Biology subjects

Liu, F.

Publications and source records attributed to Liu, F..

At least 163 records · Page 9Linked to original sources

bioRxiv2024

Lipid droplets restrict phagosome formation during Candida challenge

Lipid droplets (LDs) are intracellular organelles which can be induced and interact with phagosomes during the process of pathogen phagocytosis in macrophages. However, the function of LDs in the phagocytosis remains elusive. Here, we unveil the role of LDs in modulating phagosome formation using a fungal infection model. Specifically, LDs accumulation restricted the quantity of phagosome formation, and protected macrophages from death. Mechanistically, LDs formation competitively consumed intracellular endoplasmic reticulum membrane and altered RAC1 translocation and its GTPase activity, which resulted in limiting phagosomes formation in macrophages during fungi engulfed. Mice with Hilpda-deficient macrophages were more susceptible to the lethal sequelae of systemic infection with C. albicans. Notably, administration of ATGL inhibitor Atglistatin improved host outcomes in disseminated fungal infections. Taken together, our study elucidates the mechanism of LDs in controlling phagosomes formation to avoid immune cell death, and offers a potential drug target for treatment of C. albicans infections. HighlightsO_LIC. albicans infection induces triglycerides production and LD accumulation in macrophages. C_LIO_LILD restricts the quantity of phagosome formation and protects macrophages from death. C_LIO_LILD consumes intracellular ER membrane components and alters RAC1 translocation and its GTPase activity. C_LIO_LIAdministration of ATGL inhibitor Atglistatin improves host outcomes in disseminated fungal infections. C_LI

microbiology↗

bioRxiv2024

Transcranial Brain Atlas Based on Photon Measurement Density Function in a Triple-Parameter Standard Channel Space

Functional near-infrared spectroscopy (fNIRS) is a widely used transcranial brain imaging technique in neuroscience research. Nevertheless, its lack of anatomical information poses challenges for designing appropriate optode montage and localizing fNIRS signals to underlying anatomical regions. The photon measurement density function (PMDF) is often employed to address these issues, as it accurately measures the sensitivity of a fNIRS signal channel to perturbations of absorption coefficients at any brain locations. However, existing PMDF-based localization methods have two limitations: a limited channel space, and PMDF estimation based on single standard head models, which differ anatomically from individual subjects. To overcome these limitations, this study proposes a continuous fNIRS standard channel space and constructs a PMDF-based transcranial brain atlas (PMDF-TBA) by calculating PMDFs based on MRI images of 48 adults. PMDF-TBA contains group-averaged sensitivities of channels to gray matter and brain regions of atlases, such as Brodmann, AAL2, and LPBA40. Through leave-one-out cross-validation, we evaluated the prediction ability of PMDF-TBA for sensitivity of unseen individuals and found that it outperformed PMDFs based on single standard head models. Thus, PMDF-TBA serves as a more generalizable fNIRS spatial localization tool. Therefore, PMDF-TBA can be utilized to optimize optode montage design, improve channel sensitivity to target brain regions, and assist in the source localization of fNIRS data, thereby promoting the application of fNIRS in neuroscience research.

neuroscience↗

bioRxiv2024

Single-cell dissection of prognostic architecture and immunotherapy response in Helicobacter pylori infection associated gastric cancer

