Biology subjects

Gu, C.

Publications and source records attributed to Gu, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

cellSTAAR: Incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of non-coding regions

Whole genome sequencing (WGS) studies have identified hundreds of millions of rare variants (RVs) and have enabled RV association tests (RVATs) of these variants with complex traits and diseases. Analysis of non-coding variants is challenged by the considerable variability in regulatory function which candidate Cis-Regulatory Elements (cCREs) exhibit across cell types. We propose cellSTAAR, which integrates WGS data with single-cell ATAC-seq data to capture variability in chromatin accessibility across cell types via the construction of cell-type-specific functional annotations and variant sets. To reflect the uncertainty in cCRE-gene linking, cellSTAAR also links cCREs to their target genes using an omnibus framework which aggregates results from a variety of popular linking approaches. We applied cellSTAAR on Freeze 8 (N = 60,000) of the NHLBI Trans-Omics for Precision Medicine (TOPMed) consortium data to four lipids phenotypes: LDL cholesterol, a binary variable corresponding to high LDL cholesterol, HDL cholesterol, and triglycerides. We also provide replication results for all four phenotypes using UK Biobank (N = 190,000). Evidence from simulation studies and our real data analysis demonstrates that cellSTAAR boosts power and improves interpretation of RVATs of cCREs.

genetics↗

bioRxiv2025

Canonical Wnt Signaling Suppresses Brain Endothelial Cell Transcytosis to Maintain Blood-Brain Barrier Integrity

Canonical Wnt signaling is essential for blood-brain barrier (BBB) development and maintenance. However, the subcellular mechanisms underlying this critical regulation have remained elusive. In this study, we use a physiological paradigm examining an early phase of acutely attenuated canonical Wnt signaling in adult brain endothelial cells (ECs) to investigate how the pathway regulates BBB integrity. Following canonical Wnt signaling attenuation via EC-specific knockout of {beta}-catenin, we find that there is increased transcytosis in brain ECs, including a striking diversity of morphologically distinct vesicles, indicating multiple pathways are involved. In addition, we find that although the molecular composition of tight junctions (TJs) is altered following canonical Wnt signaling attenuation, such that Claudin-5 and ZO-1 expression is downregulated, TJs remain impermeable to molecules as small as 1.9 kDa. These findings reveal previously underappreciated role of Wnt signaling in regulating brain EC transcytosis and help illuminate subcellular mechanisms of BBB maintenance in adulthood, which is crucial for improving delivery of therapeutics to the brain.

neuroscience↗

bioRxiv2025

KIDINS220 and InsP8 safeguard the stepwise regulation of phosphate exporter XPR1

XPR1 is emerging as the only known inorganic phosphate (Pi) exporter in humans, critical for Pi homeostasis, with its activity stimulated by inositol pyrophosphate InsP8 and regulated by neuronal scaffold protein KIDINS220. Our structural studies reveal InsP8 specifically activates XPR1 in a stepwise manner, involving profound SPX domain movements. Each XPR1 subunit functions with four gating states, in which Pi permeates a constriction site via a "knock-kiss-kick" process. In contrast, KIDINS220 delicately stabilizes XPR1 in a closed conformation through multiple mechanisms, one of which involves trapping the XPR1 1 helix--critical for InsP8 binding--within an interaction hub. InsP8 serves as a key to release KIDINS220s restraint, reinforcing a "key-to-locks" mechanism to safeguard the stepwise activation. Additionally, our study provides direct structural insights into XPR1-associated neuronal disorders and highlights the evolutionary conservation and divergence among XPR1 orthologues, offering a comprehensive understanding of Pi homeostasis across species.

molecular biology↗

bioRxiv2024

Genetically Encoded Red Fluorescent Indicators for Imaging Intracellular and Extracellular Potassium Ions

