Spatial transcriptomics reveals the distinct organization of mouse prefrontal cortex and neuronal subtypes regulating chronic pain

Comparative analysis of functional network dynamics in high and low alcohol preference mice

Individual variability preference is a typical characteristic of alcohol drinking behaviors, with a higher risk for the development of alcohol use disorders (AUDs) in high alcohol preference (HP) populations. Here, we created a map of alcohol-related brain regions through c-Fos profiling, and comparatively investigated the differences of functional neural networks between the HP mice and low alcohol preference (LP) mice. We found that neuronal activity in some brain regions, such as ventral tegmental area (VTA), was altered in both HP and LP mice, indicating that these neurons were universally sensitive to alcohol. Most importantly, several brain regions, such as the prefrontal cortex and insular cortex, exhibited significantly higher c-Fos expression in HP mice than that in LP mice and displayed broader and stronger neural connections across brain networks, suggesting that these brain regions are the potential targets for individual alcohol preference. Graph theory-based analysis unraveled a decrease in brain modularity in HP networks, yet with more centralized connection patterns, and maintained higher communication efficiency and redundancy. Furthermore, LP mice switched the central network hubs, with the key differential network centered on nucleus accumbens shell (NAc Sh), nucleus accumbens core (NAc C), VTA, and anterior insular cortex (AIC), indicating that these brain regions and related neural circuits, such as NAc Sh-AIC may be involved in regulating individual alcohol preference. These results provide novel insights into the neural connections governing individual preferences to alcohol consumption, which may contribute to AUDs prediction and pharmacotherapy.

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 molecularly defined mPFC-BLA circuit specifically regulates social novelty preference

Social novelty preference is an important aspect of social interaction for evaluating new threats and opportunities for survival, but the underlying neuronal mechanism remains unclear. Here, we identify a molecularly defined medial prefrontal cortex (mPFC) excitatory neuron subtype, located in layer 5 expressing Il1rapl2, which is highly associated with social deficit disorders in genome-wide association studies and might be responsible for regulating social novelty preference. Using an Il1rapl2-Cre mouse line, we show that chemogenetic activation of the mPFC Il1rapl2-expressing neurons impairs social novelty preference but with little effect on sociability. In addition, fiber photometry recording indicates that this neuron subtype is inhibited when mice interact with novel but not with familiar mice. Furthermore, viral tracing and terminal manipulation reveal that basolateral amygdala (BLA)-projecting Il1rapl2+ neurons mediate the social novelty preference. Thus, our study uncovers a molecularly defined mPFC-BLA circuit that specifically regulates social novelty preference, highlighting that specific neuron subtypes and circuits could modulate distinct aspects of social behaviors.

Neurogenesis drives hippocampal formation-wide spatial transcription alterations in health and Alzheimer's disease

The mechanism by which neurogenesis regulates the profile of neurons and glia in the hippocampal formation is not known. Further, the effect of neurogenesis on neuronal vulnerability characterizing the entorhinal cortex in Alzheimer's disease (AD) is unknown. Here, we used in situ sequencing to investigate the spatial transcription profile of neurons and glia in the hippocampal circuitry in wild-type mice and in familial AD (FAD) mice expressing varying levels of neurogenesis. This approach revealed that in addition to the dentate gyrus, neurogenesis modulates the cellular profile in the entorhinal cortex and CA regions of the hippocampus. Notably, enhancing neurogenesis in FAD mice led to partial restoration of neuronal and cellular profile in these brain areas, resembling the profile of their wild-type counterparts. This approach provides a platform for the examination of the cellular dynamics in the hippocampal formation in health and in AD.

Shared and unique genes and pathways between neuropathic and inflammatory pain assays

BACKGROUND

Current studies mostly concentrate on behavioral differences and have not yet systematically elucidated the molecular distinctions among various chronic pain models.

