Biology subjects

Shi, S.

Publications and source records attributed to Shi, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Localising the Seizure Onset Zone from Routine Interictal and Ictal Scalp EEG Via a Factorised Spatiotemporal Ensemble Deep Learning Framework

Background: Drug-resistant focal epilepsy requires precise localisation of the epileptogenic zone (EZ) for surgical resection. Current practice depends on invasive recordings or spontaneous seizure capture, a costly and risky bottleneck. Interictal scalp EEG can exhibit localising features like spikes, but scalp EEG suffers from volume conduction (the smearing of brain signals across multiple electrodes) and low signal-to-noise ratio (SNR), which obscure subtle spatial dynamics. Neurophysiologist review of long, often multi-day recordings is time-consuming and expertise-dependent, and while computational methods exist, they tend to rely heavily on human-designed features. Deep learning for EEG localisation could therefore help to improve clinical efficiency and sensitivity. Objectives: To develop and validate a non-invasive deep learning approach for lobar-level localisation of the seizure onset zone (SOZ), the primary electrophysiological proxy for the epileptogenic zone (EZ), using interictal and ictal segments from routine scalp EEG. The model is trained on expert-annotated clinical labels and is intended to augment, not supplant, clinical judgement in EZ delineation. Methods: We curated 262 sessions (6,000+ hours) from 100 patients with unilateral focal epilepsy, tested with an extra 28-patient internal and a 9-patient external dataset. The framework integrates: (1) an online augmentation pipeline (Gaussian noise, amplitude scaling, temporal cropping, and hemispheric channel swap) to mitigate overfitting. (2) a multi-scale temporal block for 20-200 ms discharge morphologies; (3) a factorised spatiotemporal Transformer decoupling temporal and spatial attention to counter volume conduction; and (4) a hemispheric mutual exclusivity penalty encoding unilateral priors. A five-model heterogeneous ensemble, fused via model soup, was evaluated on held-out, seizure-free, and cross-institutional cohorts. Results: The ensemble achieved 88.46% session-level exact match on internal test data, outperforming EEGNet (50.00%). Performance generalised to the seizure-free holdout set (82.76%) and to cross-institutional data (84.62%). Rare occipital class (RO) recall rose from 0.500 to 1.000, with zero false positives on healthy controls (n=108). On unlabelled random segments, accuracy was 66.67% (vs. 14% chance). A full 24-hour recording was processed in 4.26 minutes, with inference under 8 seconds, highlighting localising windows for targeted expert clinical review Conclusion: Clinically actionable SOZ spatial information is encoded in routine interictal scalp EEG. Our factorised ensemble provides a safe, interpretable, and efficient tool to expedite presurgical evaluation, potentially reducing reliance on prolonged monitoring and invasive implantation.

neuroscience↗

bioRxiv2026

From sensation to action: distributed mesoscale dynamics in the primate brain

Perceptual decisions engage distributed brain networks, yet how decision-related signals are organized across and within brain areas remains unclear. Mesoscale functional domains are established in visual cortex, but whether spatially distinct domains organize perceptual decisions across the brain is unknown. Here we used 7-T functional MRI at 1-mm isotropic resolution in two awake macaques performing a contrast-discrimination task to map brain-wide activity during sensation, decision formation and saccadic report. Voxel timecourses separated into three groups with distinct temporal profiles, associated with sensory, decision-related and action-related activity. Their spatial distributions formed a broad progression from visual cortex to parietal, prefrontal and motor regions, while revealing distinct response domains within these regions. Choice-related signals were distributed across sensory, associative, and motor systems before movement, including in visual cortex responses to physically identical stimuli that differed according to the animal's eventual choice. Moreover, within the intraparietal sulcus and other regions, mesoscale domains preferentially responsive to near-threshold conditions carried choice information under uncertainty, whereas domains responsive to high-contrast conditions carried choice information when evidence was strong. These findings reveal that perceptual decisions are organized across the brain through spatially differentiated mesoscale networks whose activity varies with task phase and sensory certainty. This spatial organization provides a framework for investigating how distributed neural signals support flexible choice.

