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

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.

Whole-brain BOLD responses to graded hypoxic challenges at 7 T, 9.4 T, and 15.2 T: Implications for ultrahigh-field functional and dynamic susceptibility contrast MRI

PURPOSE

Blood oxygen-level dependent (BOLD) functional MRI signals depend on changes in deoxyhemoglobin content, which is associated with baseline cerebral blood volume (CBV) and blood oxygen saturation change. To accurately interpret activation-induced BOLD responses and quantify perfusion values by BOLD dynamic susceptibility contrast (BOLD-DSC) with transient hypoxia, it is critical to assess ΔR 2 * $$ {\mathrm{R}}_2^{\ast } $$ values in tissue and blood across varying levels of hypoxia and magnetic field strengths (B0).

METHODS

Whole-brain BOLD responses were examined using 5-s graded hypoxic challenges with 10%, 5%, and 0% O2 at ultrahigh field strengths of 7 T, 9.4 T, and 15.2 T. Both tissue and blood responses were analyzed for BOLD-DSC quantification.

RESULTS

Substantial heterogeneity in hypoxia-induced ΔR 2 * $$ {\mathrm{R}}_2^{\ast } $$ was observed among regions under different hypoxic doses and B0. Nonlinear ΔR 2 * $$ {\mathrm{R}}_2^{\ast } $$ responses with increasing field strength were observed, depending on hypoxic levels: 10% O2 condition exhibited pronounced supralinear trends, whereas 0% and 5% O2 conditions showed nearly linear dependencies. Blood arterial and venous∆ R 2 * $$ \Delta {\mathrm{R}}_2^{\ast } $$ responses showed a similar dependence as tissue. However, at 15.2 T, the venous signal saturated under 5% and 0% O2 conditions. Quantitative CBV values obtained from BOLD-DSC data showed dependency on susceptibility effects, and higher B0 and hypoxic severity resulted in slightly higher CBV, indicating that caution is needed when comparing quantitative CBV values derived from different experimental protocols. Normalizing regional CBV values to those of white matter effectively reduced the impact of varying susceptibility contrasts.

CONCLUSIONS

Our investigations provide biophysical insights into the BOLD contrast mechanism at ultrahigh fields, and address quantification issues in susceptibility-based CBV measurements.

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.

Major-depressive-disorder-associated dysregulation of ZBTB7A in orbitofrontal cortex promotes astrocyte-mediated stress susceptibility

Heightened activity in the orbitofrontal cortex (OFC), a brain region that contributes to motivation, emotion, and reward-related decision-making, is a key clinical feature of major depressive disorder (MDD). However, the cellular and molecular substrates underlying this dysfunction remain unclear. Here, we performed cell-type-specific profiling of human OFC and unexpectedly mapped MDD-linked epigenomic features (including genetic risk variants) to non-neuronal cells, revealing significant glial dysregulation in this region. Characterization of MDD-specific chromatin loci further identified ZBTB7A-a transcriptional regulator of astrocyte reactivity-as an important mediator of MDD-related alterations. In rodent models, we found that Zbtb7a induction in astrocytes is both necessary and sufficient to drive stress-mediated behavioral deficits, cell-type-specific transcriptional/epigenomic signatures, and aberrant OFC astrocyte-neuronal communication in male mice-an established MDD risk factor. These findings thus highlight essential roles for astrocytes in OFC-mediated stress susceptibility and identify ZBTB7A as a critical and therapeutically relevant regulator of MDD-related OFC dysfunction.

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.

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.

A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types

The mammalian cortex is comprised of cells classified into types according to shared properties. Defining the contribution of each cell type to the processes guided by the cortex is essential for understanding its function in health and disease. We use transcriptomic and epigenomic cortical cell-type taxonomies from mouse and human to define marker genes and putative enhancers and create a large toolkit of transgenic lines and enhancer adeno-associated viruses (AAVs) for selective targeting of cortical cell populations. We report creation and evaluation of fifteen transgenic driver lines, two reporter lines, and >1,000 different enhancer AAV vectors covering most subclasses of cortical cells. The tools reported here have been made publicly available, and along with the scaled process of tool creation, evaluation, and modification, they will enable diverse experimental strategies toward understanding mammalian cortex and brain function.

Uncovering the role of Gpr45 in obesity regulation

OBJECTIVES

G protein-coupled receptors (GPCRs) are the most druggable targets in biology due to their cell-type specificity, ligand binding, and cell surface accessibility. Underscoring this, agonists for GPCRs have recently revolutionized the treatment of diabetes and obesity. The rampant success of these compounds has invigorated interest in identifying additional GPCRs that modulate appetite and body weight homeostasis. One such potential therapeutic target is G-protein couped receptor 45 (Gpr45), an orphan GPCR expressed both centrally and peripherally. We aimed to explore the role of Gpr45 as well as neurons expressing Gpr45 in energy balance.

