Molecular Brain

Astrocytic homeostatic programs, many of which are regulated by the circadian clock, are disrupted early in neurodegenerative disease. The core clock transcription factor (TF) BMAL1 is required for normal astrocyte function, but its role during disease remains unclear. This is partly because methods for identifying cell type-specific TF binding sites are limited. Here, we developed MACS-Calling Cards (MACS-CC), a strategy for mapping astrocyte-specific TF occupancy in vivo. We used MACS-CC to define BMAL1 binding in the Cln3{Delta}ex7/8 mouse model of CLN3 disease, a fatal neurodegenerative disorder marked by early astrocyte dysfunction and circadian disruption. BMAL1 binding was extensively redistributed in Cln3{Delta}ex7/8 astrocytes: wild-type-specific binding sites enriched near glial differentiation genes, whereas Cln3{Delta}ex7/8-specific sites lacked functional enrichment. Consistent with these changes, Cln3{Delta}ex7/8 astrocytes decreased expression of mature astrocyte markers. To define mechanisms underlying BMAL1 retargeting, we tested whether altered chromatin accessibility explained the changes in BMAL1 binding. Although chromatin accessibility was broadly remodeled, differential accessibility did not predict BMAL1 redistribution. Instead, motif analysis suggested that loss of cooperative TF interactions drives BMAL1 retargeting. These findings demonstrate that MACS-CC enables astrocyte-specific TF occupancy mapping and reveals mechanisms behind early rewiring of circadian regulatory programs within a model of a neurodegenerative disease. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/721783v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1ada239org.highwire.dtl.DTLVardef@7564a3org.highwire.dtl.DTLVardef@122222forg.highwire.dtl.DTLVardef@1f2729c_HPS_FORMAT_FIGEXP M_FIG C_FIG

Parkinsons disease (PD) is associated with motor impairment and cortical synaptic dysfunction, which involve altered glutamate receptor trafficking, yet the underlying mechanisms remain incompletely understood. VPS26B, a component of the retromer complex, regulates GluA1 recycling in the trans-entorhinal cortex region. However, its role in the primary motor cortex (M1) under Parkinsonian conditions has not been explored. Here, we show that VPS26B levels are reduced in the M1 of an MPTP-induced PD mouse model, accompanied by decreased surface GluA1 and synaptic protein levels. VPS26B overexpression partially attenuated these alterations. In the accelerating rotarod test, VPS26B-deficient mice exhibited unstable motor performance following MPTP administration, whereas VPS26B overexpression was associated with improved performance in both wild-type and knockout mice. These findings suggest that cortical VPS26B may contribute to maintaining glutamate receptor surface expression and synaptic protein levels, especially under Parkinsonian conditions, with potential implications for motor learning.

CaMKII promoter is widely used to label and manipulate hippocampal pyramidal neurons via transgenic mouse lines or viral approaches. While it targets most excitatory neurons, a small subset remains unlabeled and often overlooked. We present an AAV-based strategy combined with CaMKII-driven Cre expression to access and study this remaining population. Furthermore, we provide a detailed protocol for in-house AAV production, targeted stereotaxic delivery, and functional validation of targeted neurons through slice electrophysiology and behavior. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=194 HEIGHT=200 SRC="FIGDIR/small/723440v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@3a31ccorg.highwire.dtl.DTLVardef@9b7e90org.highwire.dtl.DTLVardef@92297borg.highwire.dtl.DTLVardef@1e159eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

The cerebellar nuclei form the main output structures of the cerebellum and are composed of a deeply conserved set of cell types. Two excitatory cell classes, Class-A and -B, are present in each cerebellar nucleus and mediate all excitatory output of the cerebellum. To provide genetic access to these cell types, here we identified Acan as a marker gene for Class-B cells and generated a knock-in Acan-P2A-Cre mouse line. We demonstrate that this Acan-Cre line selectively labels Class-B neurons in the cerebellar nuclei and validate its use in viral projection tracing. This new mouse line provides a valuable genetic tool to study cerebellar nuclei organization and function.

