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Gao, L.

Publications and source records attributed to Gao, L..

At least 55 records · Page 3Linked to original sources

A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex

The genetic and spatial determinants of cell type diversity in human cerebral cortices remain poorly defined. Here, we present a population-level single-cell spatial transcriptomic atlas of human cortices from 71 donors across the lifespan. We identified 906 layer-specific genes showing conserved and divergent laminar expression patterns between humans and other species. Spatial analysis revealed neuronal vulnerability and glial activation during aging, together with a decline in the proportion of superficial SST neurons and their interactions with other cells. Disease-associated genes exhibited high cell-type and layer-specific expression, implicating the pathogenic role of spatially specific gene expression. Spatial cis-eQTL analysis identified regulatory variants linked to genes related to diseases like Tourette syndrome. Cross-species comparison demonstrated glial expansion in the human cortex, accompanied by enhanced neuron-glia communication via the neuregulin signaling. Together, we provide a comprehensive single-cell atlas of the human cortex that is essential for understanding aging, evolution, and disease pathogenesis.

neuroscience↗

Chronic Ethanol Drinking Alters Medial Prefrontal Cortex and Nucleus Accumbens Astrocyte Translatome and Extracellular Matrix Glycosaminoglycans

Alcohol Use Disorder is a leading preventable cause of morbidity and mortality, yet knowledge of mechanisms driving ethanol-related neuroplasticity remains incomplete. While research has traditionally focused on neuronal signaling, emerging evidence implicates astrocytes in addiction-related adaptations. Here, we investigated the astrocyte-specific molecular consequences of chronic ethanol consumption in the prefrontal cortex and nucleus accumbens, two brain regions critical for executive control and reward processing. Using Translating Ribosome Affinity Purification RNA-seq and bulk RNA-seq in Aldh1l1-EGFP/Rpl10a mice, expressing an EGFP tag on astrocyte ribosomes, we identified hundreds of differentially translated astrocytic genes following chronic continuous two-bottle choice ethanol drinking. Sex-specific analyses revealed greater astrocytic changes in the female PFC and male NAc. Pathway enrichment highlighted extracellular matrix remodeling, synaptic signaling, mitochondrial function, and immune-related pathways. Analyses of individual drinking levels further demonstrated distinct correlations between ethanol intake and astrocytic translation. The major components of the brain extracellular matrix are chondroitin sulfate proteoglycans, produced primarily by astrocytes and covalently bound to chondroitin sulfate glycosaminoglycan chains. Complementary mass spectrometry/liquid chromatography analyses of chondroitin sulfate, heparan sulfate, and hyaluronic acid glycosaminoglycan disaccharides revealed ethanol-induced alterations in chondroitin sulfate glycosaminoglycan sulfation patterns, with additional baseline differences identified between selectively bred high- and low-ethanol preference lines. Together, these findings indicate that astrocytes undergo profound sex- and region-specific adaptations to chronic ethanol, implicating extracellular matrix and glycosaminoglycan remodeling as key risk-factors for and mediators of chronic ethanol-related neuroplasticity.

neuroscience↗

Discovery of circulating cell-free DNA 5hmC biomarkers for peritoneal metastasis in colorectal and appendiceal cancer

IntroductionPeritoneal metastases (PM) are associated with poor prognosis in patients with colorectal cancer (CRC) or appendiceal adenocarcinoma (AA), yet detection of PM is unreliable using current circulating DNA technology. Leveraging novel 5hmC-seal technology to detect ultra-low amounts of DNA in plasma, we demonstrate the feasibility of 5-hydroxymethylcytosine (5hmC) signatures derived from circulating cell-free DNA (cfDNA) as biomarkers for PM. MethodsUsing a highly sensitive and robust 5hmC sequencing approach on genomic DNA isolated from peripheral blood samples, we developed predictive models to identify biomarkers for peritoneal metastases. ResultsWe obtained genome-wide 5hmC profiles from 71 CRC/AA patients with PM, 41 without PM, and 73 non-cancer controls. Predictive models trained on genomic region 5hmC levels in patients with cancer could distinguish PM status with high sensitivity and moderate specificity (AUC 0.827, sensitivity 92.4%, specificity 46.1%). Pathway enrichment analysis identified epigenetically dysregulated cancer, cell migration, adhesion, and immune-related pathways in PM. ConclusionNovel 5hmC-Seal technology based 5hmC signatures can detect patients with peritoneal metastases from CRC and AA, albeit with reduced specificity. This study lays a foundation for future clinical assay development for PM. Statement of significanceWe demonstrate high-sensitivity detection of peritoneal metastasis in colorectal and appendiceal adenocarcinomas using 5hmC-Seal of plasma cfDNA. Earlier detection of this condition could expand curative treatments in [~]20,000 affected U.S. patients.