neuroscience↗

bioRxiv2026

Engaging the host adaptive response to nutrient limitation delays cancer cachexia

Cancer cachexia is a debilitating wasting syndrome associated with involuntary weight loss, reduced appetite and food intake, adipose and muscle atrophy, and systemic inflammation with induction of a myriad of candidate cachexia factors. Using a multi-omic approach in a genetically engineered mouse model of lung cancer cachexia, we found that early circulating metabolic alterations preceded overt weight loss. Although both cachexia and fasting are characterized by a reduction in food intake, we show that the systemic metabolic changes in cachexia are distinct, indicating a lack of induction in the normal protective response to negative energy balance during cachexia. Cancer cachexia causes profound hepatic reprogramming, and activation of inflammatory programs, alongside muscle atrophy and elevation of circulating cytokines. However, targeting individual candidate cachectic factors such as IL-6, TNF-, GDF15, CCL2, LIF, and IL17A failed to rescue weight loss or prolong survival. In contrast, caloric restriction initiated prior to tumor induction elicited a program of protection during tumor progression that attenuated multi-tissue inflammatory and catabolic transcriptional responses, preserved lean mass, and prolonged survival. Together, these findings suggest that metabolic preconditioning broadly dampens systemic inflammation and delays the onset and progression of cancer cachexia.

cancer biology↗

bioRxiv2026

SIK3 links synaptic strength to sleep pressure through RhoA signaling

Sleep is regulated by homeostatic sleep pressure, which accumulates during wakefulness, triggering sleep, and dissipates during sleep, leading to wakefulness. Although recent evidence suggests that synaptic potentiation encodes sleep pressure, the intracellular mechanisms linking synaptic strength to sleep pressure remain unclear. Here we demonstrate that the sleep-promoting kinase SIK3 links synaptic strength and sleep pressure through RhoA signalling. We found that SIK3 is required for dendritic spine enlargement induced by chemical long-term potentiation (cLTP) in cultured cortical pyramidal neurons and positively regulates spine size in the prefrontal cortex in vivo. cLTP reduced RhoA activity in an SIK3-dependent manner during spine enlargement, whereas activation of RhoA reduced EEG delta density in vivo during non-rapid eye movement sleep (NREMS), an indicator of sleep pressure. SIK3 substrate screening identified several RhoA regulators including GEF-H1, and further biochemical analyses found that phosphorylation by SIK3 activates GEF-H1. However, contrary to our expectation, RhoA facilitation through pharmacological activation of GEF-H1 enlarged spine size in cultured neurons, and expression of constitutively active GEF-H1 increased NREMS delta density in a RhoA-dependent fashion. Together, these results indicate that SIK3 enlarges spine size and enhances NREMS delta density through two RhoA-dependent pathways, driving mutually opposing intermediate phenotypes. Our findings identify two clashing SIK3-RhoA signalling pathways that couple synaptic regulation to sleep homeostasis.

neuroscience↗

bioRxiv2026

System Identification and Control for Optogenetics in Mammalian Nucleocytoplasmic Transport

Optogenetics enables experiments in out-of-equilibrium conditions to clarify biological mechanisms and quantify biophysical parameters. However, modelling and control techniques to study mammalian cell biology under optogenetic perturbation remain underutilised. Here, we benchmark these methods within mammalian cells by steering nucleocytoplasmic transport via the optogenetic LEXY protein in outcome-driven microscopy. First, we employ system identification to obtain models that predict transport dynamics by minimising the prediction error. We quantify this prediction accuracy for one biophysical model and two black-box models. Second, we evaluate closed-loop control efficacy by steering transport along a predefined trajectory using model-free Proportional Integral (PI) control, model-based Linear Quadratic Regulation (LQR) and Model Predictive Control (MPC). Both the predictive models and the applied control techniques demonstrate robust performance against cell-to-cell variation. This biological variation is quantified by the parameter distributions obtained from model identification with single-cell trajectories. While we show that model-free techniques such as PI and gain-scheduled PI achieve steering without explict model knowledge, predictive architectures offer better performance under this cell-to-cell variation and time-varying setpoints. Moreover, black-box predictive accuracy suggests that this model-based control is possible, even when explicit mechanistic understanding is missing. Ultimately, we demonstrate that predictive modelling and optogenetics enable quantitative characterisation and precise manipulation of mammalian cells, while offering practical guidelines for the implementation of these techniques. SIGNIFICANCEOptogenetics provides the unique ability to steer cellular processes with light. Variable and localised light inputs allow us to extract more data and guide living cells to specific states. Despite this potential, application of predictive modelling and control techniques with optogenetics remain underutilised in mammalian cell biology. Here, we benchmark these techniques within mammalian cells to steer nucleocytoplasmic transport. Benchmarking these techniques demonstrates their direct applicability to mammalian systems, enabling the extraction of new biological insight in outcome-driven microscopy.

