Biology subjects

Cheng, J.

Publications and source records attributed to Cheng, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Glioblastoma Hijacks Astrocyte Ribosomes to Feul Malignancy through Translatome Reprogramming

Cancer cells demand elevated protein synthesis, yet whether they directly requisition ribosomes from microenvironmental host cells remains unknown. Here, utilizing in vivo and in vitro ribosome tracing, we show that glioblastoma (GBM) cells hijack ribosomes from surrounding astrocytes via tunneling nanotube-like structures. This transfer supports GBM malignancy in both murine and patient derived models. Single cell RNA sequencing along with whole cell and cell source traceable ribosome profiling reveal that transferred ribosomes are translationally active and selectively reprogram the tumor translatome, prioritizing cell-cycle genes and driving interferon-response-mediated immune evasion. Through a genome wide CRISPR screen, we identify INTS12 as a critical mediator of ribosome transfer. Genetic inactivation or AAV-mediated knockdown of INTS12 impairs ribosome uptake, curbs translation and proliferation, remodels the immunosuppressive landscape, and extends survival in orthotopic models. Our study uncovers a parasitic translation-support mechanism in GBM, establishing INTS12 as a therapeutic vulnerability to disrupt ribosome transfer.

cancer biology↗

bioRxiv2026

Human brain white matter charts in international populations

Brain charts provide normative references for identifying neurodevelopmental milestones and clinically meaningful deviations. Existing white matter (WM) charts are derived predominantly from European and North American populations, limiting generalizability. Here, we established the first set of population-specific WM charts of 198 morphological and microstructural phenotypes for both Chinese (N=19,215) and Western (N=15,584) populations across the human lifespan. Developmental trajectories and spatial organization of WM maturation and degeneration were broadly conserved across the populations, whereas maturational timing varied across pathways and metrics. The Chinese population showed earlier maturation in several projection and sensorimotor pathways, but more protracted maturation in higher-order association and limbic pathways. Chinese population-matched charts more accurately predicted WM phenotypes and detected more extreme disease-related deviations in brain health in the Chinese population than Western-derived models. Individual deviation patterns further discriminated patients from healthy controls and predicted cognitive performance and plasma biomarkers. Our findings reveal population-specific WM maturation and show that reference-population mismatch can reduce the accuracy and clinical sensitivity of normative brain charts.

neuroscience↗

bioRxiv2026

Three-hinge gyri link individualized folding topology to cortical and superficial white-matter diffusion organization

Individual differences in cortical folding are a hallmark of human brain anatomy, but what this variability reflects in the underlying tissue remains unclear. Three-hinge gyri (3HGs), where three gyral crests converge, provide an individualized higher-order folding landmark for probing this relationship. Using 7T diffusion MRI in six postmortem hemispheres, we found lower mean, axial, and radial diffusivity and higher fractional anisotropy at 3HGs than at matched gyral crowns, with the principal tensor pattern replicated in 414 age-matched in vivo adults. Diffusivity differences extended across the cortical ribbon, whereas anisotropy- and fiber-related differences strengthened toward and beneath the white surface. Ex vivo, diffusion measures also varied with gyral-skeleton degree, and streamlines sampled beneath 3HGs preferentially reached other 3HGs. These findings link individualized folding topology to cortical and superficial white-matter diffusion-inferred tissue properties, providing tissue-level context for understanding the microstructural correlates of individual folding variation.

neuroscience↗

bioRxiv2026

Design, Amino-Acid-Derived Analogues of FTY-720 and OSU-2S as PP2A Activators: Structure-Activity Relationships and Identification of Lead Compound XML-3D

