Biology subjects

Zou, Y.

Publications and source records attributed to Zou, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Digital molecular kinetics enabled by large-scale nanopore arrays for multidimensional biophysical profiling

While widely used, traditional technologies like surface plasmon resonance (SPR) are limited by narrow temporal windows (transient capture and baseline drift), dynamic heterogeneity, and poor physiological temperature performance. Meanwhile, early nanopore approaches are often constrained by limited throughput and heavy reliance on customized modification schemes. Here, we present a digital molecular kinetics (DMK) platform based on large-scale nanopore arrays. By introducing a universal coupling and probe reporting system, DMK achieves broad versatility across diverse molecular pairs, including proteins, peptides, small molecules, DNA, and polymerase complexes. In addition to accurately recovering classical SPR association and dissociation rate constants, by harnessing massive single-molecule event analysis, DMK breaks traditional performance boundaries: it facilitates robust thermodynamic-kinetic profiling across a wide temperature range, resolves distinct conformations in heterogeneous samples, enables ultra-low dissociation rate quantification via maximum likelihood estimation, and reveals energy wells via voltage gradients for binding analysis against environmental perturbations. Furthermore, DMK enables the capture of rapid binding events missed by SPR, offering a new perspective on molecular interaction complexity. This platform offers an effective alternative and upgrade to SPR, opening a digital paradigm for complex molecular analysis and drug discovery.

biophysics↗

bioRxiv2026

A family of metabolite damage-control phosphatases modulates ROS-induced autophagy and plant stress resilience

Autophagy is an intracellular recycling pathway with profound impacts on development, growth, and stress tolerance in eukaryotes. Therefore, unravelling signalling mechanisms that modulate the process has broad applicability. Here, we characterised a small organic molecule as an enhancer of autophagy across diverse plant lineages. Through an in vivo photoaffinity proteomics approach in Arabidopsis thaliana seedlings, we identified Domain of Unknown Function 89 (DUF89) proteins as molecular targets. Hereafter, we refer to these proteins as Reactive Metabolite Damage-Control Phosphatases (RMDPs), which are metabolite-repair phosphatases that clear reactive products. The new autophagy modulator is called RMDP inhbitor-1 (RMDPi-1) due to its demonstrated inhibitory effect on AtRMDP1 activity in vitro. Binding was further confirmed through co-incubation that thermostabilised the protein. Crystal structures of AtRMDP1 were obtained via X-ray diffraction, confirming binding of RMDPi-1 in the catalytic site and revealing a flexible region near the binding pocket that was absent in previous models. Molecular docking predicted two possible binding modes consistent with the observed electron density. RMDPi-1 treatment and the phosphatase gene knockout increased autophagic flux in Arabidopsis and Chlamydomonas reinhardtii, establishing a conserved effect. The observed autophagy response is linked to a spike in reactive oxygen species (ROS). AtRMDP knockout also results in higher ROS tolerance and greater biomass in Arabidopsis seedlings. Targeted and untargeted metabolomic experiments revealed that both pharmacological and genetic suppression of RMDP leads to accumulation of glycating agents and phosphate sugars, associating loss of RMDP activity to the ROS stress that induces alternate ROS-scavenging mechanisms, and autophagy. Taken together, our integrated chemical genetics approach reveals enhanced autophagy via inhibition of RMDP family members, which impacts on plant stress tolerance via conserved metabolite damage-control functions.

plant biology↗

bioRxiv2026

Genomic splice-donor disruption rescues systemic disease in progeria

RNA splicing determines which protein isoforms a gene produces, and aberrant splice-site activation can cause severe disease. In Hutchinson-Gilford progeria syndrome, a synonymous LMNA mutation strengthens a cryptic 5' splice donor site to produce progerin, a toxic lamin A isoform driving premature cardiovascular death. Within this cryptic donor, the activating mutation lies near the canonical GT dinucleotide required for splice-site recognition. A single guide can therefore preferentially pair with the mutant sequence while positioning Cas9 cleavage at this dinucleotide. Here we show that CRISPR/Cas9-mediated disruption of this splice site suppresses progerin without requiring precise correction of the activating mutation and prolongs lifespan in progeroid mice. In patient-derived fibroblasts and induced pluripotent stem cell-derived mesenchymal stem cells, this intervention reduced progerin by 92.7-96.8% while retaining lamin A and lamin C expression. A single neonatal injection of AAV9 carrying the corresponding mouse guide increased median survival from 115 to 279 days in Cas9-expressing LmnaG609G/G609G mice. Treatment attenuated aortic, skeletal and multiorgan pathology. Treated homozygous pairs produced 52 offspring across seven litters. These findings establish pathogenic splice signals as genomic targets for sustained suppression of toxic isoforms while retaining canonical gene outputs.

