Biology subjects

Okano, H.

Publications and source records attributed to Okano, H..

At least 19 recordsLinked to original sources

bioRxiv2026

DAP12-deficient microglia adopt a TREM2-independent antigen-presenting state with a glial-to-neuronal cascade in Nasu-Hakola disease

Nasu-Hakola disease (NHD), a dementia with about 200 cases worldwide, is caused by loss-of-function mutation of TYROBP, encoding DAP12, or its receptor TREM2. TREM2-DAP12 is the switch that converts microglia from a surveillant to a reactive state; what DAP12-deficient microglia become and to what extent they reshape their microenvironment is unknown. We profiled prefrontal cortex and hippocampus from an NHD donor and control by single-nucleus RNA sequencing and mapped the glial changes in situ by spatial transcriptomics. NHD microglia adopted a CIITA-driven, MHC class II-high antigen-presenting state with complement, iron and glycolytic programs and Fc receptors but not the TREM2-dependent lipid program. Astrocytes became pan-reactive and lost metallothionein expression, oligodendrocytes lost mature cells and cholesterol synthesis, and excitatory neurons lost presynaptic and activity programs, consistently between regions and across a published cohort. DAP12 deficiency left microglia in an antigen-presenting state short of the TREM2-dependent arm, accompanied by a glial-to-neuronal cascade.

neuroscience↗

bioRxiv2026

MECP2-mutant marmosets exhibit primate-specific phenotypes of Rett syndrome

We used genome editing to generate MECP2-knockout marmosets and establish a new primate model for Rett syndrome (RTT), a neurodevelopmental disorder. MRI analysis of this marmoset model revealed diminished cortico-cortical connections, particularly those originating in the prefrontal cortex. Detailed histological analysis revealed reduced dendritic arborization and synaptic density, particularly in the upper layers of the cerebral cortex. Cortical layer II/III excitatory neurons appeared to be immature based on single-nucleus RNA sequencing and spatial transcriptomics, while PVALB-positive interneurons exhibited upregulation of neuronal maturation-related transcripts. Moreover, the neurodevelopmental disease gene GABAB receptor 2 (GABBR2) emerged as a conserved downstream target of MECP2, illuminating a cellular cascade that could be targeted in preclinical and therapeutic drug development. Many of the gene expression changes observed in the marmoset model are common in RTT patients, thereby highlighting molecular links from cell type-specific phenotypes in the marmoset model to the RTT clinical presentation.

neuroscience↗

bioRxiv2026

IF1 restrains excessive elevation of the mitochondrial membrane potential and safeguards the epithelial state of human induced pluripotent stem cells

Human pluripotent stem cells (hPSCs) rely on glycolysis and exhibit low mitochondrial respiration, conditions under which F1Fo ATP synthase tends to run in reverse, hydrolyzing ATP. ATP synthase inhibitory factor subunit 1 (IF1) inhibits F1Fo-mediated ATP hydrolysis, but its significance in glycolytic hPSCs remains unclear. Here, we show that stable IF1 knockdown (IF1-KD) in human induced pluripotent stem cells (hiPSCs) enhanced mitochondrial ATP hydrolysis and elevated the mitochondrial membrane potential ({Delta}{Psi}m). Markers of the undifferentiated state were largely maintained, whereas IF1-KD cells exhibited reduced epithelial characteristics and a partial epithelial-mesenchymal transition (EMT)-like state. IF1-KD cells also showed enhanced store-operated Ca2 entry (SOCE) and increased nuclear NFATc3. Pharmacological reduction of {Delta}{Psi}m attenuated SOCE, whereas NFATc3 overexpression reproduced key features of the EMT-like expression pattern. Endogenous IF1 therefore acts as a constitutive restraint on reverse-mode F1Fo activity, limiting excessive {Delta}{Psi}m and downstream SOCE-NFATc3 signaling and safeguarding the epithelial state of hPSCs.

