Biology subjects

Wu, J.

Publications and source records attributed to Wu, J..

At least 415 records · Page 23Linked to original sources

bioRxiv2023

Neural mechanism of attention modulation during non-movement decision-making

Decision-making is a cognitive process, in which participants need to attend to relevant information and ignore the irrelevant information. Previous studies have described a set of cortical areas important for attention. It is unclear whether subcortical areas also serve a role. The subthalamic nucleus (STN), a part of basal ganglia, is traditionally considered a critical node in the cortico-basal ganglia-thalamus-cortico network. Given the location of the STN and its widespread connections with cortical and subcortical brain regions, the STN plays an important role in motor and non-motor cognitive processing. We would like to know if STN is also related to fluctuations in attentional task performance, and how the STN interacts with prefrontal cortical regions during the process. We examined neural activities within STN covaried with lapses of attention (defined as behavior error). We found that decreased neural activities in STN were associated with sustained attention. By examining connectivity across STN and various sub-regions of the prefrontal cortex (PFC), we found that decreased connectivity across areas was associated with sustained attention. Our results indicated that decreased STN activities were associated with sustained attention, and the STN-PFC circuit supported this process. Significance StatementAttention is a core internal state variable that governs the allocation of limited resources depending on the task demands in various cognitive processes. If the subcortical area, subthalamic nucleus (STN), related to attentional fluctuations, and how the STN interacted with cortical regions during the process remains unclear. In this study, we examined neural activities within STN, and connectivity between STN and various prefrontal sub-regions during sustained attention and lapses of attention. We found both neural activities within STN and connectivity between STN-PFC circuit decreased during sustained attention. These findings indicated that decreased STN activities were associated with sustained attention, and the STN-PFC circuit supported this process.

neuroscience↗

bioRxiv2023

Uncovering Minimal Pathways in Melanoma Initiation

Cutaneous melanomas are clinically and histologically heterogeneous. Most display activating mutations in Braf or Nras and complete loss of function of one or more tumor suppressor genes. Mouse models that replicate such mutations produce fast-growing, pigmented tumors. However, mice that combine Braf activation with only heterozygous loss of Pten also produce tumors and, as we show here, in an Albino background this occurs even with Braf activation alone. Such tumors arise rarely, grow slowly, and express low levels of pigmentation genes. The timing of their appearance was consistent with a single step stochastic event, but no evidence could be found that it required de novo mutation, suggesting instead the involvement of an epigenetic transition. Single-cell transcriptomic analysis revealed such tumors to be heterogeneous, including a minor cell type we term LNM (Low-pigment, Neural- and extracellular Matrix-signature) that displays gene expression resembling "neural crest"-like cell subsets detected in the fast-growing tumors of more heavily-mutated mice, as well as in human biopsy and xenograft samples. We provide evidence that LNM cells pre-exist in normal skin, are expanded by Braf activation, can transition into malignant cells, and persist with malignant cells through multiple rounds of transplantation. We discuss the possibility that LNM cells not only serve as a pre-malignant state in the production of some melanomas, but also as an important intermediate in the development of drug resistance.

cancer biology↗

bioRxiv2023

Lithocholic acid targets TULP3 to activate sirtuins and AMPK to retard ageing

Lithocholic acid (LCA), accumulated in the body during calorie restriction (CR), can confer administered metazoans with the ability to activate AMP-activated protein kinase (AMPK) and retard ageing. However, how LCA is signalled to activate AMPK and elicit the biological effects is unclear. Here, we show that LCA can enhance sirtuins (SIRTs) to deacetylate and subsequently inhibit vacuolar H+-ATPase (v-ATPase), thereby triggering AMPK activation via the lysosomal glucose-sensing pathway. Through proteomic analysis of SIRT1-coimmunoprecipitated proteins, we identify and validate that TUB like protein 3 (TULP3) is a constitutive component of SIRTs. Surprisingly, we found that TULP3 is an LCA receptor, and that the LCA-bound TULP3 activates SIRTs. The activated SIRTs in turn deacetylate the V1E1 subunit of v-ATPase on K52, K99 and K191 residues. Muscle-specific expression of the 3KR mutant of V1E1, mimicking the deacetylated state, dominantly activates AMPK and rejuvenates muscles in aged mice. Moreover, LCA once administered also activates AMPK and extends lifespan and healthspan in nematodes and flies, depending on the TULP3 homologues tub-1 and ktub, respectively. Our study thus elucidates that LCA triggers the TULP3-sirtuin-v-ATPase- AMPK route to manifest benefits of calorie restriction.