cell biology↗

bioRxiv2026

Within-Subject Optogenetic Model Reveals Spatiotemporal Cortical Reorganization in Artificial Vision

Visual prostheses can elicit simple percepts such as letter forms through dynamically patterned stimulation, yet naturalistic dynamic vision remains out of reach despite hardware fully capable of high-resolution temporal control. This persistent gap suggests the bottleneck lies in how artificial input is represented by the cortex itself. A fundamental question remains unresolved: when artificial vision bypasses natural retinal encoding, what is lost in cortical representation? We address this question in this paper using a retinal optogenetic mouse model that isolates the consequence of bypassing retinal encoding while preserving downstream pathways. Using within-subject V1 cortex electrophysiology and CNN-based decoding under identical dynamic stimuli, we reveal dissociable, dimension-specific gaps. Temporally, artificial vision bypassed the frequency-dependent compression imposed by natural vision, extending stimulus-locked entrainment bandwidth. Spatially, direction-selective representations underwent systematic remapping, with disrupted phase organization and reduced encoding regularity. These findings show that bypassing natural retinal encoding reorganizes cortical representation along dissociable spatiotemporal dimensions, establishing a within-subject framework that renders such structural divergences easy to locate and quantifiable.

bioengineering↗

bioRxiv2026

TEAD1 signaling modulates adrenal chromaffin maturation

Chromaffin cells synthesize and secrete catecholamines to coordinate systemic stress responses and regulate diverse neuroendocrine and metabolic functions. However, the molecular mechanisms governing chromaffin-cell differentiation and their disruption in pheochromocytoma (PC) remain incompletely understood. Here, through integrated analyses of human developmental atlases, patient-derived transcriptomic datasets, genetically engineered mouse models, and chromaffin organoids, we identify TEAD1 signaling as a critical regulator of chromaffin-cell differentiation and function. In vivo studies using a chromaffin cell-specific TEAD1 overexpression mouse model demonstrated that suppression of TEAD signaling markedly compromises chromaffin-cell differentiation and endocrine function. Additionally, compared with other TEAD family members, TEAD1 transcriptional activities are readily affected by sequences near the binding motif. To identify therapeutically actionable regulators of TEAD1 signaling, we established a TEAD activity-based screening platform and identified the serotonin receptor HTR5A antagonist SB699551 as a potent modulator of chromaffin-cell state. SB699551 suppressed PC-cell proliferation in vivo, and remodeled catecholamines synthesis in primary human PC cells. Additionally, application of SB699551 to human PC tumor revealed a subpopulation of primary chromaffin cells sensitive to this compound. Mechanistically, CXXC5 and L1CAM were identified as downstream SB699551-TEAD1 signaling effectors mediating chromaffin-cell proliferation and differentiation. Overall, we demonstrate that TEAD1 signaling is a fundamental mechanism regulating chromaffin cell differentiation and that modulation of TEAD1 signaling via SB699551 offers a new area of investigation in chromaffin cell biology.

molecular biology↗

bioRxiv2026

Spatial microRNA profiling at single-cell resolution by in situ barcoded extension

