Biology subjects

Hu, W.

Publications and source records attributed to Hu, W..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE

Recent advances in spatial transcriptomics (ST) technologies have transformed our ability to profile gene expression while retaining the crucial spatial context within tissues. However, existing ST platforms suffer from high costs, long turnaround times, low resolution, limited gene coverage, and small tissue capture areas, which hinder their broad applications. Here we present iSCALE, a method that predicts super-resolution gene expression and automatically annotates cellular-level tissue architecture for large-sized tissues that exceed the capture areas of standard ST platforms. The accuracy of iSCALE were validated by comprehensive evaluations, involving benchmarking experiments, immunohistochemistry staining, and manual annotation by pathologists. When applied to multiple sclerosis human brain samples, iSCALE uncovered lesion associated cellular characteristics that were undetectable by conventional ST experiments. Our results demonstrate iSCALEs utility in analyzing large-sized tissues with automatic and unbiased tissue annotation, inferring cell type composition, and pinpointing regions of interest for features not discernible through human visual assessment.

genomics↗

bioRxiv2025

Systematic silencing of oncogenic fusion transcripts with ultra-precise CRISPR-Cas13b

Oncogenic gene fusions are key drivers of cancer, yet most remain untargetable by current therapies. Here, we establish CRISPR-PspCas13b as a personalizable platform for systematic silencing of various fusion transcripts. We reveal that recognition and cleavage of the breakpoint sequence by PspCas13b disrupts the fusion transcript, resulting in unexpected RNA nicking and ligation near the cleavage site, which generates out-of-frame, translation-incompetent transcripts. This approach efficiently degrades canonical and drug-resistant BCR::ABL1 mutants (e.g., T315I), a primary cause of resistance to tyrosine kinase inhibitors (TKIs) and relapse in chronic myeloid leukemia (CML). Silencing T315I BCR::ABL1 mRNA in drug-resistant CML cells triggers extensive transcriptomic, proteomic, and phosphoproteomic remodelling, causing erythroid differentiation and apoptosis. Beyond BCR-ABL1 mutants, personalized design of PspCas13b effectively silences other undruggable fusions, including RUNX1::RUNX1T1 and EWSR1::FLI1, key drivers in acute myeloid leukemia and in Ewing sarcoma, respectively. Collectively, this study establishes a framework for systematic, precise, and personalizable targeting of otherwise undruggable or drug-resistant oncogenic transcripts.

molecular biology↗

bioRxiv2025

Spatial transcriptomics reveals heterogeneous cell-cell interactions among brain regions in a cuprizone model consistent with multiple sclerosis lesions

The cuprizone (CPZ) model is widely used for modeling demyelination in multiple sclerosis (MS) and for testing potential remyelination therapies. We integrated single-cell and spatial transcriptomics (ST) to fine map the spatial cellular and molecular responses during de and remyelination. ST revealed global demyelination and neuroinflammation in the brain beyond the corpus callosum, with region-specific differences. We identified oligodendroglia and microglia as two major cell types with significant transcriptomic changes in the model. Ligand receptor pairing analyses predicted growth factor and phagocytic pathway enrichment during demyelination, which is consistent with changes in MS lesions. During remyelination, while mature oligodendrocytes nearly reversed their phenotype back to the control state, microglia remained associated with the demyelination phenotype. Finally, astrocytes in the CPZ model had the greatest preservation of disease-associated modules to MS lesions, while the MOL, OPC, and microglia showed moderate to low preservation, which overall suggested that the CPZ model had moderate translatability to chronically active MS lesions.

neuroscience↗

bioRxiv2025

Ancient human extinction risk: Implications from high-precision computation and fossil evidence

