Biology subjects

Hao, Y.

Publications and source records attributed to Hao, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Brain endothelial PRMT5-ANGPTL4 axis regulates cerebellar inhibitory synaptogenesis and motor coordination

Brain vasculature is essential for central nervous system function, but its specific roles in synaptic development and motor function regulation are poorly understood. In this study, we identify a cerebrovascular signaling axis wherein endothelial PRMT5 critically regulates inhibitory synaptogenesis and motor coordination. Cerebrovascular-specific deletion of Prmt5 gene leads to excessive inhibitory synaptic input onto Purkinje cells and progressive motor deficits in mice. Mechanistically, PRMT5 deficiency epigenetically upregulates the expression of the secreted factor ANGPTL4 through reduced symmetric dimethylation of H3R8 and H4R3, along with increased H3K9 acetylation at the Angptl4 promoter, thereby driving excessive inhibitory synaptogenesis onto Purkinje cells. Importantly, Angptl4 deletion in brain endothelium normalizes inhibitory synaptic input onto Purkinje cells and restores motor coordination in PRMT5-deficient mice. Together, these findings define the endothelial PRMT5-ANGPTL4 axis as a key regulator of cerebellar inhibitory circuitry and motor function, highlighting cerebrovascular mechanisms as potential therapeutic targets for motor coordination disorders. Teaser Cerebrovascular PRMT5 prevents excessive inhibitory synaptogenesis via epigenetic repression of Angptl4.

neuroscience↗

bioRxiv2025

Disruption of Cell-Type-Specific Molecular Programs of Medium Spiny Neurons in Autism

Autism spectrum disorders (ASD) are highly heritable neurodevelopmental conditions with major contributions from rare genetic variants. Most studies have focused on cortical mechanisms; even growing evidence implicates subcortical circuits in ASD etiology. To systematically map developmental and molecular alterations beyond the cortex, we profiled lineage relationships across five brain regions in an ASD mouse model. Most prominent changes emerged in the striatum, a hub for learning and motor control. Furthermore, we performed single-nucleus multiomic profiling of human putamen from ASD and neurotypical donors revealed cell-type-specific transcriptomic and regulatory alterations. Differential expression converged on synaptic and energy metabolic dysfunctions in D1 striosome medium spiny neurons (MSNs), coupled with astrocytic remodeling of synaptic support. Gene regulatory network analysis identified EGR3 and EGR1 as key transcriptional regulators of ASD-associated programs of D1 MSNs. Together, these results establish the striatum as a central node of ASD convergence and provide a multiomic resource for dissecting its subcortical mechanisms.

neuroscience↗

bioRxiv2025

Persistent Classical and Atypical Memory B Cells Underlie Heterogeneous Vaccine Responses in Ocrelizumab-Treated Multiple Sclerosis

Background and ObjectivesPatients with multiple sclerosis (pwMS) treated with ocrelizumab (OCR), a B-cell-depleting therapy, exhibit heterogeneous humoral responses to SARS-CoV-2 mRNA vaccination. The mechanisms underlying this variability remain incompletely understood. We performed a longitudinal analysis of B-cell subset dynamics and antigen-specific T cell responses in OCR-treated pwMS and healthy controls to determine how immune cell composition, timing of OCR infusion, and lymphocyte dynamics influence humoral response outcomes. MethodsBased on post-vaccination anti-Spike IgG titers measured by multiplex bead immunoassay, pwMS were categorized as super-responders (SR), responders (R), or non-responders (NR). A 35-marker spectral flow cytometry panel was used to characterize T- and B-cell subsets longitudinally, at baseline and following stimulation with a SARS-CoV-2 peptide pool. ResultsCD4+ and CD8+ T cell populations were preserved across OCR-treated pwMS, and SARS-CoV-2-specific T cells remained detectable for more than 6 months after vaccination. In contrast, residual B-cell subset composition distinguished responders from non-responders. DN2-like B cells (CD19+CD27-IgD-T-bet+CD11c+CXCR5-) persisted despite repeated OCR infusions and were enriched in SR compared with NR. Repletion of mature naive B cells in peripheral blood correlated with time since last OCR infusion and with stronger humoral immune responses. ConclusionsB-cell subsets that resist OCR-mediated depletion may contribute to vaccine responsiveness in OCR-treated pwMS. Altered repletion kinetics of naive B cell subsets in non-responders suggest that specific B-cell populations may serve as predictive biomarkers of vaccine-induced humoral immunity, despite preserved T-cell responses.