cancer biology↗

Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance

Most advanced melanomas initially respond to targeted therapy but eventually relapse. Rather than acquiring new mutations, resistance is driven by drug-tolerant persister cells that enter a reversible drug-refractory state. We developed MeRLin, a high-resolution lineage tracing platform integrating cellular barcoding, single-cell transcriptomics, RNA fluorescence in situ hybridization (FISH), and computational analyses to track clonal and transcriptional dynamics in patient-derived melanoma models during prolonged therapy. Clonal dynamics revealed that persister subpopulations first responded to treatment but persisted and expanded during minimal residual disease, ultimately leading to tumor recurrence. Pre-treatment melanoma populations diversified into four conserved persister states characterized by stress-like, lipid metabolism, PI3K signaling, and extracellular matrix remodeling programs associated with adaptive resistance. Spatial transcriptomics showed the organization of these adaptive programs and a complex signaling network of autocrine and paracrine interactions among persister subpopulations. Barcoded RNA-FISH enabled spatial mapping of clonal identity and gene expression, revealing in situ co-localization of a dominant resistant clone with SLC2A1 expression. MeRLin provides a robust framework for dissecting cancer heterogeneity and identifying vulnerabilities in persister populations.

cancer biology↗

Design principles of a membrane-spanning ubiquitin ligase

Receptor-type E3 ubiquitin ligases are membrane-spanning assemblies that enable extracellular signals to directly control ubiquitylation in the cytoplasm. Despite playing widespread roles in tissue patterning and homeostasis, metabolism, and immunity, their structures and mechanisms remain poorly understood. Using cryo-electron microscopy, integrated with biophysical and functional studies, we visualized an E3 complex composed of two transmembrane proteins, MEGF8 and MOSMO, and the intracellular RING-family protein MGRN1. This MEGF8-MOSMO-MGRN1 (MMM) complex regulates left-right patterning of the body axis and the development of multiple organs, partly by attenuating signaling through the Hedgehog pathway. We find that the MMM complex functions like a fishing pole: a long, flexible helix attached to a membrane platform suspends an activated and precisely oriented RING domain--like a fishhook--to ubiquitylate the cytoplasmic surfaces of target receptors. Our structure explains how mutations in MEGF8 cause multi-organ birth defects in humans and defines a paradigm for receptor regulation by ubiquitylation.

biochemistry↗

A Humanized IFN-γ Mouse Model Reveals Skin Eschar Formation, Enhanced Susceptibility and Scrub Typhus Pathogenesis

