Genome-wide atlas of gene expression in the adult mouse brain

Modulation of dorsal raphe nucleus connectivity and serotonergic signalling to the insular cortex in the prosocial effects of chronic fluoxetine

Long-term exposure to fluoxetine and other selective serotonin reuptake inhibitors alters social and anxiety-related behaviours, including social withdrawal, which is a symptom of several neuropsychiatric disorders. Adaptive changes in serotonergic neurotransmission likely mediate this delayed effect, although the exact mechanisms are still unclear. Here we investigated the functional circuitry underlying the biphasic effects of fluoxetine on social approach-avoidance behaviour and explored the place of serotonergic dorsal raphe nucleus (DR) ensembles in this network, using c-Fos-immunoreactivity as a correlate of activity. Graph theory-based network analysis revealed changes in patterns of functional connectivity and identified neuronal populations in the insular cortex (IC) and serotonergic populations in the DR as central targets to the prosocial effects of chronic fluoxetine. To determine the role of serotonergic projections to the IC, a retrograde tracer was micro-injected in the IC prior to fluoxetine treatment and social behaviour testing. Chronic fluoxetine increased c-Fos immunoreactivity in insula-projecting neurons of the rostral, ventral part of the DR (DRV). Using a virally delivered Tet-Off platform for temporally-controlled marking of neuronal activation, we observed that chronic fluoxetine may affect social behaviour by influencing independent but interconnected populations of serotonergic DR ensembles. These findings suggest that sustained fluoxetine exposure causes adaptive changes in functional connectivity due to altered serotonergic neurotransmission in DR projection targets, and the increased serotonergic signalling to the IC likely mediates some of the therapeutic effects of fluoxetine on social behaviour.

Single-cell and spatial omics: exploring hypothalamic heterogeneity

Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges in capturing and analyzing individual cells. These high-throughput omics technologies now offer a remarkable opportunity to comprehend the complex spatiotemporal patterns of transcriptional diversity and cell-type characteristics across the entire hypothalamus. Current single-cell and single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes across various subregions of the hypothalamus. However, single-cell/single-nucleus RNA sequencing requires isolating the cell/nuclei from the tissue, potentially resulting in the loss of spatial information concerning neuronal networks. Spatial transcriptomics methods, by bypassing the cell dissociation, can elucidate the intricate spatial organization of neural networks through their imaging and sequencing technologies. In this review, we highlight the applicative value of single-cell and spatial transcriptomics in exploring the complex molecular-genetic diversity of hypothalamic cell types, driven by recent high-throughput achievements.

Imaging the structural connectome with hybrid MRI-microscopy tractography

Mapping how neurons are structurally wired into whole-brain networks can be challenging, particularly in larger brains where 3D microscopy is not available. Multi-modal datasets combining MRI and microscopy provide a solution, where high resolution but 2D microscopy can be complemented by whole-brain but lowresolution MRI. However, there lacks unified approaches to integrate and jointly analyse these multi-modal data in an insightful way. To address this gap, we introduce a data-fusion method for hybrid MRI-microscopy fibre orientation and connectome reconstruction. Specifically, we complement precise "in-plane" orientations from microscopy with "through-plane" information from MRI to construct 3D hybrid fibre orientations at resolutions far exceeding that of MRI whilst preserving microscopy's myelin specificity, resulting in superior fibre tracking. Our method is openly available, can be deployed on standard 2D microscopy, including different microscopy contrasts, and is species agnostic, facilitating neuroanatomical investigation in both animal models and human brains.

NECAB family of neuronal calcium-binding proteins in health and disease

The N-terminal EF-hand calcium-binding proteins 1-3 (NECAB1-3) constitute a family of predominantly neuronal proteins characterized by the presence of at least one EF-hand calcium-binding domain and a functionally less well characterized C-terminal antibiotic biosynthesis monooxygenase domain. All three family members were initially discovered due to their interactions with other proteins. NECAB1 associates with synaptotagmin-1, a critical neuronal protein involved in membrane trafficking and synaptic vesicle exocytosis. NECAB2 interacts with predominantly striatal G-protein-coupled receptors, while NECAB3 partners with amyloid-β A4 precursor protein-binding family A members 2 and 3, key regulators of amyloid-β production. This demonstrates the capacity of the family for interactions with various classes of proteins. NECAB proteins exhibit distinct subcellular localizations: NECAB1 is found in the nucleus and cytosol, NECAB2 resides in endosomes and the plasma membrane, and NECAB3 is present in the endoplasmic reticulum and Golgi apparatus. The antibiotic biosynthesis monooxygenase domain, an evolutionarily ancient component, is akin to atypical heme oxygenases in prokaryotes but is not well-characterized in vertebrates. Prokaryotic antibiotic biosynthesis monooxygenase domains typically form dimers, suggesting that calcium-mediated conformational changes in NECAB proteins may induce antibiotic biosynthesis monooxygenase domain dimerization, potentially activating some enzymatic properties. However, the substrate for this enzymatic activity remains uncertain. Alternatively, calcium-mediated conformational changes might influence protein interactions or the subcellular localization of NECAB proteins by controlling the availability of protein-protein interaction domains situated between the EF hands and the antibiotic biosynthesis monooxygenase domain. This review summarizes what is known about genomic organization, tissue expression, intracellular localization, interaction partners, and the physiological and pathophysiological role of the NECAB family.

Autism-related traits in myotonic dystrophy type 1 model mice are due to MBNL sequestration and RNA mis-splicing of autism-risk genes

Genome-wide enrichment of gene-specific tandem repeat expansions has been linked to autism spectrum disorder. One such mutation is the CTG tandem repeat expansion in the 3' untranslated region of the DMPK gene, which is known to cause myotonic muscular dystrophy type 1. Although there is a clear clinical association between autism and myotonic dystrophy, the molecular basis for this connection remains unknown. Here, we report that sequestration of MBNL splicing factors by mutant DMPK RNAs with expanded CUG repeats alters the RNA splicing patterns of autism-risk genes during brain development, particularly a class of autism-relevant microexons. We demonstrate that both DMPK-CTG expansion and Mbnl null mouse models recapitulate autism-relevant mis-splicing profiles, along with social behavioral deficits and altered responses to novelty. These findings support our model that myotonic dystrophy-associated autism arises from developmental mis-splicing of autism-risk genes.

Deep-tissue transcriptomics and subcellular imaging at high spatial resolution

Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens. We introduce cycle hybridization chain reaction (cycleHCR), a method that integrates multicycle DNA barcoding with HCR to overcome this limitation. cycleHCR enables highly multiplexed imaging of RNA and proteins using a unified barcode system. Whole-embryo transcriptomics imaging achieved precise three-dimensional gene expression and cell fate mapping across a specimen depth of ~310 μm. When combined with expansion microscopy, cycleHCR revealed an intricate network of 10 subcellular structures in mouse embryonic fibroblasts. In mouse hippocampal slices, multiplex RNA and protein imaging uncovered complex gene expression gradients and cell-type-specific nuclear structural variations. cycleHCR provides a quantitative framework for elucidating spatial regulation in deep tissue contexts for research and has potential diagnostic applications.

Molecular mechanism establishing the OFF pathway in vision

Parallel ON and OFF (positive- and negative-contrast) pathways fundamental to vision arise at the complex synapse of cone photoreceptors. Cone pedicles form spatially segregated functionally opposite connections with ON and OFF bipolar cells. Here, we discover that mammalian cones express LRFN2, a cell-adhesion molecule, which localizes to the pedicle base. LRFN2 stabilizes basal contacts between cone pedicles and OFF bipolar cell dendrites to guide pathway-specific partner choices, encompassing multiple cell types. In addition, LRFN2 trans-synaptically organizes glutamate receptor clusters, determining the contrast preferences of the OFF pathway. ON and OFF pathways converge in the inner retina to regulate bipolar cell outputs. We analyze LRFN2's contributions to ON-OFF interactions, pathway asymmetries, and neural and behavioral responses to approaching predators. Our results reveal that LRFN2 controls the formation of the OFF pathway in vision, supports parallel processing in a single synapse, and shapes contrast coding and the detection of visual threats.