Protein phosphatase 2A (PP2A) is a critical regulator of oncogenic signaling pathways, and pharmacological reactivation of PP2A through disruption of inhibitory protein interactions has emerged as a promising anticancer strategy. Although the sphingosine analogue FTY-720 and its derivative OSU-2S can restore PP2A activity, further structural diversification is needed to improve potency and expand structure-activity understanding. Here, we report the design, synthesis, and biological evaluation of three series of amino-acid-derived analogues incorporating tyrosine, homotyrosine, and tryptophan scaffolds. Docking models were used qualitatively to guide exploration of head-group functionality, hydrophobic tail variation, and stereochemical configuration; these models were hypothesis-generating and were not experimentally validated. Modular synthetic routes enabled efficient preparation of structurally diverse compounds from naturally occurring starting materials. Biological evaluation in leukemia and lymphoma cell lines revealed that hydrophobic tail length strongly influenced cytotoxic activity, while tryptophan-derived analogues were generally less potent than tyrosine-based scaffolds. Shortening the hydrophobic tail did not improve activity, contrary to the initial docking-based hypothesis. Stereochemical inversion at the amino alcohol head group yielded a lead compound, XML-3D, which demonstrated approximately two-fold enhanced cytotoxicity relative to FTY-720 and OSU-2S across leukemia cell lines (IC50 = 4.1, 1.8, and 1.5 uM in MV4-11, HL-60, and MEC-1 cells, respectively) and showed broader activity in mantle cell lymphoma lines (IC50 = 530 nM, 970 nM, and 110 nM in Jeko-1, Mino-1, and UPN1 cells). XML-3D induced increased PP2A phosphatase activity in cellular assays. Co-immunoprecipitation and pharmacological inhibition experiments were consistent with modulation of the PP2A/SET regulatory axis; however, direct binding measurements were not performed, and the mechanistic interpretation remains provisional. These findings suggest preliminary structure-activity relationships for amino-acid-derived PP2A modulators and identify stereochemical optimization as a productive direction for future development. Ongoing work aims to define molecular target engagement and refine mechanistic understanding to guide next-generation design.

molecular biology↗

bioRxiv2026

Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction

To address widespread data leakage and inconsistent evaluation in protein-ligand affinity prediction, we introduce PLABench, a leakage-controlled and target-centric benchmarking framework that enables standardized comparison across sequence- and structure-based models. We benchmark nine deep learning methods across blind CASP16 targets, leakage-controlled ChEMBL35 sets, and established Davis and KIBA datasets under rigorous data split settings, standardizing structural input via AlphaFold3 to ensure fair comparison. Although pretrained structure-based models achieve the highest overall accuracy, they show severe target-dependent variability, and increasing structural fidelity from predicted to experimental conformations yields no consistent gains. Meanwhile, sequence-based approaches surpass some structure-based methods on select targets, and protein family-level evaluations reveal uneven performance across families and substantial inter-model complementarity obscured by aggregate metrics. These findings demonstrate that training scale and structural input alone cannot guarantee cross-target generalization, highlighting the need for context-aware interaction modeling. PLABench provides an extensible open-source platform to facilitate these developments.

bioinformatics↗

bioRxiv2026

OPA1-dependent mitochondrial remodeling coordinates TCR signaling and metabolic adaptation during iNKT cell differentiation

Invariant natural killer T (iNKT) cells require mitochondrial metabolism for terminal effector development. We found iNKT cells express elevated levels of proteins regulating mitochondrial membrane dynamics, and identified Opa1, but not Drp1, as selectively required for iNKT cell differentiation. OPA1 deficiency disrupted mitochondrial cristae organization, reduced mitochondrial membrane potential, increased mitochondrial mass, and altered calcium homeostasis in iNKT cells. Bulk and single-cell transcriptomic analyses revealed impaired TCR-responsive gene expression, activation of mitochondrial stress adaptation and integrated stress response, enhanced glycolysis, and retention of immature differentiation features. SCENITH analysis demonstrated increased glycolytic dependence; LDHA became required in Opa1-deficient iNKT cells while dispensable for normal iNKT development, indicating compensatory glycolytic adaptation. EGTA in thymic organ culture partially restored NKT1 marker expression in Opa1-deficient cells. Co-deletion of Drp1 improved mitochondrial morphology, TCR signaling, stress and metabolic adaptation, and partially rescued iNKT cell differentiation, demonstrating that balanced mitochondrial dynamics coordinate mitochondrial function and terminal effector development.

immunology↗

bioRxiv2026

Division-Specific Organization of a Shared Functional Scaffold in the Early-Life Human Brain