immunology↗

bioRxiv2025

Neuronal compartmentalization results in impoverished axonal mitochondria

Mitochondria differ depending on their location within a neuron. Morphological heterogeneity between somatic, dendritic, and axonal mitochondria is well established. Emerging evidence suggests that further specialization is needed to meet the unique demands of different neuronal compartments. However, the molecular and functional diversity of mitochondria within a neuron remains poorly understood. Here, we utilized proteomics in MitoTag mice to profile somatodendritic and axonal mitochondria across four distinct neuron types, thereby generating a compendium of intracellular mitochondrial diversity. Combining proteomics, functional, and immunofluorescence analyses, we demonstrated that axonal mitochondria are not defined by the presence of unique proteins, but rather by the selective loss or preservation of specific pathways compared to their somatodendritic counterparts. This results in "impoverished" axonal mitochondria, which are characterized by diminished mtDNA expression and impaired oxidative phosphorylation yet retain other pathways, such as fatty acid metabolism. Bioinformatic analyses of multiomic data identified local translation as one mechanism underlying compartment-specific diversity. Together, these findings provide a comprehensive in vivo framework for understanding mitochondrial specialization across neuronal compartments.

neuroscience↗

bioRxiv2025

Engineering Treg-mediated immune tolerance via foxp3a overexpression to evade allograft transplantation barriers in zebrafish

In mammals, regulatory T cells (Treg) cells have been utilized to enhance tolerance in organ transplantation. Although transplanting germline stem cells (GSCs) or gonadal primordia into immunodeficient zebrafish have shown to be an important technique which can bypass the juvenile phase and expedite gamete generation, it remains challenging to raise the immunodeficient fish. Here, we achieved in vivo induction of Tregs by overexpressing the key transcription factor Foxp3a, generating transgenic zebrafish with robust immune tolerance. This was characterized by a significant downregulation of T cell development and homing-related genes, accompanied by a marked upregulation of immunosuppressive factors. Using these immune-tolerant fish as hosts for subcutaneous gonadal primordium transplantation (SGPT) and intraperitoneal GSC transplantation (IGCT), we markedly accelerated germ cell maturation and efficiently established stable transgenic lines. Transcriptomic analyses demonstrated that transgenic hosts demonstrated a phenotypic profile characterized by delayed immune activation, attenuated responsiveness, and enhanced graft survival. Thus, we present a Treg-induction-based approach in fish that resolves the intrinsic conflict between high embryonic transgenesis efficiency and early lethality, while significantly improving overall transgenesis success rates. Moreover, it offers a practical alternative to immunodeficient recipients, avoiding the challenges of complex husbandry and compromised fertility.

genetics↗

bioRxiv2025

Phosphorylation enables progressive microtubule-associated protein proteolysis and functionalisation during neural development

Neurological diseases are frequently characterised by dysregulation of the microtubule cytoskeleton, which is critical for neuronal integrity and functioning. However, the precise mechanisms by which microtubule dynamics are regulated during the development of the nervous system remain poorly understood. Here, we use global phosphoproteomic screening to identify cytoskeletal substrates of Ser-Arg Protein Kinase (SRPK), which is implicated in several neurodevelopmental and neurodegenerative conditions. We show that SRPK directly phosphorylates Microtubule Associated Protein (MAP)1S at multiple sites in a C-terminal region involved in proteolytic maturation and microtubule binding. SRPK-dependent MAP1S phosphorylation modulates the affinity of the MAP1S microtubule binding domain for microtubules and MAP1S proteolytic processing by the Calpain (CAPN)10 protease. Finally, we show that MAP1S proteolytic processing occurs progressively during neurodevelopment via a specific CAPN10 expression switch, corresponding with MAP1S acquisition of microtubule binding activity. Our results demonstrate a role for SRPK in coordinating processing and functionalisation of a key microtubule regulatory protein during neurodevelopment and provide insight into mechanisms by which the microtubule cytoskeleton may be dysregulated in neurological diseases.