Open-source antibodies as a path to enhanced research reproducibility and transparency

Antibodies are important tools with diverse uses in biomedical research. However, open access to reliable sources of well-characterized antibodies with unambiguous molecular identities remains an obstacle to research transparency and reproducibility. We propose here a community shift towards open-source antibodies, analogous to open-source computer software. The tenets of such antibodies are that 1) they are available to researchers in a ready to use form, 2) the renewable source of the antibody (e.g., hybridoma cells or plasmid) is also widely available ensuring reproducible and cost-effective access to the same antibody, and 3) the antibody sequence is publicly available. With these criteria met, the antibody can be widely used with the transparent assurance associated with a molecularly defined reagent, and the code can be edited to generate antibody variants to meet researchers' specific needs. We (the UC Davis/NIH NeuroMab Facility, the Development Studies Hybridoma Bank, and Addgene) have established a consortium to provide open-source access to a large collection of well characterized antibodies. As open-source software has benefitted both users and developers, we suggest open-source antibodies will have a similar positive impact on antibody based biomedical research. We encourage funding agencies to support initiatives to expand access to open-source antibody resources, and researchers to both utilize and to contribute to them, with a goal of enabling more reliable and cost-effective pursuit of research.

Behavioral Modulation and Molecular Definition of Wide-Field Vertical Cells in the Mouse Superior Colliculus

Visual information can have different meanings across species, and the same visual stimulus can drive appetitive or aversive behavior. The superior colliculus (SC), a visual center located in the midbrain has been involved in driving such behaviors. Within this structure, the wide-field vertical cells (WFV) are a conserved morphological cell type that is present in species ranging from reptiles to cats (Basso et al., 2021). Here, we report our investigation of the connectivity of the WFV, their visual responses, and how these responses are modulated by locomotion in male and female laboratory mice. We also address the molecular definition of these cells and attempt to reconcile recent findings acquired by RNA sequencing of single cells in the SC with the Ntsr1-Cre GN209 transgenic mouse line which was previously used to investigate WFV. We use viral strategies to reveal WFV inputs and outputs and confirm their unique response properties using in vivo two-photon imaging. Among the stimuli tested, WFV prefer looming stimuli, a small moving spot, and upward-moving visual stimuli. We find that only visual responses driven by a looming stimulus show a significant modulation by locomotion. We identify several inputs to the WFV as potential candidates for this modulation. These results suggest that WFV integrate information across multiple brain regions and are subject to behavioral modulation. Taken together, our results pave the way to elucidate the role of these neurons in visual behavior and allow us to interrogate the definition of cell types in the light of new molecular definitions.

Neural heterogeneity enhances reliable neural information processing: Local sensitivity and globally input-slaved transient dynamics

Cortical neuronal activity varies over time and across repeated trials, yet consistently represents stimulus features. The dynamical mechanism underlying this reliable representation and computation remains elusive. This study uncovers a mechanism for reliable neural information processing, leveraging a biologically plausible network model incorporating neural heterogeneity. First, we investigate neuronal timescale diversity, revealing that it disrupts intrinsic coherent spatiotemporal patterns, induces firing rate heterogeneity, enhances local responsive sensitivity, and aligns network activity closely with input. The system exhibits globally input-slaved transient dynamics, essential for reliable neural information processing. Other neural heterogeneities, such as nonuniform input connections, spike threshold heterogeneity, and network in-degree heterogeneity, play similar roles, highlighting the importance of neural heterogeneity in shaping consistent stimulus representation. This mechanism offers a potentially general framework for understanding neural heterogeneity in reliable computation and informs the design of reservoir computing models endowed with liquid wave reservoirs for neuromorphic computing.

Germline mosaicism in TCF20-associated neurodevelopmental disorders: a case study and literature review

Autosomal dominant variants in transcription factor 20 (TCF20) can result in TCF20-associated neurodevelopmental disorder (TAND), a condition characterized by developmental delay and intellectual disability, autism, dysmorphisms, dystonia, and variable other neurological features. To date, a total of 91 individuals with TAND have been reported; ~67% of cases arose de novo, while ~10% were inherited, and, intriguingly, ~8% were either confirmed or suspected to have arisen via germline mosaicism. Here, we describe two siblings with a developmental condition characterized by intellectual disability, autism, a circadian rhythm sleep disorder, and attention deficit hyperactivity disorder (ADHD) caused by a novel heterozygous single nucleotide deletion in the TCF20 gene, NM_001378418.1:c.4737del; NP_001365347.1:p.Lys1579Asnfs*36 (GRCh38/hg38). The variant was not detected in DNA extracted from peripheral blood in either parent by Sanger sequencing of PCR-generated amplicons, or by deep sequencing of PCR amplicons using MiSeq and MinION. However, droplet digital PCR (ddPCR) of DNA derived from early morning urine detected the variation in 3.2% of the father's urothelial cells, confirming germline mosaicism. This report is only the second to confirm with physical evidence TCF20 germline mosaicism and discusses germline mosaicism as a likely under-detected mode of inheritance in neurodevelopmental conditions.

Cell-Type Specific Circuits in the Mammillary Body for Place and Object Recognition Memory

Mammillary body (MB) is traditionally viewed as a structural node of an anatomic circuit for emotion and memory. However, little is known about its molecular and cellular organizations. Here, a discovery that MB contains four subtypes of neurons that occupy different spatial subregions is reported. Of these, two subtypes of neurons are tagged by parvalbumin (PV) and dopamine receptor-D2 (Drd2) markers. PV neurons are spontaneously active, whereas Drd2 neurons are inactive at rest and generate rebound bursts. These two distinct electrophysiological properties are encoded by Kcnn4 and Cacna1h. PV and Drd2 neurons generate two distinct cell-type specific circuits by receiving inputs from two discrete subiculum neuronal classes. Gain- and loss-of-function studies on these cortical-subcortical circuits demonstrate their differential roles for place and object recognition memory. This finding provides a comprehensive molecular and structural atlas of MB neurons at single-cell resolution and reveals that MB contains molecularly, structurally, and functionally dissociable streams within its serial architecture.

Spotiphy enables single-cell spatial whole transcriptomics across an entire section

Spatial transcriptomics (ST) has advanced our understanding of tissue regionalization by enabling the visualization of gene expression within whole-tissue sections, but current approaches remain plagued by the challenge of achieving single-cell resolution without sacrificing whole-genome coverage. Here we present Spotiphy (spot imager with pseudo-single-cell-resolution histology), a computational toolkit that transforms sequencing-based ST data into single-cell-resolved whole-transcriptome images. Spotiphy delivers the most precise cellular proportions in extensive benchmarking evaluations. Spotiphy-derived inferred single-cell profiles reveal astrocyte and disease-associated microglia regional specifications in Alzheimer's disease and healthy mouse brains. Spotiphy identifies multiple spatial domains and alterations in tumor-tumor microenvironment interactions in human breast ST data. Spotiphy bridges the information gap and enables visualization of cell localization and transcriptomic profiles throughout entire sections, offering highly informative outputs and an innovative spatial analysis pipeline for exploring complex biological systems.

Single-cell and spatial genomic landscape of non-small cell lung cancer brain metastases

Brain metastases frequently develop in patients with non-small cell lung cancer (NSCLC) and are a common cause of cancer-related deaths, yet our understanding of the underlying human biology is limited. Here we performed multimodal single-nucleus RNA and T cell receptor, single-cell spatial and whole-genome sequencing of brain metastases and primary tumors of patients with treatment-naive NSCLC. Chromosomal instability (CIN) is a distinguishing genomic feature of brain metastases compared with primary tumors, which we validated through integrated analysis of molecular profiling and clinical data in 4,869 independent patients, and a new cohort of 12,275 patients with NSCLC. Unbiased analyses revealed transcriptional neural-like programs that strongly enriched in cancer cells from brain metastases, including a recurring, CINhigh cell subpopulation that preexists in primary tumors but strongly enriched in brain metastases, which was also recovered in matched single-cell spatial transcriptomics. Using multiplexed immunofluorescence in an independent cohort of treatment-naive pairs of primary tumors and brain metastases from the same patients with NSCLC, we validated genomic and tumor-microenvironmental findings and identified a cancer cell population characterized by neural features strongly enriched in brain metastases. This comprehensive analysis provides insights into human NSCLC brain metastasis biology and serves as an important resource for additional discovery.

