature of cortical regions associated with post-stroke plasticity.
    Keywords:  Axonal sprouting; Contralesional cortex; Microglia; Perilesional cortex; Post-stroke plasticity; Sex-differences in stroke; Stroke; Stroke recovery
    DOI:  https://doi.org/10.1186/s12974-026-03885-1
  13. Sci Immunol. 2026 Jun 19. 11(120): eaee9584
      Macrophages in the meninges contribute to immune defense of the central nervous system (CNS), yet their site-specific origin and function remain poorly understood. Using an intravenous model of streptococcal meningoencephalitis in mice, we found bacteria predominantly in the leptomeninges and dura. Nevertheless, monocyte infiltration into the leptomeninges and parenchyma strongly correlated with disease severity. In the dura, infection triggered activation and loss of resident macrophages, followed by rapid engraftment of inflammatory monocytes that transiently replenished the macrophage niche. Under homeostasis, dural monocytes were supplied CCR2 independently from adjacent skull bone marrow. During infection, this local source was insufficient, necessitating recruitment from peripheral bone marrow. Infection further reshaped monocyte ontogeny, increasing monocyte-dendritic cell progenitor-derived monocytes, which expressed higher major histocompatibility complex class II levels and persisted in the brain alongside CD4+ T cells during resolution. Together, these findings reveal dynamic, compartment-specific remodeling of monocyte recruitment and differentiation across CNS borders during bacterial meningoencephalitis.
    DOI:  https://doi.org/10.1126/sciimmunol.aee9584
  14. J Biomed Sci. 2026 Jun 15. pii: 62. [Epub ahead of print]33(1):
       BACKGROUND: Tauopathies are neurodegenerative diseases all characterized by tau lesions in the brain. Nevertheless, a clinical and pathophysiological heterogeneity is present among them. This includes the dominant tau isoform found within aggregates (3R and/or 4R tau) along with different brain regions being affected. For some tauopathies, especially in Alzheimer's disease, a specific spatio-temporal staging of tau lesions is present. This staging has been the basis for the prion-like propagation hypothesis, which describes a cell-to-cell transfer of pathological tau species resulting in new aggregates formation in recipient neurons. Human extracellular vesicles isolated from the brain-derived fluid (BD-EVs) of Alzheimer's disease patients contain seeds that contribute to this tau pathology spreading. However, the nature of these tau species responsible for this nucleation activity remains unknown. Additionally, heterogeneity in seeding activity of BD-EVs of Alzheimer's disease, progressive supranuclear palsy and Pick's disease patients is known.
    METHODS: Here, EVs were isolated from human frozen tissue (Alzheimer's disease, Progressive Supranuclear Palsy, Pick disease and non-demented controls). We used a tau immunoprecipitation followed by high-resolution mass spectrometry to define their proteomic profile and test their seeding capacity in vitro.
    RESULTS: We show that the tau profile present within BD-EVs is different among tauopathies. Interestingly, multiple tau peptides located in the microtubule binding region were specifically enriched in Alzheimer's disease extracellular vesicles. Of these, mainly the PHF6 (VQIVYK) containing proteins mediate tau seeding activity.
    CONCLUSIONS: PHF6 is a driver for the higher EVs-mediated tau propagation in AD patients, revealing an interesting therapeutic target to prevent tau pathology spreading.
    Keywords:  Alzheimer’s disease; Extracellular Vesicles; PHF6 peptide; Seeding; Tau proteoforms; Tauopathies; Ubiquitination
    DOI:  https://doi.org/10.1186/s12929-026-01250-1
  15. PLoS Biol. 2026 Jun 18. 24(6): e3003865
      Zebrafish, in contrast to mammals, regenerate neurons after spinal cord injury, but little is known about the control mechanisms of this process. Here we use scRNA-seq and in vivo experiments to show that sema4ab, mainly expressed by lesion-reactive microglia, attenuates regenerative neurogenesis by changing the complex lesion environment. After spinal injury, disruption of sema4ab doubles the number of newly generated progenitor cells and neurons but attenuates axon regrowth and recovery of swimming function. Disruption of the plxnb1a/b receptors, selectively expressed by neural progenitor cells, increases regenerative neurogenesis. In addition, disruption of sema4ab alters activation state and cytokine expression of microglia, such that fibroblasts increase expression of the cytokine tgfb3, which strongly promotes regenerative neurogenesis. Hence, we propose that sema4ab expression in microglia attenuates regenerative neurogenesis in multiple ways, likely directly through plxnb1a/b receptors and indirectly, by controlling the inflammatory milieu and tgfb3 levels. Targeting Sema4A-dependent signaling in non-regenerating vertebrates may be a future strategy to improve regenerative outcomes.
