Biology subjects

Wu, G.

Publications and source records attributed to Wu, G..

At least 19 recordsLinked to original sources

bioRxiv2026

BiNVaST: niche boundary-preserving and synthetic data-guided variational autoencoders for concordant inference across high-resolution spatial transcriptomic platforms

High-resolution spatial transcriptomics (ST) enables subcellular spatially resolved transcript profiling but remains difficult to annotate in complex tissues because of gene coverage and super sparseness in expression. These challenges are amplified in cancer research, where neoplastic cell states and rare immune cells in tumor microenvironment are often poorly captured by generic references and/or cell typing tools exclusively built on molecular profile. Here, we present BiNVaST, a niche boundary-preserving and dual-branch variational autoencoder fused with statistical simulator for reliable cell typing across multiple spatial platforms. It generates platform-adjusted in silico training data by integrating query spatial profile and user-defined pre-annotated single-cell reference through Singular Value Decomposition and Optimal Transport, combining molecular similarity and spatial proximity to predict segmented cell labels. BiNVaST was benchmarked against existing methods across Xenium, CosMx, Stereo-seq, Visium HD platforms using six specimens from four tissue types. This tool is sensitive in detecting divergent tumor cell states and improves the cross-platform concordance, distinguishing disease-specific neoplastic and non-neoplastic cellular subpopulations and supporting robust cellular or niche inferences in heterogeneous tissues.

bioinformatics↗

bioRxiv2026

Low-Density Lipoprotein Cholesterol and Cerebral Pericyte Dysfunction in Acute Ischemic Stroke: Clinical and Experimental Evidence

Background: Low-density lipoprotein cholesterol (LDL-C) is an established risk factor for atherosclerotic cerebrovascular disease, but its effects on the cerebral microcirculation are poorly defined. We investigated whether LDL-C is associated with pericyte dysfunction in acute ischemic stroke (AIS) and explored underlying mechanisms. Methods: Serum soluble platelet-derived growth factor receptor-{beta} (sPDGFR{beta}) was measured in two independent AIS cohorts (n=97 and n=86). Cerebral pericyte transcriptional responses to LDL-C were analyzed by single-cell RNA sequencing in Apoe-knockout mice fed control or high-fat diet (n=4 [male/female: 2/2]/group), and cultured human brain pericytes were exposed to purified human LDL cholesterol with or without N-acetyl-L-cysteine. Results: Higher serum sPDGFR{beta} was associated with greater neurological deficit and circulating neurofilament light chain. LDL-C positively correlated with sPDGFR{beta} in both clinical cohorts. High-fat diet induced coordinated suppression of type-I interferon pathways, and a positive shift in reactive oxygen species-related transcriptional programs in mouse pericytes; exploratory sex-by-diet analyses suggested larger transcriptional responses in females. In cultured human pericytes, LDL-C induced oxidative-stress, lipid-handling, and ferroptosis-associated transcriptional programs while suppressing type-I interferon signaling. Cross-species enrichment analysis showed that LDL-C-induced and -repressed signatures in cultured pericytes aligned with the sex-by-diet interaction in Apoe-knockout mice. LDL-C also reduced cell-surface PDGFR{beta} and increased sPDGFR{beta} release in cultured pericytes, which were significantly attenuated by N-acetyl-L-cysteine, whereas LDH activity increased numerically but not significantly. Conclusions: Clinical and experimental findings support an LDL-pericyte axis linking atherogenic lipid stress to cerebral microvascular dysfunction, with possible sex-dependent modulation of oxidative stress and type-I interferon signaling as potential mechanisms.

neuroscience↗

bioRxiv2026

MetExPred: A Comprehensive Prediction Framework with Protein-Context-Aware Multi-view Learning for Drug Metabolism and Excretion