Most of the gastric cancer (GC) worldwide are ascribed to Helicobacter pylori (H. pylori) infections, which have a detrimental effect on the immunotherapys efficacy. Comprehensively dissecting the key cell players and molecular pathways associated with cancer immunotherapies is critical for developing novel therapeutic strategies against H. pylori infection associated GC. We performed a comprehensive single-cell transcriptome analysis of nine GC with current H. pylori infection (HpGC), three GC with previous H. pylori infection (ex-HpGC), six GC without H. pylori infection (non-HpGC), and six healthy controls (HC). We also investigated key cell players and molecular pathways associated with GC immunotherapy outcomes. We revealed the molecular heterogeneity of different cell components in GC including epithelium, immune cells, and cancer-associated fibroblasts (CAFs) at the single-cell level. The malignant epithelium of HpGC exhibited high expression level of inflammatory and epithelial-mesenchymal transition (EMT) signature, HpGC and ex-HpGC were enriched with VEGFA+ angiogenic tumor-associated macrophages (Angio-TAM) and IL11+ inflammatory CAF (iCAF), characterized by high expression levels of NECTIN2 and VEGFA/B. Additionally, we found significant correlations between the abundance of iCAF with Angio-TAM and TIGIT+ suppressive T cells, and iCAF interacted with Angio-TAM through the VEGF and ANGPTL angiogenic pathways. We also developed an immune signature and angiogenic signature and demonstrated that the iCAF abundance and angiogenic signature could predict poor immunotherapy outcomes in GC. We revealed the transcriptome characteristics and heterogeneity of various cellular constituents of HpGC and demonstrated that a synergistic combination of immunotherapy and anti-angiogenic targeted therapy may be an effective therapeutic modality for HpGC.

cancer biology↗

bioRxiv2024

Cell-type specific inference from bulk RNA-sequencing data by integrating single cell reference profiles via EPIC-unmix

Cell type specific (CTS) analysis is essential to reveal biological insights obscured in bulk tissue data. However, single-cell (sc) or single-nuclei (sn) resolution data are still cost-prohibitive for large-scale samples. Thus, computational methods to perform deconvolution from bulk tissue data are highly valuable. We here present EPIC-unmix, a novel two-step empirical Bayesian method integrating reference sc/sn RNA-seq data and bulk RNA-seq data from target samples to enhance the accuracy of CTS inference. We demonstrate through comprehensive simulations across three tissues that EPIC-unmix achieved 4.6% - 109.8% higher accuracy compared to alternative methods. By applying EPIC-unmix to human bulk brain RNA-seq data from the ROSMAP and MSBB cohorts, we identified multiple genes differentially expressed between Alzheimers disease (AD) cases versus controls in a CTS manner, including 57.4% novel genes not identified using similar sample size sc/snRNA-seq data, indicating the power of our in-silico approach. Among the 6-69% overlapping, 83%-100% are in consistent direction with those from sc/snRNA-seq data, supporting the reliability of our findings. EPIC-unmix inferred CTS expression profiles similarly empowers CTS eQTL analysis. Among the novel eQTLs, we highlight a microglia eQTL for AD risk gene AP3B2, obscured in bulk and missed by sc/snRNA-seq based eQTL analysis. The variant resides in a microglia-specific cCRE, forming chromatin loop with AP3B2 promoter region in microglia. Taken together, we believe EPIC-unmix will be a valuable tool to enable more powerful CTS analysis.

genomics↗

bioRxiv2024

Unveiling the Secrets of Extracellular Vesicles in Urban Water Systems: Understanding the Link Between Human and Environmental Health

It is crucial to gain valuable insights into the ecological health of rivers to inform management decisions and protect sustainable living conditions. Understanding biological information is vital to gaining insight into river ecosystem biodiversity, but reliable methods are challenging. Here, We investigate the potential impact of extracellular vesicles (EVs) in urban water systems on human and environmental health to promote urban sustainability. We used EXODUS to detect EVs and perform metaproteomic analysis on samples from an urban water system that contained human feces, wastewater, bacteria, plants, arthropods, and soil. We analyzed EVs collected from urban and green areas, observing taxonomic variations and discovering bacterial contributions to their protein content. According to our research, the abundance and expression levels of proteins in EVs can indicate how human activities affect microbial communities in rivers, potentially impacting public health. Our study offers a fresh perspective on the interconnectedness of urban sustainability, public health, and river ecosystem biodiversity.

ecology↗

bioRxiv2024

Persistent lung inflammation and alveolar-bronchiolization due to Notch signaling dysregulation in SARS-CoV-2 infected hamster