    DOI:  https://doi.org/10.1371/journal.pbio.3003865
  16. J Neuroinflammation. 2026 Jun 17.
      Multiple sclerosis lesions are dominated by clonally expanded CD8+ T cells within an IFNγ-rich inflammatory microenvironment and neurons may be targets of these effector cells. However, the peptide antigens that CD8+ T cells recognize on neurons are largely undefined. Neurons constitutively express low levels of HLA class I, and whether inflamed human neurons are competent to present a class I ligandome, what that ligandome contains, and whether presentation has functional consequences for autoreactive CD8+ T cells remain open questions. Here we combine human iPSC-derived neural aggregates (HNAs), HLA class I immunoprecipitation coupled to LC-MS/MS immunopeptidomics, and microfluidic co-culture assays to map IFNγ-induced HLA class I presentation by neurons and to test antigen-specific cytotoxicity. IFNγ stimulation induced HLA class I upregulation in HNAs and enabled recovery of a canonical 8-12-mer class I ligandome enriched for 9-mers. Neuron-restricted expression of a synapsin-driven polyepitope cassette yielded presentation of defined exogenous 9-mer peptides on donor HLA class I molecules and, in the presence of IFNγ, elicited activation of autologous antigen-specific CD8+ T cells and antigen-dependent neurite injury. Across four donors, comparative immunopeptidomics identified IFNγ-associated neural peptide repertoires that were distinct from those of matched fibroblasts and enriched for predicted HLA-B binding peptides. β2-microglobulin deletion ablated peptide recovery, and neuron-restricted reconstitution enabled identification of candidate neuron-derived peptides, including recurrent neurofilament light (NEFL)-derived peptides detected across donors. Together, these findings establish a human iPSC-derived platform for studying inflammatory neuronal HLA class I antigen presentation and antigen-dependent CD8+ T cell engagement.
    Keywords:  Antigen presentation; CD8+ T cells; HLA class I; Immunopeptidomics; Induced pluripotent stem cells; Interferon-γ (IFNγ); Neural organoid; Neuroinflammation
    DOI:  https://doi.org/10.1186/s12974-026-03915-y
  17. iScience. 2026 Jun 19. 29(6): 116291
      Inflammation results in increased gastrointestinal (GI) motility and diarrhea, but the mechanism remains unclear. Contrary to expectations, we found that neuronal responses to cytokine inhibited GI motility, as Nav1.8-Cre-mediated neuronal deletion of Jak1, a cytokine signaling intermediate, markedly increased GI motility at homeostasis. These cytokine-responsive neurons may reside in the enteric nervous system (ENS) based on the pattern of gene-deletion and GI motility induced by Nav1.8- and Trpv1-Cre. Cytokine receptors upstream of Jak1 that inhibit GI motility at homeostasis include IFNγ and IL-10, but not IL-4 or IFNα. While deficiency in cytokine inhibition of GI motility did not appear to affect the health of the mice at homeostasis, worse outcomes were observed after experimental Dextran sulfate sodium (DSS) colitis. Thus, we speculate that IFNγ and IL-10, cytokines associated with type 1 immune responses, may participate in a protective neuro-immune negative feedback loop to limit excessive GI motility during intestinal inflammation.