Within the ADMET continuum, metabolism and excretion (ME) form a critical bridge between drug exposure established by absorption and distribution and downstream efficacy and toxicity. However, no existing framework for drug ME prediction has simultaneously achieved broad coverage of endpoints and robust data recency and completeness. Here, we developed MetExPred, a multi-view prediction framework that comprises 17 classification endpoints and two regression endpoints, covering the overall drug ME process. The framework combines sequence-based and graph-based molecular representations, while optionally incorporating ESM-2 protein representations when experimentally annotated targets are available. A protein-aware masking strategy enables the same architecture to operate in both molecular-only and target-enhanced settings, and multi-view attention adaptively integrates the available representations. Across the classification tasks, MetExPred achieved mean AUROC, AUPRC and F1 scores of 0.844, 0.734 and 0.697, respectively. For clearance and half-life prediction, the model achieved RMSE values of 0.686 and 0.668. MetExPred showed the strongest average performance among the evaluated baselines, while ablation studies confirmed the complementary contributions of molecular sequence, graph and protein information. These results provide a unified and flexible modeling framework for systematic ME prediction of drug compounds, enabling early-stage virtual screening and pharmacokinetic assessment during lead optimization.

bioinformatics↗

bioRxiv2026

Protein hunger-driven nitrogen flow from phospholipids to amino acids inDrosophila

Protein is unique among macronutrients due to its nitrogen content and that its building blocks, essential amino acids, cannot be synthesized by animals. Additionally, animals lack specialized amino acid storage sites, necessitating a continuous dietary intake. In the face of insufficient dietary protein, how do animals manage nitrogen limitation? Using Drosophila, we reveal a previously undocumented nitrogen flow from phospholipids to amino acids, a process enhanced by protein deprivation. Protein restriction triggers the degradation of phosphatidylethanolamine (PE), releasing the nitrogen-containing headgroup, ethanolamine, which subsequently serves a dual function. Ethanolamine stimulates protein intake by activating protein hunger neurons and, remarkably, along with phosphoethanolamine, donates nitrogen for amino acid biosynthesis. This nitrogen transfer is mediated by the microbiome and ethanolamine-phosphate phospho-lyase (ETNPPL) pathway in fly cells. Together, our findings identify phospholipids as a hidden nitrogen reservoir and reveal an unrecognized metabolic plasticity that reallocates nitrogen to maintain protein homeostasis.

physiology↗

bioRxiv2026

Programmable Self-Assembly of RNA Nanostructures with >100 Unique Components

Sophisticated biomolecular functions often arise from large, precisely organized architectures, motivating efforts to construct increasingly complex structures through programmed nucleic acid self-assembly. Although RNA offers a richer repertoire of structural motifs and biological functions than DNA, RNA nanostructures constructed to date have remained substantially less complex and less scalable than their DNA counterparts, most notably DNA origami and DNA bricks, which rely on large libraries of synthetic single-stranded (ss) DNA strands. Directly adapting these strategies to RNA, however, faces two major barriers: (i) the high cost of producing large libraries of distinct synthetic ssRNA strands, and (ii) the limited stability of ssRNA under conditions commonly used for assembling multicomponent nucleic acid nanostructures. Here we present the double-stranded RNA (dsRNA) bricks approach, which addresses both barriers by adopting principles inspired by natural RNA systems: (i) many distinct RNA components ("bricks") are encoded within a single precursor transcript and released by enzymatic processing, (ii) each brick's predominantly double-stranded nature enhances stability. The resulting dsRNA bricks self-assemble through programmable branched kissing-loop interactions. Using this approach, we constructed complex two- and three-dimensional RNA nanostructures with more than 100 distinct components, representing, to our knowledge, the largest and most compositionally complex RNA nanoarchitectures reported to date. Overall, the dsRNA bricks approach establishes a scalable and robust framework for constructing complex RNA nanostructures with compositional and architectural sophistication approaching that of DNA-based systems, thereby opening new opportunities for programmable RNA materials and RNA-based devices.

synthetic biology↗

bioRxiv2026

A cross-modal generative model for incomplete and degradedprostate MRI with multicentre clinical validation