Long COVID or Post-acute sequalae of COVID-19 (PASC) defines the persistent signs, symptoms, and conditions long after initial SARS-CoV-2 infection which affecting over 10% of COVID-19 patients, with 40% of them affecting respiratory system. The lung histopathological changes and underlying mechanism remain elusive. Here we systemically investigate histopathological and transcriptional changes at 7, 14, 42, 84 and 120 days-post-SARS-CoV-2-infection (dpi) in hamster. We demonstrate persistent viral residues, chronic inflammatory and fibrotic changes from 42dpi to 120dpi. The most prominent lung histopathological lesion is multifocal alveolar-bronchiolization observed in every animal from 14dpi until 120dpi. However, none of the above are observed in hamsters recovered from influenza A infection. We show airway progenitor CK14+ basal cells actively proliferate, differentiate into SCGB1A+ club cell or Tubulin+ ciliated cells, leading to alveolar-bronchiolization. Most importantly, Notch pathway is persistently upregulated. Intensive Notch3 and Hes1 protein expression are detected in alveolar-bronchiolization foci, suggesting the association of sustained Notch signaling with dysregulated lung regeneration. Lung spatial transcriptomics show upregulation of genes positively regulating Notch signaling is spatially overlapping with alveolar-bronchiolization region. To be noted, significant upregulation of tumor-related genes was detected in abnormal bronchiolization region by spatial transcriptomics analysis, indicating possible risk of lung carcinoma. Collectively, our data suggests SARS-CoV-2 infection caused chronic inflammatory and fibrotic tissue damages in hamster lung, sustained upregulation of Notch pathway signaling contributed to the dysregulated lung regeneration and CK14+ basal cells-driven alveolar-bronchiolization. The study provides important information for potential therapeutic approaches and probable long-term surveillance of malignancy in PASC management.

microbiology↗

bioRxiv2024

Unbiased metastatic niche-labeling identifies estrogen receptor-positive macrophages as a barrier of T cell infiltration during bone colonization

Microenvironment niches determine cellular fates of metastatic cancer cells. However, robust and unbiased approaches to identify niche components and their molecular profiles are lacking. We established Sortase A-Based Microenvironment Niche Tagging (SAMENT), which selectively labels cells encountered by cancer cells during metastatic colonization. SAMENT was applied to multiple cancer models colonizing the same organ and the same cancer to different organs. Common metastatic niche features include macrophage enrichment and T cell depletion. Macrophage niches are phenotypically diverse between different organs. In bone, macrophages express the estrogen receptor alpha (ER) and exhibit active ER signaling in male and female hosts. Conditional knockout of Esr1 in macrophages significantly retarded bone colonization by allowing T cell infiltration. ER expression was also discovered in human bone metastases of both genders. Collectively, we identified a unique population of ER+ macrophages in the metastatic niche and functionally tied ER signaling in macrophages to T cell exclusion during metastatic colonization. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/593016v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@1cd65b6org.highwire.dtl.DTLVardef@1d099e2org.highwire.dtl.DTLVardef@26cd91org.highwire.dtl.DTLVardef@181f5f3_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LISAMENT is a robust metastatic niche-labeling approach amenable to single-cell omics. C_LIO_LIMetastatic niches are typically enriched with macrophages and depleted of T cells. C_LIO_LIDirect interaction with cancer cells induces ER expression in niche macrophages. C_LIO_LIKnockout of Esr1 in macrophages allows T cell infiltration and retards bone colonization. C_LI

cancer biology↗

bioRxiv2024

Single cell profiling of bone metastasis ecosystems from multiple cancer types reveals convergent and divergent mechanisms of bone colonization.