    Keywords:  Cellular neuroscience; Components of the immune system; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2026.116291
  18. Brain Commun. 2026 ;8(3): fcag202
      Pharmacological options to promote long-term rehabilitation after stroke remain limited. We investigated how short-term microglia depletion during the subacute phase after ischaemic stroke affects functional recovery and neuronal network dynamics. Using a C57BL/6 wild-type stroke model, fine motor performance was assessed with a skilled reaching task while bilateral cortical activity was recorded longitudinally through epidural electrocorticography. Microglia were depleted between days 3 and 7 post-stroke using PLX5622, a colony-stimulating factor 1 receptor inhibitor. Microglia depletion resulted in near-complete restoration of fine motor function by day 7 and was accompanied by significant functional connectivity changes in bilateral sensorimotor networks, including increased beta-band connectivity in the ipsilesional motor cortex, which correlated with contralateral fine motor improvement. Following repopulation, microglial cells showed altered morphology and gene expression profiles. These findings reveal that transient microglial modulation during the subacute phase after stroke promotes cortical network reorganization and motor recovery.
    Keywords:  CSF-1R inhibitor; ischaemic stroke; microglial repopulation; motor rehabilitation; sensorimotor networks
    DOI:  https://doi.org/10.1093/braincomms/fcag202
  19. Immunology. 2026 Jun 19.
      Immune function across development, tissue repair, aging, and disease depends not only on signaling pathways but also on epigenetic architectures that determine whether coordinated transcriptional programs can be accessed and resolved. Increasing evidence indicates that epigenetic gene networks regulate the accessibility and reversibility of semi-stable immune states, shaping plastic, homeostatic, reparative, and degenerative configurations. We propose the concept of epigenetic transition windows, defined as temporally and contextually restricted intervals during which epigenetic constraints are relaxed, permitting coordinated and reversible transitions between immune states. During development, these windows are broad and support immune tolerance and adaptive plasticity. In adulthood they become spatially and temporally restricted, preserving stability while enabling conditional adaptation. With aging, they progressively narrow, contributing to chronic inflammation, impaired repair, and increased vulnerability to neurodegeneration. Conversely, pathological persistence of regulatory permissiveness may underlie immune evasion and sustained plasticity in cancer. We outline operational genomic readouts for quantifying transition windows, including chromatin accessibility variance, enhancer switching dynamics, reversibility metrics, and cross-cell coordination indices, and derive experimentally testable predictions that distinguish this model from pathway-centric or damage-centric explanations. By reframing immune dysfunction as a failure of regulated state transition rather than excessive signaling alone, this framework integrates inflammaging, trained immunity, immune resolution failure, and tumor immune escape within a unified regulatory architecture and provides a systems-level perspective on immune adaptability across the lifespan.
    Keywords:  chromatin accessibility; epigenetic regulation; immune plasticity; immune resolution; immune state transitions; immunosenescence; inflammaging; trained immunity; tumor immune evasion
    DOI:  https://doi.org/10.1111/imm.70161
  20. Alzheimers Dement. 2026 Jun;22(6): e71566
    Alzheimer's Disease Neuroimaging Initiative
      The Alzheimer's Disease Neuroimaging Initiative (ADNI) recently celebrated its 20th anniversary, reflecting two decades of major contributions to Alzheimer's research through open data sharing and longitudinal multimodal assessments. This review synthesizes 122 high-impact studies using ADNI data or biospecimens from 2023 to mid-2025 to clarify mechanisms of Alzheimer's disease (AD) progression. Studies describe impairment of glymphatic clearance and the impact of cerebral small vessel disease, trajectories of amyloid beta and tau deposition, inflammation, metabolic disturbances, synaptic dysfunction, and neurodegeneration, leading to cognitive impairment and neuropsychiatric symptoms. Multifactorial contributions from genetic and epigenetic influences, co-pathologies and comorbidities, and mechanisms of resilience modulate disease progression. Finally, heterogeneity of clinical presentation and disease course is described in the context of multiple contributing factors, highlighting the complexity of AD. By integrating imaging, fluid biomarkers, genetics, and clinical measures, ADNI provides a comprehensive research dataset for unraveling mechanisms underlying AD progression.
