Biology subjects

Wu, R.

Publications and source records attributed to Wu, R..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Rationally Engineered Coronavirus-mimicking Protein Nanocage Platform for Glioblastoma Targeted Delivery and Immunity Regulation

Glioblastoma (GBM) is one of the most aggressive and treatment-resistant brain tumors, owing to the dual challenges of the blood-brain barrier (BBB) and a profoundly immunosuppressive tumor microenvironment. However, few existing strategies are capable of simultaneously overcoming these two barriers, underscoring a critical scientific gap and the need for innovative therapeutic platforms that enable both effective BBB traversal and tumor immune reprogramming. Here, we present a coronavirus-mimicking protein nanocage platform (EcomPC) derived from Thermotoga maritima encapsulin, rationally engineered for the targeted and sustained delivery of interferon- (IFN-) to GBM lesions. Through strategic insertion of flexible linkers, cysteine-to-serine mutations, and modular surface functionalization via SpyTag/SpyCatcher chemistry, EcomPC enables intracellular self-assembly of IFN- and glioma-specific targeting. In orthotopic GBM models, EcomPC-IFN demonstrates efficient BBB translocation, selective tumor accumulation, and potent anti-tumor efficacy. Mechanistically, localized IFN- release induces tumor cell apoptosis and reprograms the immune microenvironment--characterized by increased CD8 T cell infiltration, decreased Foxp3 regulatory T cells, and a favorable chemokine shift. These therapeutic effects are not recapitulated by free IFN- or untargeted nanocages, underscoring the essential role of both structural mimicry and ligand-guided delivery. Collectively, this work establishes EcomPC as a programmable, virus-inspired protein delivery platform capable of overcoming key physiological barriers in brain tumor immunotherapy, and lays the foundation for its broader application in CNS-targeted biologic delivery.

bioengineering↗

bioRxiv2025

Epigenetic Programming of Estrogen Receptor in Adipose Tissue by High Fat Diet Regulates Obesity-Induced Inflammation

Adipose inflammation plays a key role in obesity-induced metabolic abnormalities. Epigenetic regulation, including DNA methylation, is a molecular link between environmental factors and complex diseases. Here we found that high fat diet (HFD) feeding induced a dynamic change of DNA methylome in mouse white adipose tissue (WAT) analyzed by reduced representative bisulfite sequencing. Interestingly, DNA methylation at the promoter of estrogen receptor (Esr1) was significantly increased by HFD, concomitant with a down-regulation of Esr1 expression. HFD feeding in mice increased the expression of DNA methyltransferase 1 (Dnmt1) and Dnmt3a, and binding of DNMT1 and DNMT3a to Esr1 promoter in WAT. Mice with adipocyte-specific Dnmt1 deficiency displayed increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity upon HFD challenge; while mice with adipocyte-specific Dnmt3a deficiency showed a mild metabolic phenotype. Using a modified CRISPR/RNA-guided system to specifically target DNA methylation at the Esr1 promoter in WAT, we found that reducing DNA methylation at Esr1 promoter increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity in HFD-challenged mice. Our study demonstrates that DNA methylation at Esr1 promoter plays an important role in regulating adipose inflammation, which may contribute to obesity-induced insulin resistance.

physiology↗

bioRxiv2025

GATA6 Mediates Endoderm and Mesoderm Progenitor Fate Driven by WNT and NODAL Signaling

During gastrulation, NODAL and WNT signaling drives distinct gene regulatory networks (GRNs) to promote pluripotency exit, specify progenitor fate, and direct lineage differentiation. Here, we employ murine embryonic stem cell directed differentiation toward endoderm and mesoderm lineages to reveal a crucial role of GATA6 during anterior primitive streak-derived progenitor segregation. GATA6 is known to direct by default extra-embryonic endoderm. To promote definitive endoderm fate, GATA6 reinforces the endoderm GRN driven by NODAL while repressing the mesoderm GRN through down-regulation of WNT activity. During progression of mesoderm differentiation, GATA6 induces a switch in the transcriptional output regulated by WNT, promoting lateral mesoderm specification and repression of paraxial mesoderm fate. Thus, this single transcription factor mediates formation of four distinct tissue types, depending on integration of NODAL/WNT activities. Regulation of Eomes and T/Bra expression during anterior primitive streak progression is an essential function of GATA6 during the specification of endoderm or mesoderm fate.

developmental biology↗

bioRxiv2025

CSLAN: Cross-Species Latent Alignment Network for Trauma-Related Cell-Type Classification