Lysosomal trafficking and homeostasis are biological functions that are pivotal for DRG neurons, given their metabolic demands and extremely long axons. Previous studies indicate that lysosomal signaling is altered in a mouse model of chemotherapy-induced peripheral neuropathy (CIPN) and that blocking mitogen activated protein kinase-associated kinase (MNK1/2) signaling can alleviate pain behaviors in CIPN. Here, we investigated lysosome dynamics and lysosome-associated signaling in a mouse model of CIPN induced by paclitaxel (PTX), a chemotherapeutic agent used for various types of cancer. Using spinning disk super-resolution microscope (SPINSR), we demonstrate that PTX treatment in vivo causes reduced lysosome motility observed in vitro. PTX likewise drives the accumulation of Sequestosome 1 (SQSTM1), also known as P62, in cultured mouse DRG neurons, indicating lysosomal dysfunction in DRG neurons. The transcription factor EB (TFEB), a master regulator of lysosomal biogenesis, was also upregulated in the nucleus of cultured mouse DRG neurons treated with PTX. In line with this, increased lysosomal-associated membrane protein 1 (LAMP1) expression was observed in PTX-treated mice. Given that our previous work demonstrated PTX treatment increases MNK1/2-eIF4E signaling in DRG neurons, we examined whether MNK1/2 inhibition could rescue lysosomal dysfunction. Treatment with Tomivosertib (eFT508), a potent MNK1/2 inhibitor, restored P62 levels in DRG neurons of PTX-treated mice and reduced TFEB in DRG treated in vitro. To establish translation relevance, we further show that PTX elevates phosphorylated eiF4E (p-eIF4E) in human DRG neurons, and concurrent eFT508 administration attenuates this effect. Collectively, these findings indicated that PTX disrupts lysosome trafficking and biogenesis, and that MNK inhibition with eFT508 restores lysosomal signaling and can serve as a neuroprotective strategy for CIPN.

BackgroundMicroglial heterogeneity is a fundamental feature of brain homeostasis and pathology. The purpose of this study was to investigate the complexity of microglial plasticity by characterizing specialized oligodendrocyte-like microglial subsets. MethodsThe study was performed utilizing single-cell transcriptomics analyses and immunofluorescence staining to identify and profile microglial subpopulations. Additionally, spatial transferring and morphological analyses were conducted to determine the anatomical distribution and structural features of these specific cells. ResultsWe identified a distinct microglial subset termed dual-phenotype microglia (DPM), which co-expresses microglial and oligodendrocyte markers. DPM consisted of two subtypes with distinct functions: myelin-associated DPM (mDPM) and neuron-associated DPM (nDPM). Spatial and morphological evaluations revealed that mDPMs were sparsely distributed across the whole brain and exhibited a highly ramified architecture, whereas nDPMs were enriched in the hippocampal dentate gyrus. Mechanistically, we found that mDPM function was driven by the Sox10 regulon to modulate myelin maintenance and axonal ensheathment, while nDPM was orchestrated by Glis2, facilitating essential neuron-glia crosstalk and synaptic regulation. Furthermore, we demonstrated that nDPM and mDPM were predicted to undergo significant alterations in multiple sclerosis and Alzheimers disease. Notably, mDPMs were selectively enriched in active multiple sclerosis lesions, revealing that DPM were closely related to neuropsychiatric disorders. ConclusionsBy comprehensively characterizing the morphology, molecular signatures, and spatial logic of these oligodendrocyte-like microglial subsets, our study elucidated the complexity of microglial plasticity. These findings provided new insights into their diverse roles in central nervous system health and disease. Graphical abstractIdentification, Molecular Profiling, and Functional Modeling of Dual-Phenotype Microglia (DPM). (1) Discovery: Identification of the dual-phenotype microglia (DPM) population through single-cell transcriptomics. (2) Molecular Signatures: The transcriptomic identity of DPM subtypes is governed by specific regulatory networks. (3) Distribution & Pathology: Spatial mapping reveals divergent anatomical logic and disease relations for DPM subtypes. (4) Mechanism/Theory: A proposed functional model of mDPMs as "metabolic relay" and support units. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/724239v2_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@b7db1dorg.highwire.dtl.DTLVardef@9265e7org.highwire.dtl.DTLVardef@1605d82org.highwire.dtl.DTLVardef@19b048f_HPS_FORMAT_FIGEXP M_FIG C_FIG