bioengineering↗

bioRxiv2026

Reactivating a schizophrenia risk gene-enriched prefrontal ensemble suppresses decision noise

Schizophrenia genetics and single-cell transcriptomics implicate prefrontal excitatory neurons and synaptic programs, but how these vulnerabilities alter circuit dynamics, behavior, and pharmacological targetability remains unclear. We identify a clozapine-responsive prefrontal ensemble enriched for schizophrenia risk genes that stabilizes value-guided choice. NMDA receptor hypofunction increased value-independent decision noise and weakened the ensembles pre-choice transient, while clozapine rescued both. Chemogenetic inhibition of the ensemble increased decision noise, demonstrating causality. By integrating receptor affinities with mouse and human single-cell transcriptomes, we designed a rational multi-receptor antagonist cocktail that reactivated the ensemble and rescued decision noise without increasing NREM sleep time or NREM delta power, in contrast to clozapine. These findings link schizophrenia genetics to cortical ensemble dynamics and establish ensemble-targeted pharmacology as a strategy for ameliorating pathological computations. One-Sentence SummaryTargeting a schizophrenia risk gene-enriched prefrontal ensemble suppresses decision noise without clozapine-like sedation.

neuroscience↗

bioRxiv2026

Structural basis of substrate recognition and allosteric inhibition in human B0AT2

The SLC6 family is a major target for neuropsychiatric therapeutics. Human B0AT2 (SLC6A15) regulates amino acid homeostasis and glutamatergic transmission and is linked to major depressive disorder, yet its transport and inhibition mechanisms remain unclear. Here we report cryo-EM structures of B0AT2 in apo state and in complex with substrates (proline, leucine, methionine) and inhibitors (loratadine, tiagabine), capturing outward-open, early substrate-bound intermediate, outward-occluded, and inward-open conformations along the transport cycle. These structures reveal an early substrate-sensing mechanism at the substrate-binding pocket (S1), where a substrate-dependent rotameric switch of Phe308 remodels pocket geometry to tune substrate accommodation and selectivity. Loratadine stabilizes an outward-occluded state via allosteric inhibition at the extracellular S2 pocket, whereas tiagabine stabilizes the inward-open state through cooperative multi-site inhibition involving S1 and two previously unrecognized intracellular cavities (S3 and S4). Together with functional assays, these data define the molecular basis of B0AT2 substrate selectivity and state-dependent inhibition. Notably, the two intracellular cavities are conserved across SLC6 transporters, reflecting a shared intracellular vestibular architecture and enabling rational design of conformation-selective modulators for neuropsychiatric disorders.

biophysics↗

bioRxiv2026

ArchaicSeeker 3.0: A deep-learning framework for scalable, haplotype-resolved inference of archaic introgression