Early cognition and behavior emerge from coordinated maturation of functional systems spanning the brain, making cross-division integration essential for defining whole-brain architecture and understanding its role in neurodevelopment. Yet early human functional development is still largely investigated through cortical networks or through isolated, coarsely resolved noncortical structures, leaving unclear how this integrated architecture is organized across the cerebral cortex, subcortex and cerebellum. Moving beyond structure-isolated and adult-derived maps, we create a reproducible, fine-grained Early-Life Whole-Brain Functional Parcellation (UNC-ELF) spanning birth to six years. Using this framework, we identify a shared functional scaffold expressed through distinct division-specific modes: differentiated and dual-polarity cortical organization, spatially graded cerebellar organization with blended functional transition zones, and nucleus-constrained subcortical mosaics of multi-system affiliation. Across early childhood, the scaffold is selectively refined through heterogeneous, nonlinear connectivity trajectories, with major inflections concentrated in infancy. Age-, sex- and prospective cognition-related variation is differentially encoded across distinct connectomic components. Together, these findings reframe early functional brain development as coordinated refinement of a shared but nonuniform whole-brain scaffold and establish UNC-ELF as a unified reference for resolving typical and atypical functional organization across the developing brain.

neuroscience↗

bioRxiv2026

TransBind2: Improving Transcription Factor-DNA Binding Prediction with Multimodal Data and Bidirectional Cross Attention

Accurate genome-wide prediction of transcription factor (TF)-DNA binding remains challenging because many models focus mainly on DNA sequence and overlook chromatin context and TF structure. We previously developed TransBind, a protein-aware model that combines TF and DNA representations through cross-attention. Here, we introduce TransBind2, which improves on TransBind in several ways. It incorporates DNase-seq accessibility and genome mappability tracks as additional input, uses a biomodal protein language model (ProstT5) to capture both TF sequence and structure, and applies bidirectional cross-attention so DNA and protein features can refine each other. We also frame prediction as binary classification of individual triplets, allowing the model to generalize to new TFs and cell types. Across 690 human ChIP-seq experiments covering 161 TFs and 91 cell types, TransBind2 achieves a macro AUROC of 0.9648 and AUPR of 0.4215, outperforming TransBind and other baselines, with a [≥]12.67% relative AUPR gain. The model trained on human data also performs well in cross-species zero-shot prediction on mouse data. Saliency analysis shows that it can identify TF-binding peaks with a median error of 12-38 base pairs (bps) despite being trained on window-level labels. Ablation studies further show that TF structure, chromatin accessibility, and bidirectional attention each improve performance. Overall, these results show that combining TF structure with chromatin context leads to more accurate and generalizable TF-DNA binding predictions.

bioinformatics↗

bioRxiv2026

Site-resolved spatial and structural interactome of a human cell

The spatial and structural arrangement of proteins determine virtually every process in human cells. We combined gentle subcellular fractionation by differential ultracentrifugation with cross-linking mass spectrometry to systematically map this cellular proteome architecture with residue-level evidence, identifying 164,146 residue-to-residue links in HEK293 cells. These links capture spatial protein arrangement at a resolution sufficient to pinpoint protein localizations at sub-organelle level, determine protein orientations within cellular membranes, and identify inter-organelle contact sites. The residue-level information provides evidence for 18,074 direct protein-protein interactions (PPIs), which we integrate into AlphaFold-based pipelines to nominate PPI-mediating short linear motifs and generate assembly models of large protein complexes. Guided by these spatial and structural readouts, we discover new PPIs within the endomembrane system that regulate the compartmental localization of trafficking machinery. Leveraging a network topology-driven strategy, we augment our HEK293 dataset with PPI data from different cell lines and methods, expanding the spatial and structural interactome of human cells.

systems biology↗

bioRxiv2026

Dynamic architecture of the Rixosome reveals mechanism of activation and ITS2 processing