    Keywords:  Alzheimer's Disease Neuroimaging Initiative (ADNI); Alzheimer's disease; Lewy body disease; amyloid; amyloid beta; bioenergetic disturbances; cerebrovascular disease; disease progression; genetic variants; glymphatic system; gut microbiome; heterogeneity; multimodal data integration; neuroimaging and biomarkers; neuroinflammation; neuropsychiatric symptoms; synaptic dysfunction; tau; vascular risk
    DOI:  https://doi.org/10.1002/alz.71566
  21. Cell. 2026 Jun 18. pii: S0092-8674(26)00641-0. [Epub ahead of print]
      Elucidating the relationships among in vivo activity, brain-wide projection, and gene expression is critical for understanding neuronal functions, but characterizing these modalities for the same neuron remains technically challenging. Here, we developed a trimodal platform combining in vivo Ca2+ imaging, morphological reconstruction of single neurons in cleared whole brains, and post hoc imaging-based in situ transcriptomic profiling in thick brain sections. We applied this platform to the mouse primary visual cortex (VISp) and obtained trimodal profiles for 141 intratelencephalic (IT) and pyramidal tract (PT) neurons. We found that regional axonal arborization, soma location, transcriptomic signatures, and subcellular RNA localization emerged as informative predictors for distinguishing neurons preferentially responsive to different visual stimuli. Importantly, morphological and transcriptomic features are complementary and, when integrated, can better predict neuronal function. Thus, this trimodal platform enables a comprehensive understanding of the relationships among gene expression, morphological diversity, and functional properties of single neurons.
    Keywords:  2cEASI-FISH; brain clearing; imaging-based multimodal characterization; in vivo neuronal activity; multi-plane two-photon microscope; single-neuron profiling; spatial transcriptomics; subcellular RNA localization; whole-brain neuronal morphology
    DOI:  https://doi.org/10.1016/j.cell.2026.05.041
  22. J Transl Med. 2026 Jun 16.
       OBJECTIVE: White matter damage in Multiple Sclerosis (MS) exhibits significant heterogeneity. The cellular and molecular underpinnings of this heterogeneity are not fully understood. This study investigated cell-specific changes and spatial heterogeneity in MS white matter by integrating single-cell and spatial transcriptomics (ST) to guide potential clinical interventions.
    METHODS: Single-nucleus RNA sequencing (snRNA-seq) identified key cell types, regulons, and cellular functional heterogeneity using Gene Regulatory Network (GRN) analysis, cell communication, subpopulation classification, functional enrichment, and pseudotime analysis. ST explored functional heterogeneity and cell type distribution in MS white matter niches via correlation, enrichment analysis, and deconvolution.
    RESULTS: snRNA-seq analysis identified module M3, showing transcription factor dysregulation in MS white matter compared to controls. These genes were predominantly expressed in microglia and enriched in inflammation related signaling pathways; IKAROS Family Zinc Finger 1 (IKZF1) was identified as a candidate transcriptional regulator connected to these changes. Microglia exhibited heterogeneity, existing in dynamic regulation from homeostatic to pro-inflammatory phenotypes, the latter showing Disease-associated Microglia (DAM) characteristics. Spatial transcriptomic analysis revealed strong heterogeneity within MS white matter with distinct niche functions. The Lesion Rim (LR), a transition zone, correlated strongly with microglia and was highly enriched with DAM characteristics. The LR was identified as an inflammatory hotspot enriched for DAM and altered IKZF1 regulon activity, supporting snRNA-seq findings.
    CONCLUSION: IKZF1 regulon inactivation in microglia coincides with altered white matter lesions in MS and dysregulated inflammatory pathways. Microglial heterogeneity in MS, including DAM phenotypes, extends beyond traditional polarization models. MS white matter displays significant spatial heterogeneity. Hindered remyelination in the LR may reflect inflammation from sustained microglial activation.