biochemistry↗

bioRxiv2025

Emergence of Genetic Sex Determination in an Environmentally Sex-Determined Animal

The evolution of genetic sex determination (GSD) from environmental sex determination (ESD) remains a fundamental issue in evolutionary biology. However, the mechanisms driving such a transition, particularly in its earliest stages, are largely unknown. Here, we report on a genetic variant in the ESD species, Daphnia pulex, in which structural variations and selection on chromosome have suppressed recombination. This suppression has facilitated the accumulation of antagonistic features of the two chromosome- haplotypes, resulting in heterozygosity and differentiation of the sex-determining gene Dfh on two haplotypes. Consequently, this process has driven the emergence of a mixed-mating system, in which sex determination is jointly regulated by genetic and environmental factors. Additionally, we detected ongoing divergence in chromosomal structure between the two haplotypes at the population level. These findings suggest that processes analogous to early sex-chromosome evolution are occurring in this ESD species, offering novel insights into the molecular mechanisms underlying the emergence of GSD.

evolutionary biology↗

bioRxiv2025

APOE genotypes differentially remodel the astrocytic lipiddroplet-associated proteome to shape lipid droplet dynamics

The lipids and proteins that comprise lipid droplets regulate several cellular functions including lipid storage, stress responses, and inflammation. Glial lipid droplets have been implicated in the pathogenesis and progression of Alzheimers disease (AD), yet the mechanisms linking genetic risk to lipid droplet biology remain unclear. Here we examined how APOE, the strongest genetic modulator of late-onset AD, impacts lipid droplet composition and dynamics. We defined the lipid droplet-associated proteome and lipidome in human induced pluripotent stem cell-derived astrocytes harboring the three common APOE genotypes: APOE2 (protective), APOE3 (neutral), and APOE4 (risk). Each APOE variant displays distinct lipid droplet-associated proteins and lipids. These molecular changes yield differences in lipophagy; lipid droplets in APOE2 astrocytes undergo autophagic turnover, whereas those in APOE4 astrocytes are resistant to degradation. These findings suggest that impaired lipid droplet clearance, rather than accumulation, distinguishes APOE4-associated AD risk, and may present a new metabolic node for modulating risk.

cell biology↗

bioRxiv2025

Pharmacological Depletion of Retinal Mononuclear Phagocytes is Neuroprotective in a Mouse Model of Mitochondrial Optic Neuropathy

PurposeThe Vglut2-Cre;ndufs4loxP/loxP mouse strain with retinal ganglion cell (RGC)-specific mitochondrial complex I dysfunction develops severe RGC degeneration by postnatal day 90 (P90), with accompanying retinal mononuclear phagocyte (MNP) accumulation. We have reported that continuous exposure to hypoxia partially rescues RGC death in these mice, with minimal effect on MNP abundance. We hypothesized that pharmacological depletion of MNPs with the colony-stimulating factor-1 receptor inhibitor pexidartinib would enhance RGC neuroprotection by hypoxia. MethodsIba1+ retinal MNP depletion was assessed in C57Bl/6J mice fed control or pexidartinib-infused chow beginning at P25. Subsequently, Vglut2-Cre;ndufs4loxP/loxP mice and control littermates were raised under normoxia or hypoxia and fed control or pexidartinib chow from P25 to P90. The neuroprotective effect of pexidartinib and hypoxia alone and in combination was assessed by quantifying RGC soma and axon survival in retinal flat mounts and optic nerve cross sections. ResultsPexidartinib completely depleted retinal MNPs within one week of treatment. Untreated Vglut2-Cre;ndufs4loxP/loxP mice exhibited the expected [~]50% reduction of RGC soma and axon survival at P90 (p<0.0001 for both). Hypoxia or pexidartinib monotherapy each reduced RGC degeneration by more than one-half, while their combination resulted in complete RGC neuroprotection (p<0.001 for all three treatments). Normal myelination patterns were restored in mice receiving dual therapy. ConclusionsPexidartinib effectively depletes retinal MNPs and is neuroprotective in the setting of severe RGC mitochondrial dysfunction. This therapeutic effect is additive to that of hypoxia. Combating retinal neuro-inflammation may therefore be a useful adjunct therapy in mitochondrial optic neuropathies like Leber hereditary optic neuropathy.