Cell Biology↗

bioRxiv2026

Generalisable signatures of anaesthesia in the large-scale functional organisation of the marmoset brain

How the activity and connectivity of the brain support consciousness remains a central question in neuroscience. Recent progress driven by the use of functional MRI has seen growing recognition that large-scale distributed functional organisation of the human and non-human primate brain are systematically and consistently reshaped by anaesthetic-induced unconsciousness, across anaesthetics and across human and macaque. Here, we generalise these results to a different primate species that is gaining traction as model organism in neuroscience, the marmoset (Callithrix jacchus). We also generalise results to an additional anaesthetic, isoflurane, which we compare with propofol and sevoflurane. We report that under anaesthesia with propofol, sevoflurane, or isoflurane, distributed brain activity from functional MRI is increasingly constrained by the underlying structural connectivity across scales. Anaesthesia also induces a collapse of the principal gradient and intrinsic functional geometry of the marmoset brain, coinciding with a breakdown of hierarchical integration. Altogether, the present results indicate generalisable signatures of anaesthesia in the large-scale organisation of the primate brain.

neuroscience↗

bioRxiv2026

Ropinirole hydrochloride mitigates oxidative stress and neuroinflammation via the PI3K-mTOR pathway in TDP-43 hiPSC-derived microglial-like cells

BackgroundAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive motor neuron loss accompanied by neuroinflammation, oxidative stress, and impaired proteostasis, with pathological aggregation of TDP-43 as its defining hallmark. Microglia are recognized as central contributors to ALS pathogenesis, yet the mechanisms underlying their intrinsic dysfunction in the context of TDP-43 remain insufficiently characterized. MethodsWe characterized microglia-like cells (iMGLs) differentiated from isogenic TDP-43 M337V human induced pluripotent stem cell lines. We performed integrated functional assays, transcriptomic profiling and drug repurposing analysis to systematically compare mutant and control iMGLs. To assess therapeutic potential, we evaluated the effects of ROPI, a dopamine D2 receptor agonist previously advanced to clinical trials for ALS, on disease-relevant phenotypes in TDP-43 iMGLs. ResultsTDP-43M337V/M337V iMGLs presented ALS-associated abnormalities, including cytoplasmic TDP-43 accumulation with impaired phagocytosis and elevated oxidative stress, impaired autophagy and mitophagy, altered cytokine profiles, and reduced ferritin levels. Building on our previous identification of ropinirole hydrochloride as neuroprotective for ALS motor neurons, we now show that it confers therapeutic benefits in mitigating microglial pathology. ROPI treatment significantly reduced oxidative stress and caspase-3/7 activity and partially restored cytokine homeostasis in TDP-43M337V/M337V iMGLs, independent of autophagy/mitophagy modulation. Transcriptomic profiling revealed that ropinirole modulated disease-associated gene expression signatures involving protein folding, extracellular matrix organization, and oxidative stress responses. Furthermore, connectivity map-based analysis prioritized PI3K-Akt-mTOR inhibitors as candidates for reversing TDP-43 iMGL signatures, and ropinirole was found to modulate mTOR signaling. These converging lines of evidence support a mechanistic role for ropinirole in restoring microglial homeostasis via PI3K-mTOR pathway regulation. Taken together, our findings position ropinirole as a promising candidate dual action therapeutic candidate capable of targeting both neuronal and microglial dysfunction in ALS, suggesting broader applicability of ropinirole in modulating neuroinflammatory cascades across other neurodegenerative conditions. ConclusionRopinirole broadens ALS therapy from motor neurons to microglia, underscoring its promise for integrated and clinically meaningful treatment strategies.

neuroscience↗

bioRxiv2025

Design-of-Experiments for Nonlinear, Multivariate Biology: Rethinking Experimental Design through Perturb-seq