METHODS

To identify the similarities and differences in gene expression among mice of three kinds of pain models, i.e., spared nerve injury (SNI) model, chronic constriction injury of the sciatic nerve (CCI) model, and the complete Freund's adjuvant-induced chronic inflammatory pain (CFA) model. The lumbar enlargement segments (L5-L6) were collected. Total mRNA was extracted for RNA sequencing. The differentially expressed genes were analyzed by bioinformatics, including GO analysis, KEGG analysis, and PPI network to explore the functions.

RESULTS

Commonalities and significant variations in gene expression were observed among the three pain models. Compared with Sham, there were 60 shared differential genes among the three models, which were mainly involved in oxidative phosphorylation-related biological process (e.g., mt-Nd1). Compared with CCI, SNI upregulated genes were associated with inflammation response (e.g., Ifi204, Ifi27), while downregulated genes were linked to microtubule-based movement (e.g., Dnah7b, Hcmn1); When compared with SNI, CFA upregulated genes were related to axon development (e. g., Oprm1, Gucy1a2, Syn3), whereas downregulated genes were associated with oxidative phosphorylation (e. g., Rpl41, Rpl21); In contrast to CCI, CFA upregulated genes pertained to axon development (e. g., Zbtb16), while downregulated genes were connected to oxidative phosphorylation (e. g., Cyp3a13).

CONCLUSIONS

The three widely employed chronic pain models exhibit both similarities and distinctions, and genes that vary across all three models may serve as potential targets for chronic pain research.

Development of the rodent prefrontal cortex: circuit formation, plasticity, and impacts of early life stress

The prefrontal cortex (PFC), located at the anterior region of the cerebral cortex, is a multimodal association cortex essential for higher-order brain functions, including decision-making, attentional control, memory processing, and regulation of social behavior. Structural, circuit-level, and functional abnormalities in the PFC are often associated with neurodevelopmental disorders. Here, we review recent findings on the postnatal development of the PFC, with a particular emphasis on rodent studies, to elucidate how its structural and circuit properties are established during critical developmental windows and how these processes influence adult behaviors. Recent evidence also highlights the lasting effects of early life stress on the PFC structure, connectivity, and function. We explore potential mechanisms underlying these stress-induced alterations, with a focus on epigenetic regulation and its implications for PFC maturation and neurodevelopmental disorders. By integrating these insights, this review provides an overview of the developmental processes shaping the PFC and their implications for brain health and disease.

Development of UV-Chemometric techniques for resolving the overlapped spectra of aspirin, caffeine and orphenadrine citrate in their combined pharmaceutical dosage form

A UV-chemometric approach has been developed to analyze a ternary combination of aspirin, caffeine, and orphenadrine citrate without the need for previous separation. The method is easy, specific, accurate, and highly precise. The three medications were evaluated simultaneously utilizing CLS, PLS, and PCR, which were generated based on separate data sets that yielded superior findings. Regrettably, their accurate estimation could only be achieved using the PLS approach. In order to determine the prediction power of each chemometric approach, its validity has been tested using 8 synthetic mixes. The latent variable number varies across various models as the dataset changes. The comparison of various methodologies and the assessment of the predictive capacity of each set of data were done using the predicted residual error sum of squares (PRESS) and the root mean square error of prediction (RMSEP). The created approach was also used to statistically compare the performance of PLS in a dataset with zero absorption, as well as to compare the performance of the offered chemometric methods in various datasets. The environmental impact of the created approach was assessed to determine the overall ecological sustainability of the designed methodology. According to the new Blue Applicability Grade Index (BAGI) evaluation methodology, the suggested technique was also found to be practicable.