neuroscience↗

bioRxiv2025

Targeting FSP1 triggers ferroptosis in lung cancer

Pre-clinical and clinical studies have demonstrated how dietary antioxidants or mutations activating antioxidant metabolism promote cancer, highlighting a central role oxidative stress in tumorigenesis. However, it is unclear if oxidative stress ultimately increases to a point of cell death. Emerging evidence indicates that cancer cells are susceptible to ferroptosis, a form of cell death triggered by uncontrolled lipid peroxidation1-3. Despite broad enthusiasm about harnessing ferroptosis as a novel anti-cancer strategy, whether ferroptosis is a barrier to tumorigenesis and if it can be leveraged therapeutically remains unknown4,5. Using genetically-engineered mouse models (GEMMs) of lung adenocarcinoma (LUAD), we performed tumor specific loss-of-function studies of the two key ferroptosis suppressors, glutathione peroxidase 4 (Gpx4)6,7 and ferroptosis suppressor protein 1 (Fsp1)8,9, and observed increased lipid peroxidation and robust suppression of tumorigenesis, suggesting that lung tumors are highly sensitive to ferroptosis. Furthermore, across multiple pre-clinical models, we found that FSP1 was required for ferroptosis protection in vivo, but not in vitro, underscoring a heightened need to buffer lipid peroxidation under physiological conditions. Lipidomic analyses revealed that Fsp1-knockout (Fsp1KO) tumors had an accumulation of lipid peroxides, and inhibition of ferroptosis with genetic, dietary, or pharmacological approaches effectively restored the growth of Fsp1KO tumors in vivo. Unlike GPX4, FSP1 expression was prognostic for disease progression and poorer survival in LUAD patients, highlighting its potential as a viable therapeutic target. To this end, we demonstrated that pharmacologic inhibition of FSP1 had significant therapeutic benefit in pre-clinical lung cancer models. Our studies highlight the importance of ferroptosis suppression in vivo and pave the way for FSP1 inhibition as a therapeutic strategy in lung cancer patients.

cancer biology↗

bioRxiv2025

Structural assembly of maize CRY-GL2 photosignaling complex provides insights into its regulatory role in cuticular wax biosynthesis

Cryptochromes (CRYs) are blue-light photoreceptors in plants that regulate diverse physiological processes through oligomerization-dependent interactions with downstream effectors. While numerous light-inducible CRY-binding proteins have been identified, the structural basis for photoactivated CRY-effector assembly remains poorly understood. Here we report the crystal structure of a constitutively active maize CRY1c photolyase homology region (ZmCRY1c-PHRW368A) in complex with ZmGL2, a BAHD ptotein directing very-long-chain fatty acid (VLCFA) elongation for cuticular wax biosynthesis. Structural analysis reveals that light-activated ZmCRY1c forms a homotetrameric scaffold generating four symmetric binding sites at subunit interfaces. Each ZmCRY1c protomer engages one ZmGL2 molecule through conformational reorganization of its 16-17 loop and 17 helix, establishing a 4:4 hetero-octameric photosignaling complex validated by mutational profiling and optical design. Remarkably, structural alignment with the ZmCER6-ZmGL2 complex reveals substantial overlap (78%) in ZmGL2 binding interfaces. Biochemical quantification demonstrates that ZmCRY1c suppresses ZmCER6-GL2 enzyme activity in a dose dependent manner, unveiling a light-dependent regulatory switch controlling VLCFA elongation efficiency, though in vivo physiological investigation is awaited. Collectively, our work not only establishes the atomic model of light-activated plant CRY-effector assembly, but also uncovers a previously unrecognized spatial competition between photoreceptor and metabolic enzyme complexes that might function as a photoregulatory paradigm in cuticular wax biosynthesis.