Transcriptomic and spatial GABAergic neuron subtypes in zona incerta mediate distinct innate behaviors

Understanding the anatomical connection and behaviors of transcriptomic neuron subtypes is critical to delineating cell type-specific functions in the brain. Here we integrated single-nucleus transcriptomic sequencing, in vivo circuit mapping, optogenetic and chemogenetic approaches to dissect the molecular identity and function of heterogeneous GABAergic neuron populations in the zona incerta (ZI) in mice, a region involved in modulating various behaviors. By microdissecting ZI for transcriptomic and spatial gene expression analyses, our results revealed two non-overlapping Ecel1- and Pde11a-expressing GABAergic neurons with dominant expression in the rostral and medial zona incerta (ZIrEcel1 and ZImPde11a), respectively. The GABAergic projection from ZIrEcel1 to periaqueductal gray mediates self-grooming, while the GABAergic projection from ZImPde11a to the oral part of pontine reticular formation promotes transition from sleep to wakefulness. Together, our results revealed the molecular markers, spatial organization and specific neuronal circuits of two discrete GABAergic projection neuron populations in segregated subregions of the ZI that mediate distinct innate behaviors, advancing our understanding of the functional organization of the brain.

Precise in vivo RNA base editing with a wobble-enhanced circular CLUSTER guide RNA

Recruiting the endogenous editing enzyme adenosine deaminase acting on RNA (ADAR) with tailored guide RNAs for adenosine-to-inosine (A-to-I) RNA base editing is promising for safely manipulating genetic information at the RNA level. However, the precision and efficiency of editing are often compromised by bystander off-target editing. Here, we find that in 5'-UAN triplets, which dominate bystander editing, G•U wobble base pairs effectively mitigate off-target events while maintaining high on-target efficiency. This strategy is universally applicable to existing A-to-I RNA base-editing systems and complements other suppression methods such as G•A mismatches and uridine (U) depletion. Combining wobble base pairing with a circularized format of the CLUSTER approach achieves highly precise and efficient editing (up to 87%) of a disease-relevant mutation in the Mecp2 transcript in cell culture. Virus-mediated delivery of the guide RNA alone realizes functional MeCP2 protein restoration in the central nervous system of a murine Rett syndrome model with editing yields of up to 19% and excellent bystander control in vivo.

Fam163a knockdown and mitochondrial stress in the arcuate nucleus of hypothalamus reduce AgRP neuron activity and differentially regulate mitochondrial dynamics in mice

AIM

Mitochondria play key roles in neuronal activity, particularly in modulating agouti-related protein (AgRP) and proopiomelanocortin (POMC) neurons in the arcuate nucleus of the hypothalamus (ARC), which regulates food intake. FAM163A, a newly identified protein, is suggested to be part of the mitochondrial proteome, though its functions remain largely unknown. This study aimed to investigate the effects of Fam163a knockdown and mitochondrial dysfunction on food intake, AgRP neuron activity, and mitochondrial function in the hypothalamus.

METHODS

Male C57BL/6 and AgRP-Cre mice received intracranial injections of either Fam163a shRNA, rotenone, or appropriate controls. Behavioral assessments included food intake, locomotor activity, and anxiety-like behaviors. qRT-PCR was used to quantify the expression of the genes related to food intake, mitochondrial biogenesis, dynamics, and oxidative stress. Blood glucose, serum insulin, and leptin levels were measured. Electrophysiological patch-clamp recordings were used to assess the AgRP neuronal activity.

RESULTS

Fam163a knockdown in the ARC increased the cumulative food intake in short term (first 7 days) without altering the 25-day food intake and significantly increased the Pomc mRNA expression. Fam163a silencing significantly reduced leptin levels. Both Fam163a knockdown and rotenone significantly reduced the firing frequency of AgRP neurons. Neither Fam163a silencing nor rotenone altered locomotor or anxiety-like behaviors. Fam163a knockdown and rotenone differentially altered the expression of mitochondrial biogenesis-, mitophagy-, fusion-, and oxidative stress-related genes.

CONCLUSION

Hypothalamic FAM163A may play a role in modulating AgRP neuronal activity through regulating mitochondrial biogenesis, dynamics, and redox state. These findings provide insights into the role of FAM163A and mitochondrial stress in the central regulation of metabolism.

Spatial Transcriptomics and Proteomics Profiling After Ischemic Stroke Reperfusion: Insights Into Vascular Alterations

BACKGROUND

More than half of patients with ischemic stroke experience futile reperfusion, increasing the risk of death and disabilities despite a successful recanalization. The reason behind this is debated, and we aim to investigate cerebrovascular changes toward a broader understanding of these conditions. We hypothesize that ischemic stroke reperfusion modifies the expression profile in the microvasculature in a spatial manner toward peri-infarct brain edema and circulatory failure.

METHODS

We investigated the early (24-hour) changes in spatial gene expression in the brain parenchymal endothelial cells and mural cells following ischemia stroke reperfusion in 13- to 14-week-old C57BL/6JRj male mice (n=5). Ischemia was induced by occlusion of the middle cerebral artery for 60 minutes, and Nissl staining was used to validate infarct size. Spatial transcriptomics complemented by bulk proteomics was conducted in the peri-infarct cortex region and validated with immunohistochemical semiquantification of proteins of interest. To avoid individual biological variations, changes in the peri-infarct cortex region were expressed relatively to the matching contralateral hemisphere region.

RESULTS

Ischemic stroke reperfusion impaired the blood-brain barrier integrity through junctional Cldn5 (claudin-5) downregulation, changes of the actin cytoskeleton adhesion, and high expression of the proinflammatory Il-6 (interleukin-6). Molecules important for extracellular Ca2+ influx and intracellular Ca2+ release, Cacna1e (R-type Ca2+ channels), Orai2, Ryr3, Itpr1, and Itpka (inositol-trisphosphate 3-kinase A), were markedly reduced. Furthermore, reduced Grm5 (glutamate receptor 5) associated with upregulated Nfatc3 and Stat3 implicates suppression of the contractile phenotype, suggesting reduced poststroke vascular resistance due to loss of mural cell tone. The complete spatial transcriptomics map over the ipsilateral and contralateral hemispheres is available online as a Web tool.

CONCLUSIONS

Emphasizing the spatial molecular pattern behind blood-brain barrier disruption and loss of the vascular tone in the acute phase following ischemic stroke reperfusion suggests the gene expression contribution for a therapeutic target in ischemia-reperfusion abnormalities.

Oscillatory DeltaC Expression in Neural Progenitors Primes the Prototype of Forebrain Development

Notch signaling plays a pivotal role in regulating various developmental processes, particularly in controlling the timing of neuronal production within the developing neocortex. Central to this regulatory mechanism is the oscillatory pattern of Delta, which functions as a developmental clock modulator. Its deficiency profoundly impairs mammalian brain formation, highlighting its fundamental role in brain development. However, zebrafish carrying a mutation in the functional ortholog DeltaC (dlc) within their functional ortholog exhibit an intact forebrain structure, implying evolutionary variations in Notch signaling within the forebrain. In this study, we unveil the distinct yet analogous expression profiles of Delta and Her genes in the developing vertebrate forebrain. Specifically, for the first time, we detected the oscillatory expression of the Delta gene dlc in the developing zebrafish forebrain. Although this oscillatory pattern appeared irregular and was not pervasive among the progenitor population, attenuation of the dlc-involved Notch pathway using a γ-secretase inhibitor impaired neuronal differentiation in the developing zebrafish forebrain, revealing the indispensable role of the dlc-involved Notch pathway in regulating early zebrafish neurogenesis. Taken together, our results demonstrate the foundational prototype of dlc-involved Notch signaling in the developing zebrafish forebrains, upon which the intricate patterns of the mammalian neocortex may have been sculpted.