Understanding cellular identity and function across species is fundamental to deciphering conserved biological principles and translating insights from model organisms to human health. However, integrating single-cell transcriptomic data, particularly from resource-limited human studies, with comprehensive datasets from model organisms like mice remains a significant challenge due to evolutionary divergence and technical variability. Here, we introduce the Cross-Species Latent Alignment Network (CSLAN), a transfer learning framework that effectively bridges this gap for robust cell type classification. CSLAN employs a novel strategy involving focused feature selection on source (mouse) data followed by pretraining an encoder-decoder architecture. Crucially, for transfer to human data, only the encoder is fine-tuned while the latent space processor and the decoder, which encapsulate learned, conserved cell type signatures, remains fixed. This targeted adaptation mechanism allows CSLAN to achieve exceptional accuracy (e.g., 96.67% for human immune cells in a trauma context) by efficiently aligning human gene expression profiles to a biologically informed latent space derived from mouse data. Our findings establish a powerful and broadly applicable paradigm for cross-species knowledge transfer, enabling deeper biological insights from limited human scRNA-seq data by leveraging the wealth of information from model systems, with significant implications for translational research and the construction of comprehensive, cross-species cell atlases.

bioinformatics↗

bioRxiv2025

Structural innovations and neurogenic continuity define avian brain development and evolution

Understanding how neurogenic diversity and brain architecture emerge is crucial for deciphering the mechanisms of brain plasticity and cognitive evolution. Here, we present a comprehensive single-cell and spatial transcriptomic atlas of the budgerigar brain, a highly cognitive avian species. We uncover a striking dorsoventral symmetry in excitatory neuron distribution, precisely organized along the lamina mesopallialis intermedia (LMI), a key boundary structure. Cross-species comparisons further reveal the origins of this unique avian pallial organization, offering new insight into avian brain evolution. Our study also highlights distinct developmental trajectories and asynchronous maturation patterns between telencephalic and optic tectum excitatory neurons, underscoring their contribution to innate circuit assembly. Furthermore, we identify adult neural stem cells (NSCs) with evolutionarily conserved transcriptomic signatures across avian species, emphasizing their role in brain plasticity and adaptation. These findings refine fundamental models of avian brain development and elucidate conserved principles of cognitive plasticity.

evolutionary biology↗

bioRxiv2025

Longitudinal single-cell analysis reveals RUNX1T1 as an early driver in treatment-induced neuroendocrine transdifferentiation

Treatment-induced neuroendocrine prostate cancer (t-NEPC) is a lethal form of advanced prostate cancer that can emerge from adenocarcinoma under androgen receptor pathway inhibition, but the tumor-cell states and regulators underlying this transition remain incompletely defined. Here, we analyzed longitudinal single-cell RNA sequencing data from the LTL331/331R patient-derived xenograft model across seven disease stages, comprising 32,269 tumor-cell transcriptomes from treatment-naive adenocarcinoma, post-castration regression, and relapsed NEPC. We identified an AR-low/NE-low intermediate state that emerged after castration and before overt relapse, as well as two transcriptionally distinct terminal NEPC states marked by ASCL1high/FOXA2low and ASCL1low/FOXA2high programs. RUNX1T1 was induced in the intermediate state and remained elevated across both terminal states. RUNX1T1 enhanced NE-associated features and cell viability during enzalutamide treatment in adenocarcinoma cells, whereas its knockdown in NCI-H660 cells reduced NE-associated transcriptional programs, proliferation, and survival and shifted the transcriptome toward an intermediate-like state. Chromatin interactome analysis and co-immunoprecipitation linked RUNX1T1 to G9A/LASP1-containing chromatin repressor complexes. These findings define a temporal framework for treatment-induced NEPC progression and identify RUNX1T1 as an early-induced and sustained regulator of NE lineage transition and maintenance of established NEPC.

cancer biology↗

bioRxiv2025

Intracellular Delivery of Bone Nanoparticles to Mitigate Irradiation-Induced Damage in Bone Marrow Mesenchymal Stem Cells

Ionizing radiation (IR)-induced bone damage presents a major clinical challenge by impairing bone marrow function and disrupting normal bone remodeling. Bone regeneration depends on bone marrow-derived mesenchymal stem cells (BMSCs), which are highly sensitive to IR that causes DNA damage, oxidative stress, apoptosis, and a shift from osteogenesis to adipogenesis, ultimately leading to bone loss and impaired healing. This study evaluated the therapeutic potential of intracellularly delivered bone-derived nanoparticles (BPs) in mitigating IR-induced BMSCs damage. We found that IR exposure caused significant BMSCs dysfunction, including reduced proliferation, increased apoptosis, persistent DNA damage, and a shift toward adipogenic differentiation. Treatment with BPs led to efficient intracellular uptake, improved cell morphology, enhanced proliferation, reduced apoptosis, and preservation of balanced differentiation capacity. Transcriptomic analysis via RNA sequencing revealed that BPs restored key molecular pathways disrupted by IR, particularly those involved in cell cycle regulation, extracellular matrix (ECM) remodeling, and apoptosis. By reversing these transcriptional impairments, BPs supported genomic stability and the regenerat ive function of BMSCs. Overall, these findings suggest that BPs effectively counteract IR-induced cellular damage and enhance the regenerative capacity of BMSCs, offering a promising therapeutic strategy for radiation -induced skeletal injuries.