Eukaryotic ribosome assembly requires the coordinated processing and extensive remodeling of pre-rRNAs. During late nuclear maturation of the 60S subunit, sequential removal of the internal transcribed spacer 2 (ITS2) is initiated by endonucleolytic cleavage at site C2 by the conserved Las1 nuclease. Las1 acts together with the kinase Grc3 and the Rix1 complex to form the Rixosome, which also functions in transcriptional regulation. However, the assembly of the Rixosome, its recruitment to pre-ribosomes, and its activation for ITS2 cleavage remain unclear. Here, we present cryo-EM structures of the human LAS1 complex, two structures of the isolated Rixosome and nine transition states of Rix1-bound pre-60S particles from Schizosaccharomyces pombe. These structures reveal a dynamic Rixosome architecture in which the heterotetrameric Las1 complex engages one or two copies of the Rix1 complex. Rix1 binding is highly flexible in the human Rixosome but rigid in the yeast complex. The isolated yeast Rixosome remains inactive, but binding to the pre-60S particle triggers a structural rearrangement that allows for substrate engagement and activation of the nuclease. Together, our results define the dynamic architecture of the Rixosome and provide a structural framework for ITS2 processing during nuclear maturation of the eukaryotic 60S ribosomal subunit.

biochemistry↗

bioRxiv2026

Single-Cell Profiling of Dynamic Epicardial Cell States During Myocardial Infarction

Background: The epicardium is reactivated after myocardial infarction (MI); however, the gene expression profiles of post-MI adult epicardial subpopulations remain incompletely defined. Methods: Single-cell RNA sequencing was performed on lineage-traced Wt1+ epicardial cells from Wt1CreERT2/+; R26tdT/+; PdgfranGFP/+ adult mice after sham surgery or at 7 and 14 days after permanent artery ligation to induce MI. Immunostaining was performed on Wt1-lineage-traced cardiac tissue to validate spatial expression after ischemic injury. Results: Unbiased clustering identified nine transcriptionally distinct epicardial populations, encompassing mesothelial, fibroblast/mesenchymal, transitional, and proliferative phenotypes. Fibroblast-like epicardial cells (Wt1+/Pdgfra+) showed time-dependent expression profiles associated with upregulation of epithelial-to-mesenchymal transition (EMT) and extracellular matrix (ECM) gene programs. At 7 days post-MI, there was notable enrichment of genes related to chemokines and Wnt components. By 14 days post-MI, the expression profile shifted toward immune regulation. In contrast, a Wt1high/Msln+ population showed minimal upregulation of EMT gene programs but enhanced paracrine signaling related to wound healing and semaphorins, suggesting reactivation of reparative and angiogenic functions akin to those of the epicardium during embryonic development. Immunostaining and in situ hybridization fluorescence analyses validated laminar epicardial cell placement after MI, comprising a surface Msln+ sheet, an overlapping Wt1-lineage band, and a subadjacent PDGFR+ and Periostin+ compartment that expands 7-14 days after MI and regresses by day 28 post-ischemia. Conclusions: Our data define epicardial gene programs in which a signaling epithelial cell surface overlays an effector mesenchymal cell stroma to coordinate angiogenesis, leukocyte recruitment, and ECM remodeling. This study presents the first integrated single-cell atlas of epicardial-derived cells across multiple post-ischemic timepoints, offering new insights into their reparative potential and dynamic signaling diversity in the injured adult heart.

molecular biology↗

bioRxiv2026

A statistical framework for disease classification with scRNA-Seq Data

Motivation Bulk RNA-sequencing based disease classification obscures cell-type specific signals by aggregating gene expression across heterogeneous tissues. Although single-cell RNA-seq tackles this limitation, summarizing and deriving patient-level predictors while retaining biological interpretability remains challenging. Standard sparse methods, such as lasso, often select arbitrary scattered gene sets without leveraging the underlying cell type structures revealed by single-cell data. Results: We introduce a two-stage statistical framework for interpretable patient-level disease classification from single-cell data. We first construct a gene-by-cell-type pseudobulk matrix that summarize single-cell expression for each patient. We then fit a multinomial logistic regression model with sparse group lasso penalty, inducing sparsity at both the cell type and gene levels. Across datasets of systemic lupus erythematosus, COVID-19, and colorectal cancer, our framework either matched or outperformed lasso and random forest baselines. Importantly, our models recovered biologically coherent, cell-type specific gene signatures consistent with known disease mechanisms, demonstrating improved interpretability without sacrificing predictive accuracy. Availability: The scSGL R package implementing the Sparse Group Lasso classification framework described in this paper is available at https://github.com/zhiweixiao/scSGL (version 0.99.1). Code to reproduce the actual cross-validation, model fitting, and prediction analyses on the three datasets reported here is available at https://github.com/zhiweixiao/scSGL-manuscript.