Differing genetics of saline and cocaine self administration in the hybrid mouse diversity panel

To identify genes that regulate the response to the potentially addictive drug cocaine, we performed a control experiment using genome-wide association studies (GWASs) and RNA-Seq of a panel of inbred and recombinant inbred mice undergoing intravenous self administration of saline. A linear mixed model increased statistical power for analysis of the longitudinal behavioral data, which was acquired over 10 days. A total of 145 loci were identified for saline compared to 17 for the corresponding cocaine GWAS. Only one locus overlapped. Transcriptome-wide association studies (TWASs) using RNA Seq data from the nucleus accumbens and medial frontal cortex identified 5031434O11Rik and Zfp60 as significant for saline self administration. Two other genes, Myh4 and Npc1, were nominated based on proximity to loci for multiple endpoints or a cis locus regulating expression. All four genes have previously been implicated in locomotor activity, despite the absence of a strong relationship between saline taking and distance traveled in the open field. Our results indicate a distinct genetic basis for saline and cocaine self-administration, and suggest some common genes for saline self-administration and locomotor activity.

Reelin marks cocaine-activated striatal neurons, promotes neuronal excitability, and regulates cocaine reward

Drugs of abuse activate defined neuronal populations in reward structures such as the nucleus accumbens (NAc), which promote the enduring synaptic, circuit, and behavioral consequences of drug exposure. While the molecular and cellular effects arising from experience with drugs like cocaine are increasingly well understood, mechanisms that dictate NAc neuronal recruitment remain unknown. Here, we leveraged unbiased single-nucleus transcriptional profiling and targeted in situ detection to identify Reln (encoding the secreted glycoprotein, Reelin) as a marker of cocaine-activated neuronal populations within the rat NAc. A CRISPR interference approach enabling selective Reln knockdown in the adult NAc altered expression of calcium signaling genes, promoted a transcriptional trajectory consistent with loss of cocaine sensitivity, and decreased MSN excitability. Behaviorally, Reln knockdown prevented cocaine locomotor sensitization, abolished cocaine place preference memory, and decreased cocaine self-administration behavior. These results identify Reelin as a critical mechanistic link between neuronal activation and cocaine-induced behavioral adaptations.

GH-Releasing Hormone Neurons Regulate the Hypothalamic-Pituitary-Somatotropic Axis via Short-Loop Negative Feedback

Growth hormone (GH)-releasing hormone (GHRH) neurons are master regulators of GH secretion. However, the role of these cells in controlling pituitary GH secretion through short-loop negative feedback has not yet been fully clarified. Thus, GHRH-specific GH receptor (GHR) knockout (GHRHΔGHR) mice were generated, and possible consequences on GH secretion and body growth were determined. Approximately 60% of arcuate nucleus GHRH neurons exhibited GH-induced STAT5 phosphorylation, a marker of GHR-expressing cells. This response was practically eliminated in GHRHΔGHR mice. GHR ablation in GHRH-expressing cells increased body weight, lean mass, and naso-anal length in male and female mice without affecting fat mass. The higher body growth of GHRHΔGHR mice was associated with increases in GH secretion, mainly via higher pulsatile GH secretion and GH pulse amplitude. GHRHΔGHR female mice also showed increased GH pulse frequency and basal (non-pulsatile) secretion compared to control females. Liver Igf1 expression was increased only in GHRHΔGHR male mice. Mice carrying ablation of the insulin-like growth factor-1 (IGF-1) receptor (IGF1R) or both GHR and IGF1R in GHRH-expressing cells were generated. The increases in body growth and serum IGF-1 levels were significantly higher in GHRHΔGHR/IGF1R mice compared to GHRHΔGHR mice but similar to levels observed in GHRHΔIGF1R mice. Electrophysiological experiments showed no acute changes in the activity of GHRH neurons after GH or IGF-1 exposure. In conclusion, GH feeds back on GHRH cells to control the hypothalamic-pituitary-somatotropic axis. However, IGF1R signaling prevails over GHR as the primary signal sensed by GHRH neurons to regulate GH secretion.

Single-cell spatial transcriptomic atlas of the whole mouse brain

A comprehensive atlas of genes, cell types, and their spatial distribution across a whole mammalian brain is fundamental for understanding the function of the brain. Here, using single-nucleus RNA sequencing (snRNA-seq) and Stereo-seq techniques, we generated a mouse brain atlas with spatial information for 308 cell clusters at single-cell resolution, involving over 4 million cells, as well as for 29,655 genes. We have identified cell clusters exhibiting preference for cortical subregions and explored their associations with brain-related diseases. Additionally, we pinpointed 155 genes with distinct regional expression patterns within the brainstem and unveiled 513 long non-coding RNAs showing region-enriched expression in the adult brain. Parcellation of brain regions based on spatial transcriptomic information revealed fine structure for several brain areas. Furthermore, we have uncovered 411 transcription factor regulons showing distinct spatiotemporal dynamics during neurodevelopment. Thus, we have constructed a single-cell-resolution spatial transcriptomic atlas of the mouse brain with genome-wide coverage.

Individualized mouse brain network models produce asymmetric patterns of functional connectivity after simulated traumatic injury

The functional and cognitive effects of traumatic brain injury (TBI) are poorly understood, as even mild injuries (concussion) can lead to long-lasting, untreatable symptoms. Simplified brain dynamics models may help researchers better understand the relationship between brain injury patterns and functional outcomes. Properly developed, these computational models provide an approach to investigate the effects of both computational and in vivo injury on simulated dynamics and cognitive function, respectively, for model organisms. In this study, we apply the Kuramoto model and an existing mesoscale mouse brain structural network to develop a simplified computational model of mouse brain dynamics. We explore how to optimize our initial model to predict existing mouse brain functional connectivity collected from mice under various anesthetic protocols. Finally, to determine how strongly the changes in our optimized models' dynamics can predict the extent of a brain injury, we investigate how our simulations respond to varying levels of structural network damage. Results predict a mixture of hypo- and hyperconnectivity after experimental TBI, similar to results in TBI survivors, and also suggest a compensatory remodeling of connections that may have an impact on functional outcomes after TBI.

Brainstem neuropeptidergic neurons link a neurohumoral axis to satiation

Hunger is evolutionarily hardwired to ensure that an animal has sufficient energy to survive and reproduce. Just as important as knowing when to start eating is knowing when to stop eating. Here, using spatially resolved single-cell phenotyping, we characterize a population of neuropeptidergic neurons in the brainstem's dorsal raphe nucleus (DRN) and describe how they regulate satiation. These neurons track food from sensory presentation through ingestion, integrate these signals with slower-acting humoral cues, and express cholecystokinin (CCK). These CCK neurons bidirectionally regulate meal size, driving a sustained meal termination signal with a built-in delay. They are also well positioned to sense and respond to ingestion: they express a host of metabolic signaling factors and are integrated into an extended network known to regulate feeding. Together, this work demonstrates how DRN CCK neurons regulate satiation and identifies a likely conserved cellular mechanism that transforms diverse neurohumoral signals into a key behavioral output.

Advances in Spatial Omics Technologies

Rapidly developing spatial omics technologies provide us with new approaches to deeply understanding the diversity and functions of cell types within organisms. Unlike traditional approaches, spatial omics technologies enable researchers to dissect the complex relationships between tissue structure and function at the cellular or even subcellular level. The application of spatial omics technologies provides new perspectives on key biological processes such as nervous system development, organ development, and tumor microenvironment. This review focuses on the advancements and strategies of spatial omics technologies, summarizes their applications in biomedical research, and highlights the power of spatial omics technologies in advancing the understanding of life sciences related to development and disease.