Bone represents congenial soil for metastatic seeds and is frequently affected by metastasis of multiple cancer types. The histological and molecular characteristics of bone metastases (BMs) are diverse but poorly understood. Herein, we performed single-cell RNA-seq on 34 BMs from 6 cancer types and identified 3 ecosystem archetypes characterized by enrichment of macrophages/osteoclasts (M{varphi}-OC), regulatory/exhausted T cells (Treg-Tex), and monocytes (Mono), respectively. Breast cancer BMs are mostly the M{varphi}-OC archetype driven by the osteolytic vicious cycle, whereas kidney cancers BMs mainly belong to the Treg-Tex archetype that lacks osteoclasts. Lung cancers BMs evenly distributed across all archetypes. Further analyses revealed parallel mechanisms of immunosuppression and bone remodeling. Elevated estrogen signaling distinguishes macrophages in the M{varphi}-OC subtype, which was investigated in a companion study. Together, we elucidated that divergent mechanisms toward bone colonization and that BMs of different origins can adopt the same mechanism through convergent evolution or adaptation. HIGHLIGHTSO_LIAnalyses of bone metastases from 6 cancer types revealed three immune archetypes. C_LIO_LIArchetypes diverge on immune trajectories, and features of tumor and stromal cells. C_LIO_LIDominant cell type in each archetype undergoes convergent evolution. C_LIO_LIRegulatory networks converge on osteoclasts and Tregs to drive archetype formation. C_LI Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/593027v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@82cef6org.highwire.dtl.DTLVardef@1e1b021org.highwire.dtl.DTLVardef@1f2881eorg.highwire.dtl.DTLVardef@1c6874a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Enhancing Transcriptome Mapping with Rapid PRO-seq Profiling of Nascent RNA

Precision nuclear run-on (PRO) sequencing (PRO-seq) is a powerful technique for mapping polymerase active sites with nucleotide resolution and measuring newly synthesized transcripts at both promoters and enhancer elements. The current PRO-seq protocol is time-intensive, technically challenging, and requires a large amount of starting material. To overcome these limitations, we developed rapid PRO-seq (rPRO-seq) which utilizes pre-adenylated single-stranded DNAs (AppDNA), a dimer blocking oligonucleotide (DBO), on-bead 5 RNA end repair, and column-based purification. These modifications enabled efficient transcriptome mapping within a single day ([~]12 hours) increasing ligation efficiency, abolished adapter dimers, and reduced sample loss and RNA degradation. We demonstrate the reproducibility of rPRO-seq in measuring polymerases at promoters, gene bodies, and enhancers as compared to original PRO-seq protocols. Additionally, rPRO-seq is scalable, allowing for transcriptome mapping with as little as 25,000 cells. We apply rPRO-seq to study the role of Integrator in mouse hematopoietic stem and progenitor cell (mHSPC) homeostasis, identifying Ints11 as an essential component of transcriptional regulation and RNA processing in mHSPC homeostasis. Overall, rPRO-seq represents a significant advance in the field of nascent transcript analyses and will be a valuable tool for generating patient-specific genome-wide transcription profiles with minimal sample requirements.

molecular biology↗

bioRxiv2024

Colorectal ALOX15 as a host factor determinant of EPA and DHA effects on colorectal carcinogenesis

Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), omega-3 polyunsaturated fatty acids ({omega}-3 PUFAs) derived from fish oil, are widely used as dietary supplements and FDA-approved treatments for hypertriglyceridemia. However, studies investigating the effects of EPA and DHA on colorectal carcinogenesis (CRC) have yielded conflicting results. The factors that determine these discrepant results remain unknown. Resolvins, oxidative metabolites of EPA and DHA, inhibit key pro-tumorigenic cytokine and chemokine signaling of colorectal cancer (e.g., IL-6, IL-1{beta}, and CCL2). 15-lipoxygenase-1 (ALOX15), a critical enzyme for resolvin generation is commonly lost during human CRC. Whether ALOX15 expression, as a host factor, modulates the effects of EPA and DHA on CRC remains unknown. Therefore, we evaluated the effects of ALOX15 transgenic expression in colonic epithelial cells on resolvin generation by EPA and DHA and CRC in mouse models representative of human CRC. Our results revealed that 1) EPA and DHA effects on CRC were diverse, ranging from suppressive to promotive, and these effects were occasionally altered by the formulations of EPA and DHA (free fatty acid, ethyl ester, triglyceride); 2) EPA and DHA uniformly suppressed CRC in the presence of intestinal ALOX15 transgenic expression, which induced the production of resolvins, decreased colonic CCL3-5 and CXCL-5 expression and tumor associated macrophages while increasing CD8 T cell abundance in tumor microenvironment; and 3) RvD5, the predominant resolvin produced by ALOX15, inhibited macrophage generation of pro-tumorigenic cytokines. These findings demonstrate the significance of intestinal ALOX15 expression as a host factor in determining the effects of EPA and DHA on CRC. SignificanceEicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are widely used as dietary supplements and FDA-approved treatments for hypertriglyceridemia. Studies of EPA and DHA effects on colorectal carcinogenesis (CRC) have revealed inconsistencies; factors determining the direction of their impact on CRC have remained unidentified. Our data show that EPA and DHA effects on CRC were divergent and occasionally influenced by their formulations. More importantly, intestinal 15-lipoxgenase-1 (ALOX15) expression modulated EPA and DHA effects on CRC, leading to their consistent suppression of CRC. ALOX15 promoted EPA and DHA oxidative metabolism to generate resolvins, which inhibited key pro-tumorigenic inflammatory cytokines and chemokines, including IL-6. IL-1{beta}, and CCL2. ALOX15 is therefore an important host factor in determining EPA and DHA effects on CRC.