Archaic introgression has left a significant mark on human genetic diversity, but reliably identifying introgressed segments remains a major challenge, especially with complex demographic histories and limited sample sizes. Existing methods often rely on demographic assumptions or cohort-specific parameter fitting, which compromises robustness and scalability. We introduce ArchaicSeeker 3.0 (AS3), a deep-learning framework designed for haplotype-resolved detection of archaic introgression. AS3 integrates a tract-scale sequence model with an overlap-aware reassembly approach and boundary refinement, enabling accurate, boundary-coherent reconstruction of introgressed segments across diverse genomic contexts. By leveraging a simulation-trained model, AS3 avoids inference-time recalibration, offering stable performance across unrepresented demographic scenarios and small cohorts. In extensive simulations, AS3 outperforms existing methods in precision, recall, and F1 score, while providing more continuous segments with accurate boundary localization. It demonstrates robustness in small-target regimes and varying marker densities. Applied to 3,453 genomes from 209 populations, AS3 shows strong concordance with existing introgression callers and identifies additional introgressed regions, including high-frequency AS3-specific introgressed segments supported by locus-level haplotype and phylogenetic analyses. AS3 provides a scalable, robust solution for detecting archaic introgression from single individuals to large biobank datasets, marking a significant advancement in the field of local ancestry inference and opening new possibilities for the study of human evolutionary genetics. ArchaicSeeker 3.0 is available at https://github.com/Shuhua-Group/ArchaicSeeker3.0.

bioinformatics↗

bioRxiv2026

Population Structure and Antimicrobial Resistance Gene Transfer of Respiratory Escherichia coli Isolated from Swine in China

ABSTRACPorcine respiratory diseases caused by extraintestinal pathogenic Escherichia coli (ExPEC) pose a severe threat to swine production and public health; however, research on respiratory tract-isolated ExPEC remains limited. This study comprehensively analyzed the genomic characteristics and antibiotic resistance gene (ARG) transfer potential of 441 ExPEC strains isolated from porcine lungs across 21 Chinese provinces (including 53 newly isolated strains from 2022-2024 and 388 NCBI-deposited strains). Phylogenetic analysis revealed that 84% of the isolates belonged to phylogroups A, B1, and C, with ST410, ST101, and ST88 as the predominant STs. The strains exhibited extensive ARG diversity, harboring 111 distinct ARG subtypes, with sul2 (81.4%), floR (73.5%), and tet (A) (68.0%) being the most prevalent. Importantly, critical "last-resort" antibiotic resistance genes (e.g., blaNDM-1/5, the mcr family, and tet (X4)) were also detected. Notably, 77.2% of the ARGs presented horizontal transfer potential, with plasmids (especially IncF family replicons) serving as core vectors, followed by integrons and transposons. Cooccurrence network analysis identified aph (3)-Ib, aph (6)-Id, sul2, and floR as core subnetworks driving multidrug resistance dissemination. Pangenomic analysis confirmed an open genome architecture, with core genes accounting for only 6%, reflecting the strains capacity to acquire exogenous genetic material via horizontal transfer. From the One Health perspective, these transferable ARGs can spread to the environment and humans through fecal discharge and the food chain. These findings underscore the importance of monitoring and controlling ExPEC infections in swine, as such strains can as reservoirs of ARGs, pose potential risks to human health, and may even act as sources of pathogenic agents responsible for human infections. IMPORTANCEPorcine respiratory ExPEC-induced diseases threaten swine production and public health, yet respiratory tract-isolated ExPEC research remains scarce. This study comprehensively analyzed 441 porcine lung ExPEC strains across 21 Chinese provinces, uncovering their dominant phylogroups, high ARG diversity (111 subtypes) and the presence of "last-resort" antibiotic resistance genes. We identified 77.2% of ARGs with horizontal transfer potential, plasmids (especially IncF family) as core vectors, and a core ARG subnetwork driving multidrug resistance. The open pangenome (6% core genes) highlights ExPECs strong capacity to acquire exogenous genes. These findings fill the research gap of respiratory ExPEC, clarify ARG transmission mechanisms in swine ExPEC, and provide critical genomic data for One Health-based AMR surveillance and control, guiding targeted strategies to mitigate ARG spread from swine to humans and the environment.