Potassium ion (K+) dynamics are vital for various biological processes. However, the limited availability of detection tools for tracking intracellular and extracellular K+ has impeded a comprehensive understanding of the physiological roles of K+ in intact biological systems. In this study, we developed two novel red genetically encoded potassium indicators (RGEPOs), RGEPO1 and RGEPO2, through a combination of directed evolution in E. coli and subsequent optimization in mammalian cells. RGEPO1, targeted to the extracellular membrane, and RGEPO2, localized in the cytoplasm, exhibited positive K+-specific fluorescence response with affinities of 3.55 mM and 14.81 mM in HEK293FT cells, respectively. We employed RGEPOs for real-time monitoring of subsecond K+ dynamics in cultured neurons, astrocytes, acute brain slices, and the awake mouse in both intracellular and extracellular environments. Using RGEPOs, we were able, for the first time, to visualize intracellular and extracellular potassium transients during seizures in the brains of awake mice. Furthermore, molecular dynamics simulations provided new insights into the potassium-binding mechanisms of RGEPO1 and RGEPO2, revealing distinct K+-binding pockets and structural features. Thus, RGEPOs represent a significant advancement in potassium imaging, providing enhanced tools for real-time visualization of K+ dynamics in various cell types and cellular environments.

biochemistry↗

bioRxiv2024

A network regularized linear model to infer spatial expression pattern for single cell

Spatial transcriptomics, situated at the intersection of genomics and spatial biology, offers profound insights into the spatial organization of gene expression within tissues. However, its potential has been constrained by either limited resolution or throughput. While single-cell RNA-seq allows for in-depth profiling of cellular gene expression, the crucial spatial information is often sacrificed during sample collection. In a groundbreaking fusion of these two techniques, our research introduces the glmSMA computational algorithm. This innovative approach aims to predict cell locations by integrating scRNA-seq data with spatial-omics reference atlases. The essence of glmSMA lies in formulating cell mapping as a convex problem, strategically minimizing differences between cellular expression profiles and location expression profiles through L1 and Generalized L2 regularization. Our algorithm has undergone rigorous testing across diverse tissues, including mouse brain, drosophila embryo, and human PDAC samples. The compelling results validate glmSMAs efficacy, demonstrating its capability to faithfully recapitulate spatial gene expression and anatomical structures. This marks a significant stride forward in overcoming the limitations of existing spatial transcriptomic techniques.

bioinformatics↗

bioRxiv2024

Interpretable PROTAC degradation prediction with structure-informed deep ternary attention framework

Proteolysis Targeting Chimeras (PROTACs) are heterobifunctional ligands that form ternary complexes with Protein Of Interests (POIs) and E3 ligases, exploiting the ubiquitin-proteasome system to degrade disease-associated proteins, promising to drug the undruggable. While PROTAC research primarily relies on costly and time-consuming wet experimental approaches, deep learning offers a promising avenue to accelerate development and reduce expenses. However, existing deep learning methods for PROTAC degradation prediction often overlook the significance of hierarchical molecular representation and protein structural information, hindering effective data modeling. Moreover, their black-box nature limits the interpretability of computational outcomes, failing to provide intuitive insights into substructure interactions within the PROTAC system. This study introduces PROTAC-STAN, a structure-informed deep ternary attention network (STAN) framework for interpretable PROTAC degradation prediction. PROTAC-STAN represents PROTAC molecules across atom, molecule, and property hierarchies and incorporates structure information for POIs and E3 ligases using a protein language model infused with structural data. Furthermore, it simulates interactions among three entities at the atom and amino acid levels via a novel ternary attention network tailored for the PROTAC system, providing unprecedented insights into the degradation mechanism. By integrating hierarchical PROTAC molecule representation, structural embedding of POI and E3 ligase, and ternary attention network modeling interactions, our approach substantially improves prediction accuracy by 10.95% while enabling significant model interpretability via atomic and residue level visualization of molecule and complex. Experiments on the refined public PROTAC dataset demonstrate that PROTAC-STAN outperforms state-of-the-art baselines in overall performance. The excellent performance of PROTAC-STAN is anticipated to establish it as a foundational tool in future research on PROTAC-related drugs, thereby accelerating the development of this field.

bioinformatics↗

bioRxiv2024

In silico nanoscope to study the interplay of genome organization and transcription regulation