Scrub typhus, caused by Orientia tsutsugamushi (Ot) bacteria, is a serious acute febrile illness associated with significant mortality. An estimated one million cases occur annually, with more than one billion people at risk. No effective vaccine is currently available, largely due to the complex Ot strain diversity and an incomplete understanding of protective immune mechanisms. To overcome these challenges, there is a critical need for a suitable animal model that mimics human disease through the natural route of infection via mites. Here, we report for the first time that a genetically engineered humanized mouse strain (with triple knockout/knock-in of IFN-{gamma} and its receptors), exhibits increased susceptibility to intradermal Ot infection compared to wild-type (WT) mice. This is evidenced by greater body weight loss, elevated bacterial burden, and reduced expression of interferon-stimulated genes (ISGs). Humanized mice exhibit pronounced biochemical abnormalities and tissue pathology accompanied by dysregulated T cell and neutrophil responses following infection. Notably, these immunocompetent mice develop skin eschar-like lesions resembling those observed in human patients. Overall, our study introduces a promising humanized mouse model to dissect the immunopathogenesis of scrub typhus and evaluate future vaccine candidates. Author SummaryScrub typhus is a serious disease caused by the obligately intracellular bacterium Ot that spreads to humans through the bite of larval mites called chiggers. It affects over a million people each year, primarily in Asia, and can lead to life-threatening complications. Unfortunately, we still lack a clear understanding of how this infection causes disease, partly because there is not a good laboratory model that closely reflects how humans respond to infection. Our recent reports have suggested an important role of IFN-{gamma} in host protection against Ot infection. In this study, we used a new genetically modified mouse strain that carries human IFN-{gamma} signaling in place of its mouse counterpart. We found that these humanized mice are more vulnerable to infection, develop skin eschar lesions like those in patients, and show signs of systemic inflammation and organ damage. Their immune response also resembled what has been observed in human patients. This new mouse model can help scientists better understand the mechanisms as to how this bacterial species causes severe disease outcomes in patients. Once those mechanisms are understood, this mouse model will serve a further purpose as a tool for testing new vaccines and treatments to aid humans at-risk for scrub typhus.

immunology↗

Integrative genomic and transcriptomic analyses uncover regulatory landscape of symbiotic nitrogen fixation in soybean natural population

Symbiotic nitrogen fixation (SNF) is a key trait in legume productivity, yet the genetic and regulatory basis underlying its natural variation remains poorly understood. Here, we integrated genome, transcriptome, and chromatin accessibility data from a soybean diversity panel comprising 380 accessions, including 108 wild and 272 cultivated lines. Genome-wide association studies (GWAS) detected multiple loci for SNF traits but with limited resolution due to polygenic architecture and environmental influences. Independent component analysis (ICA) identified 136 co-expression modules; ten ICs were strongly correlated with SNF phenotypes and enriched in circadian clock components (e.g., GmLHY1a/b), lipid metabolism, or defense signaling pathways. Transcriptome-wide association studies (TWAS) linked 1,453, 806, and 178 genes to NFP, NW, and NFE traits, respectively. Among TWAS hits, 185 transcription factors were identified, with 39.0% overlapping selective sweeps, suggesting regulatory evolution under domestication. To further dissect expression regulation, we performed eQTL mapping and detected 4,654 significant eQTLs, including 1,241 local (cis), 2,505 distal (trans), and 908 mixed. By integrating ATAC-seq data from sorted nodule nuclei, we found that eQTLs, particularly local eQTLs, are significantly enriched within open chromatin regions, indicating their regulatory potential. Notably, we validated the circadian clock gene GmLHY1b as a negative regulator of nodulation using CRISPR mutagenesis and CUT&Tag. Our integrative study provides comprehensive genomic and transcriptomic resources from a diverse soybean population, offering novel insights into SNF regulatory networks and a valuable foundation for future SNF research and soybean improvement.

plant biology↗

A Maximum-Likelihood Method to Construct Phylogenetic Trees Using Low-Homoplasy Markers: New Insights into Neoaves Phylogeny

We present a novel probabilistic method for species tree reconstruction from low-homoplasy markers, termed MLRE (Maximum Likelihood for Retrotransposed Elements). MLRE uses an infinite-sites model for introducing new markers, which then evolve following a Markov process with three states: polymorphic, fixed, and lost. The model allows MLRE to optimize the likelihood of a tree with edge lengths in coalescent units. The method further incorporates variable parameters for insertion rates across lineages and missing data rates across taxa. For simulated data, MLRE consistently performs better than existing tree inference methods. Reanalyzing a retrotransposon dataset for Neoaves, we find better agreement with published trees from other data types, and we propose one strongly supported novel clade. These results underscore the value of retrotransposon markers in phylogenetics and highlight MLRE as a robust framework for species tree inference under challenging evolutionary conditions.

evolutionary biology↗

A Multimodal Adaptive Optical Microscope For In Vivo Imaging from Molecules to Organisms