Pain persists in mice lacking both Substance P and CGRPα signaling

The neuropeptides Substance P and CGRPα have long been thought important for pain sensation. Both peptides and their receptors are expressed at high levels in pain-responsive neurons from the periphery to the brain making them attractive therapeutic targets. However, drugs targeting these pathways individually did not relieve pain in clinical trials. Since Substance P and CGRPα are extensively co-expressed, we hypothesized that their simultaneous inhibition would be required for effective analgesia. We therefore generated Tac1 and Calca double knockout (DKO) mice and assessed their behavior using a wide range of pain-relevant assays. As expected, Substance P and CGRPα peptides were undetectable throughout the nervous system of DKO mice. To our surprise, these animals displayed largely intact responses to mechanical, thermal, chemical, and visceral pain stimuli, as well as itch. Moreover, chronic inflammatory pain and neurogenic inflammation were unaffected by loss of the two peptides. Finally, neuropathic pain evoked by nerve injury or chemotherapy treatment was also preserved in peptide-deficient mice. Thus, our results demonstrate that even in combination, Substance P and CGRPα are not required for the transmission of acute and chronic pain.

Stress-induced GHS-R1a expression in medial prefrontal cortical neurons promotes vulnerability to anxiety in mice

The neural basis of anxiety is unclear, which hinders the treatment of anxiety disorders. Here, we found that αCaMKII+ neurons in the medial prefrontal cortex (mPFCαCaMKII+) responded to stressors with increased activity both under physiological conditions and after repeated restraint stress (RRS) in mice. Chemogenetic activation of mPFCαCaMKII+ neurons ameliorated stress-induced anxiety. A delayed increase in the expression of growth hormone secretagogue receptor 1a (GHS-R1a), the receptor of the peripheral metabolic hormone ghrelin, in mPFCαCaMKII+ neurons coincided with reduced excitatory synaptic transmission and the development of RRS-induced enhancement of anxiety-related behavior. Virus-mediated GHS-R1a upregulation in mPFCαCaMKII+ neurons exaggerated the excitation/inhibition (E/I) imbalance and promoted anxiety-related behavior, whereas GHS-R1a knockdown had the opposite effect. We conclude that GHS-R1a signaling contributes to the development of stress-induced anxiety by shaping synaptic activity of mPFCαCaMKII+ neurons. GHS-R1a may be a new therapeutic target for treating anxiety disorders.

Distinguish risk genes functioning at presynaptic or postsynaptic regions and key connectomes associated with pathological α-synuclein spreading

Previous studies have suggested that pathological α-synuclein (α-Syn) mainly transmits along the neuronal network, but several key questions remain unanswered: (1) How many and which connections in the connectome are necessary for predicting the progression of pathological α-Syn? (2) How to identify risk gene that affects pathology spreading functioning at presynaptic or postsynaptic regions, and are these genes enriched in different cell types? Here, we addressed these key questions with novel mathematical models. Strikingly, the spreading of pathological α-Syn is predominantly determined by the key subnetworks composed of only 2% of the strongest connections in the connectome. We further explored the genes that are responsible for the selective vulnerability of different brain regions to transmission to distinguish the genes that play roles in presynaptic from those in postsynaptic regions. Those risk genes were significantly enriched in microglial cells of presynaptic regions and neurons of postsynaptic regions. Gene regulatory network analyses were then conducted to identify 'key drivers' of genes responsible for selective vulnerability and overlapping with Parkinson's disease risk genes. By identifying and discriminating between key gene mediators of transmission operating at presynaptic and postsynaptic regions, our study has demonstrated for the first time that these are functionally distinct processes.

Translatome analysis reveals cellular network in DLK-dependent hippocampal glutamatergic neuron degeneration

The conserved MAP3K12/Dual Leucine Zipper Kinase (DLK) plays versatile roles in neuronal development, axon injury and stress responses, and neurodegeneration, depending on cell-type and cellular contexts. Emerging evidence implicates abnormal DLK signaling in several neurodegenerative diseases. However, our understanding of the DLK-dependent gene network in the central nervous system remains limited. Here, we investigated the roles of DLK in hippocampal glutamatergic neurons using conditional knockout and induced overexpression mice. We found that dorsal CA1 and dentate gyrus neurons are vulnerable to elevated expression of DLK, while CA3 neurons appear less vulnerable. We identified the DLK-dependent translatome that includes conserved molecular signatures and displays cell-type specificity. Increasing DLK signaling is associated with disruptions to microtubules, potentially involving STMN4. Additionally, primary cultured hippocampal neurons expressing different levels of DLK show altered neurite outgrowth, axon specification, and synapse formation. The identification of translational targets of DLK in hippocampal glutamatergic neurons has relevance to our understanding of selective neuron vulnerability under stress and pathological conditions.

Beyond vessels: unraveling the impact of VEGFs on neuronal functions and structure

Neurons rely on the bloodstream for essential nutrients and oxygen, which is facilitated by an intricate coupling of the neuronal and vascular systems. Central to this neurovascular interaction is the vascular endothelial growth factor (VEGF) family, a group of secreted growth factors traditionally known for their roles in promoting endothelial cell proliferation, migration, and survival in the cardiovascular and lymphatic systems. However, emerging evidence shows that VEGFs also play indispensable roles in the nervous system, extending beyond their canonical angiogenic and lymphangiogenic functions. Over the past two decades, VEGFs have been found to exert direct effects on neurons, influencing key aspects of neuronal function independently of their actions on vascular cells. In particular, it has become increasingly evident that VEGFs also play crucial functions in the development, regulation, and maintenance of neuronal morphology. Understanding the roles of VEGFs in neuronal development is of high scientific and clinical interest because of the significance of precise neuronal morphology for neural connectivity and network function, as well as the association of morphological abnormalities with neurological and neurodegenerative disorders. This review begins with an overview of the VEGF family members, their structural characteristics, receptors, and established roles in vasculature. However, it then highlights and focuses on the exciting variety of neuronal functions of VEGFs, especially their crucial role in the development, regulation, and maintenance of neuronal morphology.

STsisal: a reference-free deconvolution pipeline for spatial transcriptomics data

Spatial transcriptomics has emerged as an invaluable tool, helping to reveal molecular status within complex tissues. Nonetheless, these techniques have a crucial challenge: the absence of single-cell resolution, resulting in the observation of multiple cells in each spatial spot. While reference-based deconvolution methods have aimed to solve the challenge, their effectiveness is contingent upon the quality and availability of single-cell RNA (scRNA) datasets, which may not always be accessible or comprehensive. In response to these constraints, our study introduces STsisal, a reference-free deconvolution method meticulously crafted for the intricacies of spatial transcriptomics (ST) data. STsisal leverages a novel approach that integrates marker gene selection, mixing ratio decomposition, and cell type characteristic matrix analysis to discern distinct cell types with precision and efficiency within complex tissues. The main idea of our method is its adaptation of the SISAL algorithm, which expertly disentangles the ratio matrix, facilitating the identification of simplices within the ST data. STsisal offers a robust means to unveil the intricate composition of cell types in spatially resolved transcriptomic data. To verify the efficacy of STsisal, we conducted extensive simulations and applied the method to real data, comparing its performance against existing techniques. Our findings highlight the superiority of STsisal, underscoring its utility in capturing the cell composition within complex tissues.

Pharmacological Enhancement of Adult Hippocampal Neurogenesis Improves Behavioral Pattern Separation in Young and Aged Male Mice

Background

Impairments in behavioral pattern separation (BPS)-the ability to distinguish between similar contexts or experiences-contribute to memory interference and overgeneralization seen in many neuropsychiatric conditions, including depression, anxiety, posttraumatic stress disorder, dementia, and age-related cognitive decline. Although BPS relies on the dentate gyrus and is sensitive to changes in adult hippocampal neurogenesis, its significance as a pharmacological target has not been tested.

Methods

In this study, we applied a human neural stem cell high-throughput screening cascade to identify compounds that increase human neurogenesis. One compound with a favorable profile, RO6871135, was then tested in young and aged mice for effects on BPS and anxiety-related behaviors.