Missing or degraded sequences can limit prostate multiparametric MRI. We developed MSCNet, a sequence-conditioned cross-modal generative framework for reconstructing unavailable contrasts and restoring degraded acquisitions. Across ten completion tasks, task-specific MSCNet achieved mean structural similarity of 0.818 versus 0.798 for the strongest task-matched comparators; matched-capacity analyses showed larger differences in lesion fidelity and boundary preservation. In a blinded 1,000-case reader study, overall image quality met the prespecified non-inferiority criterion for DWI, ADC and T2W completion, but not T1W. In a separate 200-case diagnostic assessment, AUCs for clinically significant cancer were 0.860 with acquired images, 0.841 with MSCNet and 0.797 with baseline-generated images. A locked 186-case three-hospital cohort supported multicentre transportability. These retrospective results support quality-controlled cross-modal reconstruction as an adjunct to acquired prostate MRI.

bioengineering↗

bioRxiv2026

Circadian clock regulates intestinal epithelial cell differentiation via NOTCH/Hes1 oscillations

The circadian clock regulates diverse cellular processes, including intestinal epithelial cell (IEC) proliferation. However, mechanisms regulating clock-dependent IEC differentiation remain unknown. We performed a time course RNA-Seq using the mouse small intestine and identified NOTCH signaling, a key mechanism regulating IEC differentiation, as one of the pathways under the control of circadian rhythms. Using mouse enteroids, we discovered that a NOTCH reporter, Hes1-luciferase, exhibits both ultradian or circadian oscillations depending on the stemness of mouse enteroids. Furthermore, single-cell analysis of Hes1-mCherry revealed that the period of Hes1 oscillations varies widely, but circadian rhythms modulate the number of Hes1-mCherry+ cells in the population. Finally, we show that Paneth cell numbers fluctuate over the circadian cycle, suggesting that circadian clock-regulated Hes1 drives the circadian dynamics of IEC composition. Our study provides a deeper insight into circadian regulation of IEC differentiation, which will be critical for applications of chronotherapies for digestive diseases.

molecular biology↗

bioRxiv2026

Impaired synthesis of both telomere strands and adaptive TERT reduction in RTEL1 ATPase-dead cells

Regulator of Telomere Elongation Helicase 1 (RTEL1) plays a critical role in telomere replication by disassembling DNA secondary structures such as G-quadruplexes and telomeric loops (T-loops). However, its precise mechanism remains unclear. Previously, we generated HeLa cells homozygous for ATPase-dead RTEL1. Here, we found that these cells have a 50-60% reduction in the synthesis of both telomere strands, indicating that RTEL1 ATPase activity is essential for both leading-strand and lagging-strand synthesis. Surprisingly, these cells also showed a substantial reduction in Telomerase Reverse Transcriptase (TERT) mRNA levels and a 60-80% reduction in telomerase activity, without activating alternative lengthening of telomeres (ALT). Forced TERT overexpression suppressed proliferation and caused late S/G2 accumulation, implying that the natural TERT reduction provides adaptive resistance. Expressing wild-type (WT) RTEL1 at levels close to physiological levels failed to rescue growth defects, suggesting a dominant-negative effect. These results reveal unexpected interactions between RTEL1 and telomerase and show how cancer cells compensate for RTEL1 dysfunction by decreasing TERT expression.

cell biology↗

bioRxiv2026

Health-associated gut bacteriocins target TLR4 to suppress intestinal inflammation

The human microbiome maintains host immune homeostasis by secreting bioactive metabolites. However, extending beyond well-characterized metabolites, the functions of most microbiome-encoded peptides remain poorly defined. In this study, we developed a multi-cohort metagenomic framework to profile protective class II bacteriocins--unmodified, ribosomally synthesized peptides--that are enriched in healthy individuals but depleted in patients with inflammatory bowel disease (IBD). We have designated these health-associated bacteriocins as gutcins. Two gutcins, which lack canonical antimicrobial activity, potently attenuate intestinal inflammation in murine models. Cryo-electron microscopy (cryo-EM) reveals that one gutcin, named gutcin 03, directly engages the C-terminus of TLR4, blocking its dimerization and downstream inflammatory signaling. Guided by this structural interface, we generated truncated variants with enhanced potency, demonstrating the amenability of these simple peptides to rational optimization. Collectively, our findings reposition class II bacteriocins from antimicrobial agents to endogenous immunomodulatory effectors and establish a structural and mechanistic foundation for their development as next-generation therapeutics for inflammatory intestinal disorders.