METHODS

Three novel transgenic mouse models were engineered to investigate the functional contribution of Gpr45 to body weight and appetite regulation: 1) a global Gpr45 knockout, 2) a conditional floxed Gpr45 allele, and 3) a Gpr45-CreERT2 knock-in. Metabolic profiling was performed in global Gpr45 knockout animals including body weight, food intake, body mass, energy expenditure, and body temperature measurements. Animals harboring a conditional floxed Gpr45 allele were bred to mice expressing Cre-recombinase in excitatory neurons labeled via Vesicular glutamate transporter 2 (Vglut2), inhibitory cells expressing Vesicular GABA transporter (Vgat), or neurons marked by the transcription factor Single-minded 1 (Sim1) and monitored for body weight and food consumption. Additionally, floxed Gpr45 mice were bilaterally injected with AAV-Cre targeting the paraventricular nucleus of the hypothalamus (PVH) and body weight and food intake were evaluated. The Gpr45-CreERT2 knock-in model was used to express chronic and acute actuators to the PVH to assess the role of PVHGpr45 neurons in energy homeostasis.

RESULTS

Global Gpr45 disruption caused marked weight gain, increased food intake and fat mass, but no detectable alterations in core temperature or energy output. Selective deletion of Gpr45 from Sim1+ or excitatory Vglut2+ but not inhibitory Vgat+, neurons produced obesity and hyperphagia. Targeted deletion of Gpr45 from the PVH phenocopies these metabolic changes suggesting a major site of action of Gpr45 signaling is glutamatergic neurons residing in the PVH. Tetanus toxin light chain (TeNT) was used to permanently silence PVHGpr45 neuronal activity in Gpr45-CreER mice leading to rapid weight accumulation and escalated food intake. These experiments highlight the critical role of both Gpr45 signaling and neural network activity in the regulation of body weight and appetite. A mutated version of the bacterial sodium channel, NaChBac, was used to constitutively activate PVHGpr45 neuronal activity in Gpr45-CreER mice with limited to no effect on body weight and food consumption, implicating redundant circuitry acting in concert to bias weight loss protection. Acute chemogenetic stimulation of PVHGpr45 neurons durably suppressed food intake regardless of caloric need state or food palatability demonstrating the capacity of these cells to curb appetite.

CONCLUSIONS

Gpr45 is a putative therapeutic candidate that could be targeted to combat obesity and overeating.

Key Connectomes and Synaptic-Compartment-Specific Risk Genes Drive 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 genes that affect pathology spreading functioning at presynaptic or postsynaptic regions, and are these genes enriched in different cell types? Here, these questions are addressed 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. Genes associated with the selective vulnerability of brain regions to pathological α-Syn transmission are further analyzed to distinguish those functioning at presynaptic versus postsynaptic regions. Those risk genes are significantly enriched in microglial cells of presynaptic regions and neurons of postsynaptic regions. Gene regulatory network analyses are 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, this study has demonstrated for the first time that these are functionally distinct processes.

Cortical circuits for cross-modal generalization

Adapting goal-directed behaviors to changing sensory conditions is a fundamental aspect of intelligence. The brain uses abstract representations of the environment to generalize learned associations across sensory modalities. The circuit organization that mediates such cross-modal generalizations remains, however, unknown. Here, we demonstrate that mice can bidirectionally generalize sensorimotor task rules between touch and vision by using abstract representations of peri-personal space within the cortex. Using large-scale mapping in the dorsal cortex at single-cell resolution, we discovered multimodal neurons with congruent spatial representations within multiple associative areas of the dorsal and ventral streams. Optogenetic sensory substitution and systematic silencing of these associative areas revealed that a single area in the dorsal stream is necessary and sufficient for cross-modal generalization. Our results identify and comprehensively describe a cortical circuit organization that underlies an essential cognitive function, providing a structural and functional basis for abstract reasoning in the mammalian brain.

Whole-brain long-range connectivity of glutamatergic, GABAergic, parvalbumin-expressing and somatostatin-expressing neurons in mouse somatosensory cortex

Understanding the composition of cortical circuits at the whole-brain scale is crucial. However, the specific ways in which particular neuronal types in the primary somatosensory cortex (SSp) establish connections with upstream and downstream brain regions remain unclear. In this study, we used whole-brain imaging technology with submicron resolution to systematically reveal the long-range connectivity patterns of glutamatergic, GABAergic, parvalbumin-expressing (PV+), and somatostatin-expressing (SOM+) neurons in the SSp. Our results show that while glutamatergic, GABAergic, PV+ , and SOM+ neurons receive similar upstream afferent, specific thalamic subregions showed numerically stronger afferent to GABAergic, PV+ , and SOM+ neurons compared to glutamatergic neurons. Additionally, glutamatergic neurons exhibit a more complex collateral projection pattern in subcortical axonal pathways compared to PV+ neurons. These findings elucidate the long-range connectivity patterns of specific neuronal types in the SSp, offering new insights into the cell-type-specific mechanisms of sensory information processing.