Lack of social interaction results in various behavioral abnormalities in rodents, including increased anxiety levels, altered sociability, and impaired cognitive ability. Epigenetic factors regulate gene expression, however, how they contribute to juvenile social isolation (jSI)-induced behavioral alterations remains largely unknown. Here, we focused on the nucleus accumbens (NAc), a critical brain region of the reward system that regulates motivation-related behaviors. We first performed RNA-seq on neuronal nuclei and found alterations in genes related to neuronal function, as well as in transcriptional and epigenetic regulation. Protein-protein interaction (PPI) analysis of differentially expressed genes (DEGs) showed that top key nodes among down-regulated genes include membrane receptors (Ntrk2, Grin3a, and Grik1) and an apoptosis regulator (Bcl2). To further investigate whether jSI-induced gene expression alterations are mediated by histone modifications, we next performed CUT&Tag for four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3), and the results implied that epigenetic alterations may also play a role in neuronal function as well as transcriptional regulation. Reanalysis of previously published RNA-seq data on the manipulation of histone modification-associated factors (including Kdm6b, Brd4, and Setd1a) suggested that these enzymes were probably involved in jSI-induced gene expression alterations. Taken together, our comprehensive analysis implies the involvement of histone modification regulation in jSI-related alterations of gene expression in NAc.

Memory impairment is a common and sometimes overlooked feature of major depressive disorder, and cognitive deficits may precede the onset of depressive symptoms in some cases. However, the cognitive benefits of first-line treatments such as SSRIs are mixed. Tianeptine is an atypical antidepressant and cognitive enhancer that neither interacts with monoamine receptors nor inhibits the reuptake of their neurotransmitters. Its antidepressant efficacy in animal models requires activation of the mu-opioid receptor (mu-OR) and phosphorylation of the AMPA receptor. However, the receptors that mediate its memory enhancing actions have never been investigated. We therefore tested the ability of tianeptine to improve spatial memory in a cross-maze task in wild-type (WT) mice compared to its effects in mice with global knockout of either the mu-OR or delta-OR. In parallel, we assessed the effects of tianeptine on hippocampal oscillatory activity and spontaneous locomotion in the same genotypes. Adult male and female WT, mu -/-, and delta -/- mice on a C57BL/6J background were implanted with hippocampal electrodes for the recording of local field potential (LFP) oscillations. Consistent with our previous observations in anaesthetised rats, injection of tianeptine (10 mg/kg and 30 mg/kg SC) caused a dose-dependent increase in beta-frequency power in WT mice that was maximal at circa 25 Hz. The same effect was observed in delta -/- mice, but the increase in beta was completely absent in mu -/- animals. As others have reported previously, tianeptine also caused a mu-OR-dependent increase in spontaneous locomotor activity, but with a time-course that was distinct from the increase in beta power. Separate groups of WT, mu -/-, and delta -/- mice were tested for their ability to learn a food-rewarded spatial memory task in a cross-maze. Over a 20-day training period, sub-groups of each genotype received either tianeptine (10 mg/kg SC) or vehicle injection 30 min before testing. Tianeptine increased the percentage of correct trials and the number of allocentric (place) responses in WT mice, but did not enhance memory in either mu -/- or delta -/- mice, even though both genotypes were able to learn the task. These results indicate that the ability of tianeptine to drive hippocampal beta oscillations is dependent on the mu-OR, whereas its memory-enhancing actions require the presence of both mu- and delta-ORs. The latter result is consistent with the actions of tianeptine on postsynaptic AMPA receptors, and we are currently exploring the signalling pathways involved in this process.