microbiology↗

bioRxiv2026

Contribution of murine strain background to Na+ reabsorption in the kidney

Kidneys play an essential role in balancing fluid and electrolyte levels. Two mouse strains, C57Bl/6 and 129S2/SV, are routinely used to study renal physiology in laboratory settings, and prior observations suggest that significant differences in salt and water handling exist between them. This study aims to further establish the sources of these observed differences at both expressional and functional levels, in male and female mice. At baseline, male 129S2/SV mice displayed decreased Na+ and increased K+ plasma concentrations compared to C57Bl/6 males, while no statistical differences were observed between female mice. Interestingly, 129S2/SV male mice had lower glomerular density than C57Bl/6 males. Immunoblotting shows that 129S2/SV mice of both sexes had increased expression of NHE3 and NKCC2 compared to their C57Bl/6 counterparts. Both total and phosphorylated NCC were more abundant in female mice as compared to males, indicating sexual dimorphism. Furthermore, 129S2/SV females had higher expression of total and phosphorylated NCC compared to C57Bl/6 females. In contrast, the expression of SGLT2, ENaC subunits, and Na+/K+-ATPase were comparable between C57Bl/6 and 129S2/SV mice of both sexes. When challenged with diuretics intended to block NKCC2, NCC or ENaC, 129S2/SV male mice responded with a smaller diuresis and natriuresis than their C57Bl/6 counterparts. Taken together, our data suggest that differential expression of key Na+ transporters along the nephron contributes to differences in Na+/K+ homeostasis between these two mouse strains. NEW & NOTEWORTHYWe assessed the influence of genetic background on the expression of key Na+ transporters along the nephron in two commonly used inbred mouse strains, C57Bl/6 and 129S2/SV. We found that the kidney expression of NHE3, NKCC2, and NCC are strain dependent. Additionally, murine strain significantly contributes to the diuretic responses induced by hydrochlorothiazide, amiloride, and furosemide.

physiology↗

bioRxiv2026

Sex-specific Genetic Regulatory Effects in Chickens

Sexual dimorphism is a defining vertebrate feature, yet its sex-specific molecular architecture remains poorly understood. Here we established a sex-balanced, uniformly reared chicken cohort to map this landscape, integrating individual whole-genome sequencing with 7,969 bulk and 779,380 single nucleus transcriptomes across 32 tissues from 280 birds. We identified 495,098 independent expression quantitative trait loci for 20,194 genes, including 10,937 loci modulated by cell-type composition. Notably, 340 genes were regulated by 449 loci in a sex-dependent manner, significantly enrichment in endocrine tissues like adipose and the adrenal gland. Furthermore, we fine-mapped 1,219 structural variants, demonstrating their unique roles to tissue- and sex-specific expression beyond SNPs. Ultimately, we showed the utility of these regulatory effects in elucidating the molecular basis of metabolism and complex traits in both chickens and humans. This comprehensive atlas of regulatory effects provides profound insights into the genomic and molecular basis of sexual dimorphism in vertebrates.

genomics↗

bioRxiv2026

Predicting mutation-rate variation across the genome using epigenetic data

Mutation rate variation is a fundamental driver of evolution, yet how it is locally patterned across genomes and structured by chromatin context remains unresolved. Here, we integrate genome-wide profiles of histone marks, DNA methylation and chromatin accessibility in Arabidopsis thaliana with de novo mutation data to model mutation probability at the level of coding sequence (CDS). Using non-negative matrix factorization, we identify 15 combinatorial epigenetic patterns whose graded mixtures stratify CDSs into six classes with distinct mutation probabilities. A generalized linear model based on pattern weights predicts local mutation probability and outperforms models based on sequence context, expression and classical genomic categories. These patterns capture context-dependent variation that is obscured by gene-level summaries and single-feature analyses. Cluster-level differences are partly retained in mutation-accumulation lines, indicating persistence into heritable mutational input. Under hypoxia, stress-responsive chromatin remodeling redistributes epigenetic contexts associated with higher predicted mutation probability toward hypoxia-responsive genes and DNA-repair pathways. Together, our results provide a CDS-resolved and interpretable framework linking combinatorial epigenomic context to mutational input, clarifying how dynamic chromatin states shape local mutation-rate heterogeneity.

bioinformatics↗

bioRxiv2026

IBDkb: an AI-enhanced integrative knowledge base for inflammatory bowel disease research and drug discovery