Results

Chronic treatment with RO6871135 (7.5 mg/kg) increased adult hippocampal neurogenesis and improved BPS in a fear discrimination task in both young and aged mice. RO6871135 treatment also lowered innate anxiety-like behavior, which was more apparent in mice exposed to chronic corticosterone. Ablation of adult hippocampal neurogenesis by hippocampal irradiation supported a neurogenesis-dependent mechanism for RO6871135-induced improvements in BPS. To identify possible mechanisms of action, in vitro and in vivo kinase inhibition and chemical proteomics assays were performed. These tests indicated that RO6871135 inhibited CDK8, CDK11, CaMKIIa, CaMKIIb, MAP2K6, and GSK-3β. An analog compound also demonstrated high affinity for CDK8, CaMKIIa, and GSK-3β.

Conclusions

These studies demonstrate a method for empirical identification and preclinical testing of novel neurogenic compounds that can improve BPS and point to possible novel mechanisms that can be interrogated for the development of new therapies to improve specific endophenotypes such as impaired BPS.

Neuron-Specific Glycine Metabolism Links Transfer RNA Epitranscriptomic Regulation to Complex Behaviors

Background

The presence of treatment resistance in neuropsychiatric disease suggests that novel mechanism-based discoveries and therapies could benefit the field, with a viable candidate being transfer RNA (tRNA) epitranscriptomics. Nsun2 tRNA methyltransferase depletion in mature neurons elicits changes in complex behaviors relevant for fear, anxiety, and other neuropsychiatric phenotypes. However, it remains unclear whether this is due to dysregulated tRNAs or metabolic shifts that impact the neuronal translatome by activation of stress messengers together with alterations in amino acid supply.

Methods

To link specific molecular alterations resulting from neuronal Nsun2 ablation to neuropsychiatric phenotypes, we used drug-induced phosphoactivation of stress response translation initiation factors together with disruption of NSUN2-regulated glycine tRNAs and cell type-specific ablation of the glycine cleavage system modeling the excessive upregulation of this amino acid in the Nsun2-deficient brain. Changes in extracellular glycine levels were monitored by an optical glycine Förster resonance energy transfer (FRET) sensor in the hippocampus, and behavioral phenotyping included cognition, anxiety-like behavior, and behavioral despair.

Results

Increased motivated escape behaviors were specifically observed in mice with neuron-specific ablation of Gldc, resulting in an excess in cortical glycine levels comparable to a similar phenotype in mice after deletion of neuronal Nsun2. None of these phenotypes were observed in mice treated with tunicamycin for chemoactivation of integrative stress response pathways or in mice genetically engineered for decreased glycine tRNA gene dosage. In the Nsun2-deficient brain, dynamic glycine profiles in the hippocampal extracellular space were fully maintained at baseline and in the context of neuronal activity.

Conclusions

Alterations in neuronal glycine metabolism, resulting from targeted ablation of the glycine cleavage system or disruption of the tRNA regulome, elicit changes in complex behaviors in mice relevant for neuropsychiatric phenotypes.

Aged hippocampal single-cell atlas screening unveils disrupted neuroglial system in postoperative cognitive impairment

Glia-neuron interaction is a crucial feature in aged hippocampus during the occurrence of postoperative cognitive impairment. However, the regulatory effects of microglia, astrocytes, and oligodendrocytes in this glia-neuron interaction, the potential mechanisms and gene targets are still to be elucidated. Here, single-cell RNA sequencing was performed to detect the perioperative genomic expression characteristics of neuroglial system in the hippocampus of aged mice, and to investigate the potential cross-cellular mechanisms and valuable treatment options for glia-neuron interaction-related cognitive impairment. We found that postoperative neurons and glia cells exhibited protein dysmetabolism and mitochondrial electron misrouting. Impaired autophagy and circadian rhythm worsened microglia activation/neuroinflammation, and exacerbated these metabolic alterations. Reactive microglia also aggravated astrocyte and oligodendrocyte cytotoxicity through the PGD2/DP and complement pathways, altering glutamate level and synaptic function via the "tripartite synapses" model, and affecting neuronal myelination. Ligand-receptor communication also indicated these synaptic and axonal dysfunctions via enhanced MDK and PTN pathways. Additionally, we found that anesthetic dexmedetomidine hold therapeutic potential within the disrupted neuroglial system. It enhanced neuronal metabolic rebalance (Atf3-related) and reduced neuroinflammation from a multicellular perspective, therefore improving postoperative cognitive impairment. Together, our study proposes an aged hippocampal cell atlas and provides insights into the role of disrupted glia-neuron cycle in postoperative cognitive impairment. Our findings also elucidate the therapeutic potential and mechanism of dexmedetomidine intervention.

Trajectories of working memory and decision making abilities along juvenile development in mice

Rodents commonly serve as model organisms for the investigation of human mental disorders by capitalizing on behavioral commonalities. However, our understanding of the developmental dynamics of complex cognitive abilities in rodents remains incomplete. In this study, we examined spatial working memory as well as odor-and texture-based decision making in mice using a delayed non-match to sample task and a two-choice set-shifting task, respectively. Mice were investigated during different stages of development: pre-juvenile, juvenile, and young adult age. We show that, while working memory abilities in mice improve with age, decision making performance peaks during juvenile age by showing a sex-independent trajectory. Moreover, cFos expression, as a first proxy for neuronal activity, shows distinct age-and brain area-specific changes that relate to task-specific behavioral performance. The distinct developmental trajectories of working memory and decision making in rodents resemble those previously reported for humans.

Benchmarking macaque brain gene expression for horizontal and vertical translation

The spatial patterning of gene expression shapes cortical organization and function. The macaque is a fundamental model organism in neuroscience, but the translational potential of macaque gene expression rests on the assumption that it is a good proxy for patterns of corresponding proteins (vertical translation) and for patterns of orthologous human genes (horizontal translation). Here, we systematically benchmark regional gene expression in macaque cortex against (i) macaque cortical receptor density and in vivo and ex vivo microstructure and (ii) human cortical gene expression. We find moderate cortex-wide correspondence between macaque gene expression and protein density, which improves by considering layer-specific gene expression. Half of the examined genes exhibit significant correlation between macaque and human across the cortex. Interspecies correspondence of gene expression is greater in unimodal than in transmodal cortex, recapitulating evolutionary cortical expansion and gene-protein correspondence in the macaque. These results showcase the potential and limitations of macaque cortical transcriptomics for translational discovery within and across species.

Brain-wide presynaptic networks of functionally distinct cortical neurons

Revealing the connectivity of functionally identified individual neurons is necessary to understand how activity patterns emerge and support behaviour. Yet the brain-wide presynaptic wiring rules that lay the foundation for the functional selectivity of individual neurons remain largely unexplored. Cortical neurons, even in primary sensory cortex, are heterogeneous in their selectivity, not only to sensory stimuli but also to multiple aspects of behaviour. Here, to investigate presynaptic connectivity rules underlying the selectivity of pyramidal neurons to behavioural state1-10 in primary somatosensory cortex (S1), we used two-photon calcium imaging, neuropharmacology, single-cell-based monosynaptic input tracing and optogenetics. We show that behavioural state-dependent activity patterns are stable over time. These are minimally affected by direct neuromodulatory inputs and are driven primarily by glutamatergic inputs. Analysis of brain-wide presynaptic networks of individual neurons with distinct behavioural state-dependent activity profiles revealed that although behavioural state-related and behavioural state-unrelated neurons shared a similar pattern of local inputs within S1, their long-range glutamatergic inputs differed. Individual cortical neurons, irrespective of their functional properties, received converging inputs from the main S1-projecting areas. Yet neurons that tracked behavioural state received a smaller proportion of motor cortical inputs and a larger proportion of thalamic inputs. Optogenetic suppression of thalamic inputs reduced behavioural state-dependent activity in S1, but this activity was not externally driven. Our results reveal distinct long-range glutamatergic inputs as a substrate for preconfigured network dynamics associated with behavioural state.