bioengineering↗

bioRxiv2025

Longitudinal single-cell RNA sequencing of a neuroendocrine transdifferentiation model reveals transcriptional reprogramming in treatment-induced neuroendocrine prostate cancer

Neuroendocrine transdifferentiation (NEtD) of prostate adenocarcinoma (PRAD) leads to aggressive neuroendocrine prostate cancer (NEPC). The LTL331 patient-derived xenograft (PDX) model consistently progresses to NEPC following castration, mimicking clinical responses to androgen-deprivation therapy. Here we tracked NEtD using longitudinal single-cell RNA sequencing (scRNA-seq) across eight time points in LTL331 from pre- to post-castration. Castration led to the loss of AR-high PRAD cells, expansion of AR-low populations, and emergence of an AR- and NE-negative (AR-/NE-) intermediate state that transitioned into NEPC. We delineate a model in which pre-EMT cells enriched in ciliogenesis and cell-adhesion pathways differentiate into EMT-like populations before branching into distinct ASCL1+ and ASCL1- NEPC states. The EMT-enriched intermediate, marked by progenitor and neural crest stem-cell genes, acts as a transition bridge, suggesting EMT-associated stemness underlies lineage plasticity. A terminal ASCL1-NEPC state also suggests that ASCL1 is not essential for NEPC maintenance. Gene regulatory analysis highlighted key regulators driving NEtD, including MSX1 and ASCL1 in early EMT-like and NEPC states, respectively. These transcriptional states were validated in both patient-derived bulk and scRNA-seq data. Our findings offer insights into intervention strategies to delay or prevent NEtD with the potential of identifying novel prognostic and therapeutic targets.

cancer biology↗

bioRxiv2025

A Single-Cell Atlas of RNA Alternative Splicing in the Glioma-Immune Ecosystem

Single-cell analysis has refined our understanding of cellular heterogeneity in glioma, yet RNA alternative splicing (AS)--a critical layer of transcriptome regulation--remains underexplored at single-cell resolution. Here, we present a pan-glioma single-cell AS analysis in both tumor and immune cells through integrating seven SMART-seq2 datasets of human gliomas. Our analysis reveals lineage-specific AS across glioma cellular states, with the most divergent AS landscapes between mesenchymal- and neuronal-like glioma cells, exemplified by AS in TCF12 and PTBP2. Comparison between core and peripheral glioma cells highlights AS-redox co-regulation of cytoskeleton organization. Further analysis of glioma-infiltrating immune cells reveals potential isoform-level regulation of protein glycosylation in regulatory T cells and a link between MS4A7 AS in macrophages and clinical response to anti-PD-1 therapy. This study emphasizes the role of AS in glioma cellular heterogeneity, highlighting the importance of an isoform-centric approach to better understand the complex biological processes driving tumorigenesis.

genomics↗

bioRxiv2025

DiNovo: high-coverage, high-confidence de novo peptide sequencing using mirror proteases and deep learning

Despite the recent advancements driven by deep learning, de novo peptide sequencing is still constrained by incomplete peptide fragmentation and insufficient protein digestion in current single protease-based proteomic experiments. Here, we present a software system, named DiNovo, for high-coverage and confidence de novo peptide sequencing by leveraging the complementarity of mirror proteases. DiNovo is empowered by several innovative algorithms, including a mirror-spectra recognition algorithm independent of pre-sequencing, two sequencing algorithms based on deep learning and graph theory, respectively, and target-decoy mapping, a method for sequencing result evaluation free of prior peptide identification. Compared with the trypsin protease used alone, DiNovo using two pairs of mirror proteases led to two to three times high-confidence amino acids sequenced. Compared with previous single-protease de novo sequencing algorithms, DiNovo achieved much higher sequence coverages. DiNovo also showed great potential as a powerful complement or alternative to database search for peptide identification with quality control.

bioinformatics↗

bioRxiv2025

A study of different pre-treatment methods for cigarettes and their aroma differences