The spatial organization of post-transcriptional regulation is a fundamental yet difficult to access layer of tissue biology. MicroRNAs (miRNAs) are small RNAs with a key role in post-transcriptional regulation, but their short length has excluded them from spatial profiling technologies, leaving them largely unexplored in spatial transcriptomics. Here, we introduce miR-Space, a method that converts individual miRNAs into extended, uniquely barcoded molecules directly in tissue, enabling their spatial detection by in situ sequencing. Across 30 mouse and human brain sections, miR-Space enabled highly multiplexed miRNA profiling at single-molecule and single-cell resolution, joint analysis with mRNA, and implementation on the automated Xenium platform. miR-Space resolved major anatomical regions and cell populations from spatial miRNA expression, identified reproducible cell-associated miRNA signatures, and uncovered previously unknown spatial and cellular distributions of multiple miRNAs. Together, these capabilities establish miR-Space as a framework for integrating miRNAs into spatial transcriptomics, enabling spatial miRNomics at anatomical and single-cell resolution.

genomics↗

bioRxiv2026

The KRAS G12C Inhibitor Divarasib Stabilizes RBM39 and Antagonizes Aryl-Sulfonamide Degraders

KRAS G12C inhibitors have demonstrated meaningful clinical benefit in KRAS G12C-mutant non-small cell lung cancer (NSCLC), yet responses remain heterogeneous and treatment-associated toxicities persist for reasons that are incompletely understood. Cysteine profiling indicates that these covalent inhibitors are highly selective for mutant KRAS; however, such approaches cannot detect noncovalent engagement of additional non-RAS proteins. Here, we used a protein-folding stability profiling technique, stability of proteins from rates of oxidation (SPROX), to identify protein targets of the clinical KRAS G12C inhibitor, divarasib (GDC-6036), in KRAS-mutant NSCLC lysates. SPROX revealed a focused set of candidate interactors, including the essential splicing factor RBM39, which was reproducibly stabilized at both divarasib concentrations tested. We subsequently confirmed that divarasib directly and noncovalently binds to RBM39 protein. In NSCLC cells, divarasib increased RBM39 protein abundance and antagonized RBM39 degradation induced by the aryl-sulfonamide molecular glue indisulam through a post-transcriptional mechanism. Divarasib and RBM39 degraders reciprocally antagonized each other's cytotoxicity, and RBM39 knockdown modestly reduced divarasib-induced cell death. Mechanistically, divarasib-mediated RBM39 stabilization regulated both INSR expression and alternative splicing, altered downstream insulin receptor signaling, and contributed to divarasib-associated cytotoxicity. Consistent with these findings, RBM39 and INSR expression were positively correlated across multiple human cancer types. Collectively, these findings identify RBM39 as a previously unrecognized noncovalent target of divarasib and uncover an RBM39-INSR signaling axis that modulates cellular responses to both divarasib and RBM39 degraders.

pharmacology and toxicology↗

bioRxiv2026

Heart rate dynamics embed a shared representation of individual brain organization and cognitive function

Idiosyncratic brain functional organization shapes intricate cardiac dynamics through central-peripheral autonomic interactions, yet a comprehensive mapping between multi-scale heart rate dynamics and whole-brain functional architecture remains lacking. Here, combining highly comparative time-series analysis with multi-modal neuroimaging and intracranial electrophysiology, we establish heart rate dynamics as a physiological fingerprint that maps onto whole-brain functional architecture. Partial least squares analysis revealed a generalizable latent axis linking reduced heart rate temporal complexity and elevated micro-scale predictability to heightened resting-state functional connectivity across default mode, salience, and sensorimotor networks. This covariance aligns spatially with serotonergic, noradrenergic, and cholinergic neuromodulatory gradients, persists across physiological confound controls and cross-session validations, derives support from human intracranial electrophysiological recordings, and extends to active cognitive states. Furthermore, brain-covarying heart rate signatures underpin the predictive capacity of heart rate dynamics for individual fluid and crystallized intelligence, demonstrating a shared representational substrate. Our findings demonstrate a robust neurovisceral coupling architecture, establishing well-characterized heart rate dynamics as a scalable, neurobiologically anchored window into human brain functional organization and cognitive traits.

neuroscience↗

bioRxiv2026

Autophagy protects pancreatic β-cells during hypoxia and islet transplantation but is compromised by TFEB-lysosomal dysfunction