Design of experiments (DOE) principles are increasingly applied to biological assays, yet it remains unclear whether the optimality of their foundational assumption--orthogonal decomposition--holds in nonlinear biological systems. We addressed this question using Perturb-seq as a case study. By benchmarking a design commonly used in Perturb-seq and related experiments against the orthogonal Plackett-Burman (PB) design via simulations, we uncovered a counter-intuitive phenomenon: while orthogonal designs generally excel, the correlated structure inherent to the common design is functionally robust in systems with significant signal amplification. This challenges the blind application of DOE to biology. Based on these findings, we developed the PB suitability index (PBSI), a simple, parameter-free metric that predicts the optimal design solely from network structure. Our work not only provides practical guidelines for Perturb-seq but also establishes a "biology-oriented DOE" framework, bridging the gap between statistical rigor and biological complexity.

bioinformatics↗

bioRxiv2025

Early pathogenesis of spinal and bulbar muscular atrophy uncovered by human iPSC-derived motor neurons highlights pathogenic neuropeptides as therapeutic targets

Spinal and bulbar muscular atrophy (SBMA) is a neuromuscular disorder caused by the expansion of the polyglutamine tract in the androgen receptor (AR). Motor neurons (MNs) derived from patient-specific induced pluripotent stem cells (iPSCs) robustl y recapitulated early SBMA phenotypes driven by endogenous mutant AR in the absence of testosterone (dihydrotestosterone) and detectable mutant AR aggregation. Notably, endoplasmic reticulum stress markedly exacerbated SBMA pathology. Cross-species integrative analyses of patient-derived neurons and spinal cords of transgenic mouse models revealed high expression of multiple disease-associated neuropeptides, including urotensin II (UTS2), in patient spinal MNs that was correlated with disease onset and progression in iPSC-derived MNs. Downstream signaling analyses of these neuropeptides revealed convergent molecular pathways whose pharmacological inhibition rescued cellular phenotypes. Together, these results establish a human disease model harboring endogenous mutant AR that closely reproduces early SBMA pathology and provides molecular leads for elucidating disease mechanisms and biomarkers and developing therapeutic targets.

neuroscience↗

bioRxiv2025

The Brain/MINDS 3D Digital Marmoset Brain Atlas Version 2.0: Population-based Cortical Region Parcellations with Multi-Modal Standard Templates

We present our new Brain/MINDS 3D digital marmoset brain atlas version 2.0 (BMA2.0), a population-based 3D digital brain atlas of the common marmoset (Callithrix jacchus), designed to overcome the limitations of previous single subject atlases that are prone to structural biases arising from individual variation. Here, manually delineated cortical regions from 10 myelin-stained brains were used to create a generalized cortical parcellation. Newly refined subcortical regions from a previous atlas and a completely new cerebellum parcellation were also incorporated, resulting in a comprehensive whole brain parcellation for both hemispheres. To facilitate multimodal data analysis, the atlas package includes co-registered average templates for myelin and Nissl staining from the same individuals, ex vivo MRI T2 (91 individuals), and in vivo MRI T2 (446 individuals). Cortical flat maps and pial, cortical mid-thickness, and white matter surfaces are also provided. BMA2.0 provides a central brain space for multimodal data integration, spatial analysis, and comparative neuroscience. Standard formats and transformations are provided for easy integration into existing workflows and interoperability with existing atlases.

neuroscience↗

bioRxiv2025

Functional connectivity, structural connectivity, and inter-individual variability in Drosophila melanogaster

Clarifying the relationship between structure and function is important for understanding the brain. In Drosophila melanogaster, FlyEM and FlyWire electron microscopy-based connectome data and whole-brain calcium imaging data are available. We applied pre-processing methods from fMRI to whole-brain calcium imaging data and comprehensively investigated the optimal parameters. Then, we found that the FC-SC (functional and structural connectivity) correlation decreased linearly with region of interest count, and this trend was the same in flies and humans. We also developed a new, more robust method to quantify the degree of pre-and post-synaptic segregation and investigated this in the fly whole-brain. This revealed that many neurons have unsegregated synapses. We extracted highly unsegregated synapses and compared them with random-extracted null SC matrices. Their FC-SC correlation was significantly higher, indicating that these synapses contribute to FC well. Conversely, highly segregated-synapses showed significantly lower FC-SC correlation and contribute less to FC. Neurons with unsegregated synapses like non-spiking neurons are spread throughout the whole-brain, and they are thought to have a significant influence on FC.

