Biology subjects

Shen, Z.

Publications and source records attributed to Shen, Z..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

A Non-Canonical Role of SMAD4 in Regulating 3D Genome Architecture to Inhibit Lung Squamous Cell Carcinoma Development

Lung squamous cell carcinoma (LUSC) lacks clearly defined key drivers and effective targeted therapies, reflecting an incomplete understanding of its molecular pathogenesis. Here, we identify SMAD4 as a critical regulator of three-dimensional (3D) genome organization in LUSC and uncover a mechanistic link between tumor suppressor loss and oncogenic transcriptional activation. By integrating clinical datasets, genetically engineered mouse models, human and murine LUSC cell lines, and multi-omics analyses, we demonstrate that SMAD4 deficiency promotes LUSC progression by unleashing EP300-mediated enhancer-promoter looping at the SOX2 locus. Mechanistically, SMAD4 does not directly bind SOX2 regulatory elements but instead constrains chromatin looping by sequestering EP300 away from loop anchor regions. Loss of SMAD4 leads to enhanced H3K27ac deposition, aberrant SOX2 activation, and increased LUSC tumor cell proliferation. Together, these findings reveal a non-canonical role for a transcription factor (e.g., SMAD4) in regulating dysregulated 3D genome architecture to inhibit tumor development.

cancer biology↗

bioRxiv2026

Polyclonal-Monoclonal Transition in Lung Squamous Cell Carcinoma Evolution

The evolutionary trajectory of lung squamous cell carcinoma (LUSC) remains poorly defined, hindering the development of effective therapies. By integrating genomic and transcriptomic sequencing from human LUSC specimens, we delineated a polyclonal-to-monoclonal evolutionary trajectory during LUSC progression. This evolutionary pattern was corroborated by single-cell RNA sequencing, which revealed consistent tumor cell heterogeneity. Specifically, the SBS5 mutational signature was enriched and correlated with poor prognosis independent of tumor stage. By further utilizing the spontaneous LUSC mouse model to identify key genomic and genetic events in LUSC progression, we observed that the JNK pathway was inhibited and that cytoskeleton-related pathways were dysregulated during LUSC development, and identified the mutations in the JNK pathway (e.g., DACT1) and cytoskeletal regulators (e.g., KIF26A). Collectively, these findings established a polyclonal-monoclonal evolution paradigm for LUSC, potentially regulated by JNK pathways, which could benefit LUSC precision therapeutics.

genomics↗

bioRxiv2026

A cerebellar cognitive rheostat bidirectionally controls attention

Attention requires filtering distractors and amplifying signals, processes classically attributed to cortico-thalamic networks. Here, we reveal that the cerebellum operates as a bidirectional "cognitive rheostat" to optimize attentional states. In mice, the anterior and posterior cerebellar vermis exert opposing control over attention. Granule cells in the anterior vermis are functionally suppressed to gate sensorimotor noise via reticular nucleus-driven feedforward inhibition. Conversely, posterior granule cells are recruited by pontine inputs to amplify cognitive signals, a process relying on Grin1-mediated NMDA receptor plasticity. Circuit-specific manipulations targeting this push-pull mechanism, or localized pharmacological modulation, successfully rescued attentional deficits in an ADHD mouse model. These findings fundamentally expand the cerebellums role beyond motor coordination, identifying a topographic circuit algorithm essential for cognitive control.

animal behavior and cognition↗

bioRxiv2026

Loss of inwardly rectifying potassium channel Kir4.2 drives Parkinson's disease-like motor, cognitive and neuropathological features in mice