physiology↗

bioRxiv2023

Lithocholic acid phenocopies rejuvenating and life-extending effects of calorie restriction

Calorie restriction (CR) is a dietary intervention to promote health and longevity. CR causes various metabolic changes in both the production and circulation of metabolites; however, it remains unclear which of the changed metabolite(s) can account for the physiological benefits of CR. Through metabolomic analysis of metabolites undergoing abundance changes during CR and subsequent functional validation, we found that lithocholic acid (LCA) is the only metabolite that alone can recapitulate the effects of CR, including activation of AMPK and the rejuvenating effects of muscle regeneration, grip strength and running capacity in mice. Interestingly, LCA also activates AMPK and exerts life- and health-extending effects in Caenorhabditis elegans and Drosophila melanogaster, indicating that these animal models are able to transmit the signalling of LCA once administered. Knockout of AMPK abrogates LCA-induced phenotypes, in nematodes and flies, as well as in mice. Together, we have identified that administration of the CR-upregulated metabolite LCA alone can confer anti-ageing benefits to metazoans, in an AMPK-dependent manner.

physiology↗

bioRxiv2023

Multilayer meta-matching: translating phenotypic prediction models from multiple datasets to small data

Resting-state functional connectivity (RSFC) is widely used to predict phenotypic traits in individuals. Large sample sizes can significantly improve prediction accuracies. However, for studies of certain clinical populations or focused neuroscience inquiries, small-scale datasets often remain a necessity. We have previously proposed a "meta-matching" approach to translate prediction models from large datasets to predict new phenotypes in small datasets. We demonstrated large improvement of meta-matching over classical kernel ridge regression (KRR) when translating models from a single source dataset (UK Biobank) to the Human Connectome Project Young Adults (HCP-YA) dataset. In the current study, we propose two meta-matching variants ("meta-matching with dataset stacking" and "multilayer meta-matching") to translate models from multiple source datasets across disparate sample sizes to predict new phenotypes in small target datasets. We evaluate both approaches by translating models trained from five source datasets (with sample sizes ranging from 862 participants to 36,834 participants) to predict phenotypes in the HCP-YA and HCP-Aging datasets. We find that multilayer meta-matching modestly outperforms meta-matching with dataset stacking. Both meta-matching variants perform better than the original "meta-matching with stacking" approach trained only on the UK Biobank. All meta-matching variants outperform classical KRR and transfer learning by a large margin. In fact, KRR is better than classical transfer learning when less than 50 participants are available for finetuning, suggesting the difficulty of classical transfer learning in the very small sample regime. The multilayer meta-matching model is publicly available at GITHUB_LINK.

neuroscience↗

bioRxiv2023

Vagus nerve stimulation by focused ultrasound attenuates acute myocardial ischemia/reperfusion injury predominantly through cholinergic anti-inflammatory pathway

BackgroundThe invasive method using electrically stimulating vagus nerve has been demonstrated to inhibit the inflammatory response against acute myocardial ischemia/reperfusion(I/R) injury. This neuro-regulatory technique used is invasive implantation of electrical stimulators which have the risk of infection and other complications. A non-invasive method of vagus nerve stimulation applying on acute myocardial I/R injury is particularly important and desirable. ObjectivesThis study aimed to test the hypothesis that focused ultrasound stimulation(FUS) of vagus nerve attenuates acute myocardial I/R injury through cholinergic anti-inflammatory pathway. MethodsThis study was completed with two parts. In the first part, ischemia was induced by left anterior descending coronary artery (LAD) occlusion for 30 minutes (min), followed by 2 hours (h) of reperfusion, FUS lasted for 50 min after reperfusion for 10 min. Infammatory markers, arrhythmia score, histopathology, infammatory markers 7 nicotinic acetylcholine receptor (7nAchR) protein were determined. In the second part, ischemia was induced by LAD occlusion for 30 min, followed by 24h of reperfusion, FUS lasted for 50 min after reperfusion for 10 min. Myocardial fibrosis, infarct size, echocardiographic measurements, biomarkers of pro-oxidative stress, antioxidant and myocardial apoptosis were determined. ResultsFUS of vagus nerve significantly decreased the level of infammatory markers in I/R+FUS group compared with the I/R group, I/R+vagotomy group and I/R+vagotomy+FUS group. FUS decreased the incidence of ventricular tachycardia (VT) and ventricular fibrillation (VF), while also reduced arrhythmia score in I/R+FUS group compared with the I/R group. These improvements were associated with the inhibition of acute inflammatory reaction through cholinergic anti-inflammatory pathway. FUS limited myocardial fibrosis and infarct size, preserved left ventricular function. This cardioprotective effect was associated with alleviation of apoptosis and oxidative stress. ConclusionsThe noninvasive method of ultrasonic neuromodulation using FUS of vagus nerve exerted protective effects on acute myocardial I/R injury. Its potential mechanisms involved the suppression of acute inflammatory reaction through cholinergic anti-inflammatory pathway.