Reconstructing ancient population size history is essential for understanding the evolutionary origin of Homo sapiens. Using the fast infinitesimal time coalescent process (FitCoal), which precisely computes the expected site frequency spectrum (SFS), we revisited the debated population bottleneck that occurred approximately 930 thousand years ago. By benchmarking FitCoal against mushi and ten billion coalescent simulations, we demonstrate that FitCoal achieves both superior speed and accuracy in expected SFS estimation. Analyses of simulated datasets confirmed that FitCoal reliably recovered the bottleneck, whereas mushi failed under identical conditions. Independent fossil and paleoclimate evidence further corroborates the timing and evolutionary impact of this bottleneck, linking it to hominin dispersals, speciation events, and a subsequent increase in brain size. These findings refine the demographic history of Homo during the Pleistocene and highlight the importance of high-precision SFS computation for revealing critical evolutionary transitions that shaped modern human ancestry.

evolutionary biology↗

bioRxiv2025

Cryo-EM structures reveal the PP2A-B55α and Eya3 interaction that can be disrupted by a peptide inhibitor

We have previously shown that Eya3 recruits PP2A-B55 to dephosphorylate pT58 on Myc, increasing Myc stability and enhancing primary tumor growth of triple-negative breast cancer (TNBC). However, the molecular details of how Eya3 recruits PP2A-B55 remain unclear. Here we determined the cryo-EM structures of PP2A-B55 bound with Eya3, with an inhibitory peptide B55i, and in its unbound state. These studies demonstrate that Eya3 binds B55 through an extended peptide in the NTD of Eya3. The Eya3 peptide and other PP2A-B55 substrates and protein/peptide inhibitors including B55i bind to a similar area on the B55 surface but the molecular details of the binding differ. We further demonstrated that the B55i peptide inhibits the B55 and Eya3 interaction in vitro. B55i peptide expressed on a plasmid increases pT58 and decreases Myc protein level in TNBC cells, suggesting the potential of B55i or similar peptides as therapies for TNBC.

molecular biology↗

bioRxiv2025

ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU.

The rise of large-scale single-cell RNA-seq data has introduced challenges in data processing due to its slow speed. Leveraging advancements in GPU computing ecosystems, such as CuPy, and building on Scanpy and rapids-singlecell package, we developed ScaleSC, a GPU-accelerated solution for single-cell data processing. ScaleSC delivers over a 20x speedup through GPU computing and significantly improves scalability, handling datasets of 10-40 million cells with over 1000 batches by overcoming the memory bottleneck on a single A100 card- far surpassing rapids-singlecells capacity of processing only 1 million cells without multi-GPU support. We also resolved discrepancies between GPU and CPU algorithm implementations to ensure consistency. In addition to core optimizations, we developed new advanced tools for marker gene identification, cluster merging, and more, with GPU-optimized implementations seamlessly integrated. Designed for ease of use, the ScaleSC package is compatible with Scanpy workflows, requiring minimal adaptation from users. The ScaleSC package (https://github.com/interactivereport/ScaleSC) promises significant benefits for the single-cell RNA-seq computational community.

bioinformatics↗

bioRxiv2025

Carbon monoxide exposure stimulates growth and activity of primary producers in diverse soil ecosystems

Carbon monoxide (CO) is both a potent poison for many aerobic organisms and a desirable energy source for diverse microorganisms. Atmospheric emissions of this gas have increased since industrialization and their levels are highly elevated in many urban and natural environments; however, it is unresolved whether elevated levels of CO at environmentally relevant concentrations are primarily stimulatory or inhibitory to soil microbial communities. Here, we showed that CO exposure minimally affects microbial abundance, richness, and composition in diverse ecosystem soils, suggesting most microbes are tolerant of this gas. Genome-resolved metagenomic profiling showed that these soils harbored diverse bacteria capable of using CO an electron donor for aerobic respiration and carbon fixation. CO stimulated the growth of several of these putative CO-oxidizing bacteria in a dose-dependent manner, especially widespread proteobacterial and actinobacterial lineages. Additionally, we found a strong relationship between CO oxidation and carbon fixation and observed an enrichment of several carboxydotrophic MAGs capable of carbon fixation in most soil types. These findings highlight that environmentally relevant CO levels do not inhibit soil microbes, but instead foster the growth of distinct carboxydotrophic bacteria, suggesting a robust soil CO sink that could help mitigate anthropogenic CO emissions and contribute to carbon cycling in terrestrial ecosystems.