    Keywords:  IKZF1; Microglia; Multiple sclerosis; Single-nucleus RNA sequencing; Spatial transcriptomics; White matter damages
    DOI:  https://doi.org/10.1186/s12967-026-08360-2
  23. Acta Neuropathol. 2026 Jun 15. pii: 67. [Epub ahead of print]151(1):
      TREM2 plays multiple functional roles in microglia and variants are associated with increased risks of Alzheimer's disease (AD). Genetic polymorphisms reducing expression of the functionally related protein CD33 are protective. Here we have contrasted cellular pathology in human post-mortem brain with and without AD to test mechanisms associated with the differential genetic risks conferred by R47H and R62H TREM2 variants (TREM2var) with and without heterozygosity for the protective rs3865444 CD33 polymorphism. Epistasis between CD33 and TREM2 was demonstrated by relative normalisation of differences in β-amyloid load in TREM2var carriers of the protective CD33 allele. These functional differences were mirrored by differential microglial transcriptomic responses to β-amyloid. Controlling for CD33 genotype, microglial transcriptional responses to increasing β-amyloid were lower for TREM2var, particularly for R47H compared to CV, and there was a reduction in expression of neuroplasticity pathways in TREM2var. R62H microglial signatures were distinguished from those of R47H by upregulation of genes associated with phagocytosis and from CV by differences in inflammatory gene expression including those involved in NF-kappaB signalling. Differential gene expression with increasing β-amyloid also suggested upregulation of β-amyloid production and binding pathways in excitatory neurons in TREM2var heterozygotes. There was lower enrichment for pathways positively adaptive to pathology and expressed in inhibitory neurons from CV samples for both TREM2var. Exploratory bulk tissue proteomics support these observations with evidence for adaptive plasticity in response to β-amyloid pathology in CV tissue not found for the TREM2var, which showed evidence of increased β-amyloid formation and neuroplasticity changes. Together, these results highlight differences in molecular pathology between CV and TREM2var and between the TREM2var risk variants. They highlight mechanisms of AD risk mediated by secondary effects on astroglial and neuronal functions. Demonstration of strong epistasis between TREM2 and CD33 with AD supports the therapeutic potential of modulators of CD33 inhibition or expression.
    Keywords:   CD33 ; TREM2 ; Alzheimer’s disease; Microglia; Proteomics; Transcriptomics
    DOI:  https://doi.org/10.1007/s00401-026-03036-z
  24. Mol Biol Rep. 2026 Jun 18. pii: 941. [Epub ahead of print]53(1):
      Neuroinflammation has been identified as a major component to the pathogenesis and progression of many neurodegenerative illnesses, going beyond its traditional role as a protective immune response within central nervous system (CNS). There is growing evidence that persistent activation of peripheral immune pathways, microglia and astrocytes causes progressive neurodegeneration, synaptic loss and progressive neurodegeneration. This review examines the mechanisms of microglia- driven neuroinflammatory signaling and its involvement in major neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and Huntington's disease. Key neuroinflammatory mechanisms covered in depth including microglial activation, astrocyte reactivity, peripheral immune cell infiltration, cytokine dysregulation, and blood brain barrier (BBB) disruption. This review also emphasizes the role of neuroinflammation in acute neurological symptoms and mental and cognitive impairments. Glial activation markers, inflammatory cytokines, BBB proteins and kynurenine pathway metabolites are emerging as promising biomarkers for disease diagnosis and monitoring. Additionally, the potential of new mathematical and systems level computational models to describe intricate neuroimmune interactions and forecast the course of disease and treatment results is investigated. Current and emerging therapies targeting neuroinflammation include anti-inflammatory and immunomodulatory drugs, lifestyle interventions, stem cell approaches, gene-editing technologies and nanoparticle-based drug delivery systems. Despite significant progress, translating preclinical findings into effective clinical therapies remains challenging. Future developments in integrative neuroimmune modeling, biomarker-guided therapies and precision medicine may make it possible to create individualized treatments plans targeted at reducing neuroinflammation and enhancing the course of neurodegenerative illnesses.