neuroscience↗

bioRxiv2025

Chiral shift toward D-serine reflects intrathecal inflammation in multiple sclerosis and counteracts motor impairment in a murine model

Multiple sclerosis (MS) is characterized by chronic inflammatory demyelination involving complex interplay between the central nervous and immune systems. Neuroinflammation triggers cellular reorganization requiring O_SCPLOWLC_SCPLOW-serine for sustained syntheses of membrane lipids and nucleic acids, whereas it causes aberrant glutamatergic neurotransmission involving O_SCPLOWDC_SCPLOW-serine. However, significance of serine metabolism in MS pathology remains unexplored. Here we show that serine chiral homeostasis is disrupted in MS and endogenous O_SCPLOWDC_SCPLOW-serine prevents motor deficits caused by inflammatory demyelination. We found in a large cohort study that patients with MS exhibit elevated O_SCPLOWDC_SCPLOW-serine levels and the O_SCPLOWDC_SCPLOW-/total serine ratio in the cerebrospinal fluid at diagnosis. Steric deviation toward O_SCPLOWDC_SCPLOW-serine accords with emergence of the intrathecal inflammatory marker oligoclonal bands, and correlates negatively with proinflammatory cytokines. An in vivo animal model of MS, genetically engineered to exhibit distinct metabolic states of O_SCPLOWDC_SCPLOW-serine, revealed that endogenous O_SCPLOWDC_SCPLOW-serine synthesis mitigates the progression of motor deficits and suppresses proinflammatory and vascular endothelial pathogenic signaling. Moreover, pre-symptomatic oral supplementation with O_SCPLOWDC_SCPLOW-serine, but not O_SCPLOWLC_SCPLOW-serine, enhances production of extracellular matrices, preserves integrity of the blood brain barrier, attenuates demyelination, and improves motor function. Contrary to the previously recognized neurotoxic nature of O_SCPLOWDC_SCPLOW-serine, our findings reveal an unrecognized significance of O_SCPLOWDC_SCPLOW-serine metabolism in MS and a protective function of O_SCPLOWDC_SCPLOW-serine against neuroinflammation involving disruption of the blood brain barrier, which may present an untapped therapeutic target in MS. One Sentence SummarySerine chiral homeostasis is disturbed in multiple sclerosis and O_SCPLOWDC_SCPLOW-serine mitigates inflammatory demyelination.

neuroscience↗

bioRxiv2025

Comprehensive profiling of anaesthetised brain dynamics across phylogeny

Intrinsic dynamics of neuronal circuits shape information processing. Combining neuroimaging with causal perturbation offers the opportunity to understand how local dynamics mediate the link between neurobiology and functional repertoire. We compile a unique dataset of multi-scale neural activity during wakefulness and anaesthetic-induced suppression of information processing encompassing human, macaque, marmoset, mouse, zebrafish and nematode. Applying massive feature extraction, we comprehensively characterise local neural dynamics across >6,000 time-series features. Using dynamics as a common space for cross-species comparison reveals a conserved dynamical profile of anaesthesia across species, characterised by shorter intrinsic timescales of neural activity and dampened interregional synchrony. This dynamical regime is experimentally reversed in vivo by deep-brain stimulation of the macaque centromedian thalamus, restoring behavioural responsiveness. Spatially, this conserved dynamical phenotype covaries with conserved transcriptional profiles of excitatory and inhibitory neurotransmission across human, macaque, marmoset and mouse cortex. Biophysical modelling provides a mechanistic link between the macroscale dynamical phenotype of anaesthesia, and microscale effects of key molecular targets on the timescales of synaptic excitation and inhibition. Altogether, comprehensive dynamical phenotyping reveals a shared neural endpoint of anaesthesia: across species and scales, anaesthetics induce spatio-temporal isolation of local neural activity.