cancer biology↗

bioRxiv2024

Singular Odorant Receptor Expression Orchestrated by Promoter Activation Specificity in Apis Mellifera Olfactory Sensory Neurons

Honeybee, positioned as an outgroup of flies and mosquitos, have exhibited intriguing duplications and expansions of OR genes in genomic studies. However, little is known about how the OR genes are expressed and regulated in honeybee olfactory sensory neurons (OSNs). In this study, we utilized a single-cell multi-omics approach to profile the transcriptome and chromatin accessibility in Apis mellifera antennal nuclei, aiming to elucidate OR gene expression and its underlying regulatory mechanisms. Our systematical analysis unveiled a similar singular expression pattern of ligand-specific receptors in Apis mellifera OSNs, parallel with those observed in Drosophila melanogaster. Mechanistically, we discovered that promoter activation of OR genes orchestrates receptor expression patterns. For instance, although multiple adjacent OR genes are co-expressed with a single active promoter through polycistronic transcription, only the first OR gene could produce functional receptor protein, as supported by transcriptome quantification in OSNs. Additionally, we found that co-expression of receptor proteins might occur only when co-expressed OR genes possess multiple accessible promoters. This scenario is less common than expected, considering the number and evolutionary age of OR genes in Apis mellifera, suggesting a selection favoring the specialization of rapidly expanded OR genes in Apis mellifera. Overall, our study provides significant insights into the insect olfaction system and the regulatory mechanisms of OR genes expression.

neuroscience↗

bioRxiv2024

Detection of High-Frequency Oscillations from Intracranial EEG Data with Switching State Space Model

High Frequency Oscillations (HFOs) is an important biomarker that can potentially pinpoint the epileptogenic zones (EZs). However, the duration of HFO is short with around 4 cycles, which might be hard to recognize when embedded within signals of lower frequency oscillatory background. In addition, annotating HFOs manually can be time-consuming given long-time recordings and up to hundreds of intracranial electrodes. We propose to leverage a Switching State Space Model (SSSM) to identify the HFOs events automatically and instantaneously without relying on extracting features from sliding windows. The effectiveness of the SSSM for HFOs detection is fully validated in the intracranial EEG recording from human subjects undergoing the presurgical evaluations and showed improved accuracy when capturing the HFOs occurrence and their duration.

bioengineering↗

bioRxiv2024

Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons

Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain-wide projections. However, investigating the complex wiring diagram, spatial organization, transcriptional, and epigenetic landscapes of brain-wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons in female mice. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.

neuroscience↗

bioRxiv2024

Comparison of therapeutic effects between pulsed field ablation and cryoballoon ablation in the treatment of atrial fibrillation: a systematic review and me-ta-analysis