IBDkb (Inflammatory Bowel Disease Knowledge Base; https://www.biosino.org/ibdkb) is a freely accessible, integrated web-based platform that systematically curates and harmonizes multi-source data related to inflammatory bowel disease (IBD). To address the fragmentation and therapeutic gaps in existing specialized resources, IBDkb establishes a unified framework featuring advanced full-text search, interactive visualizations, cross-module knowledge graphs, and AI-powered utilities for real-time literature retrieval, trend analysis, text/PDF interpretation, and domain-specific conversational assistance. The platform currently integrates 98,453 research articles, 3,390 clinical trials, 200 investigational drugs, 200,606 bioactive compounds, 103 therapeutic targets, 77 experimental models, 12 pathogenesis summaries, and 15 treatment strategies. These integrated tools facilitate efficient exploration of complex associations among drugs, targets, trials, and mechanisms, thereby accelerating hypothesis generation and translational research in IBD. The platform is openly available without registration and supports data downloads. A case study on structure-aware drug comparison further demonstrates its utility in facilitating cross-disease drug repositioning hypotheses.

bioinformatics↗

bioRxiv2026

Positron Emission Tomography of CD47/SIRPα Axis and Image-Informed Therapeutic Design

CD47/SIRP immune axis is of substantial clinical interest for innate cancer immunotherapy. Development on this axis has largely focused on monoclonal antibody agents and combination therapy strategies. Clinical use is challenging due to dose limiting side effects and severe anemia. Better understanding of the whole-body dynamics of CD47/SIRP can be used to improve the developmental and therapeutic strategies targeting this axis. Herein, we developed anti-CD47 and anti-SIRP radiotracers with good yields and stability. CD47/SIRP biodistribution showed consistent whole-body results in healthy and colorectal cancer (CT26) allograft mice, demonstrating significant uptake in normal organs liver and spleen in addition to tumor accumulation of these agents. Enhancing immunogenicity via low-dose radiotherapy had no impact on over-all biodistribution but caused small, significant changes for anti-SIRP tumor uptake. Antibody PEGylation of the anti-SIRP tracer was further able to modify the whole-body distribution and reduce splenic uptake. These findings suggest that SIRP targeted agents may benefit from co-therapies and drug delivery systems to optimize tumor uptake. Our work highlights the importance of in vivo molecular imaging in addition to in vitro and ex vivo assays when evaluating therapeutic designs.

bioengineering↗

bioRxiv2026

INS-fMRI reveals a mesoscale limbic organization associated with medial pulvinar in primates

The experience of emotion comprises not only the feelings (happiness, sadness), but also behavioral expression, internal awareness, and the bodys physiological response. However, it remains unclear how the brain integrates these disparate aspects of emotion. Here, to examine functional connectivity in the limbic system of macaque monkeys, we combined focal Infrared Neural Stimulation of a sensory gateway (medial pulvinar PM), with ultra-high-field 7T functional magnetic resonance imaging (INS-fMRI). We find connected sites are mesoscale (millimeter-scale) in size and arranged in patchy patterns across cingulate, insula, and amygdala. Non-overlapping connections evoked from three sequential stimulation sites in PM form clusters of multi-site integration, and appear related to known functional organization within these limbic regions. We suggest these mesoscale functional connections link the limbic axes of motor expression (cingulate), interoception (insula), and emotion-related processing (amygdala), and that, much like visual system, the limbic system is fundamentally quite orderly at mesoscale. Our results underscore the importance of millimeter-scale precision and organization in diagnosis and treatment of affective disorders.

neuroscience↗

bioRxiv2025

FOLR1-targeted Actinium-225-based Alpha-particle Therapy Eliminates Ovarian Cancer

Despite the advancement in therapies, ovarian cancer treatment is challenging due to poor prognosis and high relapse associated with acquired resistance. Targeting overexpression of FOLR1 in ovarian cancers has proven to be an attractive strategy. The recent FDA approval of FOLR1 targeted antibody drug conjugate has shown promising results albeit resistance with repeated use appears inevitable. Emerging targeted alpha-particle therapies, particularly Actinium-225 (225Ac), for treating refractory cancers have opened avenues for improved therapeutic options. The success of alpha-particle therapy relies on tumor specific delivery of the alpha emitters. Herein we describe the first example of FOLR1-targeted 225Ac alpha-particle therapy for treatment of ovarian cancer. Longitudinal PET imaging demonstrated high tumor-specific uptake of FOLR1 in SKOV3 xenografts. FOLR1-targeted 225Ac demonstrated high therapeutic efficacy achieving marked tumor regression, 80% survival and 40% complete response. The therapy resulted in tumor specific double stranded DNA damage, and no obvious toxicity was observed in normal tissues. Estimated human dosimetry showed high absorbed dose for tumor and minimal absorbed dose for healthy tissues establishing its safety. In totality, FOLR1-targeted 225Ac alpha-particle therapy is an efficacious and safe treatment with high feasibility for clinical translation to fight against ovarian cancer.