In eukaryotic genomes, regulated access and communication between cis-regulatory elements (CREs) are necessary for enhancer-mediated transcription of genes. The molecular framework of the chromatin organization underlying such communication remains poorly understood. To better understand it, we develop a multiscale modeling pipeline to build near-atomistic models of the 200 kb Nanog gene locus in mouse embryonic stem cells comprising nucleosomes, transcription factors, co-activators, and RNA polymerase II-Mediator complexes. By integrating diverse experimental data, including protein localization, genomic interaction frequencies, cryo-electron microscopy, and single-molecule fluorescence studies, our model offers novel insights into chromatin organization and its role in enhancer-promoter communication. The models equilibrated by high-performance molecular dynamics simulations span a scale of [~]350 nm, revealing an experimentally consistent local and global organization of chromatin and transcriptional machinery. Our models elucidate that the sequence-regulated chromatin accessibility facilitates the recruitment of transcription regulatory proteins exclusively at CREs, guided by the contrasting nucleosome organization compared to other regions. By constructing an experimentally consistent near-atomic model of chromatin in the cellular environment, our approach provides a robust framework for future studies on nuclear compartmentalization, chromatin organization, and transcription regulation.

molecular biology↗

bioRxiv2024

Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion

The SMC complex cohesin mediates interphase chromatin structural formation in eukaryotic cells through DNA loop extrusion. Here, we sought to investigate its mechanism using molecular dynamics simulations. To achieve this, we first constructed the amino-acid-residue-resolution structural models of the cohesin subunits, SMC1, SMC3, STAG1, and NIPBL. By simulating these subunits with double-stranded DNA molecules, we predicted DNA binding patches on each subunit and quantified the affinities of these patches to DNA using their dissociation rate constants as a proxy. Then, we constructed the structural model of the whole cohesin complex and mapped the predicted high-affinity DNA binding patches on the structure. From the spatial relations of the predicted patches, we identified that multiple patches on the SMC1, SMC3, STAG1, and NIPBL subunits form a DNA clamping patch group. The simulations of the whole complex with double-stranded DNA molecules suggest that this patch group facilitates DNA bending and helps capture a DNA segment in the cohesin ring formed by the SMC1 and SMC3 subunits. In previous studies, these have been identified as critical steps in DNA loop extrusion. Therefore, this study provides experimentally testable predictions of DNA binding sites implicated in previously proposed DNA loop extrusion mechanisms and highlights the essential roles of the accessory subunits STAG1 and NIPBL in the mechanism.

molecular biology↗

bioRxiv2024

Multi-omics delineate growth factor network underlying exercise effects in an Alzheimer's mouse model

Physical exercise represents a primary defense against age-related cognitive decline and neurodegenerative disorders like Alzheimers disease (AD). To impartially investigate the underlying mechanisms, we conducted single-nucleus transcriptomic and chromatin accessibility analyses (snRNA-seq and ATAC-seq) on the hippocampus of mice carrying AD-linked NL-G-F mutations in the amyloid precursor protein gene (APPNL-G-F) following prolonged voluntary wheel-running exercise. Our study reveals that exercise mitigates amyloid-induced changes in both transcriptomic expression and chromatin accessibility through cell type-specific transcriptional regulatory networks. These networks converge on the activation of growth factor signaling pathways, particularly the epidermal growth factor receptor (EGFR) and insulin signaling, correlating with an increased proportion of immature dentate granule cells and oligodendrocytes. Notably, the beneficial effects of exercise on neurocognitive functions can be blocked by pharmacological inhibition of EGFR and the downstream phosphoinositide 3-kinases (PI3K). Furthermore, exercise leads to elevated levels of heparin-binding EGF (HB-EGF) in the blood, and intranasal administration of HB-EGF enhances memory function in sedentary APPNL-G-F mice. These findings offer a panoramic delineation of cell type-specific hippocampal transcriptional networks activated by exercise and suggest EGF-related growth factor signaling as a druggable contributor to exercise-induced memory enhancement, thereby suggesting therapeutic avenues for combatting AD-related cognitive decline.