SLIMBRAIN database: A multimodal image database of in vivo human brains for tumour detection

Hyperspectral imaging (HSI) and machine learning (ML) have been employed in the medical field for classifying highly infiltrative brain tumours. Although existing HSI databases of in vivo human brains are available, they present two main deficiencies. First, the amount of labelled data are scarce, and second, 3D-tissue information is unavailable. To address both issues, we present the SLIMBRAIN database, a multimodal image database of in vivo human brains that provides HS brain tissue data within the 400-1000 nm spectra, as well as RGB, depth and multiview images. Two HS cameras, two depth cameras and different RGB sensors were used to capture images and videos from 193 patients. All the data in the SLIMBRAIN database can be used in a variety of ways, for example, to train ML models with more than 1 million HS pixels available and labelled by neurosurgeons, to reconstruct 3D scenes or to visualize RGB brain images with different pathologies, offering unprecedented flexibility for both the medical and engineering communities.

SMOPCA: spatially aware dimension reduction integrating multi-omics improves the efficiency of spatial domain detection

Technological advances have enabled us to profile multiple omics layers with spatial information, significantly enhancing spatial domain detection and advancing a variety of biomedical research fields. Despite these advancements, there is a notable lack of effective methods for modeling spatial multi-omics data. We introduce SMOPCA, a Spatial Multi-Omics Principal Component Analysis method designed to perform joint dimension reduction on multimodal data while preserving spatial dependencies. Extensive experiments reveal that SMOPCA outperforms existing single-modal and multimodal dimension reduction and clustering methods, across both single-cell and spatial multi-omics datasets derived from diverse technologies and tissue structures.

Spatial and Temporal Single-Cell Profiling of RNA Compartmentalization in Neurons with Nanotweezers

Emerging techniques for mapping mRNAs within the subcellular compartments of live cells hold great promise for advancing our understanding of the spatial distribution of transcripts and enabling the study of single-cell dynamics in health and disease. This is particularly critical for polarized cells, such as neurons, where mRNA compartmentalization is essential for regulating gene expression, and defects in these localization mechanisms are linked to numerous neurological disorders. However, many subcellular analysis techniques require a compromise between subcellular precision, live-cell measurements, and nondestructive access to single cells in their native microenvironment. To overcome these challenges, we employ a single-cell technology that we have recently developed, the nanotweezer, which features a nanoscale footprint (∼100 nm), avoids cytoplasmic fluid aspiration, and enables rapid RNA isolation from living cells with minimal invasiveness. Using this tool, we investigate single-cell mRNA compartmentalization in the soma and dendrites of hippocampal neurons at different stages of neuronal development. By combining precise targeting with sequential sampling, we track changes in mRNA abundance at dendritic spine regions of the same neuron, both before and after stimulation. This minimally invasive approach enables time-resolved, subcellular gene expression profiling of the same single cell. This could provide critical insights into polarized cells and advance our understanding of biological processes and complex diseases.

The Competitive Loss of Cerebellar Granule and Purkinje Cells Driven by X-Linked Mosaicism in a Female Mouse Model of CASK-Related Disorders

CASK-related disorders are a form of female-restricted intellectual disabilities associated with cerebellar and pontine hypoplasia. The CASK gene is regulated by X-chromosome inactivation, which results in a mosaic distribution of CASK-expressing and CASK-deficient neurons in the female brain. This mosaic distribution is believed to play a key role in the pathophysiology of X-linked neurological disorders; however, the detailed brain structure has not been extensively characterized. In this study, we used CASK heterozygous knockout (CASK-hKO) mice combined with X-linked GFP reporter mice to investigate motor abilities and the distribution of CASK-expressing cells in the brains of female CASK-hKO mice. The CASK-hKO mice exhibited motor deficits and cerebellar hypoplasia similar to those observed in patients with CASK-related disorders. Interestingly, although half of the cerebellar granule cells were CASK-negative during early postnatal development, almost all Purkinje cells and cerebellar granule cells were CASK-positive in adulthood, suggesting that CASK expression may determine the survival of cerebellar granule cells during postnatal development. We also analyzed CASK-hypomorphic mice, which express 50% less CASK than wild-type mice, and compared hemizygous males and heterozygous females. The CASK-hypomorphic heterozygous females displayed a thinner cerebellar cortex and a higher probability of CASK-positive granule cells in CASK-hKO females, suggesting that the survival of cerebellar granule cells is regulated by a combination of cell-autonomous and cell-competitive mechanisms between CASK-expressing and CASK-deficient cells, which are generated by X-chromosome inactivation. These findings provide new insights into the relationship between the mosaic distribution of cells established by X-chromosome inactivation and the pathophysiology of CASK-related disorders.