neuroscience↗

bioRxiv2024

Dual fragmentation via collision-induced and oxygen attachment dissociations using water and its radicals for C=C position-resolved lipidomics

Oxygen attachment dissociation (OAD) is a tandem mass spectrometry (MS/MS) technique used to annotate the positions of double bonds (C=C) in complex lipids. Although OAD has been used for untargeted lipidomics, its availability has been limited to the positive-ion mode, requiring the independent use of a collision-induced dissociation (CID) method. In this study, we demonstrated the OAD-MS/MS technique in the negative-ion mode for profiling phosphatidylserines, phosphatidylglycerols, phosphatidylinositols, and sulfatides, where the fragmentation mechanism remained consistent with that in the positive-ion mode. Furthermore, we proposed optimal conditions for the simultaneous acquisition of CID- and OAD-specific fragment ions, termed OAciD. In the collision cell for OAD, oxygen atoms and hydroxy radicals facilitate C=C position-specific fragmentation, while residual water vapor induces cleavage of low-energy covalent bonds, such as ester and peptide bonds, at higher collision energy values, preserving OAD-specific ions under high collision energy conditions. Finally, theoretical fragment ions were implemented in MS-DIAL 5 to accelerate C=C position-resolved untargeted lipidomics. The OAciD methodology was applied to lipid profiling of five marmoset brain regions: the frontal lobe, hippocampus, midbrain, cerebellum, and medulla. Region-specific marmoset lipidomes were characterized with C=C positional information, where the ratios of C=C positional isomers such as delta 9- and delta 11 of fatty acid 18:1 in phosphatidylcholine were also estimated using OAciD-MS/MS. In addition, we characterized the profiles of polyunsaturated fatty acid-containing complex lipids with C=C positional information, where lipids containing omega-3 fatty acids were enriched in the cerebellum, while those containing omega-6 fatty acids were more abundant in the hippocampus and frontal lobe.

bioengineering↗

bioRxiv2024

Glial scar formation by reactive astrocytes derived from oligodendrocyte progenitor cells after closed-head injury

The diversity of reactive astrocytes is key to understanding complicated pathological processes in the brain. The accumulation of reactive astrocytes expressing the neural stem/precursor cell marker Nestin is common after brain injury, but the pathological implications of this reactive astrocyte subpopulation remain elusive. This study initially aimed to determine the origin and fate of these reactive astrocytes expressing Nestin by characterizing cells labeled with green fluorescent protein (GFP) after closed-head injury, using a Nestin promoter region widely utilized to study neural stem/precursor cells. Unexpectedly, oligodendrocyte progenitor cells (OPCs), rather than astrocytes, were robustly and selectively labeled with GFP. A fraction of these cells showed a subsequent upregulation of astrocyte markers and were incorporated into glial scars. These glial scars are aggregates of reactive astrocytes that form between lesion cores and the perilesional recovering region. Deletion of the Stat3 gene, which is essential for astrocyte activation, using a Nestin promoter reduced glial scars, further confirming that OPCs are involved in glial scar formation. Reactive astrocytes labeled with a glial fibrillary acidic protein promoter differed in morphology and distribution from astrocytes derived from OPCs. This confirms that astrocytes and OPCs produce distinct reactive astrocyte subpopulations. Some GFP-labeled OPCs lacking astrocyte markers were found to distribute in perilesional recovering regions. The reduced expression of Nestin and OPC markers in these non-astrocytic descendants of OPCs, coupled with a significant fraction of these cells remaining olig2-positive, suggests that OPCs give rise to both reactive astrocytes and oligodendrocytes. These findings suggest that OPCs are activated by a novel process after brain injury.