neuroscience↗

bioRxiv2023

Spatially resolved molecular and cellular atlas of the mouse brain

A comprehensive atlas of genes, cell types, and their spatial distribution across a whole mammalian brain is fundamental for understanding function of the brain. Here, using snRNA-seq and Stereo-seq techniques, we generated a mouse brain atlas with spatial information for 308 cell clusters with single-cell resolution involving over 6 million cells as well as for 29,655 genes. We have identified new astrocyte clusters, and demonstrated that distinct cell clusters exhibit preference for cortical subregions. In addition, we identified 155 genes exhibiting regional specificity in the brainstem, and 513 long non-coding RNA exhibited regional specificity in the adult brain. Parcellation of brain regions based on spatial transcriptomic information showed large overlap with that by traditional method. Furthermore, we have uncovered 411 transcription factor regulons with spatiotemporal specificity during development. Thus, our study has discovered genes and regulon with spatiotemporal specificity, and provided a high-resolution spatial transcriptomic atlas of the mouse brain.

neuroscience↗

bioRxiv2023

Human mutations in high-confidence Tourette disorder genes affect sensorimotor behavior, reward learning, and striatal dopamine in mice

Tourette disorder (TD) is poorly understood, despite affecting 1/160 children. A lack of animal models possessing construct, face, and predictive validity hinders progress in the field. We used CRISPR/Cas9 genome editing to generate mice with mutations orthologous to human de novo variants in two high-confidence Tourette genes, CELSR3 and WWC1. Mice with human mutations in Celsr3 and Wwc1 exhibit cognitive and/or sensorimotor behavioral phenotypes consistent with TD. Sensorimotor gating deficits, as measured by acoustic prepulse inhibition, occur in both male and female Celsr3 TD models. Wwc1 mice show reduced prepulse inhibition only in females. Repetitive motor behaviors, common to Celsr3 mice and more pronounced in females, include vertical rearing and grooming. Sensorimotor gating deficits and rearing are attenuated by aripiprazole, a partial agonist at dopamine type II receptors. Unsupervised machine learning reveals numerous changes to spontaneous motor behavior and less predictable patterns of movement. Continuous fixed-ratio reinforcement shows Celsr3 TD mice have enhanced motor responding and reward learning. Electrically evoked striatal dopamine release, tested in one model, is greater. Brain development is otherwise grossly normal without signs of striatal interneuron loss. Altogether, mice expressing human mutations in high-confidence TD genes exhibit face and predictive validity. Reduced prepulse inhibition and repetitive motor behaviors are core behavioral phenotypes and are responsive to aripiprazole. Enhanced reward learning and motor responding occurs alongside greater evoked dopamine release. Phenotypes can also vary by sex and show stronger affection in females, an unexpected finding considering males are more frequently affected in TD. Significance StatementWe generated mouse models that express mutations in high-confidence genes linked to Tourette disorder (TD). These models show sensorimotor and cognitive behavioral phenotypes resembling TD-like behaviors. Sensorimotor gating deficits and repetitive motor behaviors are attenuated by drugs that act on dopamine. Reward learning and striatal dopamine is enhanced. Brain development is grossly normal, including cortical layering and patterning of major axon tracts. Further, no signs of striatal interneuron loss are detected. Interestingly, behavioral phenotypes in affected females can be more pronounced than in males, despite male sex bias in the diagnosis of TD. These novel mouse models with construct, face, and predictive validity provide a new resource to study neural substrates that cause tics and related behavioral phenotypes in TD.

neuroscience↗

bioRxiv2023

A combination of physicochemical tropism and affinity moiety targeting of lipid nanoparticles enhances organ targeting