Persistent large-scale changes in alternative splicing in prefrontal cortical neuron types following psychedelic exposure

Psychedelics engage the serotonergic system as potent neuromodulators, increasing neuroplasticity in humans and rodents. Persistent changes in cognitive flexibility, emotional regulation, and social cognition are thought to underlie the therapeutic effects of psychedelics. However, the underlying molecular and cellular basis of psychedelic-induced plasticity remains unclear. Here, we identify persistent, cell type-specific alternative splicing changes in the mouse medial prefrontal cortex (mPFC) induced by a single dose of psychedelics. Combining deep RiboTag sequencing and bioinformatics, we find that a single dose of psychedelics modestly alters gene expression while dramatically shifting patterns of alternative splicing lasting at least a month. We connect our functional enrichment and alternative splicing analysis with changes in the extracellular matrix, synaptic physiology, and intrinsic physiology in parvalbumin interneurons days to a week after psychedelic treatment. Our dataset is an essential resource for understanding the persistent, cell type-specific effects of psychedelics on cortical cell types and functions.

Single Cell Data Enables Dissecting Cell Types Present in Bulk Transcriptome Data

The quality of organoid models can be assessed by single-cell-RNA-sequencing (scRNA-seq) but often only bulk transcriptome data is available. Here we present a pipeline for the analysis of scRNA-seq data and subsequent "deconvolution," which is a method for estimating cell type fractions in bulk transcriptome data based on expression profiles and cell types found in scRNA-seq data derived from biopsies. We applied this pipeline on bulk iPSC-derived kidney and brain organoid transcriptome data to identify cell types employing two scRNA-seq kidney datasets and one brain dataset. Relevant cells present in kidney (e.g., proximal tubules, distal convoluted tubules, and podocytes) and brain (e.g., neurons, astrocytes, oligodendrocytes, and microglia) with obligatory endothelial and immune-related cells were identified. We anticipate that this pipeline will also enable estimation of cell type fractions in organoids of other tissues.

Knowledge mapping and emerging trends in cognitive impairment associated with chronic pain: A 2000-2024 bibliometric study

Chronic pain is commonly recognized as a distressing symptom or a standalone disease, with over half of those affected experiencing cognitive impairment, which significantly impacts their quality of life. Despite a recent surge in literature on cognitive impairment associated with chronic pain, a comprehensive bibliometric analysis in this field has yet to be conducted. In this study, we performed a bibliometric analysis on this topic. We retrieved English-language publications on chronic pain and cognitive impairment from 2000 to 2024 using the Web of Science Core Collection database. These publications were visually analyzed using tools such as VOSviewer, CiteSpace, and the R package "bibliometrix." We identified 1656 publications from 72 countries/regions across 722 journals on the topic of chronic pain and cognitive impairment. Publication numbers showed a steady increase, peaking in 2022. The United States led in contributions, with Harvard Medical School emerging as the most prominent institution involved. The journal Pain was the most prolific and frequently co-cited in this area. Among the authors, Stefan Duschek was the most productive, while Frederick Wolfe was the most frequently co-cited. Key research areas include investigating the bidirectional long-term effects between chronic pain and cognitive impairment and exploring the mechanisms underlying cognitive changes associated with chronic pain. In conclusion, this study highlights a global surge in research on cognitive impairment related to chronic pain. Emerging hotspots and future research trends point towards brain imaging mechanisms and neuronal circuit-mediated processes.

SMART: spatial transcriptomics deconvolution using marker-gene-assisted topic model

While spatial transcriptomics offer valuable insights into gene expression patterns within the spatial context of tissue, many technologies do not have a single-cell resolution. Here, we present SMART, a marker gene-assisted deconvolution method that simultaneously infers the cell type-specific gene expression profile and the cellular composition at each spot. Using multiple datasets, we show that SMART outperforms the existing methods in realistic settings. It also provides a two-stage approach to enhance its performance on cell subtypes. The covariate model of SMART enables the identification of cell type-specific differentially expressed genes across conditions, elucidating biological changes at a single-cell-type resolution.