A critical barrier to therapeutic development in Parkinsons disease (PD) is the lack of endogenous genetic models that spontaneously recapitulate the diseases progressive, anatomically selective nigrostriatal pathology. Genetic studies have linked KCNJ15, encoding the inwardly rectifying potassium channel Kir4.2, to familial PD via a loss-of-function dominant-negative variant; however, its mechanistic role in neurodegeneration remains unexplored. Here, we demonstrate that Kcnj15-/- mice spontaneously develop a progressive PD-like phenotype, exhibiting a "coordination-first" motor syndrome, anxiety-like behavioural changes and spatial memory impairments. Crucially, neuropathology reveals selective degeneration of substantia nigra pars compacta neurons, sparing the ventral tegmental area, with marked microglial hyperactivation and phosphorylated -synuclein accumulation, faithfully recapitulating the topography of human PD. Striatal transcriptomics further reveals upregulation of oligodendrocyte- and myelin-associated genes, implicating compensatory glial remodeling. These findings identify Kir4.2 as a critical homeostatic regulator of nigrostriatal integrity and establish the Kcnj15-/- mouse as a new physiologically accurate and translatable model for PD research.

neuroscience↗

bioRxiv2026

AlphaGenome -enabled analysis of non-coding regulatory variants underlying RHD Expression

Systematic identification of functional non-coding regulatory variants remains a major challenge in human genetics. Conventional approaches such as large-scale CRISPR screening and genome-wide association studies (GWAS) are powerful but often prohibitively expensive, time-consuming, and experimentally intensive, limiting their scalability for locus-specific mechanistic studies. Recent advances in artificial intelligence offer the potential to partially replace or substantially augment these approaches by prioritizing regulatory variants with high functional likelihood. The RHD antigen, a major contributor to red blood cell alloimmunization, hemolytic transfusion reactions, and hemolytic disease of the fetus and newborn, serves as an excellent model for this paradigm, since coding variants alone do not fully account for differences in RHD expression. Here, we present an integrated artificial intelligence (AI)-guided and experimental framework to identify and validate functional non-coding regulatory variants governing RHD expression. We first applied AlphaGenome (AG), a deep-learning model released in 2025 for non-coding variant impact prediction, to systematically interrogate the RHD locus. By integrating multi-omics datasets, AG prioritized regulatory regions within the promoter, 5' untranslated region (5'UTR), and intragenic regions. In silico deletion- and Single Nucleotide Polymorphism (SNP)-based perturbation analyses consistently predicted that variants within the promoter and its proximal regions, as well as within intragenic regions, exert strong suppressive effects on RHD expression. To experimentally validate these predictions, we performed CRISPR-mediated base editing in K562 cells at AG-prioritized non-coding SNP sites. Editing of a high-score predicted variant (chr1:25272434 G>A) achieved efficient base conversion and was accompanied by additional nearby edits, all predicted by AG to downregulate RHD expression. In contrast, editing of low-score predicted sites (chr1:25272422 C>T) produced much smaller functional effects. Quantitative polymerase chain reaction (qPCR) analysis of full-length RHD transcripts, together with flow cytometry-based analysis of RHD expression, confirmed strong concordance between AI-based predictions and transcriptional as well as phenotypic outcomes. Taken together, our results demonstrate that the combination of AI-guided regulatory variant prioritization and targeted base editing provides a potentially scalable and cost-effective alternative to traditional CRISPR screening for decoding functional non-coding variants in blood group genes, with direct implications for genomics-based RHD typing and transfusion medicine. To our knowledge, this study also represents the first validation of AlphaGenome predictions at the phenotypic level using wet-lab experiments.

genomics↗

bioRxiv2026

High-Affinity Protein Binder Design via Flow Matching and In Silico Maturation

The de novo design of high-affinity protein binders remains a central challenge in protein engineering and therapeutic discovery. While deep generative models have advanced backbone generation and interface design, achieving picomolar or nanomolar binding affinities typically demands extensive experimental screening or iterative in vitro maturation. A general computational approach for the direct production of high-affinity binders has remained elusive. Here, we introduce an integrated framework that synergizes PPIFlow, a flow-matching-based generative model, with a novel in silico maturation strategy. PPIFlow employs a pairformer architecture to explicitly reason over pair-wise geometric and chemical interactions, modeling protein backbone rigid-body transformations as continuous flows. To bridge the affinity gap, we implement a dedicated in silico affinity maturation stage that combines interface rotamer enrichment with partial flow refinement to optimize energetic packing. This pipeline is further accelerated by AF3Score, a score-only adaptation of AlphaFold3 that enables high-fidelity and computationally efficient candidate prioritization. Across a diverse set of therapeutic targets, this synergistic approach consistently produces picomolar and nanomolar affinity binders without experimental affinity maturation. Notably, the framework proves highly effective for the de novo design of single-domain antibodies (VHHs), producing sub-nanomolar binders across multiple targets. These results establish that coupling robust backbone generation with focused in silico maturation renders the purely computational design of high-affinity binders feasible.