Two camps have emerged in the targeting of nanoparticles to specific organs and cell types: affinity moiety targeting, which conjugates nanoparticles to antibodies or similar molecules that bind to known surface markers on cells; and physicochemical tropism, which achieves specific organ uptake based on the nanoparticles physical or chemical features (e.g., binding to endogenous proteins). Because these camps are largely non-overlapping, the two targeting approaches have not been directly compared or combined. Here we do both, using intravenous (IV) lipid nanoparticles (LNPs) whose original design goal was targeting to the lungs endothelial cells. For an affinity moiety, we utilized PECAM antibodies, and for physicochemical tropism, we used cationic lipids, both having been heavily studied for lung targeting. Surprisingly, the two methods yield nearly identical levels of lung uptake. However, aPECAM LNPs display much greater specificity for endothelial cells. Intriguingly, LNPs that possess both targeting methods had >2-fold higher lung uptake than either method alone. The combined-targeting LNPs also achieved greater uptake in already inflamed lungs, and greater uptake in alveolar epithelial cells. To understand how the macro-scale route of delivery affects organ targeting, we compared IV injection vs. intra-arterial (IA) injection into the carotid artery. We found that IA combined-targeting LNPs achieve 35% of the injected dose per gram (%ID/g) in the brain, a level superior to any other reported targeting method. Thus, combining affinity moiety targeting and physicochemical tropism provides benefits that neither targeting method achieves alone. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=56 SRC="FIGDIR/small/568061v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@281d31org.highwire.dtl.DTLVardef@1948026org.highwire.dtl.DTLVardef@693f99org.highwire.dtl.DTLVardef@1ce74cb_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

Insights into spinach domestication from genomes sequences of two wild spinach progenitors, Spinacia turkestanica and S. tetrandra

Cultivated spinach (Spinacia oleracea) is a dioecious species (with male and female flowers on separate individuals). We report high-quality genome assemblies for its two closest wild relatives, S. turkestanica and S. tetrandra, which are also dioecious, to study the genetics of spinach domestication. Using a combination of genomic approaches, we assembled genome sequences of both these species, and analysed them in comparison to the previously assembled S. oleracea genome. These species diverged approximately 6.3 million years ago (Mya), while cultivated spinach split from S. turkestanica (its probable direct progenitor) 0.8 Mya. A common feature of all three species is that all six chromosomes include very large gene-poor, repeat-rich regions. In S. oleracea, these correspond with pericentromeric regions with very low recombination rates in both male and female genetic maps, and we infer that the similar pericentromeric regions in the wild species also recombine rarely. Although these regions include a low proportion of Spinacia genes, many genes are nevertheless within them, and they must be considered when analyzing selection during domestication. As a first approach to the difficult question of detecting genes involved in spinach domestication, we characterized 282 structural variants (SVs) whose frequencies are higher in a set of spinach accessions than in the wild species, suggesting that they mark genome regions that have been selected during domestication. These regions include genes associated with leaf margin type and flowering time. We also describe evidence that the downy mildew resistance loci of cultivated spinach are derived from introgression from both wild spinach species.

genomics↗

bioRxiv2023

Two wild Spinacia species, S. turkestanica and S. tetrandra, genomes reveal a sex chromosome turnover in the genus

Spinach (Spinacia oleracea) is a dioecious species (with male and female flowers on separate individuals). Spinach and its closest wild relative, S. turkestanica, has homomorphic sex chromosomes, but the more distant relative S. tetrandra has heteromorphic sex chromosomes. We report high-quality genome assemblies for S. turkestanica and S. tetrandra. These diverged approximately 6.3 million years ago (Mya), while S. turkestanica split from S. oleracea much more recently, around 0.8 Mya, supporting previous suggestions that S. turkestanica is the direct progenitor of cultivated spinach. Using a combination of genomic approaches, we identified a sex-linked region (SLR) of [~]133 Mb in S. tetrandra. In all three species, the SLRs are within a large pericentromeric region of chromosome 4. We describe evidence that, in S. tetrandra, this region has completely stopped recombining in male meiosis, creating a large Y-linked region (YLR) that has partially degenerated; loss of recombination appears to have evolved in two events that created two "evolutionary strata", one of which and is highly rearranged, relative to the X. The SLRs of S. turkestanica and S. oleracea are much smaller: both include only a 10 Mb Y-specific region which is not detected in S. tetrandra. This was duplicated into a 14 Mb inverted region, and is termed the Y-duplicated region, or "YDR". These findings suggest that a turnover event created the YDR before these species diverged, replacing an extensive ancestral Y-linked region like the S. tetrandra YLR.