neuroscience↗

bioRxiv2024

A graph-based practice of evaluating collective identities of cell clusters

The rise of single-cell RNA-sequencing (scRNA-seq) and evolved computational algorithms have significantly advanced biomedical science by revealing and visualizing the multifaceted and diverse nature of single cells. These technical advancements have also highlighted the pivotal role of cell clusters as representations of biologically universal entities such as cell types and cell states. However, to some extent, these clusterings remain dataset-specific and method-dependent. To improve comparability across different datasets or compositions, we previously introduced a graph-based representation of cell collections that captures the statistical dependencies of their characteristic genes. While our earlier work focused on theoretical insights, it was not sufficiently adapted and fine-tuned for practical implementation. To address this, the present paper introduces an improved practice to define and evaluate cellular identities based on our theory. First, we provide a concise summary of our previous theory and workflow. Then, point-by-point, we highlight the issues that needed fixing and propose solutions. The frameworks utility was enhanced by leveraging alternative formats of cellular features such as gene ontology (GO) terms and effectively handling dropouts. Supplemental techniques are offered to reinforce the versatility and robustness of our method.

bioinformatics↗

bioRxiv2024

Selective agonism of GPR34 stimulates microglial uptake and clearance of amyloid β fibrils

Microglia, the primary immune cells of the central nervous system, play a crucial role in maintaining brain homeostasis through phagocytosis of various substrates, including amyloid-{beta} (A{beta}) fibrils, a hallmark of Alzheimer disease (AD) pathology. However, the molecular mechanisms regulating microglial A{beta} uptake remain poorly understood. Here, we identified GPR34, a Gi/o-coupled receptor highly expressed in microglia, as a novel regulator of fibrillar A{beta} phagocytosis. Treatment with a selective GPR34 agonist, M1, specifically enhanced uptake of A{beta} fibrils, but not its monomer or oligomer, in both mouse and human microglia. Mechanistically, M1 reduced intracellular cAMP levels, which inversely correlated with A{beta} uptake activity. Importantly, a single intrahippocampal injection of M1 in an AD mouse model significantly increased microglial A{beta} uptake in vivo. Furthermore, single-nucleus RNA-sequencing analysis of Japanese AD patient samples revealed a significant reduction of GPR34 expression in microglia from AD patients compared to controls. We also observed an age-dependent decline in microglial GPR34 expression in both human and mouse datasets, suggesting a potential contribution of GPR34 downregulation to age-related A{beta} accumulation and AD risk. Collectively, our findings identify GPR34 as a promising target for modulating microglial A{beta} clearance and highlight the therapeutic potential of GPR34 agonists in AD. Significance statementAlzheimer disease (AD) is characterized by amyloid-{beta} (A{beta}) accumulation in the brain. Microglia, the brains immune cells, play a crucial role in the metabolism of A{beta}. We discovered that activating the microglial receptor GPR34 with a selective agonist enhances the phagocytosis of A{beta} fibrils, a key pathogenic form of A{beta}. Importantly, GPR34 expression decreases with aging and AD progression, potentially contributing to impaired A{beta} clearance. Our findings highlight GPR34 as a promising therapeutic target for AD, as boosting its activity could promote A{beta} clearance and slow disease progression. This study provides valuable insights into microglial function in AD and offers a novel strategy for developing disease-modifying therapies.

neuroscience↗

bioRxiv2024

Establishment of a novel amyotrophic lateral sclerosis patient-derived blood-brain barrier model: Investigating barrier dysfunction and immune cell interaction