Adeno-associated viral (AAV) vectors are foundational tools for dissecting brain structure-function relationships, but AAV serotype tropism varies across brain regions and species, requiring empirical validation to inform experimental design. This need is especially important in non-model organisms, where molecular neuroscience tools remain underdeveloped and access to research subjects is often limited. The Arctic ground squirrel (AGS, Urocitellus parryii) is a valuable model for studying extreme physiology, including metabolic suppression during hibernation and resistance to cerebral ischemia/reperfusion, yet no studies have evaluated AAV performance in the AGS brain. Here, we investigated the ability of AAV serotypes 1, 8, 9, and DJ to transduce the AGS hypothalamus using the human synapsin (hSyn) promoter and directly compared cellular transduction rates in a region implicated in thermoregulation and hibernation. To maximize data collection from a limited experimental population, we used a within-animal, contralateral stereotaxic injection design. Recombinant AAV vectors expressing enhanced green fluorescent protein or mCherry were delivered bilaterally, and reporter expression was analyzed four weeks later. All tested serotypes produced clear and reproducible reporter expression, establishing AAV as a viable molecular tool in the AGS hypothalamus. AAV1 produced significantly greater cellular transduction rates than AAV-DJ (17.2% {+/-} 3.5% vs 8.4% {+/-} 2.9%, paired t-test, p = 0.032). AAV8 and AAV9 showed transduction rates of 22.8% {+/-} 0.6% and 20.1% {+/-} 1.5%, respectively; however, with only two biological replicates per serotype, formal statistical comparison was not performed. These findings provide the first direct characterization of AAV-mediated gene delivery in the AGS brain and establish a foundation for future molecular interrogation of hypothalamic circuits in this extreme mammalian hibernator.

Disease variants in GABR genes encoding {gamma}-Aminobutyric acid type A receptor (GABAAR) subunits are major causes of developmental and epileptic encephalopathies (DEEs). There is no effective treatment for these DEEs although the GABAAR is a major target for antiseizure drugs. We previously identified the therapeutic effect of 4-phenyl-butyrate (PBA) in Gabrg2+/Q390X knockin DEE mice and now test the effect of the drug in GABRA1 variants that encode the 1 subunit. We used a multidisciplinary approach including in silico structural modeling, flow cytometry, patch clamp recordings and bio-chemistry in conjunction with differential tagging of the wild-type and the mutant alleles to evaluate the effect of PBA on rescue of GABAAR subunit expression, surface trafficking, and function in vitro in heterologous HEK293T cell model and in vivo in Gabra1+/A322D mice. We found that both total and cell surface 1 expression was reduced when the variant 1 protein was present; suggesting reduced functional receptor on the cell membrane and synapse. Patch clamp recordings identified 1 variants reduced GABA-evoked current amplitude. In silico prediction indicated reduced protein stability for GABRA1 variants indicated by negative {Delta}{Delta}G values. PBA increased both total and surface expression of wildtype 1 and 1 variants; and improved expression of both wildtype and variant 1 alleles when these were co-expressed. Importantly, PBA also increased the GABAAR expression in the thalamus of the Gabra1+/A322D mice. This study indicates that PBA is a promising treatment option for DEEs associated with GABRA1 mutations. Our previous work has demonstrated that PBA improves proteostasis by enhancing expression of the wildtype allele, repairing the mutant allele, and reducing endoplasmic reticulum stress. Therefore, it can mitigate seizures and improve neurobehavioral phenotypes at behavioral levels. Based on this and our previous work on GABRG2 and SLC6A1 mutations, we propose that PBA holds promise as a common medicine for multiple genetic neurologic disorders that share the proteostasis pathology with a broad clinical application in DEEs.