biochemistry↗

bioRxiv2025

Coordination of distinct sources of excitatory inputs enhances motion selectivity in the mouse visual thalamus

Multiple sources innervate the visual thalamus to influence image-forming vision prior to the cortex, yet it remains unclear how non-retinal and retinal input coordinate to shape thalamic visual selectivity. Using dual-color two-photon calcium imaging in the thalamus of awake mice, we observed similar coarse-scale retinotopic organization between axons of superior colliculus neurons and retinal ganglion cells, both providing strong converging excitatory input to thalamic neurons. At a fine scale of [~]10 {micro}m, collicular boutons often shared visual feature preferences with nearby retinal boutons. Inhibiting collicular input significantly suppressed visual responses in thalamic neurons and specifically reduced motion selectivity in neurons preferring nasal-to-temporal motion. The reduction in motion selectivity could be the result of silencing sharply tuned direction-selective colliculogeniculate input. These findings suggest that the thalamus is not merely a relay but selectively integrates inputs from multiple regions to build stimulus selectivity and shape the information transmitted to the cortex. HIGHLIGHTSChronic dual-color calcium imaging reveals diverse visual tuning of collicular axonal boutons. Nearby collicular and retinal boutons often share feature preferences at [~]10 {micro}m scale Silencing of collicular input suppresses visual responses in the majority of thalamic neurons. Silencing of collicular input reduces motion selectivity in thalamic neurons.

neuroscience↗

bioRxiv2025

AAVone: A Cost-Effective, Single-Plasmid Solution for Efficient AAV Production with Reduced DNA Impurities

Currently, the most common approach for manufacturing GMP-grade adeno-associated virus (AAV) vectors involves transiently transfecting mammalian cells with three plasmids that carry the essential components for production. The requirement for all three plasmids to be transfected into a single cell and the necessity for high quantities of input plasmid DNA, limits AAV production efficiency, introduces variability between production batches, and increases time and labor costs. Here, we developed an all-in-one, single-plasmid AAV production system, called AAVone. In this system, the adenovirus helper genes (E2A, E4orf6, and VA RNA), packaging genes (rep and cap), and the vector transgene cassette are consolidated into a single compact plasmid with a 13-kb backbone. The AAVone system achieves a two- to four-fold increase in yields compared to the traditional triple-plasmid system. Furthermore, the AAVone system exhibits low batch-to-batch variation and eliminates the need for fine-tuning the ratios of the three plasmids, simplifying the production process. In terms of vector quality, AAVs generated by the AAVone system show similar in vitro and in vivo transduction efficiency, but a substantial reduction in sequences attributed to plasmid backbones and a marked reduction in non-functional snap-back genomes. In Summary, the AAVone platform is a straightforward, cost-effective, and highly consistent AAV production system - making it particularly suitable for GMP-grade AAV vectors.

bioengineering↗

bioRxiv2025

Development of Proton Density Fat Fraction Micro-MRI for Non-Invasive Quantitative Assessment of Bone Marrow Changes with Age and Radiation in Mouse Models