animal behavior and cognition↗

bioRxiv2024

Jumbo phages possess independent synthesis and utilization systems of NAD+

Jumbo phages, phages with genomes >200 kbp, contain some unique genes for successful reproduction in their bacterial hosts. Due to complex and massive genomes analogous to those of small-celled bacteria, how do jumbo phages complete their life cycle remain largely undefined. In this study, we assembled 668 high-quality jumbo phage genomes from over 15 TB of intestinal metagenomic data from 955 samples of five animal species (cow, sheep, pig, horse, and deer). Within them, we obtained a complete genome of 716 kbp in length, which is the largest phage genome so far reported in the gut environments. Interestingly, 174 out of the 668 jumbo phages were found to encode all genes required for synthesis of NAD+ by the salvage pathway or Preiss-Handler pathway, referred as NAD-jumbo phage. Besides synthesis genes of NAD+, these NAD-jumbo phages also encode at least 15 types of NAD+-consuming enzyme genes involved in DNA replication, DNA repair, and counterdefense, suggesting that these phages not only have the capacity to synthesize NAD+ but also redirect NAD+ metabolism towards phage propagation need in hosts. Phylogenetic analysis and environmental survey indicated NAD-jumbo phages are widely present in the Earths ecosystems, including the human gut, lakes, salt ponds, mine tailings, and seawater. In summary, this study expands our understanding of the diversity and survival strategies of phages, and in-depth study of the NAD-jumbo phages is crucial for understanding their role in ecological regulation.

microbiology↗

bioRxiv2023

Vitamin D attenuates diabetic myocardial injury via the Erbb4/ferroptosis axis

BackgroundHyperglycemia and hyperlipidemia lead to the ferroptosis, well as the phosphorylation of Erbb4, and thereby increase the risk of cardiac hypertrophy. Thus, our investigation aims to explore whether vitamin D could mitigate diabetic cardiac injury through modulation of the Erbb4/ferroptosis axis. Methods and resultsKKAy mice fed on a high-fat diet were utilized to construct the prediabetic model, which showed an up-regulated phosphorylation of Erbb4, with concurrent ferroptosis in cardiac tissues. Following the intervention with vitamin D for 16 weeks, the activity of Erbb4/YAP signaling was suppressed and the severeness of ferroptosis was improved. Meanwhile disturbances in glucose-lipid metabolism and insulin secretion induced by high fat were alleviated, along with improvements in cardiac hypertrophy and myocardial function. Moreover, we established an in vitro damage model by introducing H9c2 myocardial cells to high glucose (HG, 33.3 mM) and palmitic acid (PA, 0.25 mM). Unsurprisingly, similar results have been acquired after vitamin D supplementation. Subsequently, selective inhibitors of Erbb4 (Dacomitinib) and ferroptosis (Ferrostatin-1) were applied to evaluate the efficiency of Erbb4 signaling on modulating ferroptosis in vitro, and conclusively confirming that inhibiting of Erbb4 indeed reduce ferroptosis under HG and PA stimulus. Additionally, treatment of vitamin D was found to reduce cardiomyocyte hypertrophy and prevent cell death by inhibiting Erbb4 activity. Interestingly, the combined intervention of Vitamin D and Dacomitinib exerted a synergistic effect on ameliorating the abnormal conditions. ConclusionsOur study unveils, the correlation between Erbb4 and ferroptosis in diabetic heart. Providing evidences that vitamin D supplementation can improve ferroptosis related diabetic cardiac injury through inactivation of Erbb4. Proposing that the combination treatment of vitamin D and Erbb4 inhibitors may emerge as a highly feasible clinical strategy for diabetic myocardial injury.

pharmacology and toxicology↗

bioRxiv2023

Multiscale Bayesian Simulations Reveal Functional Chromatin Condensation of Gene Loci

Chromatin, the complex assembly of DNA and associated proteins, plays a pivotal role in orchestrating various genomic functions. To aid our understanding of the principles underlying chromatin organization, we introduce Hi-C metainference, a Bayesian approach that integrates Hi-C contact frequencies into multiscale prior models of chromatin. This approach combines both bottom-up (the physics-based prior) and top-down (the data-driven posterior) strategies to characterize the 3D organization of a target genomic locus. We first demonstrate the capability of this method to accurately reconstruct the structural ensemble and the dynamics of a system from contact information. We then apply the approach to investigate the Sox2, Pou5f1, and Nanog loci of mouse embryonic stem cells using a bottom-up chromatin model at 1kb resolution. We observe that the studied loci are conformationally heterogeneous and organized as crumpled globules, favoring contacts between distant enhancers and promoters. Using nucleosome-resolution simulations, we then reveal how the Nanog gene is functionally organized across the multiple scales of chromatin. At the local level, diverse chromatin folding motifs correlate with epigenetics, with open chromatin predominantly observed at cis-regulatory elements and compact tetranucleosomes in between. At the larger scale, we find that enhancer-promoter contacts are driven by the transient condensation of chromatin into compact domains stabilized by extensive inter-nucleosome interactions. Overall, this work highlights the condensed, but dynamic nature of chromatin in vivo, contributing to a deeper understanding of gene structure-function relationships.