Hypoxia is a potent stressor and a major cause of {beta}-cell failure and loss after islet transplantation. Autophagy is a critical homeostatic mechanism that preserves organelle integrity and metabolic balance in cells under stress, but whether it supports {beta}-cell adaptation to sustained oxygen deprivation is unclear. Here, we used {beta}-cell-specific Atg5 knockout together with hypoxia and transplantation models, to demonstrate that autophagy is a major determinant of {beta}-cell survival during oxygen limitation and supports islet graft function. However, prolonged hypoxia suppressed autophagic flux, reduced lysosomal activity, and led to autophagosome accumulation, indicating failure of the lysosomal clearance pathway. This was accompanied by a marked reduction in transcription factor EB (TFEB) and its lysosomal target genes. Genetic and pharmacological activation of TFEB restored lysosomal gene expression and cathepsin B activity and improved {beta}-cell viability under hypoxia, implicating TFEB decline as a contributor to autophagy-lysosome dysfunction. Together, these findings outline a sequence in which autophagy initially safeguards {beta}-cells but becomes ineffective under sustained hypoxia as TFEB levels fall, identifying TFEB as a potential target to strengthen {beta}-cell resilience and survival in islet transplantation.

cell biology↗

bioRxiv2026

Same-section spatial metabolo-transcriptomics using Stereo-meta-seq reveals DHA-driven kidney maturation

A central unresolved question in developmental biology is whether local metabolites merely accompany, or actively instruct, tissue maturation. Addressing this question requires direct spatial coupling of metabolic states with genome-wide transcriptional programs in situ at high spatial resolution, which existing approaches do not readily achieve. Here, we introduce Stereo-meta-seq, a workflow that integrates quantitative MALDI-MSI with Stereo-seq spatial transcriptomics within a single tissue section. A conductive adapter was designed to overcome the electrical incompatibility of non-conductive Stereo-seq chips with vacuum MALDI platforms, improving efficiency of MSI detection that preserves RNA integrity. MALDI laser-ablation marks are retained in downstream Stereo-seq data and serve as intrinsic fiducials for direct co-registration at 10 m or 20 m resolution, enabling fine grained spatial metabolite-transcript integration. Applying Stereo-meta-seq to human kidney development, we uncover selective enrichment of docosahexaenoic acid (DHA) in maturing proximal tubules. Functional studies in human kidney organoids demonstrate that DHA activates PPAR-and HNF4-driven transcriptional programs and promotes proximal tubule maturation in vitro and after transplantation in vivo. These findings identify lipid metabolism as an instructive regulator of human nephrogenesis and establish Stereo-meta-seq as a practical platform for dissecting metabolite-gene coupling and tissue heterogeneity in situ.

Cell Biology↗

bioRxiv2026

WTAP-mediated epitranscriptomic program in alveolar macrophages confers prolonged protection against postinfluenza bacterial pneumonia

Secondary bacterial infections remain an intractable problem of seasonal influenza, primarily due to the depletion and defunctionalization of alveolar macrophages (AMs). Here, we described that N6-methyladenosine (m6A), the most prevalent RNA modification in eukaryotes, critically orchestrates trained immunity (TRIM) establishment in AMs. Influenza A virus (IAV)-trained AMs maintained low Wilms tumor 1-associated protein (WTAP) expression and reduced global m6A deposition for over two months. Mechanistically, this IAV-induced m6A decrease promotes TRIM by enhancing the RNA stability of phagocytic and metabolic genes, thereby boosting antibacterial function. Mimicking this m6A reduction pharmacologically or genetically recapitulates the IAV-trained TRIM phenotype, which improves phagocytosis and protects mice from secondary infection. Clinically, elevated WTAP in AMs correlates with impaired phagocytosis and disease severity in COVID-19 and COPD. These findings for the first time unveil how respiratory virus infection shapes AM TRIM via epitranscriptomic reprogramming, and offer prospective strategies for the prevention and treatment of post-viral bacterial complications.

immunology↗

bioRxiv2026

Comprehensive Complete-Genome Analysis of Lactobacillaceae and Bifidobacteriaceae Reveals Strain-Specific Metabolic Interactions in Chinese Gut Microbiota