plant biology↗

bioRxiv2025

ZmCRY1s interact with GL2 in a blue light dependent manner to regulate epidermal wax composition in Zea mays

Cryptochromes (CRYs) are photolyase-like blue-light / ultraviolet-A (UV-A) receptors that regulate diverse aspects of plant growth. Maize (Zea mays), a major crop often grown under high UV-B radiation, possesses four copies of CRY. However, it remains unclear whether the multiple copies of CRY in maize have evolved to improve UV tolerance or to acquire new functions. In this study, CRISPR-Cas9-engineered Zmcry mutants were used to investigate the functions of four cryptochromes (ZmCRYs) in maize. The findings revealed that ZmCRYs play a redundant role in mediating blue light signaling and in inhibiting the elongation of the mesocotyl. The results also demonstrated that ZmCRYs mediated blue light-enhanced UV-B stress tolerance in Zea mays by upregulating the expression of genes involved in UV-B stress tolerance-related metabolites such as phenylpropanoid, flavonoid, and fatty acid biosynthesis. Furthermore, blue light was found to influence both the accumulation and composition of epidermal waxes, suggesting that blue light enhances epidermal wax accumulation for UV-B stress tolerance. Additionally, it was discovered that ZmCRY1 directly interacted with GLOSSY2 (GL2) in a blue light dependent manner to mediate blue light promoted C32 aldehyde accumulation, shedding new light on the enigma of aldehyde-forming. These results highlight the critical roles of ZmCRY1s in mediating blue light regulated epidermal wax biosynthesis and UV-B tolerance in Zea mays.

plant biology↗

bioRxiv2025

A trade-off mechanism underpins the evolution of a young two-gene sex-determining system in plants

Sexual systems in animals and plants are remarkably diverse, with dioecy having evolved independently in numerous lineages. In plants, dioecy often evolved more recently than in the best-studied animal systems, making plants especially important for understanding how separate sexes evolved independently from functionally hermaphrodite ancestors. Despite long-standing theories of developmental trade-offs in sex allocation, the underlying genetic mechanisms remain elusive. Here, we show that the XY sex determination system in the dioecious plant species Eurycorymbus cavaleriei in Sapindaceae involves two Y-linked mutations that act jointly within the developmental male-female trade-off: YUN{Delta}, a truncated allele that lowers the dosage of the D-class MADS-box gene YUN, and SUNMAO, a novel sRNA locus that silences the X-linked SUN allele. In females, SUN stabilizes the HD-ZIP transcription factor KUN, which is a known sex determinant in another dioecious plant, thereby promoting femaleness by increasing YUN expression; loss of SUN expression, together with the effect of YUN{Delta}, shifts development toward males. Two interlocking regulatory loops in this "SKY" module (SUN-KUN-YUN) fine-tunes YUN dosage. This dioecious system in E. cavaleriei likely evolved by sequential mutations in genes acting in the predicted male-female trade-off system, with their close linkage reflecting a translocation, and later recombination-suppressing inversions.

plant biology↗

bioRxiv2025

MITScan: Score-Based Genome-Wide Association Analysis of the Microbiome and Host Transcriptome