Cognitive impairments significantly impact the daily life of people with Down syndrome (DS). Overinhibition mediated by interneurons in the central nervous system was proposed as a key pathophysiological mechanism. Previous studies demonstrated cognitive rescue in the Ts65Dn mouse model using 5IA, a negative allosteric modulator of the 5 subunit-containing GABAA receptors. Here, we evaluated the effect of this drug in a mouse model carrying a more accurate duplication of the orthologous region to the human chromosome 21, namely the Dp(16)1Yey mouse model. First, we expanded the phenotypic characterization of Dp(16)1Yey mice using translationally more relevant behavioral tests. We confirmed spatial memory deficits in Dp(16)1Yey mice in the Barnes maze, and highlighted robust learning deficits in the pattern dissociation task and impairments in motor coordination. Next, we evaluated the effect of 5IA treatment on cognitive and motor performance. While 5IA treatment improved motor coordination in the Dp(16)1Yey mice, it failed to restore cognitive performance in the Barnes maze or in the pattern dissociation task. These findings could suggest divergent pathophysiological mechanisms between the Dp(16)1Yey and the Ts65Dn models. Potentially, it could explain the limited efficacy of similar pharmacological intervention in clinical trials for DS. Further preclinical studies should prioritize refined behavioral paradigms and probably the use of more complex DS models to enhance the translational potential of candidate therapies.

Triggering receptor expressed on myeloid cells 2 (TREM2) plays a crucial role in regulating various microglial functions, including phagocytosis, inflammation, chemotaxis, and proliferation. Recent studies have demonstrated that TREM2 cooperates with DAP12 to mediate intracellular signaling essential for these processes. Despite the importance of the TREM2-DAP12 complex in microglial physiology, the mechanisms controlling its expression and activity remain poorly understood. In this study, we report that the soluble ectodomain of TREM2 (sTREM2) regulates microglial phagocytic activity by attenuating the surface expression of DAP12. We found that stimulation of the microglial cell line BV2 with recombinant sTREM2 reduces the membrane expression of DAP12, but not that of TREM2. In addition, sTREM2 binds to full-length TREM2, leading to the uncoupling of TREM2 from DAP12. Furthermore, pre-treatment of BV2 cells with sTREM2 significantly inhibited amyloid-{beta} incorporation. These findings suggest that sTREM2 negatively regulates TREM2 signaling through the destabilization of the TREM2-DAP12 complex, and act as a novel bioactive molecule that modulates TREM2 signaling under physiological and pathological conditions.

Assessing reproducibility across different molecular profiling studies is a persistent methodological challenge (Zhang et al., 2009; Sweeney et al., 2017; Ioannidis, 2005). Differences in platform technology, cohort composition, analytical pipelines, and feature definitions often make it difficult to interpret cross-study comparisons based solely on gene-identity overlap. In this study, we conducted a retrospective computational analysis of seven publicly available analytical datasets (including alternative analytical pipelines applied to the same cohort) derived from five biologically independent peripheral blood transcriptomic and DNA methylation cohorts, comprising 3,487 samples (1,824 Parkinsons disease cases and 1,663 controls). Reproducibility was evaluated using gene-identity overlap, enrichment-based comparisons, and a permutation-based framework to assess directional consistency of effect estimates across datasets. We also tested the robustness of results by varying false discovery rate thresholds and applying alternative probe-to-gene collapsing strategies. All analyses were performed using reproducible workflows implemented in R and Python with fixed random seeds. Across independent cohorts, gene-identity overlap was generally limited, with enrichment ratios close to one, especially when datasets were generated using different platforms. In several datasets, limited numbers of statistically significant features further constrained overlap-based comparisons. In contrast, directional consistency showed greater stability. High levels of directional consistency were observed across independent cohort comparisons when restricted to overlapping statistically significant features and remained stable across statistical thresholds (90.0% at FDR < 0.05 and 82.8% at FDR < 0.10). When evaluated across the full shared gene universe without conditioning on statistical significance, directional consistency was substantially lower ([~]30 to 32%) but remained significantly above permutation-based null expectations. Permutation testing confirmed that the observed directional consistency exceeded what would be expected by chance. A combined analysis including methodological replicates (n [&ge;] 3 datasets) showed 98.3% directional consistency; however, this estimate includes non-independent analytical pipelines applied to the same cohort and reflects analytical stability rather than independent biological replication. Rather than introducing a new statistical method, this study examines how commonly used reproducibility metrics behave under crossstudy heterogeneity and identifies their practical limitations and appropriate use boundaries.