biochemistry↗

bioRxiv2025

Histone Demethylase KDM6B Promotes Postnatal Oligodendrocyte Development and Cortical Myelination

Myelination in the postnatal cortex requires epigenetic programs that activate oligodendrocyte gene networks. Here we show that the histone H3K27me3 demethylase KDM6B promotes this process in vivo. Conditional Kdm6b deletion (Kdm6b-cKO) in Emx1 dorsal telencephalic progenitors caused delayed cortical myelination. Lineage-specific RNA-seq revealed that the oligodendrocyte master regulator Sox10 was significantly reduced, as well as myelination effectors, indicating impaired oligodendrocyte maturation. Chromatin immunoprecipitation assays of the same lineage showed increased H3K27me3 at promoter-proximal regions of Sox10, consistent with loss of KDM6B-mediated de-repression. Temporally controlled Sox10 induction partially rescued myelination in Kdm6b-cKO mice. These findings define a KDM6B[->]SOX10 axis that licenses oligodendrocyte development and cortical myelination by removing repressive H3K27me3 and sustaining active chromatin, with implications for KDM6B-related neurodevelopmental disorders.

neuroscience↗

bioRxiv2025

Skin microbiome composition and function in the development of atopic diseases during infancy

BackgroundAtopic dermatitis (AD), food sensitization (FS), and food allergy (FA) frequently co-occur in infancy, but the factors driving distinct atopic phenotypes remain unclear. While FLG null mutations are major genetic risk factors for AD, they explain only a fraction of disease heritability, suggesting a potential role for the skin microbiome. ObjectiveTo determine how early-life skin microbiome composition and its interaction with host genetics contribute to distinct atopic phenotypes in infancy. MethodsWe analyzed >1,000 skin swabs from 429 infants in the VITALITY cohort using deep shotgun metagenomic sequencing at 2-3 months (pre-diagnosis) and 12 months (post-diagnosis). Differential abundance, strain-level, and microbial genome-wide association analyses were performed to identify taxonomic and functional features associated with AD, FS, FA, and their co-occurrence, as well as with FLG mutation status. ResultsWithin AD, microbial signatures differed by co-occurring FA or FS. At 12 months, Staphylococcus epidermidis was enriched in infants with AD alone, whereas infants with AD and FA exhibited decreased Staphylococcus hominis and Lactococcus species, along with increased Dermacoccus nishinomiyaensis and Malassezia slooffiae. At 2-3 months, early skin dysbiosis characterized by enrichment of Staphylococcus species was associated with subsequent development of AD with FS or FA, but not AD alone. Among infants with AD, FLG mutation carriers exhibited additional microbial shifts, including reduced Streptococcus species and increased Malassezia slooffiae. Strain-level analyses revealed mother-infant sharing of skin microbial taxa associated with AD, and microbial genome-wide association analyses identified species-specific genes linked to AD severity. ConclusionsInfant atopic phenotypes are associated with distinct, phenotype-specific features of the skin microbiome that emerge both before and after clinical disease onset. By resolving microbial differences within AD according to allergic co-occurrence, host genetics, and early-life timing, this study highlights the infant skin microbiome as a potential target for early risk stratification.

microbiology↗

bioRxiv2025

TaoChongBao: A Large-Scale Caenorhabditis elegans Mutagenesis and Missense Variant Database Bridging Worm and Human Genomes