Up-regulation of IL-1β and sPLA2-III in the medial prefrontal cortex contributes to orofacial and somatic hyperalgesia induced by malocclusion via glial-neuron crosstalk

The medial prefrontal cortex (mPFC) has been identified as a key brain region involved in the modulation of chronic pain. Our recent study demonstrated that unilateral anterior crossbite (UAC) developed the comorbidity model of temporomandibular disorders (TMD) and fibromyalgia syndrome (FMS), which was characterized by both orofacial and somatic hyperalgesia. In the present study, UAC rats exhibited significant changes in gene expression in the mPFC. Enrichment analysis revealed that the significantly involved pathways were cytokines-cytokine receptor interaction and immune response. The expression of group III secretory phospholipase A2 (sPLA2-III) was significantly increased in the mPFC of UAC rats. Silencing sPLA2-III expression in the mPFC blocked the orofacial and somatic hyperalgesia. Immunofluorescence showed that sPLA2-III was mainly localized in neurons. The expression of interleukin-1β (IL-1β) in the mPFC significantly increased after UAC. Injection of IL-1β antibody into the mPFC blocked orofacial and somatic hyperalgesia. IL-1β was mainly localized in microglia cells. Furthermore, injection of IL-1β antibody significantly reduced the expression of sPLA2-III. These results indicate that neuroinflammatory cascade responses induced by glial-neuron crosstalk in the mPFC may contribute to the development of TMD and FMS comorbidity, and IL-1β and sPLA2-III are identified as novel potential therapeutic targets for the treatment of chronic pain in the comorbidity of TMD and FMS.

Parvalbumin interneuron impairment causes synaptic transmission deficits and seizures in SCN8A developmental and epileptic encephalopathy

SCN8A developmental and epileptic encephalopathy (DEE) is a severe epilepsy syndrome resulting from mutations in the voltage-gated sodium channel Nav1.6, encoded by the gene SCN8A. Nav1.6 is expressed in excitatory and inhibitory neurons, yet previous studies primarily focus on how SCN8A mutations affect excitatory neurons, with limited studies on the importance of inhibitory interneurons. Parvalbumin (PV) interneurons are a prominent inhibitory interneuron subtype that expresses Nav1.6. To assess PV interneuron function within SCN8A DEE, we used 2 mouse models harboring patient-derived SCN8A gain-of-function variants, Scn8aD/+, where the SCN8A variant N1768D is expressed globally, and Scn8aW/+-PV, where the SCN8A variant R1872W is selectively expressed in PV interneurons. Expression of the R1872W SCN8A variant selectively in PV interneurons led to development of spontaneous seizures and seizure-induced death. Electrophysiology studies showed that Scn8aD/+ and Scn8aW/+-PV interneurons were susceptible to depolarization block and exhibited increased persistent sodium current. Evaluation of synaptic connections between PV interneurons and pyramidal cells showed synaptic transmission deficits in Scn8aD/+ and Scn8aW/+-PV interneurons. Together, our findings indicate that PV interneuron failure via depolarization block along with inhibitory synaptic impairment likely elicits an overall inhibitory reduction in SCN8A DEE, leading to unchecked excitation and ultimately resulting in seizures and seizure-induced death.

An emerging multi-omic understanding of the genetics of opioid addiction

Opioid misuse, addiction, and associated overdose deaths remain global public health crises. Despite the tremendous need for pharmacological treatments, current options are limited in number, use, and effectiveness. Fundamental leaps forward in our understanding of the biology driving opioid addiction are needed to guide development of more effective medication-assisted therapies. This Review focuses on the omics-identified biological features associated with opioid addiction. Recent GWAS have begun to identify robust genetic associations, including variants in OPRM1, FURIN, and the gene cluster SCAI/PPP6C/RABEPK. An increasing number of omics studies of postmortem human brain tissue examining biological features (e.g., histone modification and gene expression) across different brain regions have identified broad gene dysregulation associated with overdose death among opioid misusers. Drawn together by meta-analysis and multi-omic systems biology, and informed by model organism studies, key biological pathways enriched for opioid addiction-associated genes are emerging, which include specific receptors (e.g., GABAB receptors, GPCR, and Trk) linked to signaling pathways (e.g., Trk, ERK/MAPK, orexin) that are associated with synaptic plasticity and neuronal signaling. Studies leveraging the agnostic discovery power of omics and placing it within the context of functional neurobiology will propel us toward much-needed, field-changing breakthroughs, including identification of actionable targets for drug development to treat this devastating brain disease.