microbiology↗

bioRxiv2026

Chemokine-Dependent Natural Killer Cells Prevent Pulmonary Metastasis in a Newly Established Mouse Osteosarcoma Model

Rampant genomic instability of osteosarcoma (OS) and associated inter- and intratumoral heterogeneity convey a high risk of metastasis despite contemporary multimodal therapy. A mouse primary OS tumor model, originating from Myc-overexpressing Trp53-null mesenchymal progenitor cells, closely mimics cardinal genetic features and gene expression patterns of human OS samples. Subcutaneous injection of OS cells into immunocompromised NSG mice produced extensive metastases, whereas many fewer metastases occurred in T cell-deficient nude mice, suggesting a principal role for innate immunity in controlling OS dissemination. Depletion of natural killer (NK) cells in nude mice facilitated OS metastasis. OS cells released a suite of chemokines, with CCL2 the most prominent. A genome-wide CRISPR/Cas9 screen in OS cells identified 11 genes, including Ccl2, whose loss facilitated pulmonary metastasis in nude mice. Disruption of CCL2 in OS cells partially phenocopied the effects of antibody-dependent NK cell depletion, underscoring a plausible OS-NK signaling pathway that limits OS metastasis. SignificanceOsteosarcoma exhibits complex genomic instability and a propensity for pulmonary metastasis that limit chemotherapeutic response and patient survival. Despite the plethora of heterogeneous genetic alterations that connote poor prognosis, a novel preclinical in vivo model for studying metastasis highlights potentially targetable signaling between osteosarcoma cell-derived chemokines and pulmonary NK cells.

cancer biology↗

bioRxiv2026

Circadian misalignment underlies immune escape in breast cancer

Circadian regulation shapes tissue physiology, yet how it organizes cellular and molecular dynamics within the tumor microenvironment (TME) and influences tumor immunity remains unclear. Using temporal single-nucleus multiomic profiling of mouse breast tumors, we uncovered extensive circadian programs that are both cell-type-specific and shared across the TME, governing proliferation and immune responses. Notably, cancer epithelial cells exhibited global acrophase misalignment relative to immune populations. This intercellular desynchrony manifests as temporal decoupling between tumor proliferation and immune activation, discordant antigen presentation and T cell recognition with intrinsic activation-exhaustion overlap in T cells, and asynchronous PD-1/PD-L1 oscillations that sustain checkpoint-mediated suppression. Similar patterns were observed in human triple-negative breast cancer (TNBC). Together, these findings establish intercellular circadian misalignment as a mechanism of tumor immune evasion and position the circadian architecture of the tumor-immune ecosystem as a previously underappreciated determinant of tumor development and therapeutic response. HIGHLIGHTSO_LISingle-cell multiomics maps circadian regulation of tumor-immune programs. C_LIO_LICircadian regulation in cancer epithelial cells is misaligned with immune cell populations. C_LIO_LITumor-immune temporal misalignment undermines antitumor immunity. C_LIO_LICircadian misalignment in human TNBC suggests relevance for immunotherapy timing. C_LI

cancer biology↗

bioRxiv2026

Alternative organelle targeting of OPA1 mediates fatty acid release from lipid droplets