Sleep disturbances are common among individuals with schizophrenia and can exacerbate disruptions in cognitive processes like learning and memory. Elucidating pharmacologically targetable molecular pathways perturbed by schizophrenia genes may uncover new treatment avenues. Here, we investigated the relationship of the schizophrenia-associated gene znf804a with sleep and circadian pathways. Using multi-day behavior tracking, we showed that znf804a zebrafish mutants displayed changes in sleep and circadian behaviors when light cues were removed. Through bulk RNA sequencing of fish raised under normal light cycling and dark-only conditions, we identified altered gene expression in the core and auxiliary pathways controlling circadian rhythms. Expression of fbxl3a, which encodes a modulator of the core negative feedback regulator of the clock, decreased in a dose-dependent manner as znf804a mutant copy number increased. Further analysis also revealed shifts in the relative abundance of specific transcripts, including idh1, suggesting znf804a could influence transcript processing or stability. Together, these findings link a ZNF804A ortholog to sleep and circadian behaviors and identify the regulation of fbxl3a and transcript processing as candidate mechanisms through which this schizophrenia risk gene may influence circadian biology.

BackgroundDirect conversion of human somatic cells into functional neurons could offer a faster way to generate patient-specific neurons for use in regenerative medicine, disease modelling, and drug development. Although it has been reported that neuronal direct reprogramming bypasses the intermediate pluripotent state, no reports have included time-lapse experiments, potentially overlooking transient intermediate states. Recent studies have shown that the conversion of human mesenchymal stromal cells (hMSCs) into neuron-like cells involves a transition through a transient intermediate state. Therefore, further research is needed to fully understand the process by which human somatic cells can become neurons without cell division. In this study we investigates whether direct neuronal reprogramming of human bone marrow-derived MSC (hBM-MSCs), dental pulp-derived MSC (hDP-MSCs), and adult human dermal fibroblasts (HDFa), involves a transient intermediate state, and sought to further validate the neuronal identity of hMSC-derived induced neurons. MethodsIn this study, we conducted time-lapse experiments to observe the transformation of hBM-MSCs, hDP-MSCs and HDFa, into neurons using a small-molecule-based direct reprogramming protocol. Cellular and ultrastructural changes were further characterized by confocal and electron microscopy. ResultsDirect conversion of hBM-MSCs, hDP-MSCs and HDFa into neuron-like cells occurred rapidly and in absence of cell division. Time-lapse analyses revealed that reprogramming proceeds through a transient intermediate state characterized by distinct morphological changes and dynamic nuclear remodelling. Furthermore, we found that neuron-like cells derived from hBM-MSCs and hDP-MSCs exhibit neuronal polarization, expressed specific neuronal and synaptic markers, formed interconnected cellular networks, and exhibited functional plasticity, providing further evidence that hMSCs can become functional neurons. ConclusionsThis study provides clear evidence that the direct neuronal reprogramming process involves a transition through an intermediate, transient state. Our findings also provide further evidence that hMSCs can become functional neurons. In summary, our work provides new insights into the direct neuronal reprogramming process, which is essential for advancing both developmental biology and regenerative medicine.