Hypothalamic Median Eminence Thyrotropin-Releasing Hormone-Degrading Ectoenzyme Activity Is Dispensable for Basal Thyroid Axis Activity in Lean Rodents

The amplitude of the phasic output of thyrotropin-releasing hormone (TRH) into the hypothalamus-pituitary portal capillaries is likely controlled by the TRH-degrading ectoenzyme (TRH-DE) expressed on the surface of median eminence (ME) β2-tanycytes. To extend this hypothesis, we performed experiments on adult rodents reared in standard conditions. TRH-DE was close to the putative sites of TRH release in the male rat external layer of the ME. In global Trhde knockout mice, basal hypothalamus-pituitary-thyroid (HPT) axis parameters were not altered but we detected an increased vimentin (a tanycyte marker) positive coverage of the portal vessels. We then overexpressed TRH-DE or a dominant negative isoform by microinjection of adeno-associated virus 1 (AAV1) vectors into the third ventricle of adult male rats. Two weeks after microinjection, cold-stress-induced serum TSH concentration was decreased if ME TRH-DE activity had been enhanced. However, the long-term modification of TRH-DE activity in the ME had only a small impact on basal serum TSH concentration but increased Trhr expression in the anterior pituitary of animals transduced with AAV1-TRH-DE. Thus, long-term modifications of ME TRH-DE activity lead to limited changes in serum TSH concentration in adult rodents reared in standard conditions, possibly because of adaptations of TRH communication in the ME and/or anterior pituitary.

Antianxiety effects of dexmedetomidine: systematic review and meta-analysis

BACKGROUND

Despite numerous studies of the anxiolytic effects of dexmedetomidine compared with those of other drugs or saline, the results have been inconsistent. Here we report a systematic review and meta-analysis to comprehensively evaluate the evidence of the anxiolytic effects of dexmedetomidine.

METHODS

This research has been registered in the International Prospective Register of Systematic Reviews. The PubMed, Embase, Cochrane Library, Web of Science, and ClinicalTrials.gov database were searched for clinical trials that compared the anxiolytic effects of dexmedetomidine with those of a control group with valid anxiety scores from inception to December 29, 2024.

RESULTS

Overall, this systematic review and meta-analysis included 25 clinical studies with 2159 participants who underwent surgery. The primary outcome revealed that patients who were treated with dexmedetomidine had significantly lower anxiety scores than others did overall (MD = - 1.73, 95% CI = [ - 2.33, - 1.13], p < 0.00001, I2 = 86.5%). Dexmedetomidine was found to be more effective than benzodiazepines in relieving anxiety (MD = - 1.34, 95% CI = [ - 2.08, - 0.60], p = 0.0004, I2 = 83.3%). The secondary outcomes revealed no significant differences in satisfaction, pain level, sedation scores or the risk of postoperative nausea and vomiting between patients who were treated with dexmedetomidine and controls. However, the occurrence of bradycardia was more common in the dexmedetomidine groups.

CONCLUSIONS

Overall, this meta-analysis provided evidence of the potential of dexmedetomidine for relieving anxiety among patients who undergo surgery, with superior antianxiety effects compared with those of benzodiazepines.

A transgenic mouse line for rabies virus-mediated trans-synaptic tracing in the postnatal developing brain

Neural circuits are composed of numerous neurons that perform diverse functions. Understanding the mechanisms of neural processing requires elucidating the connections among individual neurons. Rabies virus (RV)-mediated trans-synaptic tracing enables the visualization of direct presynaptic neurons of a defined neural population, facilitating the precise mapping of neural circuits across various brain regions. This method relies on RV mutants that require the expression of the TVA receptor and rabies glycoprotein to infect and spread to presynaptic neurons. Traditionally, adeno-associated virus (AAV) has been used to express these proteins. However, because AAV requires several weeks to achieve sufficient gene expression, it is challenging to use this approach for studying neural connections during postnatal development. To address this limitation, we generated a transgenic mouse line, termed Ai162-nCTG, which expresses nuclear-localized mCherry, the TVA receptor, and rabies glycoprotein in a Cre-dependent manner. As a proof-of-principle, we crossed the Ai162-nCTG line with the vasopressin-Cre line. In the paraventricular hypothalamic nucleus, where a major cluster of vasopressin neurons exists, mCherry expression was highly specific to vasopressin neurons, although not all vasopressin neurons co-expressed mCherry. We injected RV into the paraventricular hypothalamic nucleus and compared the labeling patterns with those of the conventional AAV-based approach. Although both methods labeled input cells in similar brain regions, the AAV-based approach was superior in terms of labeling efficiency. We also demonstrated that the Ai162-nCTG-based method enables rabies virus-mediated trans-synaptic tracing in mice at postnatal day 7 and 30. The distribution of presynaptic neurons was largely similar in the juvenile and adult stages, suggesting that paraventricular vasopressin neurons do not significantly change their presynaptic inputs during post-weaning development. Taken together, these findings suggest that the Ai162-nCTG line can be used for rabies virus-mediated trans-synaptic tracing when AAV administration is challenging. We also acknowledge and discuss the technical constraints associated with this mouse line.