Cross-ancestry genome-wide association study and systems-level integrative analyses implicate new risk genes and therapeutic targets for depression

Deciphering the genetic architecture of depression is pivotal for characterizing the associated pathophysiological processes and development of new therapeutics. Here we conducted a cross-ancestry genome-wide meta-analysis on depression (416,437 cases and 1,308,758 controls) and identified 287 risk loci, of which 49 are new. Variant-level fine mapping prioritized potential causal variants and functional genomic analysis identified variants that regulate the binding of transcription factors. We validated that 80% of the identified functional variants are regulatory variants, and expression quantitative trait loci analysis uncovered the potential target genes regulated by the prioritized risk variants. Gene-level analysis, including transcriptome and proteome-wide association studies, colocalization and Mendelian randomization-based analyses, prioritized potential causal genes and drug targets. Gene prioritization analyses highlighted likely causal genes, including TMEM106B, CTNND1, AREL1 and so on. Pathway analysis indicated significant enrichment of depression risk genes in synapse-related pathways. Finally, knockdown of Tmem106b in mice resulted in depression-like behaviours, supporting the involvement of Tmem106b in depression. Our study identified new risk loci, likely causal variants and genes for depression, providing important insights into the genetic architecture of depression and potential therapeutic targets.

Suprachiasmatic Neuromedin-S Neurons Regulate Arousal

Mammalian circadian rhythms, which orchestrate the daily temporal structure of biological processes, including the sleep-wake cycle, are primarily regulated by the circadian clock in the hypothalamic suprachiasmatic nucleus (SCN). The SCN clock is also implicated in providing an arousal 'signal,' particularly during the wake-maintenance zone (WMZ) of our biological day, essential for sustaining normal levels of wakefulness in the presence of mounting sleep pressure. Here we identify a role for SCN Neuromedin-S (SCN NMS ) neurons in regulating the level of arousal, especially during the WMZ. We used chemogenetic and optogenetic methods to activate SCN NMS neurons in vivo, which potently drove wakefulness. Fiber photometry confirmed the wake-active profile of SCN NM neurons. Genetically ablating SCN NMS neurons disrupted the sleep-wake cycle, reducing wakefulness during the dark period and abolished the circadian rhythm of body temperature. SCN NMS neurons target the dorsomedial hypothalamic nucleus (DMH), and photostimulation of their terminals within the DMH rapidly produces arousal from sleep. Pre-synaptic inputs to SCN NMS neurons were also identified, including regions known to influence SCN clock regulation. Unexpectedly, we discovered strong input from the preoptic area (POA), which itself receives substantial inhibitory input from the DMH, forming a possible arousal-promoting circuit (SCN->DMH->POA->SCN). Finally, we analyzed the transcriptional profile of SCN NMS neurons via single-nuclei RNA-Seq, revealing three distinct subtypes. Our findings link molecularly-defined SCN neurons to sleep-wake patterns, body temperature rhythms, and arousal control.

Significance Statement

Our study's findings provide a cellular and neurobiological understanding of how Neuromedin-S (NMS)-containing SCN neurons contribute to regulating circadian rhythms, sleep-wake patterns, body temperature, and arousal control in mammals. This research illuminates the circuit, cellular, and synaptic mechanisms through which SCN neurons regulate daily cycles of wakefulness and sleep, with implications for understanding and potentially manipulating these processes in health and disease.

A SMARTTR workflow for multi-ensemble atlas mapping and brain-wide network analysis

In the last decade, activity-dependent strategies for labelling multiple immediate early gene (IEG) ensembles in mice have generated unprecedented insight into the mechanisms of memory encoding, storage, and retrieval. However, few strategies exist for brain-wide mapping of multiple ensembles, including their overlapping population, and none incorporate capabilities for downstream network analysis. Here, we introduce a scalable workflow to analyze traditionally coronally-sectioned datasets produced by activity-dependent tagging systems. Intrinsic to this pipeline is simple multi-ensemble atlas registration and statistical testing in R (SMARTTR), an R package which wraps mapping capabilities with functions for statistical analysis and network visualization, and support for import of external datasets. We demonstrate the versatility of SMARTTR by mapping the ensembles underlying the acquisition and expression of learned helplessness (LH), a robust stress model. Applying network analysis, we find that exposure to inescapable shock (IS), compared to context training (CT), results in decreased centrality of regions engaged in spatial and contextual processing and higher influence of regions involved in somatosensory and affective processing. During LH expression, the substantia nigra emerges as a highly influential region which shows a functional reversal following IS, indicating a possible regulatory function of motor activity during helplessness. We also report that IS results in a robust decrease in reactivation activity across a number of cortical, hippocampal, and amygdalar regions, indicating suppression of ensemble reactivation may be a neurobiological signature of LH. These results highlight the emergent insights uniquely garnered by applying our analysis approach to multiple ensemble datasets and demonstrate the strength of our workflow as a hypothesis-generating toolkit.

Comparative molecular landscapes of immature neurons in the mammalian dentate gyrus across species reveal special features in humans

Immature dentate granule cells (imGCs) arising from adult hippocampal neurogenesis contribute to plasticity, learning and memory, but their evolutionary changes across species and specialized features in humans remain poorly understood. Here we performed machine learning-augmented analysis of published single-cell RNA-sequencing datasets and identified macaque imGCs with transcriptome-wide immature neuronal characteristics. Our cross-species comparisons among humans, monkeys, pigs, and mice showed few shared (such as DPYSL5), but mostly species-specific gene expression in imGCs that converged onto common biological processes regulating neuronal development. We further identified human-specific transcriptomic features of imGCs and demonstrated functional roles of human imGC-enriched expression of a family of proton-transporting vacuolar-type ATPase subtypes in development of imGCs derived from human pluripotent stem cells. Our study reveals divergent gene expression patterns but convergent biological processes in the molecular characteristics of imGCs across species, highlighting the importance of conducting independent molecular and functional analyses for adult neurogenesis in different species.

Single-cell genomics meets systems neuroscience: Insights from mapping the brain circuitry of stress

Responses to external and internal dangers is essential for survival and homeostatic regulation. Hypothalamic corticotropin-releasing hormone neurons (CRHNs) play a pivotal role in regulating neuroendocrine responses to fear and stress. In recent years, the application of neurogenetic tools, such as fiber photometry, chemogenetics and optogenetics, have provided new insights into the dynamic neuronal responses of CRHNs during stressful events, offering new perspectives into their functional significance in mediating neurobehavioural responses to stress. Transsynaptic viral tracers have facilitated the comprehensive mapping of neuronal inputs to CRHNs. Furthermore, the development and application of innovative single-cell genomic tools combined with viral tracing have begun to pave the way for a deeper understanding of the transcriptional profiles of neural circuit components, enabling molecular-anatomical circuit mapping. Here, I will discuss how these systems neuroscience approaches and novel single-cell genomic methods are advancing the molecular and functional mapping of stress neurocircuits, their associated challenges and future directions.

Utility of a commercial antibody against NTRK1 for western blotting and potential application to immunohistochemistry in adult mouse brain

Ntrk1 (also known as TrkA) is a nerve growth factor receptor with essential roles in the development and function of the cholinergic nervous system. Ntrk1 is expressed in a few specific and defined brain areas. Specific antibodies are necessary to identify the expression and localization of Ntrk1 in the brain, and validating signal authenticity is critical. These issues have not been investigated sufficiently. We evaluated the utility of commercial antibodies for Ntrk1 using western blotting in brain lysates from Ntrk1 knockout mice and tested the utility of the antibody that showed specificity in western blotting for immunohistochemistry applications in the adult mouse brain. We confirmed specificity for one of the seven commercial antibodies in western blots, in which the specific bands were absent in the knockout samples. Using this antibody, we performed immunohistochemical staining of the brain tissues of adult mice to examine Ntrk1 localization. Distinct signals were observed in regions with known Ntrk1 expression, such as the striatum and basal forebrain. The characteristic expression pattern of Ntrk1 in the paraventricular thalamic nucleus (PVT) was verified at the protein level, with high and low expression levels in the anterior and posterior PVT, respectively.