bioinformatics↗

bioRxiv2026

Extracellular vesicles drive cross-genus mycovirus transmission and suppress two fungal diseases

Mycoviruses are typically transmitted vertically through fungal reproduction or horizontally via hyphal anastomosis, but identical viruses in phylogenetically divergent fungi hint at unknown inter-species transmission mechanisms. Here, we identify fungal extracellular vesicles (EVs) as mediators of cross-genus mycovirus transmission. Using the hypovirulent Botrytis cinerea strain IBc-374 (harboring 16 mycoviruses) as a donor, we show that up to 13 mycoviruses are horizontally transmitted to Sclerotinia sclerotiorum during dual culture or plant co-inoculation, even though these two fungi belong to different genera and are generally considered incapable of hyphal anastomosis. Electron microscopy reveals abundant vesicle structures in IBc-374 hyphae, and nanoparticle tracking analysis showed that the strain secretes >11-fold more EVs than a virus-free strain. RT-PCR detects genomic RNAs of 7 mycoviruses in purified EVs, and the full-length viral genome in EVs was further validated with BcHV5 as example by fluorescence in situ hybridization and RT-PCR. Incubation of protoplast-derived germlings of S. sclerotiorum or B. cinerea with IBc-374 EVs leads to infection by 4-6 donor mycoviruses, demonstrating EV-mediated cross-genus transmission. Injection of mycovirus-carrying EVs into tobacco leaves followed by fungal inoculation also transmits two hypoviruses to both species. Application of IBc-374 hyphal fragment suspension significantly reduces lesion sizes caused by both pathogens on plants, and rescued two pathogens carrying multiple mycoviruses exhibit hypovirulence and impaired growth. Our findings reveal EVs as a cell-free vector that bypasses vegetative incompatibility, providing a mechanistic basis for cross-species viral spread and opening avenues for EV-based virus cocktails to control multiple fungal diseases. IN BRIEFWu et al. discover that fungal extracellular vesicles (EVs) can package and transmit multiple mycoviruses across genera from Botrytis cinerea to Sclerotinia sclerotiorum. EV-mediated delivery overcomes vegetative incompatibility barriers and reduces disease caused by both fungal pathogens, offering a cell-free strategy for mycovirus-based biological control.

microbiology↗

bioRxiv2026

SOLAR Mediates Lysosomal Membrane Repair and Redox Defense

Lysosomal damage is increasingly recognized as a hallmark of aging. Understanding lysosomal quality control may open new therapeutic strategies to enhance lysosomal resilience. Here, we identify SOLAR (SQSTM1/p62 Oligomer-mediated Lysosomal Antioxidant Defense And Membrane Repair), a lysosomal quality control pathway that links CASM (conjugation of ATG8 to single membranes) to p62-driven membrane repair and redox signaling. In this pathway, CASM, but not macroautophagy, recruited p62 to damaged lysosomes. Efficient lysosomal recruitment of p62 required its ATG8-binding and self-oligomerizing domains, enabling p62 assemblies to promote membrane repair. p62 mutations associated with neurodegeneration interfered with p62 recruitment and compromised lysosomal repair. Besides membrane repair, the SOLAR pathway also activated the p62-KEAP1-NRF2 redox signaling axis, driving transcriptional upregulation of antioxidative genes and cholesterol biosynthesis. By integrating membrane repair and redox defense, SOLAR establishes a coordinated lysosomal quality control pathway with implications for aging and degenerative disease.

cell biology↗

bioRxiv2026

Internalized Components of Membrane Attack Complexes Disrupt Proteostasis and Acquire Alarmin-Like Properties