genomics↗

bioRxiv2023

Optical segmentation-based compressed readout of neuronal voltage dynamics

Functional imaging of biological dynamics generally begins with acquiring time-series images, followed by quantifying spatially averaged intensity traces for the regions of interest (ROIs). The conventional pipeline discards a substantial portion of the acquired data when quantifying intensity traces, indicative of inefficient data acquisition. Here we propose a conceptually novel acquisition pipeline that assigns each ROI to a single pixel in the detector, enabling optimally compressed acquisition of the intensity traces. As a proof-of-principle, we implemented a detection module composed of a pair of spatial light modulators and a microlens array, which segments the original image into multiple subimages by introducing distinct angular shifts to each ROI. Each subimage exclusively encodes the signal for the corresponding ROI, facilitating the compressed readout of its intensity trace using a single pixel. This spatial compression allowed for maximizing the temporal information without compromising the spatial information on ROIs. Harnessing our novel approach, we demonstrate the recording of circuit-scale neuronal voltage dynamics at over 5 kHz sampling rate, revealing the individual action potential waveforms within subcellular structures, as well as their submillisecond-scale temporal delays.

neuroscience↗

bioRxiv2023

Does winterkill explain contrasting demographics of winter-breeding freshwater mussel populations in Ishikari River floodplain?

O_LIEnvironmental conditions bottlenecking species population demographics are less known in cold regions with harsh winters despite of global concerns of declining freshwater mussels (Unionidae). Few studies examined both cold and summer environments in attempts to promote habitat conservation of Unionidae species. C_LIO_LIWe identified the taxonomically confused Unionidae species using phylogenetic analysis with mtDNA (COI region) and tested the hypothesis that winter mortality is the main cause of contrasting population demographics and structures in floodplain lakes in northern Japan. Demographic surveys were conducted in two lakes, which contrasted in recruitment rates, over one year including 4-month ice-covered periods C_LIO_LIAlthough previous studies have identified freshwater mussels as introduced Anemina arcaeformis (Heude 1877) based on morphology, this study confirmed the focal species as potentially native Buldowskia iwakawai (Suzuki, 1939). High winter mortality (30-40%) of adult mussels was found, although the mortality did not significantly differ between the populations with contrasting recruitment. C_LIO_LISurprisingly, the annual mortality was much lower in juveniles (10%) than in gravid and nongravid adult individuals (40-75%). The main inter-population difference was attributed to the higher summer mortality of gravid females, but not juveniles and non-gravid individuals, in the population with low recruitment. C_LIO_LIThese results collectively suggest that summer hypoxia combined with physiological stresses on females in winter is a likely population growth-limiting mechanism. To prevent a chain of adult abundance decreases in winter and high mortality of gravid mussels and newly born juveniles in summer, improvements in summer habitat conditions are necessary, while winter conditions need to be considered simultaneously. Increases in water circulation rates and alleviations of hypoxic conditions is an option for short-term habitat improvement approach. The current study sheds light on the winter-mediated mortality of freshwater mussels in shallow eutrophic floodplain lakes and contributes to improved management strategies for degraded floodplain waterbodies. C_LI