BackgroundPulmonary vein isolation (PVI) is the cornerstone of atrial fibrillation (AF) ablation surgery. Cryoballoon ablation (CBA), a conventional thermal ablation technique, enjoys widespread clinical application. In contrast, Pulsed field ablation (PFA) is a novel non thermal ablation technique for the treatment of atrial fibrillation (AF) patients, with safety comparable to traditional thermal ablation surgery. The present study aims to evaluate and compare the procedural efficiency and safety profiles of PFA and CBA in the management of AF. MethodWe performed a systematic search across PubMed, the Cochrane Library, and Embase databases, encompassing the literature up to February 2024, to inform our systematic review and meta-analysis. When assessing outcome indicators, the risk ratio (RR) and its corresponding 95% confidence interval (CI) were calculated for dichotomous variables. For continuous variables, the mean difference (MD) and the associated 95% CI were determined. In this context, an RR less than 1 and an MD less than 0 were considered advantageous for the PFA group. ResultIn this analysis, nine observational studies encompassing 2,875 patients with AF were included. Among these, 38% (n=1105) were treated with PFA, while 62% (n=1,770) received CBA. The results indicated that PFA was associated with a significantly shorter surgical duration compared to CBA, with a mean difference (MD) of -10.49 minutes (95% CI [-15.50, -5.49]; p<0.0001). Additionally, the PFA group exhibited a reduced risk of perioperative complications relative to the CBA group, with a risk ratio (RR) of 0.52 (95% CI 0.30-0.89; p=0.02). Nevertheless, no statistically significant differences were observed when comparing the two treatment cohorts concerning fluorescence irradiation time (MD 0.71; 95% CI [-0.45, 1.86]; p=0.23) and the recurrence of atrial arrhythmias during follow-up (RR 0.95; 95% CI 0.78-1.14; p=0.57). ConclusionThe outcomes of this investigation reveal that PFA holds a relative advantage over CBA in certain respects, notably by reducing both surgical duration and the incidence of perioperative complications. However, no significant distinction was identified between the two modalities concerning the duration of fluorescence irradiation or the rate of atrial arrhythmia recurrence. To enhance the robustness of these estimates, further research is needed, especially by incorporating additional randomized controlled trials.

physiology↗

bioRxiv2024

CBP/P300 BRD Inhibition Reduces Neutrophil Accumulation and Activates Antitumor Immunity in TNBC

Tumor-associated neutrophils (TANs) have been shown to promote immunosuppression and tumor progression, and a high TAN frequency predicts poor prognosis in triple-negative breast cancer (TNBC). Dysregulation of CREB binding protein (CBP)/P300 function has been observed with multiple cancer types. The bromodomain (BRD) of CBP/P300 has been shown to regulate its activity. In this study, we found that IACS-70654, a novel and selective CBP/P300 BRD inhibitor, reduced TANs and inhibited the growth of neutrophil-enriched TNBC models. In the bone marrow, CBP/P300 BRD inhibition reduced the tumor-driven abnormal differentiation and proliferation of neutrophil progenitors. Inhibition of CBP/P300 BRD also stimulated the immune response by inducing an IFN response and MHCI expression in tumor cells and increasing tumor-infiltrated CTLs. Moreover, IACS-70654 improved the response of a neutrophil-enriched TNBC model to docetaxel and immune checkpoint blockade. This provides a rationale for combining a CBP/P300 BRD inhibitor with standard-of-care therapies in future clinical trials for neutrophil-enriched TNBC. SummaryIn neutrophil-enriched triple-negative breast cancer (TNBC) models, CREB binding protein (CBP)/P300 bromodomain (BRD) inhibition reduces tumor growth and systemic neutrophil accumulation while stimulating an antitumor immune response. This improves standard-of-care therapies, suggesting a potential therapeutic benefit of CBP/P300 BRD inhibitors for neutrophil-enriched TNBC.

cancer biology↗

bioRxiv2024

Electrophysiological Brain Network Estimation with Simultaneous Scalp EEG and Intracranial EEG: Inference Algorithm and Applications