    Keywords:  Alzheimer's disease; Amyotrophic lateral sclerosis; Astrocytes; Microglia; Multiple sclerosis; Parkinson's disease
    DOI:  https://doi.org/10.1007/s11033-026-12128-8
  25. PLoS Biol. 2026 Jun;24(6): e3003821
      Adiponectin is the most abundant hormone in the circulation. Plasma adiponectin decreases in obesity but increases in leanness, including during caloric restriction (CR) in animals and humans. In obesity, adiponectin deficiency promotes cardiometabolic dysfunction. In contrast, the roles of adiponectin in CR, when it is at its highest, are largely unknown. To address this, we studied global adiponectin knockout (KO) in male and female mice fed either ad libitum (AL) or a 30% CR diet from 9-13 weeks of age. We show that adiponectin KO did not alter CR effects on body mass, body composition, or energy expenditure. However, KO unexpectedly decreased blood glucose levels during CR, both with fasting and following an oral glucose challenge. This is opposite to the effects of adiponectin deficiency during AL feeding or obesity and occurred without changes in insulin concentrations or sensitivity. Moreover, adiponectin KO augmented CR-induced increases in plasma fatty acids in both sexes and, in males only, impaired systemic triglyceride clearance on both AL and CR diets. These effects on lipid metabolism were associated with sex- and diet-specific KO effects on white adipose tissue, including altered adipocyte size and expression of key regulators of adipocyte lipid metabolism. Indirect calorimetry further revealed that adiponectin KO alters the shifts between carbohydrate and lipid utilization that occur during transitions between fed and fasted states. To determine potential molecular mechanisms, we investigated effects of adiponectin KO on the liver, a major adiponectin target that plays key roles entraining metabolism to nutritional state. Hepatic transcriptomics revealed that, in both sexes, adiponectin KO upregulates sterol and fatty acid synthesis genes under AL while increasing amino acid catabolic genes during CR. However, the latter occurred without altering plasma or hepatic amino acid concentrations. Together, our findings suggest that adiponectin exerts sexually dimorphic effects on glucose, lipid, and amino acid metabolism during CR, in whole or in part through effects on the liver. Thus, the roles adiponectin in CR differ markedly from its widely reported functions in obesity, insulin resistance, and other pathological states.
    DOI:  https://doi.org/10.1371/journal.pbio.3003821
  26. Neuropharmacology. 2026 Jun 13. pii: S0028-3908(26)00250-9. [Epub ahead of print]298 111076
      Neuroimmune signaling is increasingly implicated in alcohol use disorder (AUD). Microglia, the brain's resident immune cells, signal in part through the adaptor protein myeloid differentiation primary response 88 (MyD88), a key mediator of innate immune responses. Here, we investigated whether microglial-specific MyD88 signaling regulates voluntary alcohol consumption in adulthood, as whole-body loss of MyD88 was previously shown to increase drinking. We further determined if alcohol altered parvalbumin-expressing interneurons (PVIs) and microglia within the pre-frontal cortex, based on our previously described role for MyD88 signaling on perineuronal net (PNN) deposition on PVIs in several brain regions, and the well characterized role of inhibitory signaling in alcohol use disorders. Loss of microglial-MyD88 had minimal effects on voluntary alcohol intake and anxiety-like behaviors. Alcohol exposure did not modify observed MyD88-dependent changes in PVIs/PNNs, despite altering microglial morphology in the male prefrontal cortex independent of genotype. The addition of an early life endotoxin challenge was sufficient to induce an increase in adult alcohol consumption in both MyD88-deficient and control males. However, injection of saline alone also induced an increase in adult drinking in MyD88-deficient males. These findings suggest that microglial-MyD88 signaling does not strongly regulate alcohol intake under baseline conditions in a one-bottle, voluntary binge-drinking paradigm, however there may be a role for microglial-MyD88 signaling in modulating the impact of developmental environmental contexts, such as stress, in later-life male drinking behavior. This work highlights the importance of developmental context, such as stress or inflammatory history, in understanding underlying microglia signaling mechanisms in conferring AUD risk.