Divergent subregional information processing in mouse prefrontal cortex during working memory

Working memory (WM) is a critical cognitive function allowing recent information to be temporarily held in mind to inform future action. This process depends on coordination between prefrontal cortex (PFC) subregions and other connected brain areas. However, few studies have examined the degree of functional specialization between these subregions throughout WM using electrophysiological recordings in freely-moving mice. Here we record single-units in three neighboring mouse medial PFC (mPFC) subregions-supplementary motor area (MOs), dorsomedial PFC (dmPFC), and ventromedial (vmPFC)-during a freely-behaving non-match-to-position WM task. The MOs is most active around task phase transitions, when it transiently represents the starting sample location. Dorsomedial PFC contains a stable population code, including persistent sample-location-specific firing during the delay period. Ventromedial PFC responds most strongly to reward-related information during choices. Our results reveal subregionally segregated WM computation in mPFC and motivate more precise consideration of the dynamic neural activity required for WM.

A distinct neuronal ensemble of prelimbic cortex mediates spontaneous pain in rats with peripheral inflammation

The absence of a comprehensive understanding of the neural basis of spontaneous pain limits the development of therapeutic strategies targeting this primary complaint of patients with chronic pain. Here we report a distinct neuronal ensemble within the prelimbic cortex which processes signals related to spontaneous pain in rats with chronic inflammatory pain. This neuronal ensemble specifically encodes spontaneous pain-related behaviors, independently of other locomotive and evoked behaviors. Activation of this neuronal ensemble elicits marked spontaneous pain-like behaviors and enhances nociceptive responses, whereas prolonged silencing of its activities alleviates spontaneous pain and promotes overall recovery from inflammatory pain. Notably, afferents from the primary somatosensory cortex and infralimbic cortex bidirectionally modulate the activities of the spontaneous pain-responsive prelimbic cortex neuronal ensemble and pain behaviors. These findings reveal the cortical basis of spontaneous pain at the neuronal level, highlighting a distinct neuronal ensemble within the prelimbic cortex and its associated pain-regulatory brain networks.

Spatiotemporal omics for biology and medicine

The completion of the Human Genome Project has provided a foundational blueprint for understanding human life. Nonetheless, understanding the intricate mechanisms through which our genetic blueprint is involved in disease or orchestrates development across temporal and spatial dimensions remains a profound scientific challenge. Recent breakthroughs in cellular omics technologies have paved new pathways for understanding the regulation of genomic elements and the relationship between gene expression, cellular functions, and cell fate determination. The advent of spatial omics technologies, encompassing both imaging and sequencing-based methodologies, has enabled a comprehensive understanding of biological processes from a cellular ecosystem perspective. This review offers an updated overview of how spatial omics has advanced our understanding of the translation of genetic information into cellular heterogeneity and tissue structural organization and their dynamic changes over time. It emphasizes the discovery of various biological phenomena, related to organ functionality, embryogenesis, species evolution, and the pathogenesis of diseases.