Microbiome research explores how microbial communities interact with the human body to influence health and well-being, offering insights for advancing personalized medicine and targeted treatments. Microbiome profiles can be measured, for example, by 16S rRNA sequencing, where sequencing reads are clustered into genus-or species-level operational taxonomic units (OTUs), yielding count-based abundance data. In addition, these data are often characterized by sparsity with extra zeros. Emerging evidence suggests that imbalances in microbial composition, potentially regulated by host gene expression, have been associated with various diseases. Investigating the associations between the microbiome and host transcriptome can help uncover the mechanisms underlying human health and disease. Current existing approaches for evaluating their associations largely rely on Pearson or Spearman correlations, ignoring the fact that microbiome data are sparse count data, leading to potentially biased results. To overcome this issue, we present MITScan, a genome-wide MI crobiome-host T ranscriptome Score-based association an alysis, employing zero-inflated negative binomial models to accommodate extra zeros commonly observed in microbiome data. To address the large number of paired association tests arising from two high-dimensional omics datasets, we utilize score tests and matrix calculations for computational efficiency. We further apply an empirical permutation method with genomic control to effectively control the family-wise error rate in studies with small sample sizes. With real datasets, we demonstrate that MITScan achieves computational gains of three orders of magnitude compared to commonly used Wald or t tests, while identifying similar significant OTU-gene pairs. The MITScan R package is accessible on GitHub at https://github.com/yajing-hao/MITScan.

genomics↗

bioRxiv2025

Bidirectional regulation of glycoprotein nonmetastatic melanoma protein B by β-glucocerebrosidase deficiency in GBA1 isogenic dopaminergic neurons from a patient with Gaucher disease and parkinsonism

Variants in GBA1 are common genetic risk factors for several synucleinopathies. The increased risk has been attributed to the toxic effects of misfolded glucocerebrosidase (GCase) (gain-of-function), and the accumulation of lipid substrates due to reduced enzyme activity (loss-of-function). To delineate GBA1 pathogenicity, an iPSC line was generated from a patient with both type 1 Gaucher disease (GBA1: N370S/N370S; p.N409S/p.N409S) and Parkinson disease (PD). From this line, we created a reverted wild-type (WT) line and a GBA1 knockout (KO) line to eliminate misfolded GCase and intensify lipid accumulation. N370S/N370S and KO dopaminergic neurons (DANs) exhibited decreasing GCase levels and progressive accumulation of lipid substrates compared to WT DANs. Notably, the expression of GPNMB, whose levels correlate with PD risk, was upregulated by the mild lipid accumulation in N370S/N370S DANs but disrupted in KO DANs. These findings refine the loss-of-function mechanism by associating PD risk levels of GPNMB with lipid levels specific to GBA1 risk variants.

neuroscience↗

bioRxiv2025

Advancing Ligand Binding Affinity Prediction with Cartesian Tensor-Based Deep Learning

0.We present PBCNet2.0, a cartesian tensor-based Siamese Neural Network for protein-ligand relative binding affinity prediction. Trained on 8.6 million protein-ligand complex structure pairs, PBCNet2.0 achieves zero-shot performance comparable to computationally intensive physics-based simulations. Our prioritization experiments show that PBCNet2.0 speeds up binding affinity optimization by 718% while reducing resource use by 41%. Through extensive retrospective experiments, we demonstrate that PBCNet2.0 intrinsically comprehends protein-ligand interactions, showing high sensitivity to intermolecular interactions and exceptional perception of spatial geometric information. Strikingly, PBCNet2.0 exhibits an emergent capability to predict affinity changes induced by binding residue variations, highlighting its potential for identifying resistance mutation. We prospectively validated these capabilities on two targets ENPP1 and ALDH1B1, where PBCNet2.0 successfully identified affinity shifts arising from subtle molecular interactions and conformational differences, and pinpointed critical binding residues with an 83% hit rate. This combination of computational efficiency, spatial geometric perception of binding site, and generalizable affinity prediction establishes PBCNet2.0 as a transformative tool for developing pharmacological probes for all human proteins.

molecular biology↗

bioRxiv2025

Unbiased genetics identifies a glutamatergic signaling network as a mediator of daily sleep patterns.