The study innovatively utilized a combination of smoking machine and Cambridge filter to effectively extract the aroma compounds generated during smoking of cigarettes, and employed three different pretreatment methods to obtain optimal cigarette pretreatment procedures. In addition, the aroma components of different cigarettes were identified by different instruments such as gas chromatography-mass spectrometry. Combined with the calculation of Odor Activity Values (OAV), PCA analysis and sensory evaluation were performed on the five types of cigarettes to reveal differences and similarities in their aroma profiles.

biochemistry↗

bioRxiv2025

clusIBD: Robust Detection of Identity-by-descent (IBD) Segments Using Unphased Genetic Data from Poor-quality DNA Samples

Inferring relatedness through the detection of identity-by-descent (IBD) segments is widely used in many fields. However, existing methods are often powerless for poor-quality DNA samples. Here, we propose a method, clusIBD, which can robustly detect IBD segments using unphased genetic data with high genotype errors. We evaluated and compared the performance of clusIBD with IBIS, TRUFFLE, and IBDseq using simulated data, artificial poor-quality materials and ancient DNA samples. The results showed that clusIBD outperformed these state-of-the-art existing tools and may be a promising tool for kinship inference in fields such as ancient DNA analysis and criminal investigation (freely available at https://github.com/Ryan620/clusIBD/).

genetics↗

bioRxiv2025

Chimeric Collagen-like Proteins with Tunable Structural Heterogeneity for Precise Control and Targeted Doxorubicin Delivery

Protein-based drug delivery systems offer advantages such as genetic tunability, structural homogeneity, and high biocompatibility. However, precisely controlling the assembly of protein nanoparticles and establishing correlations between their macroscopic properties and molecular architecture remain significant challenges. Here, inspired by chimeric collagen-like proteins, we rationally designed a series of de novo chimeric proteins comprising an N-terminal globular domain fused to a linear collagen-like domain. These structurally heterogeneous proteins were conjugated with doxorubicin (DOX) and homogenized to form chimeric collagen-like protein-DOX nanocomplexes (CDCNs). By fine-tuning the protein structure and domain organization, we achieved precise control over CDCN architecture and drug release kinetics. Furthermore, to enhance tumor specificity, triple-negative breast cancer (TNBC)- and glioblastoma (GBM)-targeting peptides were genetically fused to the chimeric proteins, respectively. In both in vitro and in vivo models of TNBC and GBM, CDCNs facilitated selective tumor accumulation, enhanced cellular uptake, and promoted apoptosis while minimizing off-target toxicity. This work establishes a strategy for designing protein-based nanoplatforms with programmable structures and tunable functionalities, offering promising potential for precisely controlling of protein-based delivery system.

bioengineering↗

bioRxiv2025

A piece of evidence for pathogenesis of cerebral small vessel disease caused by blood-brain barrier dysfunction

BackgroundBlood-brain barrier (BBB) dysfunction caused by endothelial cell injury is one of the widely accepted pathogenesis of small cerebral vessel disease (CSVD). However, the early microcirculation studies were notably deficient in providing compelling imaging evidence, which has hampered a comprehensive understanding of the pathophysiological processes underlying BBB dysfunction in CSVD. The onset of CSVD is insidious and the clinical manifestations are diverse, diagnosis of CSVD relies primarily on neuroimaging information currently. These MRI imaging features mainly represent the end-stage brain parenchyma injury, rather than the vascular lesion itself. Therefore, clarifying the pathophysiological processes related to cerebral microcirculation in CSVD is of great significance for early treatment intervention of CSVD. MethodsTwenty rats were used to prepare CSVD animal model by ultrasound combined with ultrasonic microbubble contrast agent. MRI, functional ultrasound (fUS) imaging and ultrasound localization microscopy (ULM) were used to evaluate microcirculation changes in acute and chronic models. ResultsCurrently, our research has successfully validated that the imaging characteristics of this model align with the four established criteria outlined in the STRIVE-2 classification. FUS shows increased microflow velocity in the molding area, which can be used for initial evaluation of CSVD models in the acute phase. ULM has revealed a progressive reduction in the density of both the short cortical arteries and the long medullary arteries, along with their respective branches, over time. Concurrently, there has been a noted deviation in blood flow velocity. ConclusionThis model offers compelling evidence at the microvascular level, suggesting that blood-brain barrier (BBB) dysfunction is a central pathophysiological mechanism in the etiology of CSVD. Then it provides a straightforward, efficient, and widely applicable tool and continuous monitoring method for the further investigation of CSVD from the macroscopic to the microscopic circulation level, with significant long-term implications for CSVD diagnosis and treatment.