    Keywords:  Anxiety-like behavior; DID; Microglia; MyD88; Neuroimmunology; Parvalbumin interneuron; Perineuronal nets
    DOI:  https://doi.org/10.1016/j.neuropharm.2026.111076
  27. Cell Rep. 2026 Jun 19. pii: S2211-1247(26)00639-X. [Epub ahead of print]45(7): 117561
      Microglia are central nervous system (CNS)-resident macrophages, with key roles in immune surveillance, phagocytosis, and synaptic pruning. Yolk sac-derived microglia show minimal turnover from hematopoietic stem/progenitor cells (HSPCs) under steady-state conditions in mice. However, clinical benefits observed in patients receiving HSPC gene therapies for CNS disorders suggest functional integration of HSPC-derived cells. To investigate microglia replacement and the impact of clonal hematopoiesis (CH) on microglia, we analyzed microglia in rhesus macaques receiving barcoded or CRISPR-edited (TET2-mutant) HSPC transplants. We found that <2% microglia were derived from HSPCs many years following transplant, with no evidence of enhanced replacement in CH. The rare HSPC-derived tissue-resident cells exhibited a macrophage-like gene expression profile. Our results demonstrate limited long-term microglia replacement from adult HSPCs, even with CH, contrasting prior human studies. This work provides insights into microglia ontogeny and informs strategies for CNS-targeted HSPC gene therapies and interpretation of CH-related neuroprotection.
    Keywords:  CP: neuroscience; CP: stem cell research; clonal hematopoiesis; hematopoietic stem cell transplantation; microglia; rhesus macaques
    DOI:  https://doi.org/10.1016/j.celrep.2026.117561
  28. Cell Rep. 2026 Jun 17. pii: S2211-1247(26)00577-2. [Epub ahead of print]45(6): 117499
    Alzheimer Gut Microbiome Project Consortium
      The etiology of Alzheimer's disease (AD) remains unclear but is likely driven by gene-environment interactions. We present a multi-organ untargeted metabolomics atlas (n = 2,271) paired with metagenomics data (n = 666) from two AD transgenic mouse models (3xTg and 5xFAD) under colonized and germ-free conditions. Systems-level analyses revealed clusters of dysregulated molecules across tissues, including carnitines, bile acids, B vitamins, neurotransmitters, and N-acyl lipids. Metabolic shifts were associated with the depletion of Akkermansia muciniphila and enrichment of Mucispirillum schaedleri in the 3xTg model. We identify previously unexplored carnitines linked to microbial metabolism of phenylalanine. Using tissueMASST-a mass spectrometry search tool we developed to translate animal-model findings into a human clinical context-we trace phenylacetyl-carnitine in human plasma and serum samples (n = 1,470) from independent cohorts, revealing associations with aging, cognitive impairment, and diminished memory performance. This public resource and associated tools will aid future research in AD etiology.
    Keywords:  3xTg; 5xFAD; Alzheimer's disease; CP: metabolism; CP: neuroscience; metagenomics; tissueMASST; untargeted metabolomics
    DOI:  https://doi.org/10.1016/j.celrep.2026.117499
  29. Nat Cell Biol. 2026 Jun 19.
      Lysosomes are integral organelles that communicate cellular status to an entire tissue through mechanisms that are poorly defined. Here we developed an unbiased platform, integrating human plasma metabolomes and single-lysosome metabolomics, and show the byproducts of proteolysis are an unexpected class of signalling molecules. We show that dimethylarginine is a lysosomal-derived metabolite and a predictor of patient morbidity. Genetic depletion of a lysosomal exporter, cystinosin, accumulated dimethylarginine in lysosomes. Leveraging a lysosomal storage disease with cystinosin mutations, we show that the rapid plasticity of dimethylarginine compartmentalization ensures cell and tissue homeostasis. Strikingly, lysosomal entrapment of dimethylarginine in patients and disease models corresponds with lipid accumulation, lipid droplets and lipotoxicity. Exogenously restoring asymmetric dimethylarginine buffers oxidative stress, decreasing lipid peroxidation and cell death. These data show that dimethylarginine engages an interorganellar process-with peroxisomes, lysosomes and lipid droplets-that confers a crucial adaptive response mechanism.
    DOI:  https://doi.org/10.1038/s41556-026-01970-4