Atypical hippocampal excitatory neurons express and govern object memory

Classically, pyramidal cells of the hippocampus are viewed as flexibly representing spatial and non-spatial information. Recent work has illustrated distinct types of hippocampal excitatory neurons, suggesting that hippocampal representations and functions may be constrained and interpreted by these underlying cell-type identities. In mice, here we reveal a non-pyramidal excitatory neuron type - the "ovoid" neuron - that is spatially adjacent to subiculum pyramidal cells but differs in gene expression, electrophysiology, morphology, and connectivity. Functionally, novel object encounters drive sustained ovoid neuron activity, whereas familiar objects fail to drive activity even months after single-trial learning. Silencing ovoid neurons prevents non-spatial object learning but leaves spatial learning intact, and activating ovoid neurons toggles novel-object seeking to familiar-object seeking. Such function is doubly dissociable from pyramidal neurons, wherein manipulation of pyramidal cells affects spatial assays but not non-spatial learning. Ovoid neurons of the subiculum thus illustrate selective cell-type-specific control of non-spatial memory and behavioral preference.

Large Donor CRISPR for Whole-Coding Sequence Replacement of Cell Adhesion Molecule LRRTM2

The cell adhesion molecule leucine-rich repeat transmembrane neuronal protein 2 (LRRTM2) is crucial for synapse development and function. However, our understanding of its endogenous trafficking has been limited due to difficulties in manipulating its coding sequence (CDS) using standard genome editing techniques. Instead, we replaced the entire LRRTM2 CDS by adapting a two-guide CRISPR knock-in method, enabling complete control of LRRTM2. In primary rat hippocampal cultures dissociated from embryos of both sexes, N-terminally tagged, endogenous LRRTM2 was found in 80% of synapses, and synaptic LRRTM2 content correlated with PSD-95 and AMPAR levels. LRRTM2 was also enriched with AMPARs outside synapses, demonstrating the sensitivity of this method to detect relevant new biology. Finally, we leveraged total genomic control to increase the synaptic levels of LRRTM2 via simultaneous mutation of its C-terminal domain, which did not correspondingly increase AMPAR enrichment. The coding region of thousands of genes span lengths suitable for whole-CDS replacement, suggesting this simple approach will enable straightforward structure-function analysis in neurons.

Persistent Disruptions in Prefrontal Connectivity Despite Behavioral Rescue by Environmental Enrichment in a Mouse Model of Rett Syndrome

Rett Syndrome, a neurodevelopmental disorder caused by loss-of-function mutations in the MECP2 gene, is characterized by severe motor, cognitive and emotional impairments. Some of the deficits may result from changes in cortical connections, especially downstream projections of the prefrontal cortex, which may also be targets of restoration following rearing conditions such as environmental enrichment that alleviate specific symptoms. Here, using a heterozygous Mecp2 +/- female mouse model closely analogous to human Rett Syndrome, we investigated the impact of early environmental enrichment on behavioral deficits and prefrontal cortex connectivity. Behavioral analyses revealed that enriched housing rescued fine motor deficits and reduced anxiety, with enrichment-housed Mecp2 +/- mice performing comparably to wild-type (WT) controls in rotarod and open field assays. Anatomical mapping of top-down anterior cingulate cortex (ACA) projections demonstrated altered prefrontal cortex connectivity in Mecp2 +/- mice, with increased axonal density in the somatosensory cortex and decreased density in the motor cortex compared to WT controls. ACA axons revealed shifts in hemispheric distribution, particularly in the medial network regions, with Mecp2 +/- mice exhibiting reduced ipsilateral dominance. These changes were unaffected by enriched housing, suggesting that structural abnormalities in prefrontal cortex connectivity persist despite behavioral improvements. Enriched housing rescued brain-derived neurotrophic factor (BDNF) levels in the hippocampus but failed to restore BDNF levels in the prefrontal cortex, consistent with the persistent deficits observed in prefrontal axonal projections. These findings highlight the focal nature of changes induced by reduction of MeCP2 and by exposure to environmental enrichment, and suggest that environmental enrichment starting in adolescence can alleviate behavioral deficits without reversing abnormalities in large-scale cortical connectivity.

Microvascular structure variability explains variance in fMRI functional connectivity

The influence of regional brain vasculature on resting-state fMRI BOLD signals is well documented. However, the role of brain vasculature is often overlooked in functional connectivity research. In the present report, utilizing publicly available whole-brain vasculature data in the mouse, we investigate the relationship between functional connectivity and brain vasculature. This is done by assessing interregional variations in vasculature through a novel metric termed vascular similarity. First, we identify features to describe the regional vasculature. Then, we employ multiple linear regression models to predict functional connectivity, incorporating vascular similarity alongside metrics from structural connectivity and spatial topology. Our findings reveal a significant correlation between functional connectivity strength and regional vasculature similarity, especially in anesthetized mice. We also show that multiple linear regression models of functional connectivity using standard predictors are improved by including vascular similarity. We perform this analysis at the cerebrum and whole-brain levels using data from both male and female mice. Our findings regarding the relation between functional connectivity and the underlying vascular anatomy may enhance our understanding of functional connectivity based on fMRI and provide insights into its disruption in neurological disorders.

Epigenetic Control of an Auxiliary Subunit of Voltage-Gated Sodium Channels Regulates the Strength of Drug-Cue Associations and Relapse-Like Cocaine Seeking

BACKGROUND

Repeated use of addictive drugs produces long-lasting and prepotent drug-cue associations that increase vulnerability for relapse in individuals with a substance use disorder. Epigenetic factors, such as HDAC5 (histone deacetylase 5), play a key role in regulating the formation of drug-cue associations, but the underlying mechanisms remain unclear.

METHODS

We used a combination of molecular biology, cultured cells, tandem mass spectrometry, deacetylase activity measurements, co-immunoprecipitation, and molecular dynamics simulations to assess HDAC5 structure-activity relationships. In male and female Long Evans rats, we used viral-mediated expression of HDAC5 mutants in the nucleus accumbens (NAc) to test effects on cocaine intravenous self-administration and cue-reinstated cocaine seeking. We also used in silico analysis of single-nucleus RNA sequencing data, quantitative reverse transcriptase-polymerase chain reaction, viral-mediated expression of Scn4b short hairpin RNA, patch-clamp electrophysiology, and rat cocaine or sucrose SA to assess Scn4b's effects on NAc intrinsic excitability and cued reward seeking.

RESULTS

We discovered that 2 conserved cysteines located near HDAC5's catalytic domain were required for its intrinsic deacetylase activity and that HDAC5's deacetylase activity was required in NAc medium spiny neurons (MSNs) to limit relapse-like cue-reinstated cocaine seeking. Moreover, we found that HDAC5 limited cocaine-seeking, but not sucrose-seeking, behavior by reducing NAc MSN intrinsic excitability through the deacetylase-dependent repression of Scn4b, which codes for an auxiliary subunit of voltage-gated sodium channels.

CONCLUSIONS

Our findings suggest that HDAC5's control of NAc Scn4b expression governs the formation of cocaine-cue, but not sucrose-cue, associations through modulation of NAc MSN intrinsic excitability and drug-induced NAc plasticity mechanisms.

Searching for the cellular underpinnings of the selective vulnerability to tauopathic insults in Alzheimer's disease

Neurodegenerative diseases such as Alzheimer's disease exhibit pathological changes in the brain that proceed in a stereotyped and regionally specific fashion. However, the cellular underpinnings of regional vulnerability are poorly understood, in part because whole-brain maps of a comprehensive collection of cell types have been inaccessible. Here, we deployed a recent cell-type mapping pipeline, Matrix Inversion and Subset Selection (MISS), to determine the brain-wide distributions of pan-hippocampal and neocortical cells in the mouse, and then used these maps to identify general principles of cell-type-based selective vulnerability in PS19 mouse models. We found that hippocampal glutamatergic neurons as a whole were significantly positively associated with regional tau deposition, suggesting vulnerability, while cortical glutamatergic and GABAergic neurons were negatively associated. We also identified oligodendrocytes as the single-most strongly negatively associated cell type. Further, cell-type distributions were more predictive of end-time-point tau pathology than AD-risk-gene expression. Using gene ontology analysis, we found that the genes that are directly correlated to tau pathology are functionally distinct from those that constitutively embody the vulnerable cells. In short, we have elucidated cell-type correlates of tau deposition across mouse models of tauopathy, advancing our understanding of selective cellular vulnerability at a whole-brain level.