Mitochondria and lipid droplets (LDs) are functionally coupled to coordinate fatty acid utilization and storage. However, a comprehensive understanding of mitochondria-LD alliances remains elusive. We have identified a previously unrecognized role for optical atrophy 1 (OPA1), a mitochondrial fusion factor, in the regulation of fatty acid release from LDs. We demonstrated that OPA1s exon 4 adapts an amphipathic helix to target OPA1 to LDs. OPA1 localized to LDs promote fatty acid release by facilitating the recruitment of lipases to LDs. In addition, OPA1s residence on LDs competes with its mitochondrial entry, influencing mitochondria fusion and connectivity. Furthermore, the S158N polymorphism within OPA1s exon 4 exhibiting attenuated fatty acid release from LDs is associated with changes in metabolic traits in pediatric cancer survivors. Altogether, our findings reveal that OPA1 actively mediates fatty acid release from LDs and provide a mechanistic link between OPA1 and human metabolism.

cell biology↗

bioRxiv2026

Cell fusion reprograms tumor cells and promotes RUNX1-mediated invasion and dissemination in colorectal cancer

Metastasis remains the primary cause of cancer-related morbidity and mortality, despite significant advances in targeted therapies. Although metastatic dissemination requires tumor cells to escape the primary lesion and colonize distant organs, the mechanisms by which primary tumor cells gain metastatic competence remain poorly understood. Increasing evidence demonstrates that fusion of tumor (i.e., neoplastic) and immune (e.g., macrophages) cells generate a distinct population of tumor-immune hybrid cells with enhanced functional ability to migrate and disseminate into peripheral blood. Herein, our study investigates tumor-macrophage hybrid cells, an underexplored population of disseminated tumor cells, and their inherent heterogeneity and acquisition of molecular mechanisms underlying their dissemination as metastatic effectors in colorectal cancer (CRC). Through hybrid cell phenotyping utilizing integrative single-cell RNA sequencing (scRNA-seq), cyclic immunofluorescence (cyCIF) and functional assays with an in vitro model of CRC hybrid cells, we identify Runt-related transcription factor 1 (Runx1) as a central regulator of hybrid cell motility and invasion. Runx1 depletion in hybrid cells suppressed functional protease expression, chemotactic activity and extracellular matrix (ECM) invasion. Furthermore, pharmacologic inhibition of RUNX1 in an in vivo model reduced hybrid tumor growth and dissemination into peripheral blood, key attributes of metastatic spread of disease. In patients with CRC, RUNX1+ hybrid cells were identified in both primary tumor and peripheral blood, where circulating hybrid cells (CHCs) exhibited enriched migratory and epithelial-to-mesenchymal transition (EMT) phenotypes. Taken together, these findings reveal a mechanistic role for RUNX1 in driving invasive behavior of tumor-immune hybrids and highlight disseminated CHCs as an under-recognized contributor to metastatic spread and a promising noninvasive biomarker for tumor progression.

cancer biology↗

bioRxiv2026

CellPheno: A High-throughput Computational Platform for Quantifying Cellular Resolution Whole Brain Microscopy Images

Advances in tissue clearing and light-sheet microscopy enable cellular resolution whole-brain 3D imaging. However, whole-brain quantification tools do not yet meet demands for efficiency or assess morphometry. Here we present CellPheno, a 3D nuclei instance segmentation framework for high-throughput cellular phenotyping. CellPheno quantifies an entire P4 mouse brain within 15 hours. We showcase whole-brain morphometry, enhanced stitching, and co-localization across multiple cell types in 53 brains.

neuroscience↗

bioRxiv2026

Chd8 haploinsufficiency leads to molecular layer heterotopias and age-dependent cortical expansion

Mutations in the chromatin remodeler CHD8 are associated with autism and macrocephaly. While mouse models of Chd8 haploinsufficiency recapitulate brain overgrowth, the specific cellular mechanisms and developmental timing that lead to these anatomical abnormalities remain poorly understood. Here, we conducted 3D imaging of Chd8V986*/+ mouse brains using magnetic resonance imaging followed by tissue clearing and cellular resolution light-sheet microscopy across embryonic and postnatal developmental stages. We found that brain overgrowth occurs postnatally, driven by an increase in non-neuronal cells prior to volumetric expansion. Unexpectedly, we identified prevalent molecular layer heterotopias (MLH) within the frontal cortex of Chd8V986*/+ mice composed of neurons breaking through the pial surface during embryonic development and persisting throughout life. Increased incidence of MLH, previously identified in individuals with idiopathic autism, was replicated across three independent Chd8+/- mouse models and present across multiple genomic backgrounds, establishing aberrant neuronal migration as a core feature of Chd8 haploinsufficiency.