Understanding how neuronal populations interact to encode and transform sensory information is a fundamental challenge in computational neuroscience. Most existing studies, however, study neural encoding, behavioral readout, and functional connectivity as disjoint problems. Two-photon calcium imaging enables simultaneous recording of large neuronal ensembles in vivo, driven by diverse stimuli and eliciting distinct behaviors. However, extracting directional functional connectivity metrics as well as encoding and readout properties of neurons from such data remains difficult due to indirect and noisy observations of spiking activity, slow temporal dynamics, and the latent interplay between external stimuli and endogenous neural processes. Here, we introduce a unified conceptual and operational modeling and inference framework for directly extracting functional Granger causal (GC) effects between neurons, from external stimuli to neurons, and from neurons to behavior, from two-photon imaging data, in the sense of Granger. Inspired by the intersection information framework, we also identify neurons that encode features of sensory stimuli that inform behavioral readout. The resulting GC networks together with the taxonomy of functional sensori-behavioral relevance, which we call G-taxonomy, provides a powerful statistical analysis framework, enabled by the integration of several techniques including state-space modeling and inference, variational inference, and point processes. We applied the proposed framework to simulated and experimentally-recorded two-photon imaging from the mouse auditory cortex (A1) during both passive listening and active tone discrimination. Our simulation studies reveal significant improvement of our proposed methodology over existing techniques. Analysis of experimental data from the mouse A1 identifies distinct groups of cells with diverse sensori-behavioral relevance, as well as changes in functional connectivity associated with correct vs. incorrect behavior. In summary, this work provides a principled and data-driven methodology for uncovering directional interactions among the neurons, sensory stimuli, and behavior, all within the same statistical framework, offering new insights into how distributed cortical populations transform sensory inputs into behaviorally relevant representations. Author SummaryThe brain processes sensory inputs through the coordinated activity of large networks of neurons and produces readouts that elicit behavior. Understanding how information flows and is processed through these networks is a central goal of neuroscience. In this study, we present a new computational framework that identifies directional interactions among neurons in an ensemble as well as from sensory stimuli to neurons and from neurons to behavior. Utilizing the Granger formalism to identify directional effects, as opposed to common correlational measures, our framework extracts said effects directly from two-photon calcium imaging data. We tested our proposed method on both simulated data and recordings from the auditory cortex of mice during passive listening and active tone discrimination tasks. Our method revealed diverse groups of neurons in the auditory cortex with distinct functional roles and relevance to sensori-behavioral integration. Our framework provides a new way to study the flow of information in the brain and can be broadly applied to uncover neural computations across sensory and cognitive systems.

Microglia are the brains resident immune cells that exhibit complex signaling behavior, including phagocytic activity in response to threats and prolonged neuronal activity. Adenosine triphosphate (ATP) is a chemoattractant for microglia. In the nucleus accumbens (NAc), ATP is co-packaged and released with DA, and microglia express dopamine (DA) receptors and ATP receptors. The present work examines microglia chemotactic motility for these transmitters using iontophoresis and multiphoton microscopy approaches in NAc brain slices from GFP-monocyte labeled transgenic mice. ATP chemoattraction was more regularly observed than DA chemoattraction, and DA chemoattraction occurred in only a small subset of microglia. The DA chemoattraction of this subset was blocked by DA D1 antagonism. Microglia are reactive oxygen species (ROS) scavengers. Application of glucose oxidase produces mild but consistent increases in ROS and induced inflammatory-related changes in microglial morphology and motility. Glucose oxidase application decreased DA release but had variable effects on ATP release. The toll-like receptor 4 (TLR4) agonist lipopolysaccharide (LPS) transitioned microglia from ramified to amoeboid morphology over a period of 4 hours, and increased DA and ATP release across this same period. These studies highlight the complex relationship between local immune activation and DA terminal functionality.

Plasma Membrane Calcium ATPase (PMCA) is essential for maintaining intracellular calcium homeostasis. Previously, we used constitutive PMCA downregulation in Drosophila melanogaster dopaminergic neurons as a model to increase intracellular calcium and mimic early neuronal alterations associated with Parkinsons disease. Here, we examined the mechanisms underlying the effects mediated by the conditional, adult-specific downregulation of PMCA in dopaminergic neurons in Drosophila melanogaster, both in vivo and in primary neuronal cultures. Adult-specific conditional silencing of PMCA in dopaminergic neurons reduced lifespan but to a lesser extent than the constitutive model and impaired locomotor performance. At the cellular level, PMCA-downregulated dopaminergic neurons exhibited elevated basal calcium, indicating disrupted calcium regulation. This was associated with a progressive increase in presynaptic vesicles and extracellular dopamine levels, suggesting enhanced neurotransmitter release. Notably, the synaptic active zone structure was preserved, indicating primarily functional rather than structural alterations. In primary neuronal cultures, PMCA downregulation reduced dopaminergic neuron survival and induced transient increases in neurite branching. Together, these findings show that PMCA downregulation leads to calcium dysregulation and presynaptic dysfunction without overt neurodegeneration in vivo, while promoting premature neuronal death in culture, indicating increased vulnerability and supporting a pre-degenerative state in which synaptic alterations precede neuronal loss.