Background/ObjectivesBone marrow (BM) adipocytes are critical in progressing solid tumor metastases and hematological malignancies across pediatric to aging populations. Single-point biopsies remain the gold standard for monitoring BM diseases, including hematologic malignancies, but are limited in capturing the full complexity of loco-regional and global BM microenvironments. Non-invasive imaging techniques like Magnetic Resonance Imaging (MRI), could offer valuable alternatives for real-time evaluation of BM diseases in both preclinical translational and clinical studies. MethodsWe developed a preclinical proton density fat fraction (PDFF) MRI technique for quantitative BM composition assessment, focusing on fat fraction (FF) within mouse femurs. We validated this method using aging mice and young mice subjected to 10 Gy X-ray irradiation, compared with young unirradiated mice as controls. Water-fat phantoms (0% to 100% fat content) were used to optimize the imaging sequence, and immunohistochemical (IHC) staining with H&E validates equivalent adipose content in the femur BM regions. ResultsSignificant differences in FF were observed across age groups (p = 0.001 for histology and p = 0.0002 for PDFF) and between irradiated and control mice (p = 0.005 for histology and p = 0.002 for PDFF). A strong correlation (R2 [~] 0.84) between FF values from PDFF and histology validates the accuracy of the technique. ConclusionsThese findings demonstrate the potential of PDFF MRI as a non-invasive real-time imaging biomarker for quantifying BM fat fraction in preclinical mice model studies, particularly in evaluating the effects of aging, disease progression, and irradiation therapy in pediatric and translational oncology research.

biophysics↗

bioRxiv2024

Mycobacterium tuberculosis CrgA Forms a Dimeric Structure with Its Transmembrane Domain Sandwiched between Cytoplasmic and Periplasmic β-Sheets, Enabling Multiple Interactions with Other Divisome Proteins

CrgA is a key transmembrane (TM) protein in the cell division process of Mycobacterium tuberculosis (Mtb), the pathogen responsible for tuberculosis. While many of the Mtb divisome proteins have been identified, their structures and interactions remain largely unknown. Previous studies of CrgA using oriented-sample solid-state NMR have defined the tilt and rotation of the TM helices, but the cytoplasmic and periplasmic domains and even the oligomeric state were uncharacterized. Here, combining oriented-sample and magic-angle spinning solid-state NMR spectra, we solved the full-length structure of CrgA. The structure features a dimer with a TM domain sandwiched between a cytoplasmic {beta}-sheet and a periplasmic {beta}-sheet. The {beta}-sheets stabilize dimerization, which in turn increases CrgAs ability to participate in multiple protein interactions. Within the membrane, CrgA binds FtsQ, CwsA, PbpA, FtsI, and MmPL3 via its TM helices; in the cytoplasm, Lys23 and Lys25 project outward from the {beta}-sheet to interact with acidic residues of FtsQ and FtsZ. The structural determination of CrgA thus provides significant insights into its roles in recruiting other divisome proteins and stabilizing their complexes for Mtb cell wall synthesis and polar growth.

biophysics↗

bioRxiv2024

Assessing Extracellular Vesicle Turnover In vivo Using Highly Sensitive Phosphatidylserine-Binding Reagents

Phosphatidylserine (PS) is a well-established marker for apoptotic cells and activated platelets, and it is also found on extracellular vesicles (EVs). However, the frequency of PS+ EVs remains a topic of debate, probably due to the distinct lipid composition of EVs, which varies with the source material. This variation underscores the need for highly sensitive detection reagents to accurately differentiate between PS+ and PS- EVs. To address this issue, we compared several PS-binding reagents for the staining of blood EVs, including milk fat globule factor E8 (MFG-E8, lactadherin), a derivative of MFG-E8, and Annexin V, the most used compound in the literature. Here, we demonstrate the predominance of PS+ EVs in both murine and human blood and reveal significant differences in the affinities of the PS-binding proteins. With approximately 90% of the detected blood EVs being PS+, we utilized a derivative of MFG-E8 for in vivo monitoring of both circulating and cell-bound EVs, providing a novel tool to analyze endogenous EV kinetics. Our findings showed that murine PS+ plasma EVs were rapidly cleared from circulation ([~]50% after 30 minutes), yet they remained present on splenic B cells and monocytes/macrophages. In conclusion, MFG-E8-based reagents enable externalized PS to serve as a universal EV marker, greatly improving EV isolation, standardizing EV quantification, and facilitating diagnostic EV monitoring and disease biomarker discovery.

cell biology↗

bioRxiv2024

SpatialPPI 2.0: Enhancing Protein-Protein Interaction Prediction through Inter-Residue Analysis in Graph Attention Networks