Neural and vascular contributions to sensory impairments in a human alpha-synuclein transgenic mouse model of Parkinson's disease

Parkinson's disease (PD) is a complex progressive neurodegenerative disorder involving hallmarks such as α -Synuclein (α Syn) aggregation and dopaminergic dysfunction that affect brain-wide neural activity. Although movement disorders are prominent in PD, sensory impairments also occur relatively early on, mainly in olfactory and, to a lesser extent visual systems. While these deficits have been described mainly at the behavioral and molecular levels, the underlying network-level activity remains poorly understood. Here, we harnessed a human α Syn transgenic mouse model of PD with in vivo functional MRI (fMRI) to map evoked activity in the visual and olfactory pathways, along with pseudo-Continuous Arterial Spin Labeling (pCASL) and c-FOS measurements to disentangle vascular from neuronal effects. Upon stimulation with either odors or flickering lights, we found significant decreases in fMRI responses along both olfactory and visual pathways, in multiple cortical and subcortical sensory areas. Average Cerebral Blood Flow rates were decreased by ∼10% in the α Syn group, while c-FOS levels were reduced by over 50%, suggesting a strong neural driver for the dysfunction, along with more modest vascular contributions. Our study provides insight into brain-level activity in an α Syn-based model, and suggests a novel target for biomarking via quantification of simple sensory evoked responses.

Quantitative 3D histochemistry reveals region-specific amyloid-β reduction by the antidiabetic drug netoglitazone

A hallmark of Alzheimer's disease (AD) is the extracellular aggregation of toxic amyloid-beta (Aβ) peptides in form of plaques. Here, we identify netoglitazone, an antidiabetic compound previously tested in humans, as an Aβ aggregation antagonist. Netoglitazone improved cognition and reduced microglia activity in a mouse model of AD. Using quantitative whole-brain three-dimensional histology (Q3D), we precisely identified brain regions where netoglitazone reduced the number and size of Aβ plaques. We demonstrate the utility of Q3D in preclinical drug evaluation for AD by providing a high-resolution brain-wide view of drug efficacy. Applying Q3D has the potential to improve pre-clinical drug evaluation by providing information that can help identify mechanisms leading to brain region-specific drug efficacy.

Nitrous oxide enhances MR-guided focused ultrasound delivery of gene therapy to the murine hippocampus

Transcranial Magnetic Resonance Guided Focused Ultrasound can oscillate intravenously delivered microbubbles and transiently open the blood brain barrier (BBB) in a targeted brain region. However, high microbubble doses or Focused ultrasound pressures (FUS) leads to injury. So, we administered nitrous oxide (N2O), an anesthetic gas to determine reduced need of FUS pressure and microbubble dose for opening BBB. Swiss Webster mice were treated with N2O or medical air (MA) at varying FUS pressures, while the microbubble dose was kept constant and the vice-versa. Consequently, BBB opening was quantified by acoustic emissions and enhancement rate on T1-weighted MR. To compare the effect of N2O on gene delivery, following BBB opening with either MA or N2O, a viral vector expressing GFP was subsequently delivered. Additionally, Immunohistochemical studies quantified viral transfection efficacy and assessed acute cell injury. We observed that N2O significantly potentiates acoustic emissions and enhancement rate on post-contrast MRI images, compared to MA at all measured pressures (0.39, 0.45, 0.67 MPa). Furthermore, N2O reduces the microbubble dose to 0.02μl/kg and FUS pressures to 0.28 and 0.39 MPa for BBB disruption and enhanced viral gene delivery, respectively. Hence, N2O potentiates microbubble oscillations, allowing reduced microbubble dose and FUS pressures and improved viral gene delivery.