Understanding biological systems requires observing features and processes across vast spatial and temporal scales, spanning nanometers to centimeters and milliseconds to days, often using multiple imaging modalities within complex native microenvironments. Yet, achieving this comprehensive view is challenging because microscopes optimized for specific tasks typically lack versatility due to inherent optical and sample handling trade-offs, and frequently suffer performance degradation from sample-induced optical aberrations in multicellular contexts. Here, we present MOSAIC, a reconfigurable microscope that integrates multiple advanced imaging techniques including light-sheet, label-free, super-resolution, and multi-photon, all equipped with adaptive optics. MOSAIC enables non-invasive imaging of subcellular dynamics in both cultured cells and live multicellular organisms, nanoscale mapping of molecular architectures across millimeter-scale expanded tissues, and structural/functional neural imaging within live mice. MOSAIC facilitates correlative studies across biological scales within the same specimen, providing an integrated platform for broad biological investigation.

cell biology↗

Occludin Acts as a Dynein Adaptor Regulating Permeability and Collateral Angiogenesis

Previous studies of the tight junction protein occludin (OCLN) suggest that multiple phosphorylation sites on the carboxy-terminal domain contribute a regulatory role in vascular barrier properties. However, gene deletion studies failed to identify a clear functional role for OCLN, despite multiple phenotypic alterations. Importantly, previous studies targeting exon 3 allowed expression of a splice variant starting at exon 4, (isoform 4) that expresses the full carboxy-terminal tail. Here we show that the OCLN carboxy-terminus forms a complex with the light intermediate chain (LIC) of dynein to link tight junction cargo to the minus end directed motor protein. Mutational analysis revealed S471 phosphorylation is required for binding to the LIC while S490 phosphorylation is required for trafficking. Expressing OCLN S490A mutant prevented endothelial cell proliferation and collateral angiogenesis. OCLN gene deletion targeting exon 5, preventing full length and isoform 4 expression, resulted in embryonic lethality. In summary, OCLN links tight junction cargo to the dynein motor, regulating trafficking in a phosphorylation dependent manner and contributing to both VEGF-induced vascular permeability and collateral angiogenesis.

cell biology↗

Cross-Platform Omics Pipeline for Integrated Transcriptomics

The fragmentation of single-cell RNA-seq (scRNA-seq) and spatial transcriptomics (ST) tools across Python/R ecosystems, coupled with escalating computational demands for million-cell datasets, creates critical barriers to reproducible analysis. To overcome this, we present CrosPIT (Cross-Platform Omics Pipeline for Integrated Transcriptomics), a cloud-native framework that unifies cross-language analysis in Google Colab with versioned storage on Google Drive. Pre-configured environments enable rapid switching between CPU/GPU/R runtimes, eliminating local hardware constraints. To demonstrate biological utility, we embedded several modules, such as a module for precision detection of malignant epithelial cells in colorectal cancer. CrosPIT thus delivers a scalable, language-agnostic solution that standardizes workflows through native AnnData/Seurat object interoperability, accelerates integrative omics research, and democratizes access to high-performance transcriptomic analysis.

bioinformatics↗

A novel tool for labeling intermediary proteins between two non-interacting proteins

Decoding the complexities of signaling pathways is fundamental for deciphering the mechanisms underlying tissue development, homeostasis, and disease pathogenesis. Proximity labeling tools have been instrumental in identifying upstream or downstream effectors of specific proteins within signaling pathways. However, currently, there are no tools available to directly label and capture intermediary proteins that bridge two non-interacting proteins. Here, we developed STUPPIT (Split-TurboID and PUP-IT based Protein Identification Tool), a novel method combining split-TurboID and PUP-IT to biotinylate intermediary proteins of two non-interacting proteins through a two-step enzymatic reaction. Two approaches of STUPPIT were validated using three well-characterized protein triad, including YAP1/AMOT/{beta}-actin, YAP1/LATS1/MOB1A, and {beta}-catenin/-catenin/{beta}-actin. Combining STUPPIT and proteomics, we identified novel intermediary proteins including RNF20, ERC1, USP7 and TRIM33, which interact both with {beta}-catenin and SMAD4, key components of the Wnt and BMP signaling pathways. In conclusion, STUPPIT represents a powerful tool for labeling and capturing intermediary proteins between non-interacting partners, offering new insights into protein-protein interactions and advancing signal transduction research.