Amyotrophic lateral sclerosis (ALS) is a major neurodegenerative disease for which there is currently no effective treatment. The main feature of the disease is the loss of motor neurons in the central nervous system (CNS), but other CNS components and the immune system also appear to be involved in the pathogenesis of the disease. The blood-brain barrier (BBB) is formed by specialized brain microvascular endothelial cells (BMECs) and plays a crucial role in maintaining homeostasis within the central nervous system (CNS). Autopsy studies have reported BBB abnormalities in ALS patients, and studies in animal models suggest that BBB breakdown may precede neurodegeneration. However, the difficulty of obtaining patient samples has hampered further studies. We used the method of differentiating BMEC-like cells from human induced pluripotent stem cells (hiPSCs), which have robust barrier functions and express adhesion molecules necessary for immune cell adhesion, to investigate BBB functions in ALS patients. We also established a method using automated analysis techniques to analyze immune cell adhesion to the BBB in multiple samples simultaneously and with minimal bias. BMEC-like cells derived from ALS patients carrying TARDBP N345K/WT mutations exhibited increased permeability to small molecules due to loss of tight junction, as well as increased expression of cell surface adhesion molecules, leading to enhanced immune cell adhesion. BMEC-like cells derived from hiPSCs with other types of TARDBP gene mutations (TARDBP K263E/K263E and TARDBP G295S/G295S) introduced by genome editing technology did not show such BBB dysfunction compared to the isogenic control. These results indicate that our model can recapitulate BBB abnormalities reported in ALS patients using patient (TARDBP N345K/WT) -derived hiPSCs and that two types of missense mutation, TARDBP K263E/K263E and TARDBP G295S/G295S, do not contribute to the BBB dysfunction. This novel ALS patient-derived BBB model is useful for the challenging analysis of the involvement of BBB dysfunction in the pathogenesis and to promote therapeutic drug discovery.

cell biology↗

bioRxiv2023

A single-cell atlas of transcribed cis-regulatory elements in the human genome

Transcribed cis-regulatory elements (tCREs), such as promoters and enhancers, are fundamental to modulate gene expression and define cell identity. The detailed mapping of tCREs at single-cell resolution is essential for understanding the regulatory mechanisms that govern cellular functions. Prior tCRE catalogs, limited by bulk analysis, have often overlooked cellular heterogeneity. We have constructed a tCRE atlas using single-cell 5-RNA-seq, capturing over 340,000 single-cells from 23 human tissues and annotating more than 175,000 tCREs, substantially enhancing the scope and granularity of existing cis-regulatory element annotations in the human genome. This atlas unveils patterns of gene regulation, revealing connections between broadly expressed promoters and cell type-specific distal tCREs. Assessing trait heritability at single-cell resolution with a novel tCRE module-based approach, we uncovered the nuanced trait-gene regulatory relationships across a continuum of cell populations, offering insights beyond traditional gene-level and bulk-sample analyses. Our study bridges the gap between gene regulation and trait heritability, underscoring the potential of single-cell analysis to elucidate the genetic foundations of complex traits. These insights set the stage for future research to investigate the impact of genetic variations on diseases at the individual level, advancing the understanding of cellular and molecular basis of trait heritability.

genomics↗

bioRxiv2023

Epileptic responses in marmosets induced by knockdown of CREB Regulated Transcription Coactivator 1 (CRTC1)

Animal models have contributed greatly to the development of anticonvulsant drugs. However, 20-30% of epilepsy patients still do not achieve adequate seizure control. It is important to understand the biological mechanisms of epilepsy in order to develop treatments and novel anticonvulsant drugs. Here we report CRTC1 knockdown (KD) induced abnormal cFOS expression beyond the injection sites followed by epileptic response by three local injections of short hairpin RNA (shRNA) in marmoset V1. Longitudinal monitoring of cortical-wide neural activity revealed transient changes in high frequency oscillations by cortical electrocorticography throughout the cortex, and a lesion in the temporal lobe was observed by MRI and postmortem histology. shCRTC1 KD marmosets showed severe lesions surrounding the injection site several months after injection. Glial cell activation may occur simultaneously or prior to IEG induction after shCRTC1 injection. Thus, the epileptic process from seizure onset to remission can be studied in this animal model.

neuroscience↗