Activity in the human brain is composed of complex firing patterns and interactions among neurons and neuronal circuits. The neuroimaging field underwent a paradigm shift over the past decades from mapping tasked evoked brain regions of activations towards identifying and characterizing the dynamic brain networks of coordinating brain regions. Electrophysiological signals are the direct manifestation of brain activities, thus characterizing the whole brain electrophysiological networks (WBEN) can serve as a fundamental tool for neuroscience studies and clinical applications. The electrophysiological network inferred from electroencephalogram (EEG) source imaging suffers from low accuracy limited by the Restricted Isometry Property (RIP), while the invasive EEG-derived electrophysiological networks can only characterize partial brain regions where invasive electrodes reside. In this work, we introduce the first framework for the integration of scalp EEG and intracranial EEG (iEEG) for WBEN estimation with a principled estimation framework based on state-space models, where an Expectation-Maximization (EM) algorithm is designed to infer the state variables and brain connectivity simultaneously. We validated the proposed method on synthetic data, and the results revealed improved performance compared to traditional two-step methods using scalp EEG only, which demonstrates the importance of the inclusion of iEEG signal for WBEN estimation. For real data with simultaneous EEG and iEEG, we applied the developed framework to understand the information flows of the encoding and maintenance phases during the working memory task. The information flows between the subcortical and cortical regions are delineated, which highlights more significant information flows from cortical to subcortical regions compared to maintenance phases. The results are consistent with previous research findings, however with the view of the whole brain scope, which underscores the unique utility of the proposed framework.

neuroscience↗

bioRxiv2024

Molecular architecture of synaptic vesicles.

Synaptic vesicles (SVs) store and transport neurotransmitters to the presynaptic active zone for release by exocytosis. After release, SV proteins and excess membrane are recycled via endocytosis, and new SVs are formed in a clathrin-dependent manner. This process maintains the morphology and complex molecular composition of SVs through multiple recycling rounds. Previous studies explored the molecular composition of SVs through proteomic analysis and fluorescent microscopy, proposing a model for an average SV1,2. However, the structural heterogeneity and molecular architecture of individual SVs are not well described. Here we used cryo-electron tomography to visualize morphological and molecular details of SVs isolated from mouse brains and inside cultured neurons. We describe several classes of small proteins on the SV surface and long proteinaceous densities inside SVs. We identified V-ATPases, determined a structure using subtomogram average, and showed them forming a complex with the membrane-embedded protein synaptophysin. Our bioluminescence assay revealed pairwise interactions between VAMP2 and synaptophysin and V-ATPase Voe1 domains. Interestingly, V-ATPases were randomly distributed on the surface of SVs irrespective of vesicle sizes. A subpopulation of isolated vesicles and vesicles inside neurons contained a partially assembled clathrin coat with a soccer-ball symmetry. We observed a V-ATPase under clathrin cage in several isolated clathrin-coated vesicles. Additionally, from isolated SV preparations and within hippocampal neurons we identified clathrin baskets without vesicles. We determined their preferential location in proximity to the cell membrane. Our analysis advances the understanding of individual SVs diversity and their molecular architecture.

biophysics↗

bioRxiv2024

Identification and characterization of a synaptic active zone assembly protein

At presynaptic active zones (AZs), scaffold proteins play a crucial role in coordinating synaptic vesicle (SV) release and forming intricate nanoarchitectures essential for synaptic function. Despite their suspected importance, factors governing the assembly of nanoscale AZ scaffolds have remained elusive. Here, we identify "Blobby" as a novel regulator of AZ nanopatterning, localized within the AZ scaffold. Genetic loss of the extended Blobby protein led to aberrant accumulation of AZ scaffold proteins ("blobs") and disrupted the nanoscale architecture of the AZ scaffold, resulting in a significant reduction in the packing density of voltage-gated Ca2+ channels at AZs, as observed through intravital single-molecule imaging. This disruption correlated with decreased evoked synaptic currents and SV release probability. Our findings suggest that Blobby plays a crucial role in switching the AZ scaffold into a state which allows to fine-tune the dynamic nanopatterning of Ca2+ channels to maintain proper release.

neuroscience↗