ecology↗

bioRxiv2023

Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics

The COVID-19 disease is an ongoing global health concern. Although vaccination provides some protection, people are still susceptible to re-infection. Ostensibly, certain populations or clinical groups may be more vulnerable. Factors causing these differences are unclear and whilst socioeconomic and cultural differences are likely to be important, human genetic factors could influence susceptibility. Experimental studies indicate SARS-CoV-2 uses innate immune suppression as a strategy to speed-up entry and replication into the host cell. Therefore, it is necessary to understand the impact of variants in immunity-associated human proteins on susceptibility to COVID-19. In this work, we analysed missense coding variants in several SARS-CoV-2 proteins and its human protein interactors that could enhance binding affinity to SARS-CoV-2. We curated a dataset of 19 SARS-CoV-2: human protein 3D-complexes, from the experimentally determined structures in the Protein Data Bank and models built using AlphaFold2-multimer, and analysed impact of missense variants occurring in the protein-protein interface region. We analysed 468 missense variants from human proteins and 212 variants from SARS-CoV-2 proteins and computationally predicted their impacts on binding affinities to SARS-CoV-2 proteins, using 3D-complexes. We predicted a total of 26 affinity-enhancing variants from 14 human proteins implicated in increased binding affinity to SARS-CoV-2. These include key-immunity associated genes (TOMM70, ISG15, IFIH1, IFIT2, RPS3, PALS1, NUP98, RAE1, AXL, ARF6, TRIMM, TRIM25) as well as important spike receptors (KREMEN1, AXL and ACE2). We report both common (e.g., Y13N in IFIH1) and rare variants in these proteins and discuss their likely structural and functional impact, using information on known and predicted functional sites. Potential mechanisms associated with immune suppression implicated by these variants are discussed. Occurrence of certain predicted affinity-enhancing variants should be monitored as they could lead to increased susceptibility and reduced immune response to SARS-CoV-2 infection in individuals/populations carrying them. Our analyses aid in understanding the potential impact of genetic variation in immunity-associated proteins on COVID-19 susceptibility and help guide drug-repurposing strategies.

bioinformatics↗

bioRxiv2023

Vina-GPU 2.1: towards further optimizing docking speed and precision of AutoDock Vina and its derivatives

AutoDock Vina and its derivatives have established themselves as a prevailing pipeline for virtual screening in contemporary drug discovery. Our Vina-GPU method leverages the parallel computing power of GPUs to accelerate AutoDock Vina, and Vina-GPU 2.0 further enhances the speed of AutoDock Vina and its derivatives. Given the prevalence of large virtual screens in modern drug discovery, the improvement of speed and accuracy in virtual screening has become a longstanding challenge. In this study, we propose Vina-GPU 2.1, aimed at enhancing the docking speed and precision of AutoDock Vina and its derivatives through the integration of novel algorithms to facil-itate improved docking and virtual screening outcomes. Building upon the foundations laid by Vina-GPU 2.0, we introduce a novel algorithm, namely Reduced Iteration and Low Complexity BFGS (RILC-BFGS), designed to expedite the most time-consuming operation. Additionally, we implement grid cache optimization to further enhance the docking speed. Furthermore, we employ optimal strategies to individually optimize the structures of ligands, receptors, and binding pockets, thereby enhancing the docking precision. To assess the performance of Vina-GPU 2.1, we conduct extensive virtual screening experiments on three prominent targets, utilizing two fundamental compound libraries and seven docking tools. Our results demonstrate that Vina-GPU 2.1 achieves an average 4.97-fold acceleration in docking speed and an average 342% improvement in EF1% compared to Vina-GPU 2.0. The source code and tools for Vina-GPU 2.1 are freely available at https://github.com/DeltaGroupNJUPT/Vina-GPU-2.1, accompanied by comprehensive instructions and illustrative examples.

developmental biology↗

bioRxiv2023

Human iPSC-derived microglia sense and dampen hyperexcitability of cortical neurons carrying the epilepsy-associated SCN2A-L1342P mutation

Neuronal hyperexcitability is a hallmark of seizures. It has been recently shown in rodent models of seizures that microglia, the brains resident immune cells, can respond to and modulate neuronal excitability. However, how human microglia interacts with human neurons to regulate hyperexcitability mediated by epilepsy-causing genetic mutation found in human patients remains unknown. The SCN2A genetic locus is responsible for encoding the voltage-gated sodium channel Nav1.2, recognized as one of the leading contributors to monogenic epilepsies. Previously, we demonstrated that the recurring Nav1.2-L1342P mutation identified in patients with epilepsy leads to hyperexcitability in a hiPSC-derived cortical neuron model from a male donor. While microglia play an important role in the brain, these cells originate from a different lineage (yolk sac) and thus are not naturally present in hiPSCs-derived neuronal culture. To study how microglia respond to diseased neurons and influence neuronal excitability, we established a co-culture model comprising hiPSC-derived neurons and microglia. We found that microglia display altered morphology with increased branch length and enhanced calcium signal when co-cultured with neurons carrying the Nav1.2-L1342P mutation. Moreover, the presence of microglia significantly lowers the action potential firing of neurons carrying the mutation. Interestingly, we further demonstrated that the current density of sodium channels in neurons carrying the epilepsy-associated mutation was reduced in the presence of microglia. Taken together, our work reveals a critical role of human iPSCs-derived microglia in sensing and dampening hyperexcitability mediated by an epilepsy-causing mutation present in human neurons, highlighting the importance of neuron-microglia interactions in human pathophysiology. Significance StatementSeizure studies in mouse models have highlighted the role of microglia in modulating neuronal activity, particularly in the promotion or suppression of seizures. However, a gap persists in comprehending the influence of human microglia on intrinsically hyperexcitable neurons carrying epilepsy-associated pathogenic mutations. This research addresses this gap by investigating human microglia and their impact on neuronal functions. Our findings demonstrate that microglia exhibit dynamic morphological alterations and calcium fluctuations in the presence of neurons carrying an epilepsy-associated SCN2A mutation. Furthermore, microglia suppressed the excitability of diseased hyperexcitable neurons, suggesting a potential beneficial role. This study underscores the role of microglia in the regulation of abnormal neuronal activity, providing insights into therapeutic strategies for neurological conditions associated with hyperexcitability.