cell biology↗

CellLoop: Identifying single-cell 3D genome chromatin loops

Single-cell 3D genome mapping offers insights into chromatin architecture, yet the inherent sparsity and high dimensionality of contact maps hinder reliable identification of chromatin loops at the single-cell level. Here, we present CellLoop, a single-cell chromatin loop detection algorithm based on a density-based center detection framework that integrates intra-cellular and neighboring inter-cellular contacts via a re-voting strategy. Applied to Dip-C data from the mouse brain, CellLoop demonstrates superior accuracy based on the genome spatial distance and compartment signals at the single-cell level. It reveals cell-specific chromatin loops linked to transcriptional regulation and improved cell state classification. In HiRES embryogenesis data, CellLoop refines cell subtype definitions by minimizing cell cycle effects. Integrating GAGE-seq with MERFISH in mouse cortex, CellLoop redefines spatial domain functions through chromatin loop dynamics. Together, CellLoop enables robust, scalable, and biologically meaningful single-cell chromatin loop detection.

bioinformatics↗

Quantifying Uncertainty in Phasor-Based Time-Domain Fluorescence Lifetime Imaging Microscopy

The phasor approach to time-domain fluorescence lifetime imaging microscopy (FLIM) offers a powerful, fit-free method for analyzing complex fluorescence decay signals. However, its quantitative accuracy is fundamentally limited by noise--particularly photon shot noise--which introduces variability and bias in lifetime estimation and fluorophore unmixing. In this study, we present a theoretical uncertainty model for phasor-based time-domain FLIM that analytically captures the propagation of shot noise and quantifies its impact on phasor coordinates and fluorophore weight estimation. We validate the model using Monte Carlo simulations and experimental data acquired from standard fluorescent dyes and biological tissue samples. Our model improves the overall reliability and efficiency of phasor-based time-domain FLIM, particularly in photon-limited imaging applications.

bioinformatics↗

Decoding the Moving Mind: Multi-Subject fMRI-to-Video Retrieval with MLLM Semantic Grounding

Decoding dynamic visual information from brain activity remains challenging due to inter-subject neural heterogeneity, limited per-subject data availability, and the substantial temporal resolution gap between fMRI signals (0.5 Hz) and video dynamics (30 Hz). Current approaches face persistent challenges in addressing these temporal mismatches, demonstrate limited capacity to integrate subject-specific neural patterns with shared representational frameworks, and lack adequate semantic granularity for aligning neural responses with visual content. To bridge these gaps, we propose a framework addressing these limitations through three innovations: (1) a Dynamic Temporal Alignment module that resolves temporal mismatches via exponentially weighted multi-frame fusion with adaptive decay coefficients; (2) a Brain Mixture-of-Experts architecture that combines subject-specific extractors with shared expert layers through parameter-efficient tri-modal contrastive learning; and (3) a Multi perspective Semantic Hyper-Anchoring module that resolves cross-subject attention bias via multi-dimensional semantic decomposition, leveraging multimodal LLMs for fine-grained video semantic extraction--enabling the model to match individual attention patterns as different subjects naturally focus on distinct aspects of the same visual stimulus. This module boosts Top-10/Top-100 retrieval by 17.7%/6.6%. Experiments on two video-fMRI datasets demonstrate state-of-the-art performance, with 39%/30% improvements in Top-10/Top-100 accuracy over single-subject baselines and 27% gains against multi-subject models. The framework exhibits remarkable few-shot adaptability, retaining 97% performance when using only 10% training data for new subjects. Visualization analysis confirms this generalization capability stems from effective disentanglement of subject-specific and shared neural representations.

neuroscience↗

HRCHY-CytoCommunity identifies hierarchical tissue organization in cell-type spatial maps