biophysics↗

bioRxiv2023

A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies

Large-scale whole-genome sequencing (WGS) studies have improved our understanding of the contributions of coding and noncoding rare variants to complex human traits. Leveraging association effect sizes across multiple traits in WGS rare variant association analysis can improve statistical power over single-trait analysis, and also detect pleiotropic genes and regions. Existing multi-trait methods have limited ability to perform rare variant analysis of large-scale WGS data. We propose MultiSTAAR, a statistical framework and computationally-scalable analytical pipeline for functionally-informed multi-trait rare variant analysis in large-scale WGS studies. MultiSTAAR accounts for relatedness, population structure and correlation among phenotypes by jointly analyzing multiple traits, and further empowers rare variant association analysis by incorporating multiple functional annotations. We applied MultiSTAAR to jointly analyze three lipid traits (low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides) in 61,861 multi-ethnic samples from the Trans-Omics for Precision Medicine (TOPMed) Program. We discovered new associations with lipid traits missed by single-trait analysis, including rare variants within an enhancer of NIPSNAP3A and an intergenic region on chromosome 1.

genetics↗

bioRxiv2023

Ventral hippocampus neurons encode meal-related memory

The ability to encode and retrieve meal-related information is critical to efficiently guide energy acquisition and consumption, yet the underlying neural processes remain elusive. Here we reveal that ventral hippocampus (HPCv) neuronal activity dynamically elevates during meal consumption and this response is highly predictive of subsequent performance in a foraging-related spatial memory task. Targeted recombination-mediated ablation of HPCv meal-responsive neurons impairs foraging-related spatial memory without influencing food motivation, anxiety-like behavior, or escape-mediated spatial memory. These HPCv meal-responsive neurons project to the lateral hypothalamic area (LHA) and single-nucleus RNA sequencing and in situ hybridization analyses indicate they are enriched in serotonin 2a receptors (5HT2aR). Either chemogenetic silencing of HPCv-to-LHA projections or intra-HPCv 5HT2aR antagonist yielded foraging-related spatial memory deficits, as well as alterations in caloric intake and the temporal sequence of spontaneous meal consumption. Collective results identify a population of HPCv neurons that dynamically respond to eating to encode meal-related memories.

neuroscience↗

bioRxiv2023

Western diet consumption impairs memory function via dysregulated hippocampus acetylcholine signaling

Western diet (WD) consumption during development yields long-lasting memory impairments, yet the underlying neurobiological mechanisms remain elusive. Here we developed an early life WD rodent model to evaluate whether dysregulated hippocampus (HPC) acetylcholine (ACh) signaling, a pathology associated with memory impairment in human dementia, is causally-related to WD-induced cognitive impairment. Rats received a cafeteria-style WD (access to various high-fat/high-sugar foods; CAF) or healthy chow (CTL) during the juvenile and adolescent periods (postnatal days 26-56). Behavioral, metabolic, and microbiome assessments were performed both before and after a 30-day healthy diet intervention beginning at early adulthood. Results revealed CAF-induced HPC-dependent contextual episodic memory impairments that persisted despite healthy diet intervention, whereas CAF was not associated with long-term changes in body weight, body composition, glucose tolerance, anxiety-like behavior, or gut microbiome. HPC immunoblot analyses after the healthy diet intervention identified reduced levels of vesicular ACh transporter in CAF vs. CTL rats, indicative of chronically reduced HPC ACh tone. To determine whether these changes were functionally related to memory impairments, we evaluated temporal HPC ACh binding via ACh-sensing fluorescent reporter in vivo fiber photometry during memory testing, as well as whether the memory impairments could be rescued pharmacologically. Results revealed dynamic HPC ACh binding during object-contextual novelty recognition was highly predictive of memory performance and was disrupted in CAF vs. CTL rats. Further, HPC alpha-7 nicotinic receptor agonist infusion during consolidation rescued memory deficits in CAF rats. Overall, these findings identify dysregulated HPC ACh signaling as a mechanism underlying early life WD-associated memory impairments.