We generated and sequenced 12,069 viable Caenorhabditis elegans strains produced by ethyl methanesulfonate mutagenesis, identifying 20,315,536 variants, including 541,102 unique missense mutations across 20,914 genes. To organize and visualize this resource, we developed TaoChongBao, an open-access database and strain repository that integrates C. elegans mutation data with AlphaMissense-predicted pathogenicity scores and ClinVar clinical annotations. TaoChongBao enables users to explore worm missense variants, identify conserved residues corresponding to human pathogenic sites, and access viable strains for experimental validation. Compared with the previous Million Mutation Project in C. elegans, TaoChongBao expands mutation coverage over twenty-fold and emphasizes amino acid-altering variants. This resource provides a scalable platform for functional residuomics, variant interpretation, and comparative analyses between C. elegans and human genomes.

bioinformatics↗

bioRxiv2025

ERAD Activity Distinguishes the Functional Heterogeneity of Hematopoietic Stem Cells

Hematopoietic stem cells (HSCs) rely on precisely controlled proteostasis to sustain lifelong self-renewal, yet whether intrinsic proteostatic characteristics can prospectively define functional diversity within the HSC pool remains unknown. In this study, we developed a dual-fluorescence reporter system to visualize endoplasmic reticulum-associated degradation (ERAD) activity in vivo and discovered that ERAD activity can prospectively predicts the long-term reconstitution potential of HSCs. Remarkably, ERAD states were maintained through self-renewal, revealing an inheritable "proteostatic memory" within the HSC pool. Transcriptomic and functional analyses identified SOCS2 as a key regulator of this process: SOCS2 inhibits JAK2 signaling to sustain ERAD activity, whereas hyperactive JAK2 interacts with the ERAD E3 ligase Hrd1 and suppresses VCP-mediated misfolded substrate. These findings define a SOCS2-JAK2-ERAD axis that connects cytokine signaling to intrinsic proteostasis remodeling, establishing ERAD activity as a predictive and heritable marker of HSC function and providing a conceptual framework for understanding hematopoietic stem cell heterogeneity.

cell biology↗

bioRxiv2025

AKAP1 regulates mitochondrial and synaptic homeostasis to enable neuroprotection and repair in retinal ganglion cell degeneration

Glaucoma is a leading cause of irreversible blindness, characterized by progressive retinal ganglion cell (RGC) loss and optic nerve degeneration. Mitochondrial dysfunction plays a central role in this neurodegeneration, yet effective targeted therapies remain limited. Here, we identify the mitochondrial scaffold A-kinase anchoring protein 1 (AKAP1) as a critical regulator of RGC resilience and axon regeneration. AKAP1 expression is diminished in human glaucomatous retinas and experimental glaucoma models, correlating with elevated intraocular pressure, disrupted mitochondrial dynamics, oxidative stress, and synaptic instability. Restoration of AKAP1 via adeno-associated virus serotype 2-mediated gene therapy preserves RGC survival, promotes mitochondrial fusion and cristae integrity, enhances ATP production, and mitigates oxidative and apoptotic stress in mouse models of glaucoma and optic nerve injury. Transcriptomic profiling of AKAP1 knockout retinas reveals widespread dysregulation of mitochondrial and synaptic gene networks. Mechanistically, AKAP1 stabilizes synapses by promoting mitochondrial biogenesis, modulating calcium/calmodulin-dependent kinase II and synapsin phosphorylation, maintaining synaptophysin expression, and suppressing complement component C1q expression, thereby preventing early synaptic loss in glaucomatous neurodegeneration. Moreover, restoring AKAP1 expression facilitates axonal regeneration, preserves the central visual pathway, and maintains visual function. Collectively, these findings establish AKAP1 as a master regulator of mitochondrial and synaptic homeostasis and axonal regeneration and a promising therapeutic target for vision preservation in glaucomatous neurodegeneration. One Sentence SummaryAKAP1 protects retinal ganglion cells and preserves vision by restoring mitochondrial and synaptic health in experimental glaucoma models.