An orbitocortical-thalamic circuit suppresses binge alcohol-drinking

Alcohol consumption remains a significant global health challenge, causing millions of direct and indirect deaths annually. Intriguingly, recent work has highlighted the prefrontal cortex, a major brain area that regulates inhibitory control of behaviors, whose activity becomes dysregulated upon alcohol abuse. However, whether an endogenous mechanism exists within this brain area that limits alcohol consumption is unknown. Here we identify a discrete GABAergic neuronal ensemble in the medial orbitofrontal cortex (mOFC) that is selectively recruited during binge alcohol-drinking and intoxication. Upon alcohol intoxication, this neuronal ensemble suppresses binge drinking behavior. Optogenetically silencing of this population, or its ablation, results in uncontrolled binge alcohol consumption. We find that this neuronal ensemble is specific to alcohol and is not recruited by other rewarding substances. We further show, using brain-wide analysis, that this neuronal ensemble projects widely, and that its projections specifically to the mediodorsal thalamus are responsible for regulating binge alcohol drinking. Together, these results identify a brain circuit in the mOFC that serves to protect against binge drinking by halting alcohol intake. These results provide valuable insights into the complex nature of alcohol abuse and offers potential avenues for the development of mOFC neuronal ensemble-targeted interventions.

Pathology of pain and its implications for therapeutic interventions

Pain is estimated to affect more than 20% of the global population, imposing incalculable health and economic burdens. Effective pain management is crucial for individuals suffering from pain. However, the current methods for pain assessment and treatment fall short of clinical needs. Benefiting from advances in neuroscience and biotechnology, the neuronal circuits and molecular mechanisms critically involved in pain modulation have been elucidated. These research achievements have incited progress in identifying new diagnostic and therapeutic targets. In this review, we first introduce fundamental knowledge about pain, setting the stage for the subsequent contents. The review next delves into the molecular mechanisms underlying pain disorders, including gene mutation, epigenetic modification, posttranslational modification, inflammasome, signaling pathways and microbiota. To better present a comprehensive view of pain research, two prominent issues, sexual dimorphism and pain comorbidities, are discussed in detail based on current findings. The status quo of pain evaluation and manipulation is summarized. A series of improved and innovative pain management strategies, such as gene therapy, monoclonal antibody, brain-computer interface and microbial intervention, are making strides towards clinical application. We highlight existing limitations and future directions for enhancing the quality of preclinical and clinical research. Efforts to decipher the complexities of pain pathology will be instrumental in translating scientific discoveries into clinical practice, thereby improving pain management from bench to bedside.

Targeting Prefrontal Cortex Dysfunction in Pain

The prefrontal cortex (PFC) has justifiably become a significant focus of chronic pain research. Collectively, decades of rodent and human research have provided strong rationale for studying the dysfunction of the PFC as a contributing factor in the development and persistence of chronic pain and as a key supraspinal mechanism for pain-induced comorbidities such as anxiety, depression, and cognitive decline. Chronic pain alters the structure, chemistry, and connectivity of PFC in both humans and rodents. In this review, we broadly summarize the complexities of reported changes within both rodent and human PFC caused by pain and offer insight into potential pharmacological and nonpharmacological approaches for targeting PFC to treat chronic pain and pain-associated comorbidities. SIGNIFICANCE STATEMENT: Chronic pain is a significant unresolved medical problem causing detrimental changes to physiological, psychological, and behavioral aspects of life. Drawbacks of currently approved pain therapeutics include incomplete efficacy and potential for abuse producing a critical need for novel approaches to treat pain and comorbid disorders. This review provides insight into how manipulation of prefrontal cortex circuits could address this unmet need of more efficacious and safer pain therapeutics.

Divergent Subregional Information Processing in Mouse Prefrontal Cortex During Working Memory