Protein-protein interactions (PPIs) are fundamental to cellular functions, and accurate prediction of these interactions is crucial to understanding biological mechanisms and facilitating drug discovery. SpatialPPI 2.0 is an advanced graph neural network-based model that predicts PPIs by utilizing interresidue contact maps derived from both structural and sequence data. By leveraging the comprehensive PINDER dataset, which includes interaction data from the RCSB PDB and the AlphaFold database, SpatialPPI 2.0 improves the specificity and robustness of the prediction of PPI. Unlike the original SpatialPPI, the updated version employs interaction interface prediction as an intermediate step, allowing for a more effective assessment of interactions between isolated proteins. The model utilizes Graph Attention Networks (GAT) and Graph Convolutional Networks (GCN) to capture both local and global structural features. SpatialPPI 2.0 outperforms several state-of-the-art PPI and interface predictors, demonstrating superior accuracy and reliability. Furthermore, the model shows robustness when using structures predicted by AlphaFold, indicating its potential to predict interactions for proteins without experimentally determined structures. SpatialPPI 2.0 offers a promising solution for the accurate prediction of PPIs, providing insight into protein function and supporting advances in drug discovery and synthetic biology. SpatialPPI 2.0 is available at https://github.com/ohuelab/SpatialPPI2.0

bioinformatics↗

bioRxiv2024

Chromosome-scale assembly and annotation of the wildwheat relative Aegilops comosa

Wild relatives of wheat are valuable sources for enhancing the genetic diversity of common wheat. Aegilops comosa, an annual diploid species with an MM genome constitution, possesses numerous agronomically valuable traits that can be exploited for wheat improvement. In this study, we report a chromosome-level genome assembly of Ae. comosa accession PI 551049, generated using PacBio high-fidelity (HiFi) reads and high-throughput chromosome conformation capture (Hi-C) data. The assembly spans 4.47 Gb, featuring a contig N50 of 23.59 Mb and a scaffold N50 of 619.05 Mb. A total of 39,063 gene models were annotated through a combination of homoeologous proteins, Iso-Seq, and RNA-Seq data. Comparative genome analysis revealed a terminal intrachromosomal translocation in chromosome 2M of Ae. comosa (and Ae. umbellulata) compared to its homoeologous chromosomes in other diploid wheat species. Phylogenetic analysis showed a close relationship between Ae. comosa and Ae. umbellulata. This newly constructed reference genome of Ae. comosa will serve as an important genomic resource for comparative genomic studies and the cloning of agriculturally important genes.

genomics↗

bioRxiv2024

General purpose genotypes and evolution of higher plasticity in clonality underlie knotweed invasion

Many widespread invasive plant species express high phenotypic variation across novel environments, providing a unique opportunity to examine ecological and evolutionary dynamics under global change. However, biogeographical studies often lack information about the origin of introduced populations, limiting our understanding of post-introduction evolution of introduced species in the new range. Here, we assessed the responses of Reynoutria japonica from 128 populations spanning three latitudinal transects in the native ranges of China and Japan, and the introduced ranges of North America and Europe. When grown in two common gardens in the native range, plants from introduced populations in North America and Europe differed in almost all traits from those from native Chinese populations, but were similar to plants from native Japanese populations. Compared to Chinese populations, North American, European and Japanese populations expressed lower trait values and plasticity in most traits. However, plants from both introduced ranges and from Japanese populations expressed higher clonality and plasticity in clonality than plants from Chinese populations. In addition, introduced populations expressed higher plasticity in clonality but lower plasticity in basal diameter compared to Japanese populations. Our study showed heritable differences in phenotypes between plants from the native ranges of Japan and China, and those from the introduced ranges were similar to the putative source of origin in Japan. However, we found that introduced populations may have evolved higher plasticity in clonal growth. Our findings emphasize the critical role of clonality and plasticity in invasion success, demonstrating the importance of discriminating between source and non-source native populations to identify ecological and evolutionary responses of invasive plants to novel environments.