Bifidobacteriaceae and Lactobacillaceae are key probiotic families and widely used in food production, yet a comprehensive understanding of strain functions and their gut microbial interactions based on complete genomes remain understudied. Here we constructed a complete-genome dataset of 3,300 strains from these two families, including 1,151 newly isolated from China. Compared with draft assemblies, complete genomes substantially recovered a gene functional landscape encompassing stress tolerance, surface exopolysaccharide synthesis, nutrient utilization, and mobile genetic elements. Major species from both families exhibited a prevalence >60% in the Chinese population, far higher than that in US/Dutch cohorts. Notably, as a core probiotic species with remarkable genomic plasticity and gut-adaptive potential, Lactiplantibacillus plantarum stood out in our dataset for its enriched functional profile and was particularly abundant in the Chinese population. Moreover, compared with non-Chinese genomes, our isolates of key species displayed less metabolic complementarity and stronger competition with potentially pathogenic keystone species in the gut, thereby linking strain origin to enhanced probiotic potential and ecological fitness to benefit human gut health.

microbiology↗

bioRxiv2026

The Magnaporthe oryzae Effector AvrPii Attenuates Rice Immunity by Targeting the Calcium-Associated ANK Protein AVIN8

Rice blast, caused by the fungus Magnaporthe oryzae, poses a severe threat to global rice production. Although numerous M. oryzae effectors have been identified, the molecular mechanisms remain poorly understood. The effector AvrPii triggers ETI upon recognition by NLR receptor Pii and has been shown to target host exocytosis and oxidative metabolic pathways to suppress immunity. Here, we identify AVIN8 (AvrPii-interacting protein 8) as a new target of AvrPii. AVIN8 is an ankyrin-repeat (ANK) protein localized to the plasma membrane and nuclear envelope, with sequence similarity to known ANK calcium channels. AVIN8 expression is induced during early M. oryzae infection. Overexpression of AVIN8 enhances blast resistance, whereas its silencing increases susceptibility. AVIN8 promotes chitin-triggered ROS production in a Ca2+-dependent manner. In contrast, AvrPii impairs Ca2+ influx and chitin-triggered ROS burst. Our findings reveal a virulence strategy in which M. oryzae effector AvrPii hijacks the Ca2+ influx-associated ANK protein AVIN8 to suppress early calcium and PTI signaling in rice.

plant biology↗

bioRxiv2026

Midkine Dependency Defines a Therapeutically Actionable Vulnerability in Medulloblastoma

Medulloblastoma (MB), the most common malignant pediatric brain tumor, remains associated with high recurrence rates and substantial treatment-related morbidity despite aggressive multimodal therapy. Here, we identify midkine (MDK), a secreted growth factor/cytokine, as a previously unrecognized central regulator of MB growth and survival. Tissue microarray analysis revealed elevated MDK protein expression in MB specimens, and single-cell RNA sequencing datasets showed tumor cell-specific MDK expression. Genetic depletion or antibody-mediated neutralization of MDK suppressed proliferation and survival and induced apoptosis across multiple MB cell lines, whereas recombinant MDK supplementation exerted the opposite effect. Mechanistically, phosphokinase profiling and immunoblot analyses showed that MDK signals through multiple receptors, including nucleolin (NCL), LRP1, and syndecan-2 (SDC2), to sustain oncogenic ERK1/2 and Akt-mTOR-S6 signaling. Transcriptomic profiling following MDK silencing or depletion revealed marked suppression of ribosome biogenesis, global protein translation, and MYC-driven programs, coupled with activation of inflammatory and apoptotic responses. Consistently, mechanistic studies utilizing RPS6 staining, ribosomal RNA quantification, puromycin SUnSET, and OPP incorporation assays confirmed that loss of MDK impairs ribosome biogenesis and protein synthesis. Notably, MDK suppression also triggered robust activation of the IFN-cGAS-STING pathway, linking translational stress to innate immune signaling. In orthotopic xenograft models, CRISPR-mediated MDK knockout significantly reduced tumor growth and prolonged survival. Together, these findings establish MDK as a key integrator of oncogenic signaling, translational control, and innate immunity in MB, highlighting MDK as a compelling therapeutic target.

cancer biology↗

bioRxiv2026

Complete genome-derived metabolic interactions reveal impact of gut ecology on human health