neuroscience↗

bioRxiv2025

Single-Cell Immune Profiling Reveals Non-classical Monocyte-Driven Immunodepression in Tuberculosis Treatment Non-Responders

Sputum culture conversion (SCC) at 2 months is a critical predictor of tuberculosis (TB) treatment outcomes, yet the underlying immune alterations driving treatment non-response remain unclear. We performed single-cell RNA sequencing on peripheral blood mononuclear cells from 8 TB patients, stratified by 2-month SCC status, to characterize cellular heterogeneity and intercellular communication. Treatment non-responders exhibited marked expansion and terminal differentiation of non-classical monocytes with elevated TB progression risk signatures. These cells showed reduced outgoing but enhanced incoming signaling, prominently via IL-16 and TRAIL pathways, potentially amplifying regulatory T cell (Treg)-mediated immunosuppression. CD4 Tregs in non-responders engaged in intensified GALECTIN signaling toward CD8 cytotoxic T cells and mature NK cells, contributing to effector cell exhaustion. NK cell subsets, particularly mature NK c2, displayed increased inhibitory receptor expression and terminal differentiation states. Our findings delineate a dysregulated "non-classical monocyte -Treg -cytotoxic lymphocyte" axis in TB treatment failure, highlighting candidate biomarkers and host-directed therapeutic targets.

bioinformatics↗

bioRxiv2025

Persistence of vestibular function in the absence of glutamatergic transmission from hair cells

Quantal synaptic transmission in vestibular end-organs is glutamatergic. Although genetic deletion of Slc17a8 (termed Vglut3) leads to deafness in mice, the dependence of vestibular function on VGLUT3-mediated quantal transmission is unknown. Here, we investigated the vestibular phenotype of Vglut3-/- mice at the cellular, systems, and behavioral levels. The type-II vestibular hair cells (VHCs) in Vglut3+/+mice were strongly immunoreactive for VGLUT3, while type-I VHCs showed poor immunoreactivity. In Vglut3-/- mice quantal synaptic transmission in utricular calyces was reduced in rate and amplitude by > 95%. In vivo recordings of spontaneous activity in the vestibular nerve revealed similar action potential rates and regularity in Vglut3+/+and Vglut3-/- mice, suggesting a divergent underlying mechanism compared to the silent Vglut3-/- auditory nerve. In behavioral studies, Vglut3-/- mice did not exhibit considerable sensorimotor or balance deficits. Collectively, these data support the view that non-quantal transmission is the predominant mode of neurotransmission between type I VHCs and vestibular calyceal afferent neurons. We propose that non-quantal transmission alone underlies the apparently normal vestibular nerve physiology and behavioral function in Vglut3-/- mice.

neuroscience↗

bioRxiv2025

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

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

neuroscience↗

bioRxiv2025

Changes in Urinary Proteome Post-Translational Modifications Following Short-Term Intake of Specific Magnesium, Calcium, Zinc, and Iron Supplements in Rats

Magnesium, calcium, zinc, and iron are essential mineral elements indispensable for maintaining physiological functions in mammals. This study investigated changes in post-translational modifications (PTMs) of the urinary proteome in Sprague-Dawley (SD) rats of different ages following short-term intragastric administration of magnesium L-threonate (MgT), calcium gluconate, zinc gluconate, and polysaccharide-iron complex. The results revealed PTM alterations in the urinary proteins of rats in all mineral supplement groups, with the most pronounced changes observed in the polysaccharide-iron complex group. Notably, rats of different ages exhibited distinct responses to the same mineral supplement. The proteins carrying differential PTMs were involved in a wide range of biological functions, and several of them, including serotransferrin and beta-2-microglobulin, are closely associated with mineral metabolism. This study explores the functional changes in urinary proteins from a PTM perspective following short-term mineral supplementation in rats, providing a novel viewpoint for investigating the physiological functions of mineral elements.