ecology↗

bioRxiv2024

Structural Insights into Selective and Dual Antagonism of EP2 and EP4 Prostaglandin Receptors

Prostaglandin E2 (PGE2) signaling through EP2 and EP4 receptors plays a crucial role in inflammation, pain, and cancer progression. Selective and dual antagonists of these receptors have shown promising therapeutic potential. However, the structural basis for their binding modes and selectivity remained unclear. Here, we present cryo-EM structures of human EP2 and EP4 receptors in complex with selective antagonists PF-04418948 and grapiprant, respectively, as well as the dual antagonist TG6-129. These structures reveal distinct binding pockets and interaction networks that govern antagonist selectivity and efficacy. Combining the structural data and functional studies, we uncover the key residues and structural features that differentiate EP2 and EP4 binding sites, including a unique {pi}-{pi} stacking interaction in EP2 and variations in pocket shape and charge distribution. The dual antagonist TG6-129 exhibited a novel binding mode, interacting deeply with EP2 but only shallowly with EP4 in a two-warhead manner. These findings provide a structural framework for understanding prostanoid receptor pharmacology and offer valuable insights for the rational design of improved selective and dual antagonists targeting EP2 and EP4 receptors.

biochemistry↗

bioRxiv2024

Molecular mechanisms of uric acid transport by the native human URAT1 and its inhibition by anti-gout drugs

Gout, a common and painful disease, stems from hyperuricemia, where elevated blood uric acid levels lead to urate crystal formation in joints and kidneys. The human urate transporter 1 (hURAT1) plays a critical role in urate homeostasis by facilitating urate reabsorption in the renal proximal tubule, making it a key target for gout therapy. Pharmacological inhibition of hURAT1 with drugs such as dotinurad, benzbromarone, lesinurad, and verinurad promotes uric acid excretion and alleviates gout symptoms. Here we present cryo-electron microscopy structures of native hURAT1 bound with these anti-gout drugs in the inward-open state, and with uric acid in inward-open, outward-open, and occluded states. Complemented by mutagenesis and cell-based assays, these structures reveal the mechanisms of uric acid reabsorption and hURAT1 inhibition. Our findings elucidate the molecular basis of uric acid transport and anti-gout medication action, and provide a structural framework for the rational design of next-generation therapies for hyperuricemia and gout.

biochemistry↗

bioRxiv2024

A novel bifunctional peptide VAMP mined from hemp seed protein hydrolysates improves glucose homeostasis by inhibiting intestinal DPP-IV and increasing the abundance of Akkermansia muciniphila

Discovery of new dipeptidyl peptidase IV (DPP-IV) inhibitory peptides from natural protein resources capable of regulating glucose metabolism in type 2 diabetic populations has been a significant challenge. In this study, we constructed a molecular docking- and machine learning-aided DPP-IV inhibitory peptide library and combined a functional screening approach based on intestinal organoids to discover efficient and new DPP-IV-inhibiting peptides from hemp seed protein hydrolysates. A novel tetrapeptide, VAMP, was then identified to strongly inhibit DPP-IV (IC50=1.00 M in vitro), which competitively binds to DPP-IV and improves glucose metabolism in vivo with high safety by increasing active glucagon-like peptide-1 (GLP-1) levels in obese mouse models. Interestingly, VAMP specifically promoted the growth and abundance of intestinal Akkermansia muciniphila in vivo, at the same time, which was responsible for the improved intestinal barrier function and insulin resistance. Our study demonstrated that the novel bifunctional VAMP can effectively target the DPP-IV-GLP-1 axis and simultaneously regulate the abundance of the gut microbial A. muciniphila, to regulate glucose homeostasis, providing a promising nutraceutical and therapeutic tetrapeptide for hyperglycaemia treatment by targeting the gut-microbiata axis. TeaserVAMP improves glucose metabolism by increasing the active GLP-1 level and promoting the growth of A. muciniphila to improve intestinal barrier function.

molecular biology↗