bioengineering↗

bioRxiv2025

PIWIL3-piRNA Pathway Is Essential for Rabbit Oogenesis and Embryogenesis via Broad Regulation of the Transcriptome and Proteome

Female infertility represents a significant challenge in reproductive medicine. Although it is known to be primarily due to oogenic and early embryonic failures, the molecular mechanisms underlying these failures remain elusive. The Piwi-piRNA pathway is crucial for gametogenesis in diverse organisms. Yet, its role in mammalian female fertility is unclear. This is partly because most studies are done in mice, which contain only PIWIL1, PIWIL2, and PIWIL4 that are essential for spermatogenesis but not for oogenesis. PIWIL3 emerges in higher mammals and is highly expressed in human oocytes. Interestingly, female PIWIL3-knockout golden hamsters exhibit only reduced fertility without detectable defects in oogenesis. This has left the function of PIWIL3 in higher mammals, including humans, unexplored. Here, we discovered that PIWIL3 in the rabbit (Oryctolagus cuniculus) shares high homology with human PIWIL3. It is the predominant PIWI protein in oocytes in both species. Using CRISPR-cas9-mediated knockout, we demonstrated that rabbit PIWIL3 is essential for female fertility. Its loss leads to severe defects in oogenesis. Moreover, embryos lacking maternal PIWIL3 arrest developmentally at the 8-cell stage. Mechanistically, rabbit PIWIL3 binds [~]18-nucleotide piRNAs, mirroring the behavior of human PIWIL3, and is critical for piRNA biogenesis. Moreover, it regulates transcriptomic and proteomic landscapes and silences a broad array of transposons during late oogenesis yet activates another set of transposons during early embryogenesis. These findings establish PIWIL3 as a pivotal dual regulator of gene expression and transposon activity, which is essential for oogenesis and early embryogenesis in non-rodent mammals, potentially including humans.

developmental biology↗

bioRxiv2025

Integrative metabolome-genome analysis reveals the genetic architecture of metabolic diversity in sorghum grain

Natural variation in the grain metabolome plays a central role in shaping nutritional quality and end-use traits in grass crops. Understanding the genetic basis of this metabolic diversity is therefore essential, yet population-scale integration of metabolomics and genomics remains limited in sorghum, a climate-resilient C4 crop renowned for its exceptional heat and drought tolerance. Here, we integrated large-scale untargeted metabolomic profiling, population genomics, and artificial intelligence (AI)-based machine learning to systematically dissect grain metabolic diversity and its genetic architecture in sorghum. Untargeted metabolomic profiling of mature grains of the Sorghum Association Panel (SAP) identified 4,877 compounds, revealing extensive quantitative variation relevant to grain nutritional improvement. Metabolite-based genome-wide association studies (mGWAS) identified [~]4.15 million significant SNP-metabolite associations, revealing the heterogeneous genetic architecture of metabolic traits. Associated variants were enriched in genic and regulatory regions but depleted in intergenic regions, consistent with functional constraint. A total of 38 metabolite gene clusters revealed coordinated genetic control of core metabolic pathways. We further applied machine learning to identify key metabolites that underlie grain color variation and to prioritize associated candidate genes, demonstrating the utility of predictive models integrating genotype, metabolome, and end trait. Collectively, this work establishes a population-scale atlas of sorghum grain metabolomic and genetic diversity, available through the Sorghum Grain Metabolite Diversity Atlas (SorGMDA). This resource enables integrated metabolomics and genomic analyses and supports systems-level breeding strategies for improving grain nutritional quality.

genomics↗