neuroscience↗

bioRxiv2025

Biological function and mechanism of flpL gene in regulating pathogenicity of Aeromonas hydrophila

Aeromonas hydrophila is human-animal commensal bacterium that seriously threatens the development of aquaculture and human health. Type IV pili (T4P) are essential for bacterial physiological function. The relationship between the molecular mechanism of flpL gene affiliated to T4P and the pathogenicity is still unclear. In the research, A. hydrophila with a genetically stable deletion of flpL gene ({Delta}flpL) was constructed. The median lethal dose of {Delta}flpL for Crucian carp was 4.87 times higher compared to wild-type strain, suggesting that {Delta}flpL significantly reduced pathogenicity. The attenuation may be attributed to a reduced capacity for biofilm formation and downregulation of the expression levels of virulence-related genes in {Delta}flpL. Meanwhile, the significant increase in swimming capacity and adhesion can be related to the upregulation of flpC, tapM, tapB and tapP genes. In conclusion, flpL gene plays essential role in the pathogenicity, adhesion, motility, and capacity for biofilm formation in A. hydrophila. The research aims to clarify the pathogenesis of A. hydrophila, and lay the foundation for developing live attenuated vaccines through the targeted modification flpL gene.

microbiology↗

bioRxiv2025

A versatile miniature two-photon microscope enabling multicolor deep-brain imaging

Here we present the FHIRM-TPM 3.0, a 2.6 g miniature two-photon microscope capable of multicolor deep-brain imaging in freely behaving mice. The system was integrated with a broadband anti-resonant hollow-core fiber featuring low transmission loss, minimal dispersion from 700-1060 nm, and high tolerance of laser power. By correcting chromatic and spherical aberrations and optimizing the fluorescence collection aperture, we achieved cortical neuronal imaging at depths exceeding 820 m and, using a GRIN lens, hippocampal Ca2+ imaging at single dendritic spine resolution. Moreover, we engineered three interchangeable parfocal objectives, allowing for a tenfold scalable field-of-view up to 1x0.8 mm{superscript 2}, with lateral resolutions ranging from 0.68 to 1.46 m. By multicolor imaging at excitation wavelengths of 780 nm, 920 nm and 1030 nm, we investigated mitochondrial and cytosolic Ca2+ activities relative to the deposition of amyloid plaques in the cortex of awake APP/PS1 transgenic mice. Thus, the FHIRM-TPM 3.0 provides a versatile imaging system suitable for diverse brain imaging scenarios.

neuroscience↗

bioRxiv2025

Neural circuits between nodose ganglion and pulmonary neuroendocrine cells regulate lung inflammatory responses

The lungs are organs exposed to the external environment, and the air we inhale contains various pathogens, such as endotoxins. The vagus nerve, which innervates the lungs, may play a role in detecting pathogens that invade the lungs. Through transcriptome analysis, tissue clearance imaging, electrical excitability recording, and gene- and cell-specific knockout experiments, we found that vagus nerve endings innervate pulmonary neuroendocrine cells (PNECs). These nerve endings sense bacterial endotoxins via pain receptors (TRPA1) rather than toll-like receptors (TLR4), eliciting electrical excitation and enhancing the production of neuropeptides (CGRP) in the nodose ganglia. In turn, CGRP released by sensory neurons from the nodose ganglia promotes both neuropeptide production and the proliferation of PNECs, thereby amplifying endotoxin-induced lung inflammatory responses. This reveals that the neural circuits between the nodose ganglion and PNECs play a critical role in regulating lung inflammatory responses.

neuroscience↗

bioRxiv2024

Synergy and antagonism in a genome-scale model of metabolic hijacking by bacteriophage

Bacteriophage auxiliary metabolic genes (AMGs) alter host metabolism by hijacking reactions. Previous studies used functional annotations to infer AMG impacts but neglected propagation effects on global metabolism and phage production. We demonstrate the first integration of AMGs and phage assembly into a genome-scale metabolic model, using a general method applied to the infection of Prochloroccocus marinus MED4 by P-HM2. We experimentally validate our approach to predicting AMG impact on growth using cp12 mutations in Syne-chococcus elongatus. We predict that 17 directly hijacked reactions substantially impact over 30% of the metabolism, including carbon fixation, photosynthesis, and nucleotide synthesis. We find that indirect impacts are synergistically and antagonistically coupled and are either phage-aligned--shifting feasible reaction velocities in accordance with maximal phage production--or phage-antialigned. Pareto optimization reveals that phage-aligned reactions limit host growth, while phage-antialigned reactions do not. We provide systems-level insight into AMG perturbations, highlighting how nontrivial cascading effects shape microbial functions.

systems biology↗