neuroscience↗

bioRxiv2023

Supraclavicular brown adipocytes originate from Tbx1+ myoprogenitors

Brown adipose tissue (BAT) dissipates energy as heat, contributing to temperature control, energy expenditure, and systemic homeostasis. In adult humans, BAT mainly exists in supraclavicular areas and its prevalence is associated with cardiometabolic health. However, the developmental origin of supraclavicular BAT remains unknown. Here, using genetic fate mapping in mice, we demonstrate that supraclavicular brown adipocytes do not develop from the Pax3+/Myf5+ epaxial dermomyotome that gives rises to interscapular BAT. Instead, the Tbx1+ lineage that specifies the pharyngeal mesoderm marks the majority of supraclavicular brown adipocytes. Tbx1Cre-mediated ablation of peroxisome proliferator-activated receptor gamma (PPAR{gamma}) or PR/SET Domain 16 (PRDM16), components of the transcriptional complex for brown fat determination, leads to supraclavicular BAT paucity or dysfunction, thus rendering mice more sensitive to cold exposure. Moreover, human deep neck BAT expresses higher levels of the TBX1 gene than subcutaneous neck white adipocytes. Taken together, our observations reveal location-specific developmental origins of BAT depots and call attention to Tbx1+lineage cells when investigating human relevant supraclavicular BAT.

developmental biology↗

bioRxiv2023

Nondestructive Spatial Lipidomics for Glioma Classification

Mapping the molecular composition of tissues using spatial biology provides high-content information for molecular diagnostics. However, spatial biology approaches require invasive procedures to collect samples and destroy the investigated tissue, limiting the extent of analysis, particularly for highly functional tissues such as those of the brain. To address these limitations, we developed a workflow to harvest biomolecules from brain tissues using nanoneedles and characterise the distribution of lipids using desorption electrospray ionization mass spectrometry imaging. The nanoneedles preserved the original tissue while harvesting a reliable molecular profile and retaining the original lipid distribution for mouse and human brain samples, accurately outlining the morphology of key regions within the brain and tumour lesions. The deep neural network analysis of a cohort containing 23 human glioma biopsies showed that nanoneedle samples maintain the molecular signatures required to accurately classify disease state. Thus, nanoneedles provide a route for tissue-preserving spatial lipidomic and molecular diagnostics.

bioengineering↗

bioRxiv2023

MANF stimulates autophagy and restores mitochondrial homeostasis to treat toxic proteinopathy

Misfolded protein aggregates may cause toxic proteinopathy, including autosomal dominant tubulointerstitial kidney disease due to uromodulin mutations (ADTKD-UMOD), one of the leading hereditary kidney diseases, and Alzheimers disease etc. There are no targeted therapies. ADTKD is also a genetic form of renal fibrosis and chronic kidney disease, which affects 500 million people worldwide. For the first time, in our newly generated mouse model recapitulating human ADTKD-UMOD carrying a leading UMOD deletion mutation, we show that autophagy/mitophagy and mitochondrial biogenesis are severely impaired, leading to cGAS- STING activation and tubular injury. Mesencephalic astrocyte-derived neurotrophic factor (MANF) is a novel endoplasmic reticulum stress-regulated secreted protein. We provide the first study that inducible tubular overexpression of MANF after the onset of disease stimulates autophagy/mitophagy and clearance of the misfolded UMOD, and promotes mitochondrial biogenesis through p-AMPK enhancement, resulting in protection of kidney function. Conversely, genetic ablation of endogenous MANF upregulated in the mutant mouse and human tubular cells worsens autophagy suppression and kidney fibrosis. Together, we discover MANF as a novel biotherapeutic protein and elucidate previously unknown mechanisms of MANF in regulating organelle homeostasis to treat ADTKD, which may have broad therapeutic application to treat various proteinopathies.

cell biology↗