neuroscience↗

bioRxiv2026

Orion Microbiome Database: mapping constellations in the microbiome universe

BackgroundPublicly available microbiome sequencing data have grown rapidly in scale and diversity, but secondary use remains limited by fragmentation across repositories, inconsistent annotations, heterogeneous processing pipelines, and incomplete metadata. These barriers complicate cross-study comparisons and restrict the reproducibility of large-scale microbiome research. ObjectiveThe Orion Microbiome Database was developed to overcome these challenges by providing a standardized, accessible, and reproducible resource for the integration and analysis of whole-genome shotgun (WGS) microbiome datasets. MethodsOrion aggregates raw metagenomic datasets from public repositories and harmonizes them into computed microbial profiles using automated and transparent analysis pipelines. Metadata are curated to ensure consistency and enable systematic cross-cohort comparisons. The platform provides interactive tools for data exploration, visualization, and downstream analysis, reducing redundancies in data preprocessing and lowering the barrier for both novice and expert users. Beyond research applications, Orion also serves as an educational resource, enabling microbiome data exploration in classroom settings. ConclusionBy unifying fragmented sequencing resources into a reproducible framework, Orion accelerates microbiome discovery, supports scalable cross-study investigations, and fosters integration of microbiome science into teaching and training. This database has the potential to serve as a model for future large-scale, community-driven platforms in microbiome research.

microbiology↗

bioRxiv2026

Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

The conserved multifunctional chromatin modulator and oncogene DEK exhibits context-dependent genomic binding and function, but how these activities are regulated in cancer remains poorly understood. Using multi-omics and biochemical approaches, we find that while DEK predominantly occupies promoter-proximal regions in HeLa cells and primary melanocytes, its chromatin binding is dramatically reduced in melanoma cell lines--despite DEK overexpression. We attributed this to CK2-mediated phosphorylation, which governs DEK chromatin association and transcriptional output in a cell-type-specific manner. Phosphoproteomics identified 34 phosphorylation sites, including S287 and S288 within the DEK C-terminal DNA-binding domain. Strikingly, CK2 inhibition and concomitant loss of phosphorylation at S287/S288 triggered DEK redistribution to promoter regions, coinciding with transcriptional repression of oncogenic pathways and global chromatin compaction. Melanoma subtypes showed divergent responses: NRAS-mutant cells displayed dynamic, phosphorylation-dependent DEK redistribution, whereas BRAF-mutant cells lacked detectable DEK binding. Our work establishes DEK as a phosphorylation-sensitive regulator of chromatin states, with CK2-mediated modification orchestrating its tumor-specific regulatory functions. These findings nominate phospho-DEK as a potential biomarker and therapeutic target in melanoma and possibly other cancers.

biochemistry↗

bioRxiv2026

Asymmetric Division in a Two-Cell-Like State Rejuvenates Embryonic Stem Cells

A fundamental question in biology is whether cellular aging is inevitable. Embryonic stem cells (ESCs) challenge this paradigm as rare normal cells capable of indefinite in vitro passage. However, the mechanisms underlying ESC lineage immortality remain unresolved. Using long-term live-cell imaging to follow fates of single ESCs, we show here that ESC lineage renewal is achieved through sporadic entry into a state characterized by the expression of two-cell embryo-specific markers. During this state, cells undergo asymmetric divisions, segregating accumulated DNA damage into one daughter lineage destined for elimination, while producing a second lineage that reverts to the pluripotent state. Importantly, the latter lineage exhibits signs of rejuvenation, including reduced DNA damage and enhanced chimeric efficiency. These findings underscore the crucial role of asymmetric cell division in maintaining the long-term health of the ESC lineage against mounting damage within individual cells, a potential model for studying cellular aging and rejuvenation in mammalian cells.

cell biology↗