Metabolic interactions govern gut microbiome assembly, yet functional rules remain obscured by genomic incompleteness and fragmentation. Here, we leverage 1,150 complete genomes to construct genome-scale metabolic models, demonstrating that draft genomes introduce systemic artifacts missing critical transport functions. We observe that metabolic interactions are intrinsically driven by genomic traits and niche specialization rather than random association. We stratifies strains into four ecological groups, including active players, resource predators, utilizers, and contributors, each of which exhibits distinct metabolite exchange/competition signatures. This functional architecture is strongly coupled to secondary metabolism. Applying this framework to inflammatory bowel disease revealed distinct temporal dynamics of ecological groups across disease subtypes, where group-specific dysbiosis predicted clinical phenotypes better than whole community profiles. Furthermore, integrating metabolic and co-occurrence networks to identify keystone for classifiers as features significantly improved disease diagnosis. Our study provides novel insights into gut metabolic interaction landscape, bridging the gap between genomic potential and clinical utility for precision microbiome therapeutics.

microbiology↗

bioRxiv2026

Starvation-induced autophagy occurs independently of the ATG1 complex in Chlamydomonas

The survival of eukaryotes during starvation depends on effective nutrient recycling via autophagy. Accordingly, loss of autophagy-related (ATG) proteins, including the nutrient-sensing ATG1 kinase complex, typically results in reduced fitness or lethality under nutrient limitation. The green alga Chlamydomonas reinhardtii provides a tractable model for autophagy studies, as its ATG repertoire is encoded by single-copy genes. Here, we generated a comprehensive library of ATG deletion mutants and examined their growth and autophagy during starvation. Surprisingly, starvation-induced autophagy occurred in the absence of ATG1 complex components (ATG1, ATG11, ATG13, and ATG101), revealing ATG1-independent autophagy and challenging the canonical model for autophagy initiation.

molecular biology↗

bioRxiv2026

Complete Genomes of Cultivated Gut Bacteria Reveal Mobile Genetic Element-Driven Functional Diversity with Therapeutic Implications

Cultivated bacterial isolates are essential for elucidating gut microbiota functions, yet reliance on fragmented draft genomes and limited mobile genetic element (MGE) annotation has constrained high-resolution analyses. Here, we present the Cultivated Complete Genome Reference (CCGR), a comprehensive compendium of 1,150 fully circularized human gut bacterial genomes. Overcoming draft limitations, CCGR achieves chromosome-scale resolution and reveals distinct evolutionary strategies shaping gene topological organization in response to bacterial growth. Furthermore, we decode the dynamic landscape of MGEs, demonstrating that broad-host-range phages follow strict positional patterns by integrating at conserved chromosomal hotspots flanked by nutrient transporter loci. Importantly, we provide mechanistic in vivo evidence that accessory genomic elements drive strain-level functional heterogeneity. Specifically, the plasmid-encoded scrK gene in Levilactobacillus brevis involved in fructose catabolism is required to mitigate fructose-diet-exacerbated colitis. Collectively, CCGR establishes a framework linking chromosomal architecture and MGEs to bacterial evolution and host health, enabling precise, strain-resolved functional investigations.

microbiology↗

bioRxiv2026

A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination

Closely related prophages are frequently found in phylogenetically distant bacteria in the human gut, despite limited evidence of productive phage infections across broad host ranges. Thus, it remains unclear how the wide distribution of prophages could emerge. Here, we identify a potential mechanism of prophage dissemination. We describe two deeply diverged groups of conjugative megaplasmids (>300 kilobases) in the human gut microbiome, which we term Hodors. Hodors encode conserved replication, partitioning, and type IV secretion systems, together with a complex surface-associated gene module. A subset of Hodors harbor complete, intact prophage genomes, and closely related prophages are detected across phylogenetically distant Bacillota lineages, including both Bacilli and Clostridia. Further analysis indicates that Hodor-associated prophages can exist as extracellular particles and demonstrate their transcriptional activity. Our findings support a model in which conjugative megaplasmids act as composite mobile platforms that disseminate prophage genomes across bacterial lineages, providing a mechanistic explanation for the widespread occurrence of closely related prophages in phylogenetically distant gut bacteria and effectively decoupling lysogenic host range from infective host range.

microbiology↗