Working memory (WM) is a critical cognitive function allowing recent information to be temporarily held in mind to inform future action. This process depends on coordination between key subregions in prefrontal cortex (PFC) and other connected brain areas. However, few studies have examined the degree of functional specialization between these subregions throughout the phases of WM using electrophysiological recordings in freely-moving animals, particularly mice. To this end, we recorded single-units in three neighboring medial PFC (mPFC) subregions in mouse - supplementary motor area (MOs), dorsomedial PFC (dmPFC), and ventromedial (vmPFC) - during a freely-behaving non-match-to-position WM task. We found divergent patterns of task-related activity across the phases of WM. The MOs is most active around task phase transitions and encodes the starting sample location most selectively. Dorsomedial PFC contains a more stable population code, including persistent sample-location-specific firing during a five second delay period. Finally, the vmPFC responds most strongly to reward-related information during the choice phase. Our results reveal anatomically and temporally segregated computation of WM task information in mPFC and motivate more precise consideration of the dynamic neural activity required for WM.

fMRI, LFP, and anatomical evidence for hierarchical nociceptive routing pathway between somatosensory and insular cortices

The directional organization of multiple nociceptive regions, particularly within obscure operculoinsular areas, underlying multidimensional pain processing remains elusive. This study aims to establish the fundamental organization between somatosensory and insular cortices in routing nociceptive information. By employing an integrated multimodal approach of high-field fMRI, intracranial electrophysiology, and transsynaptic viral tracing in rats, we observed a hierarchically organized connection of S1/S2 → posterior insula → anterior insula in routing nociceptive information. The directional nociceptive pathway determined by early fMRI responses was consistent with that examined by early evoked LFP, intrinsic effective connectivity, and anatomical projection, suggesting fMRI could provide a valuable facility to discern directional neural circuits in animals and humans non-invasively. Moreover, our knowledge of the nociceptive hierarchical organization of somatosensory and insular cortices and the interface role of the posterior insula may have implications for the development of targeted pain therapies.

Unique Spatial Transcriptomic Profiling of the Murine Femoral Fracture Callus: A Preliminary Report

Fracture callus formation is a dynamic stage of bone activity and repair with precise, spatially localized gene expression. Metastatic breast cancer impairs fracture healing by disrupting bone homeostasis and imparting an altered genomic profile. Previous sequencing techniques such as single-cell RNA and in situ hybridization are limited by missing spatial context and low throughput, respectively. We present a preliminary approach using the Visium CytAssist spatial transcriptomics platform to provide the first spatially intact characterization of genetic expression changes within an orthopedic model of impaired fracture healing. Tissue slides prepared from BALB/c mice with or without MDA-MB-231 metastatic breast cancer cells were used. Both unsupervised clustering and histology-based annotations were performed to identify the hard callus, soft callus, and interzone for differential gene expression between the wild-type and pathological fracture model. The spatial transcriptomics platform successfully localized validated genes of the hard (Dmp1, Sost) and soft callus (Acan, Col2a1). The fibrous interzone was identified as a region of extensive genomic heterogeneity. MDA-MB-231 samples demonstrated downregulation of the critical bone matrix and structural regulators that may explain the weakened bone structure of pathological fractures. Spatial transcriptomics may represent a valuable tool in orthopedic research by providing temporal and spatial context.

High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labeling

Deciphering patterns of connectivity between neurons in the brain is a critical step toward understanding brain function. Imaging-based neuroanatomical tracing identifies area-to-area or sparse neuron-to-neuron connectivity patterns, but with limited throughput. Barcode-based connectomics maps large numbers of single-neuron projections, but remains a challenge for jointly analyzing single-cell transcriptomics. Here, we established a rAAV2-retro barcode-based multiplexed tracing method that simultaneously characterizes the projectome and transcriptome at the single neuron level. We uncovered dedicated and collateral projection patterns of ventromedial prefrontal cortex (vmPFC) neurons to five downstream targets and found that projection-defined vmPFC neurons are molecularly heterogeneous. We identified transcriptional signatures of projection-specific vmPFC neurons, and verified Pou3f1 as a marker gene enriched in neurons projecting to the lateral hypothalamus, denoting a distinct subset with collateral projections to both dorsomedial striatum and lateral hypothalamus. In summary, we have developed a new multiplexed technique whose paired connectome and gene expression data can help reveal organizational principles that form neural circuits and process information.