Exploring the role of AMPA receptor auxiliary proteins in synaptic functions and diseases

α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) ionotropic glutamate receptors (AMPARs) mediate rapid excitatory synaptic transmission in the mammalian brain, primarily driven by the neurotransmitter glutamate. The modulation of AMPAR activity, particularly calcium-permeable AMPARs (CP-AMPARs), is crucially influenced by various auxiliary subunits. These subunits are integral membrane proteins that bind to the receptor's core and modify its functional properties, including ion channel kinetics and receptor trafficking. This review comprehensively catalogs all known AMPAR auxiliary proteins, providing vital insights into the biochemical mechanisms governing synaptic modulation and the specific impact of CP-AMPARs compared to their calcium-impermeable AMPA receptor (CI-AMPARs). Understanding the complex interplay between AMPARs and their auxiliary subunits in different brain regions is essential for elucidating their roles in cognitive functions such as learning and memory. Importantly, alterations in these auxiliary proteins' expression, function or interactions have been implicated in various neurological disorders. Aberrant signaling through CP-AMPARs, in particular, is associated with severe synaptic dysfunctions across neurodevelopmental, neurodegenerative and psychiatric conditions. Targeting the distinct properties of AMPAR-auxiliary subunit complexes, especially those involving CP-AMPARs, could disclose new therapeutic strategies, potentially allowing for more precise interventions in treating complex neuronal disorders.

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.

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.

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.

StereoMM: a graph fusion model for integrating spatial transcriptomic data and pathological images

Spatial omics technologies, generating high-throughput and multimodal data, have necessitated the development of advanced data integration methods to facilitate comprehensive biological and clinical treatment discoveries. Based on the cross-attention concept, we developed an AI learning based toolchain called StereoMM, a graph based fusion model that can incorporate omics data such as gene expression, histological images, and spatial location. StereoMM uses an attention module for omics data interaction and a graph autoencoder to integrate spatial positions and omics data in a self-supervised manner. Applying StereoMM across various cancer types and platforms has demonstrated its robust capability. StereoMM outperforms competitors in identifying spatial regions reflecting tumour progression and shows promise in classifying colorectal cancer patients into deficient mismatch repair and proficient mismatch repair groups. The comprehensive inter-modal integration and efficiency of StereoMM enable researchers to construct spatial views of integrated multimodal features efficiently, advancing thorough tissue and patient characterization.

GPR171 is necessary for normal physiological functions and mood-related behaviors in males, but not females

GPR171 is a recently deorphanized G protein-coupled receptor that has been implicated in feeding, mood regulation, and pain. However, the role of this receptor in other physiological functions and in female mice is largely unexplored. Using a novel genetic GPR171 knockout mouse model, we examined general physiological behaviors and mood-related behaviors in both sexes. In male GPR171 knockout mice, we observed increased feeding, reduced water intake, heightened ataxia, and decreased anxiety-like behaviors. Male GPR171 knockout mice showed greater depressive-like behaviors compared to female knockout mice, but this did not correspond to a change in cFos activity in the basolateral amygdala. No significant changes were detected in female GPR171 knockout mice in other behaviors measured. These findings corroborate previous studies linking GPR171 to feeding and mood regulation in males, but highlight notable sex differences that were previously unknown. These sex differences indicate that future studies should focus on elucidating the behavioral effects of GPR171 in females to provide a more comprehensive understanding of its physiological roles.

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.

Sainsc: A Computational Tool for Segmentation-Free Analysis of In Situ Capture Data

Spatially resolved transcriptomics (SRT) has become the method of choice for characterising the complexity of biomedical tissue samples. Until recently, scientists were restricted to SRT methods that can profile a limited set of target genes at high spatial resolution or transcriptome-wide but at a low spatial resolution. Through recent developments, there are now methods that offer both subcellular spatial resolution and full transcriptome coverage. However, utilising these new methods' high spatial resolution and gene resolution remains elusive due to several factors, including low detection efficiency and high computational costs. Here, we present Sainsc (Segmentation-free analysis of in situ capture data), which combines a cell-segmentation-free approach with efficient data processing of transcriptome-wide nanometre-resolution spatial data. Sainsc can generate cell-type maps with accurate cell-type assignment at the nanometre scale, together with corresponding maps of the assignment scores that facilitate interpretation of the local confidence of cell-type assignment. We demonstrate its utility and accuracy for different tissues and technologies. Compared to other methods, Sainsc requires lower computational resources and has scalable performance, enabling interactive data exploration. Sainsc is compatible with common data analysis frameworks and is available as open-source software in multiple programming languages.