Diverse cell types within a tissue assemble into multicellular structures to shape the functions of the tissue. These structural modules typically comprise specialized subunits, each performing unique roles. We present HRCHY-CytoCommunity, a graph neural network-based framework that leverages differentiable graph pooling and graph pruning to identify hierarchical multicellular structures in cell phenotype-annotated single-cell spatial maps. HRCHY-CytoCommunity ensures the robustness of the result by employing a hierarchical majority voting strategy. To extend the utility of HRCHY-CytoCommunity in cross-sample comparative analysis, an additional cell-type enrichment-based clustering can be used to generate a unified set of nested multicellular structures across all tissue samples. Using single-cell-resolution spatial proteomics and transcriptomics data, we demonstrate that HRCHY-CytoCommunity outperforms the existing state-of-the-art method in discerning coarse-grained tissue compartments (TCs) and fine-grained tissue cellular neighborhoods (TCNs). To further validate the utility of multi-level nested multicellular structures, we apply HRCHY-CytoCommunity to breast cancer data with clinical information and reveal that large-scale TCs and small-scale TCNs enable the stratification of patients with different prognoses in a hierarchical manner.

bioinformatics↗

AIPAMPDS: an AI platform for antimicrobial peptide design and screening

Antimicrobial resistance (AMR) presents a pressing global health crisis, particularly in the post-pandemic era, underscoring the urgent need for innovative therapeutics. Antimicrobial peptides (AMPs) hold promises for combating multidrug-resistant infections but are hindered by challenges in clinical translation, including limited hemocompatibility and inefficient design processes. To overcome these obstacles, we developed AIPAMPDS, an AI-driven computational platform that integrates a deep generative model with multi-stage screening to design highly active, non-haemolytic AMPs. The platform features two key modules: (1) a Generative Pre-trained Transformer (GPT)-based framework for target-specific AMP generation, enabling rapid exploration of novel peptide sequences, and (2) a multi-neural network screening pipeline for dual evaluation of antimicrobial activity and toxicity. By systematically evaluating both AI-generated and natural candidate AMPs, we identified ten lead peptides for experimental validation, of which 90% exhibited negligible haemolytic activity while maintaining robust antimicrobial potency. AIPAMPDS bridges computational design and therapeutic application, significantly advancing AMP discovery and providing a powerful tool for next-generation antimicrobial development. The platform is freely accessible via a web server at https://amps.pianlab.cn/AIPAMPDS/. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/644774v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@14e9a20org.highwire.dtl.DTLVardef@168e811org.highwire.dtl.DTLVardef@5bd9beorg.highwire.dtl.DTLVardef@344c34_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

The E3 ubiquitin ligase MGRN1 targets melanocortin receptors MC1R and MC4R via interactions with transmembrane adapters

E3 ubiquitin ligases play a crucial role in modulating receptor stability and signaling at the cell surface, yet the mechanisms governing their substrate specificity remain incompletely understood. Mahogunin Ring Finger 1 (MGRN1) is a membrane-tethered E3 ligase that fine-tunes signaling sensitivity by targeting surface receptors for ubiquitination and degradation. Unlike cytosolic E3 ligases, membrane-tethered E3s require transmembrane adapters to selectively recognize and regulate surface receptors, yet few such ligases have been studied in detail. While MGRN1 is known to regulate the receptor Smoothened (SMO) within the Hedgehog pathway through its interaction with the transmembrane adapter Multiple Epidermal Growth Factor-like 8 (MEGF8), the broader scope of its regulatory network has been speculative. Here, we identify Attractin (ATRN) and Attractin-like 1 (ATRNL1) as additional transmembrane adapters that recruit MGRN1 and regulate cell surface receptor turnover. Through co-immunoprecipitation, we show that ATRN and ATRNL1 likely interact with the RING domain of MGRN1. Functional assays reveal that MGRN1 requires these transmembrane adapters to ubiquitinate and degrade the melanocortin receptors MC1R and MC4R, in a process analogous to its regulation of SMO. Loss of MGRN1 leads to increased surface and ciliary localization of MC4R in fibroblasts and elevated MC1R levels in melanocytes, with the latter resulting in enhanced eumelanin production. These findings expand the repertoire of MGRN1-regulated receptors and provide new insight into a shared mechanism by which membrane-tethered E3 ligases utilize transmembrane adapters to dictate substrate receptor specificity. By elucidating how MGRN1 selectively engages with surface receptors, this work establishes a broader framework for understanding how this unique class of E3 ligases fine-tunes receptor homeostasis and signaling output.

cell biology↗