biochemistry↗

bioRxiv2025

Discovery of A Small Molecule non-IMiD Degrader of ZBTB7A for the Treatment of β-hemoglobinopathies

Sickle cell disease and {beta}-thalassemia, two major {beta}-hemoglobinopathies, pose significant clinical challenges globally. Current treatments often face limitations in efficacy and tolerability. The transcription factor ZBTB7A has emerged as a promising therapeutic target for reactivating fetal hemoglobin expression. Here, we report the discovery and characterization of SH6, a small molecule non-IMiD degrader of ZBTB7A. SH6 induces fetal hemoglobin in erythroid cell lines in a CRBN and ZBTB7A-dependent manner, and it is capable of inducing fetal hemoglobin expression in healthy donor, SCD and {beta}-thalassemia patient CD34+ cell derived erythroid cells. The efficacy of SH6 is confirmed in a xenotransplantation humanized mouse model. SH6 outperforms currently available therapeutic agents in vitro, and shows synergy with hypomethylating agents. SH6 exhibits a favorable in vivo toxicity profile. Our findings establish SH6 as a promising therapeutic lead candidate for further optimization towards clinical development for treatment of sickle cell disease and {beta}-thalassemia.

cell biology↗

bioRxiv2025

Fully Automated and Scalable Pipeline for Macaque Brain Registration

With the rapid development of various whole-brain ex vivo imaging technologies, there is a growing need to develop cross-modal 3D image registration methods to integrate multimodal imaging datasets. While comprehensive cross-modality registration tools such as D-LMBmap and mBrainAligner have been successfully implemented for mouse brains, macaque whole-brain registration presents unique challenges. These include more pronounced non-uniform deformations in larger ex vivo specimens, greater modality-specific contrast differences relative to standard space, and increased inter-individual variability. To address these challenges, we developed Macaca-Star, which incorporates deep learning models and self-individual MRI to tackle cross-modal and ex vivo sample deformation challenges in macaque whole-brain registration. Macaca-Star provides fully automated alignment of fMOST and 2D fluorescent slice images to the NMT MRI standard space, allowing for comprehensive integration of anterograde axonal projections and retrograde-traced neuronal soma profiles.

neuroscience↗

bioRxiv2025

An increase of NPY1 expression leads to inhibitory phosphorylation of PIN-FORMED (PIN) proteins and suppression of pinoid (pid) null mutants

The PINOID (PID) protein kinase is required for flower initiation in Arabidopsis. The pid mutants fail to initiate flowers on inflorescences, a phenotype that is mimicked by disrupting either the NAKED PINS IN YUC MUTANTS (NPY) gene family or PIN FORMED 1 (PIN1). Both PID and NPY1 have been reported to positively modulate PIN-mediated polar auxin transport. Here, we show that overexpression of NPY1 (NPY1 OE) completely suppressed pid null mutants, demonstrating that NPY1 functions downstream of PID. NPY1 OE triggered phosphorylation of PIN proteins at multiple sites that are mostly different from the previously characterized phosphorylation sites regardless of the presence of PID. Phosphorylation of the newly identified PIN sites in NPY1 OE plants likely leads to the inhibition of PIN functions, as we previously showed that pid is suppressed by decreasing PIN1 gene dosage or decreasing PIN1 activity. Furthermore, we show that the Ser/Thr rich C-terminal motif in NPY1 is phosphorylated and is required for pid suppression by NPY1 OE. Overexpression of NPY1 that lacked the C-terminal motif (NPY1{Delta}C) failed to rescue pid, but overexpression of NPY1{Delta}C was still able to trigger phosphorylation of PIN proteins including PIN2, which is known to cause agravitropic roots when mutated. NPY1{Delta}C overexpression plants displayed a complete loss of root gravitropic response, likely caused by PIN2 phosphorylation. Our results suggest a pathway for auxin mediated-flower initiation, in which PID regulates NPY1 accumulation and/or activity, and subsequently, NPY1 triggers phosphorylation of PIN proteins and inhibition of PIN functions.

plant biology↗