High-Throughput Proteoform Imaging for Revealing Spatial-Resolved Changes in Brain Tissues Associated with Alzheimer's Disease

Spatially resolved characterization of proteoforms has substantial potential to significantly advance the understanding of physiological and disease mechanisms. However, challenges remain regarding throughput and coverage. A robust method is developed for high-throughput proteoform imaging (HTPi) by combining matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) and region-specific top-down proteomic analysis. MALDI MSI enables the imaging of proteoforms on tissue sections at a rate of 7 h cm-2 (100-µm spatial resolution), and the identification sensitivity of the proteoforms is improved by narrow-bore monolithic columns with low adsorption, yielding 366 annotated proteoform images from the mouse brain. The obtained proteoform images reveals differential expression of individual proteoforms across the brain regions, and distinct spatial distribution patterns of various proteoforms generated from a single gene. Given its ability to visualize proteoform, HTPi is further applied to explore spatial pathological changes associated with Alzheimer's disease (AD) in 5 × FAD mice. 158 annotated proteoform images are obtained in hippocampal regions at 50-µm spatial resolution, illuminating 14 differential proteoforms in the subiculum region and highlighting their significant associations with amyloid-β pathology in AD. The results highlight the power of HTPi in unraveling the intricate molecular landscape of brain tissues and its potential in elucidating disease mechanisms.

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.

Synchrotron Radiation-Based Tomography of an Entire Mouse Brain with Sub-Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte Data

Synchrotron radiation-based X-ray microtomography is uniquely suited for post-mortem 3D visualization of organs such as the mouse brain. Tomographic imaging of the entire mouse brain with isotropic cellular resolution requires an extended field-of-view and produces datasets of multiple terabytes in size. These data must be reconstructed, analyzed, and made accessible to domain experts who may have limited image processing knowledge. Extended-field X-ray microtomography is presented with0.65 μ m $0.65 \,\umu \mathrm{m}$ voxel size covering an entire mouse brain. The 4495 projections from 8 × 8 offset acquisitions are stitched to reconstruct a volume of 150003 voxels. The microtomography volume was non-rigidly registered to the Allen Mouse Brain Common Coordinate Framework v3 based on a combination of image intensity and landmark pairs. The data were block-wise transformed and stored in a public repository with a hierarchical format for navigation and overlay with anatomical annotations in online viewers such as Neuroglancer or siibra-explorer. This study demonstrates X-ray imaging and data processing for a full mouse brain, augmenting current atlases by improving resolution in the third dimension by an order of magnitude. The 3.3-teravoxel dataset is publicly available and easily accessible for domain experts via browser-based viewers.

Modeling functional connectivity with learning and memory in a mouse model of Alzheimer's disease

Introduction

Functional connectivity (FC) is a metric of how different brain regions interact with each other. Although there have been some studies correlating learning and memory with FC, there have not yet been, to date, studies that use machine learning (ML) to explain how FC changes can be used to explain behavior not only in healthy mice, but also in mouse models of Alzheimer's Disease (AD). Here, we investigated changes in FC and their relationship to learning and memory in a mouse model of AD across disease progression.

Methods

We assessed the APP/PS1 mouse model of AD and wild-type controls at 3-, 6-, and 10-months of age. Using resting state functional magnetic resonance imaging (rs-fMRI) in awake, unanesthetized mice, we assessed FC between 30 brain regions. ML models were then used to define interactions between neuroimaging readouts with learning and memory performance.

Results

In the APP/PS1 mice, we identified a pattern of hyperconnectivity across all three time points, with 47 hyperconnected regions at 3 months, 46 at 6 months, and 84 at 10 months. Notably, FC changes were also observed in the Default Mode Network, exhibiting a loss of hyperconnectivity over time. Modeling revealed functional connections that support learning and memory performance differ between the 6- and 10-month groups.

Discussion

These ML models show potential for early disease detection by identifying connectivity patterns associated with cognitive decline. Additionally, ML may provide a means to begin to understand how FC translates into learning and memory performance.

GHS-R1a signaling drives anxiety-related behavior by shaping excitability of ventromedial hypothalamic neurons

The neural substrates of anxiety are poorly understood, which hinders treatment of anxiety disorders. Here we found, αCaMKII+ neurons in the ventral medial hypothalamic nucleus (VMH) responded to stressors with increased activity in male mice, both under physiological conditions and after repeated restraint stress. Activation of VMH αCaMKII+ neurons were necessary and sufficient to ameliorate stress-induced anxiety. The peripheral metabolic hormone ghrelin and receptor GHS-R1a play a complex role in emotion regulation; however, the mechanism is uncertain. A delayed increase in GHS-R1a expression in VMH αCaMKII+ neurons coincided with the development of stress-induced enhancement of anxiety-related behavior. GHS-R1a expression in VMH αCaMKII+ neurons promoted anxiety-related behavior, whereas GHS-R1a knockdown had the opposite effect. GHS-R1a upregulation inhibited the excitability of VMH αCaMKII+ neurons. We conclude that GHSR1a signaling drives stress-induced anxiety by shaping the activity of VMH αCaMKII+ neurons. GHS-R1a may be a therapeutic target for treating anxiety disorders such as post-traumatic stress disorder.