neuroscience↗

bioRxiv2023

Combining Blood-Based Biomarkers and Structural MRI Measurements to Distinguish Persons With and Without Significant Amyloid Plaques

BackgroundAmyloid-{beta} (A{beta}) plaques play a pivotal role in Alzheimers disease. The current positron emission tomography (PET) is expensive and limited in availability. In contrast, blood-based biomarkers (BBBMs) show potential for characterizing A{beta} plaques more affordably. We have previously proposed an MRI-based hippocampal morphometry measure to be an indicator of A{beta}-plaques. ObjectiveTo develop and validate an integrated model to predict brain amyloid PET positivity combining MRI feature and plasma A{beta}42/40 ratio. MethodsWe extracted hippocampal multivariate morphometry statistics (MMS) from MR images and together with plasma A{beta}42/40 trained a random forest classifier to perform a binary classification of participant brain amyloid PET positivity. We evaluated the model performance using two distinct cohorts, one from the Alzheimers Disease Neuroimaging Initiative (ADNI) and the other from the Banner Alzheimers Institute (BAI), including prediction accuracy, precision, recall rate, F1 score and AUC score. ResultsResults from ADNI (mean age 72.6, A{beta}+ rate 49.5%) and BAI (mean age 66.2, A{beta}+ rate 36.9%) datasets revealed the integrated multimodal (IMM) models superior performance over unimodal models. The IMM model achieved prediction accuracies of 0.86 in ADNI and 0.92 in BAI, surpassing unimodal models based solely on structural MRI (0.81 and 0.87) or plasma A{beta}42/40 (0.73 and 0.81) predictors. ConclusionOur IMM model, combining MRI and BBBM data, offers a highly accurate approach to predict brain amyloid PET positivity. This innovative multiplex biomarker strategy presents an accessible and cost-effective avenue for advancing Alzheimers disease diagnostics, leveraging diverse pathologic features related to A{beta} plaques and structural MRI.

neuroscience↗

bioRxiv2023

Dense Sampling of Taxa and Genomes Untangles the Phylogenetic Backbone of a Non-model Plant Lineage Rife with Deep Hybridization and Allopolyploidy

Phylogenetic networks, rather than purely bifurcating trees, more accurately depict the intricate evolutionary dynamics of most lineages, especially those characterized by extensive hybridization and allopolyploidization events. However, the challenges of achieving complete taxon sampling, and limited financial resources for studying non-model plant lineages, have hindered comprehensive and robust estimation of phylogenetic backbones with guidance from networks. The bellflower tribe, Campanuleae, characterized by a reticulate evolutionary history, serves as an ideal model to investigate how to diagnose nested ancient reticulation events. Here, by integrating multiple genomic data sources and a range of phylogenetic inference methods, we produced a robust phylogenetic backbone for the tribe Campanuleae. Our investigation of reticulate evolution indicates that hybridization and allopolyploidization were instrumental in shaping the diversity of the bellflower tribe, particularly during the initial diversification of the subtribe Phytematinae. Additionally, we ascertained that conflicting topologies resulting from distinct genomic datasets and inference methodologies significantly impact downstream estimates of divergence dating, ancestral area construction, and diversification rates. This study offers a universally relevant framework for deciphering how to use network-based phylogenetic structures using various genomic sources and inference methods. [Campanulaceae, Campanuleae, Cytonuclear discordance, paralog, phylogenomics, reticulate evolution]

plant biology↗