Sleep is a fundamental, conserved behavior important for survival. In many species, sleep behavior is controlled by poorly understood interactions between a system of circadian rhythms (CR), which promote sleep at ecologically appropriate times, and a homeostatic sleep drive that accumulates with time awake. The CR is a cellular phenomenon, driven by molecular oscillations of "clock genes" in nearly all cells. Emerging evidence indicates neuronal synapses are a key locus for the accumulation and resolution of sleep need, supporting a cellular basis of sleep need. Indeed, efforts to understand the genetic basis of sleep need identified Homer1a, a regulator of synapse homeostasis. To develop further insight into the genetic basis of sleep regulation, we measured daily sleep patterns in genetically diverse strains of mice from the Collaborative Cross. Strains with 1) highly consolidated light-phase sleep, or 2) fragmented, arrhythmic sleep, were identified for genetic analysis using quantitative trait loci (QTL) mapping. Excitingly, in F2 hybrids, 19 of 32 metrics of sleep and circadian behavior mapped to a narrow QTL containing GRM5, a postsynaptic glutamate receptor and binding partner of Homer1a, and GCPII, an astrocytic enzyme that regulates NAAG, a peptide agonist for the presynaptic/astrocytic glutamate receptor GRM3. Collectively, these genes form a coordinated glutamatergic signaling network across the tri-partite synapse. Pharmacology targeting GRM5, GCPII, and GRM3 strongly modulated sleep, functionally validating them as sleep-regulating genes. Our findings support a model in which synapses act as a cellular site for integration of circadian and sleep-need signals to regulate daily sleep patterns. Significance StatementSleep is a fundamental pillar of human health. Restorative sleep is supported by circadian rhythms (CR). Sleep and CR disruptions are prevalent in neuropsychiatric conditions and are increasingly understood as causal drivers of altered brain function and behavior. Therefore, sleep and CR are attractive therapeutic targets to improve health. However, the basic biological mechanisms that couple our need to sleep with the CR are not understood. Genetic discovery using diverse strains of mice identifies a glutamatergic signaling network coordinated across the synapse as an underlying genetic basis for daily sleep patterns. This work builds upon a growing body showing that excitatory synapses are a cellular site for the resolution of sleep need and interaction with the CR.

neuroscience↗

bioRxiv2025

Large-scale HLA immunopeptidome and interactome profiling in microglia

Microglia are immune cells of the brain and act as major antigen presenting cells. Antigen presentation involves the human leukocyte antigen (HLA) complex, which is implicated in genetic risk of multiple neurodegenerative diseases. How HLA affects the function of microglia in the context of neurodegenerative disease remains unclear. Here, we investigated the HLA epitopes and their protein interactome in human induced pluripotent stem cell (iPSC)-derived microglia-like cells (iMGLs) using systematic mass spectrometry (MS)-based immunopeptidomics, whole-cell proteomics, affinity purification, and prediction algorithms. Our results revealed the presence of almost 7,000 peptides presented by HLA class I and II within microglia. We further showed that the immunopeptidome landscapes of iPSCs, iMGLs and interferon-gamma (IFN{gamma}) stimulated iMGLs are all readily distinguishable. Furthermore, HLA interacts with different groups of proteins in iPSCs compared to iMGLs which involve proteins in immune response. Importantly, we detected 25 HLA epitopes derived from 15 genes associated with Alzheimers and related dementias such as Tau, PLD3 (Alzheimers disease), TDP-43, FUS (Frontotemporal dementia), and PARK7, VPS35 (Lewy Body dementia). We predicted 31 mutant epitopes derived from these ADRD genes that could be presented with strong interaction to HLA molecules. Along with these epitopes, we observed an enrichment of immune-related interaction proteins in microglia treated with IFN{gamma}. These results provide evidence that aggregated and mutated proteins can interact with HLA alleles and be presented on the cell surface by microglia cells. This study sheds light on the antigen presenting and adaptive immunity mechanism within the central nervous system and its possible effects on neurodegenerative diseases.

immunology↗