SGTB: A graph representation learning model combining transformer and BERT for optimizing gene expression analysis in spatial transcriptomics data

In recent years, spatial transcriptomics (ST) has emerged as an innovative technology that enables the simultaneous acquisition of gene expression information and its spatial distribution at the single-cell or regional level, providing deeper insights into cellular interactions and tissue organization, this technology provides a more holistic view of tissue organization and intercellular dynamics. However, existing methods still face certain limitations in data representation capabilities, making it challenging to fully capture complex spatial dependencies and global features. To address this, this paper proposes an innovative spatial multi-scale graph convolutional network (SGTB) based on large language models, integrating graph convolutional networks (GCN), Transformer, and BERT language models to optimize the representation of spatial transcriptomics data. The Graph Convolutional Network (GCN) employs a multi-layer architecture to extract features from gene expression matrices. Through iterative aggregation of neighborhood information, it captures spatial dependencies among cells and gene co-expression patterns, thereby constructing hierarchical cell embeddings. Subsequently, the model integrates an attention mechanism to assign weights to critical features and leverages Transformer layers to model global relationships, refining the ability of learned representations to reflect variations in spatial patterns. Finally, the model incorporates the BERT language model, mapping cell embeddings into textual inputs to exploit its deep semantic representation capabilities for high-dimensional feature extraction. These features are then fused with the embeddings generated by the Transformer, further optimizing feature learning for spatial transcriptomics data. This approach holds significant application value in improving the accuracy of tasks such as cell type classification and gene regulatory network construction, providing a novel computational framework for deep mining of spatial multi-scale biological data.

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.

Reanalysis of Published Histological Data Can Help to Characterize Neuronal Death After Spinal Cord Injury

Neuronal death is a central event in spinal cord injury (SCI) pathophysiology. Despite its importance, we have a fragmentary vision of the process. In our opinion, the research community has accumulated enough information to provide a more detailed, integrated vision of neuronal death after SCI. This work embeds this vision by creating an open repository to store and share data and results from their analysis. We have employed this repository to upload raw images of spinal cord sections from a mouse model of contusive SCI and used this information to compare manual-, threshold-, and neural network-based neuron identifications and to explore neuronal death at the injury penumbra 21 days after injury and the effects of the anti-apoptotic drug ucf-101. Results indicate that, whereas the three identification methods assayed yield coherent estimates of the total number of neurons per section, neural network (NN) outperforms the other two methods. Combining NN identification and image registration has allowed us to characterize neuron distribution among Rexed laminae in the mice T11, revealing spatial patterns in the neuronal death that follows injury and in their survival following ucf-101 treatment.

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.

The role of dorsal raphe nucleus neuropeptides in reward and aversion

The dorsal raphe nucleus is a critical node for affective and motivated circuits in the brain. Though typically known as a serotonergic hub, the dorsal raphe nucleus is also highly enriched in a variety of neuropeptides. Recent advances in biotechnology and behavioral modeling have led to a resurgence in neuropeptide research, allowing investigators to target unique peptide systems with unprecedented clarity. Here, we review and discuss multiple neuropeptide systems in dorsal raphe and consider how their activity may contribute to reward and aversion. While this is not an exhaustive review, this short overview will highlight the many opportunities available to refine our understanding of multiple dorsal raphe neuropeptides. By more thoroughly studying dorsal raphe neuropeptides, we will reveal novel pathways to design more effective therapeutics and tailor treatments for millions of patients.

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.

Advances in Microfluidic Single-Cell RNA Sequencing and Spatial Transcriptomics

The development of micro- and nano-fabrication technologies has greatly advanced single-cell and spatial omics technologies. With the advantages of integration and compartmentalization, microfluidic chips are capable of generating high-throughput parallel reaction systems for single-cell screening and analysis. As omics technologies improve, microfluidic chips can now integrate promising transcriptomics technologies, providing new insights from molecular characterization for tissue gene expression profiles and further revealing the static and even dynamic processes of tissues in homeostasis and disease. Here, we survey the current landscape of microfluidic methods in the field of single-cell and spatial multi-omics, as well as assessing their relative advantages and limitations. We highlight how microfluidics has been adapted and improved to provide new insights into multi-omics over the past decade. Last, we emphasize the contributions of microfluidic-based omics methods in development, neuroscience, and disease mechanisms, as well as further revealing some perspectives for technological advances in translational and clinical medicine.

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.

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.

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.