Immune effects of membrane attack complexes (MAC) have been widely attributed to their abilities to cause cell death. Here, we show that the MAC component, C9, forms non-cytolytic aggregates with pro-inflammatory effects. Intracellular aggregates of C9 are detected within inflamed tissues of patients in association with endothelial cell (EC) activation but not increased cell death. We identify NUMBL as a Rab35 effector that directly binds surface-bound C9 to promote C9 internalization and entry into the endolysosomal pathway. Within acidified endolysosomes, C9 forms insoluble aggregates that are targeted for degradative aggrephagy in a process that activates NF-{kappa}B. For C9 aggrephagy to occur, ZFYVE21, a Rab5 effector, complexes with RNF34 to bridge C9 aggregates to LC3B+ aggresome membranes. We detect C9 aggregates in vivo, and we show that a ZFYVE21-RNF34 signaling axis is required for C9 aggrephagy and NF-{kappa}B -dependent EC activation in three separate mouse models. Mice with conditional loss of ZFYVE21 in ECs show reduced aggregraphy, resulting in attenuated systemic inflammation and reduced tissue injury following skin transplantation. Our data show that the C9 component of MACs forms intracellular aggregates with alarmin-like properties.

biochemistry↗

bioRxiv2026

SpatialDataAgent: Autonomous Spatial Omics Data Curation at Decade Scale

Fragmented metadata in spatial omics archives has rendered large volumes of multimodal molecular-histological data inaccessible as dark data. Here, we introduce SpatialDataAgent, an agentic workflow for autonomous spatial omics data curation, combining schema-constrained evidence evaluation with a self-refining standardization agent. Applied to a decade of GEO records, SpatialDataAgent identified 769 paired H&E-spatial transcriptomics (ST) datasets, representing a 6.4-fold scale expansion over existing manually curated baselines. Within the benchmarking window, the framework achieved a 141% increase in high-confidence Class A paired datasets. We further assembled a recent high-confidence subset into HESRT, a standardized datalake containing 29.2 million spots/cells, establishing a blueprint for evidence-grounded autonomous curation of multimodal biomedical archives.

bioinformatics↗

bioRxiv2026

Widespread use of invalid statistical tests in biomedical machine learning

Cross-validation is routinely used to compare performance in biomedical artificial intelligence. Standard tests ignore correlation across cross-validation folds, inflating false-positive rates. In a PRISMA-guided meta-analysis of 184 studies (impact factor [≥] 15) across 30 biomedical fields, 97% use invalid tests. Among studies with abstract-level claims supported by invalid tests, 59% rely on a spurious comparison: one that loses significance after correcting for this correlation. On average, regaining significance requires a 43% larger effect. Extending these findings to the broader literature, we estimate that spurious comparisons occur in nearly two in three studies and support abstract-level claims in nearly one in three studies. Simulations confirm false-positive rates paradoxically approach 100% when cross-validation is repeated to improve stability. We introduce SHARP, a redesign of cross-validation, which best balances false-positive control and power among 13 benchmarked tests. These results reveal widespread fragility in biomedical artificial intelligence and offer a practical route to valid comparisons.

bioinformatics↗

bioRxiv2026

Student-Driven Microbiome Exploration: A Low-Cost 16S rRNA Sequencing Curriculum for Undergraduate Biology Education

Microbiome science is increasingly important in modern biology education because microbial communities influence human health, ecosystems, and environmental processes. However, undergraduate microbiome instruction is often limited by the high cost and technical complexity of sequencing-based workflows, restricting opportunities for authentic student-driven research. To address this challenge, we developed a low-cost, inquiry-based curriculum that enables undergraduate students to conduct complete microbiome studies using 16S rRNA gene sequencing. The module integrates project design, environmental sample collection, microbial cell processing, PCR amplification, sequencing, and bioinformatic analysis using open-source tools such as QIIME 2. Cost-reduction strategies included centrifugation-based cell collection and a surfactant-assisted direct PCR workflow that eliminated the need for commercial DNA extraction kits. Students designed independent research projects investigating microbial communities in local environments, including campus water sources and gym equipment surfaces. Assessment data from post-course surveys, knowledge checks, and student research products demonstrated strong learning gains in microbiome concepts, molecular biology techniques, scientific communication, and computational analysis. Students reported high confidence in PCR, experimental design, and microbiome interpretation, while also identifying bioinformatics as the most challenging yet rewarding component of the curriculum. All participants expressed increased interest in future research in microbiology or bioinformatics. Overall, this curriculum provides an accessible, scalable framework for integrating next-generation sequencing into undergraduate education while promoting inquiry-driven learning, student ownership, and engagement in authentic scientific research.

microbiology↗