The hippocampal formation (HPF) provides neural substrates integrating disparate sensory cues into episodic memories and coherent action. Whereas HPF structures are formed by birth, the functional circuits evolve over postnatal development. Our previous studies showed that transient perinatal expression of the serotonin (5-HT) transporter SERT/Slc6a4 in CA3 pyramidal neurons, which do not synthesize 5-HT but take up extracellular 5-HT thus termed "5-HT-absorbing neurons", exerts sex-biased effects on long-term activity-dependent HPF synaptic plasticity and behavior in mice. This study investigates SERT impact on circuit development, through single-nucleus transcriptomics of postnatal HPF from CA3-pyramidal neuron SERT knockout (SERTPyramid{Delta}) mice. We demonstrate that SERTPyramid{Delta} mice preserve cell identities across the HPF but alter gene expression in specific neuronal types in a sex-biased manner. We observed SERTPyramid{Delta} male-biased upregulation of genes preferentially in glutamatergic neurons, particularly affecting the CA2 and parasubiculum (PaS) when they develop social novelty and spatial representations, respectively. In both the CA2 and PaS, altered genes center on two categories -- modulators of gene expression patterning including chromatin plasticity, RNA processing and ubiquitin-dependent protein degradation, and aspects of synaptic transmission. >20% of the dysregulated genes in the CA2 and PaS are associated with Autism and engaged in cell-type distinct functional networks, showing CA3 SERT regulation of ASD-vulnerable genes in intersecting biological processes in specific neurons during social and spatial circuits development. The data, available at https://scviewer.shinyapps.io/hippocampus_sertKO, provide an entry map for further deducing anatomical neuronal origin and the molecular and cellular pathways impaired by 5-HT dysfunction during HPF circuits development leading to lifetime cognitive deficits.

Down syndrome (DS), caused by trisomy of human chromosome 21, is characterized by intellectual disability and cognitive deficits, partly driven by the overexpression of Dual-specificity tyrosine-(Y)-phosphorylation Regulated Kinase 1A (DYRK1A). While postnatal DYRK1A inhibition has shown promise in improving cognition in DS models, its therapeutic potential during embryonic development, a critical window for neurogenesis, remains unexplored. Here, we tested the hypothesis that prenatal inhibition of DYRK1A could mitigate long-term cognitive impairments in DS. We administered Leucettine L41, a potent and selective DYRK1A inhibitor, to pregnant dams carrying two DS mouse models: Ts65Dn and Dp(16)1Yey, both of which recapitulate trisomy of genes homologous to human chromosome 21, including Dyrk1a. Treatment was designed to suppress DYRK1A kinase activity during embryogenesis. In adulthood, we evaluated the progeny for cognitive performance, gene expression profiles linked to DS phenotypes, and neuronal maturation markers. Prenatal L41 treatment produced lasting effects in both models, rescuing specific behavioral deficits and modulating the expression of DS-implicated genes, including the excitatory/inhibitory balance regulator GAD67. However, model-specific responses were observed: hyperactivity, working memory deficits, and GAD67-positive cell counts remained uncorrected in Ts65Dn mice, suggesting divergent molecular pathways underlying shared DS phenotypes. This study demonstrates the therapeutic potential of prenatal DYRK1A inhibition for DS and provides novel insights into its role in neurodevelopmental trajectories and cognitive outcomes. Our findings underscore the importance of timing and genetic context in DS intervention strategies.