Biology subjects

Qin, L.

Publications and source records attributed to Qin, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Seasonal influenza vaccine strain selection by quantifying viral fitness

The long-standing challenge of seasonal influenza vaccines providing poor protection is attributed to the rapid and continuous evolution of the virus. In theory, the recommendation of vaccine strain is to predict the dominant strain with best fitness in the upcoming season. Here, we develop FutureFlu, a biologically-grounded framework that quantifies the fitness score of influenza variants in upcoming seasons, by integrating metrics on three levels: molecular genetic divergence, individual immune escape, and population-scale transmission dynamics. The fitness scores of influenza variants present strong positive correlation with their actual observed frequencies in the next seasons. Validation across 24 seasons of three influenza subtypes shows FutureFlu recommends antigenically matched vaccine strains more frequently than annual recommendations, particularly for challenging subtypes: 83.3% versus 45.8% seasons for A/H3N2, and 75.0% versus 33.3% seasons for B/Victoria. Furthermore, FutureFlu significantly outperforms the currently used methods in vaccine strain selection whether or not there is available antigenic data from hemagglutination inhibition (HI) assay, which provides a valuable supplement for WHO vaccine recommendation. To support global public health implementation, an open online platform (futureflu.com.cn) has been established to offer real-time viral fitness predictions and vaccine recommendations.

evolutionary biology↗

bioRxiv2026

Decorin-mediated Extracellular Matrix Stabilization Maintains Cartilage Integrity During Aging

Aging is a primary risk factor for osteoarthritis (OA), yet the mechanisms that preserve extracellular matrix integrity in long-lived connective tissues remain poorly defined. The function of articular cartilage depends on maintaining extracellular matrix integrity over a lifetime of mechanical use. Here we identify failure of matrix stabilization as an initiating mechanism of age-associated OA. Cartilage-specific deletion of decorin in mature mice disrupted the superficial collagen II fibrillar network, reduced aggrecan retention, and impaired poroelastic fluid pressurization by 9 months of age, preceding substantial transcriptional changes in resident chondrocytes. With advancing age, these matrix defects culminated in cartilage erosion, fibrotic remodeling, and spontaneous OA by 18 months. Mechanistically, decorin attenuated force-induced collagen II fibril realignment and reinforced the superficial fibrillar network, preserving matrix architecture under sustained physiological loading. These findings establish decorin-mediated extracellular matrix stabilization as a critical determinant of cartilage longevity and support a matrix-first model of age-associated degeneration.

biophysics↗

bioRxiv2026

Evolutionary Origins and Synthetic Reconstruction of Gingerols

How new enzymatic activities become integrated with existing metabolic networks to generate lineage-restricted plant chemistry remains a central question in metabolic evolution, exemplified by gingerol biosynthesis in Zingiberaceae, whose complete enzymatic basis has remained elusive. Here, we resolve this problem by elucidating the evolutionary origins and the full biosynthetic pathway of gingerol through single-cell transcriptomics, functional screening, structural biology, comparative genomics and pathway reconstruction. A coordinated metabolic program operates in ginger oil cells, thereby guiding the identification of diketide-CoA synthases, gingerol synthases (GS) and gingerol reductases that together constitute the complete pathway. GS remodels the conserved type III polyketide synthase scaffold to organize a fatty acyl-CoA and a phenylpropanoid-derived intermediate for gingerol formation. Furthermore, GS arose through duplication and limited active-site remodeling of a curcumin synthase-like enzyme, accompanied by coordinated recruitment of precursor-supply and reduction pathways. Translating these principles into yeast achieves the first de novo microbial production of 6-gingerol from glucose at 12.4 mg/L. These findings reveal the evolutionary logic by which plants recruit and coordinate novel enzymatic activities to establish lineage-restricted metabolic program, providing a framework for understanding and engineering specialized metabolism across the plant kingdom.

synthetic biology↗

bioRxiv2026

Medulloblastoma Forms Symbiotic Metabolic Partnerships with Macrophages to Establish Leptomeningeal Metastases

Leptomeningeal metastases are the primary source of morbidity and mortality for pediatric medulloblastoma patients. Due to limited surgical sampling of metastases in patients, little is understood of the mechanisms of metastasis. Here, we identify biologically distinct quiescent small metastases (designated as micrometastases) and mitotically active larger metastases (macrometastases). Macrometastases are more metabolically active than micrometastases and contain higher levels of lipids, particularly cholesterol. Macrometastases secrete CXCL12, which attracts lipid-laden macrophages into the tumor. Lipid-laden macrophages upregulate the cholesterol transporter ABCG1, promoting the efflux of free cholesterol, which is then taken up by tumor cells via the HDL receptor SCARB1. CXCL12-driven macrophage recruitment and exogenous cholesterol are sufficient and necessary to drive progression of medulloblastoma leptomeningeal metastases in vivo. High fat diets drive metastatic progression in vivo. Dietary or pharmacological interventions targeting the CXCL12-SCARB1-cholesterol axis represent therapeutic strategies to either prevent or treat medulloblastoma leptomeningeal metastases.

cancer biology↗

bioRxiv2026

Yawning reveals energy-dynamics mismatch and neural inertia across state transitions

Yawning is a highly conserved behavior, yet its neural dynamics across arousal state transitions remain poorly understood. Classical reflex models fail to account for the precise timing of yawns during large-scale changes in brain network organization. Here, we investigated the neural signatures of yawning using simultaneous electroencephalography (EEG), electromyography (EMG), and kinematic recordings in a beagle model during wakefulness and propofol anesthesia. Propofol-associated yawning exhibited marked temporal asymmetry, with 89.2% of events occurring during emergence from anesthesia. To resolve the fast neural dynamics surrounding these events, we applied empirical mode decomposition coupled with the Hilbert-Huang transform (EMD-HHT) analyses. Across induction, recovery, and wakefulness, yawning was consistently associated with a transient decoupling between local and global network dynamics: a brief increase in local {gamma}-band power coincided with a drop in network flexibility, quantified by instantaneous frequency volatility; IFV). We termed this reproducible motif as "Energy-Dynamics Mismatch" (EDM). A machine learning classifier leveraging EDM features reliably decoded the brain state immediately preceding yawning. We further validated the presence of this signature in an independent human cohort during anesthesia induction. These findings indicate that yawning is not a passive reflex, but is tightly linked to moments of network instability during state transitions. From a computational perspective, EDG may reflect a transient "control effort" that preserves information integration in the presence of "neural inertia." This dynamic signature may provide a quantitative biomarker for monitoring arousal transitions brain-computer interface (BCI) interface state-alerting. Significance StatementYawning is a ubiquitous and evolutionarily conserved behavior, yet its neural basis remains elusive. Using high-resolution neural recordings in a cross-species model, we show that yawning is not a passive reflex, but reliably coincides with a distinct, transient brain-state signature. Specifically, yawning occurs when local high-frequency cortical activity briefly increases while global network flexibility decreases - a pattern we term an "Energy-Dynamics Mismatch" (EDM). We propose that EDM reflects a compensatory neural process engaged during moments of network instability, consistent with overcoming neural inertia to preserve information integration. By identifying this conserved neural marker, this work advances the biological understanding of yawning and suggests a potential biomarker for detecting critical brain states in future BCI.

neuroscience↗

bioRxiv2026

Mechano-activation of synovial fibroblasts and macrophages during OA progression in the dynamically stiffening synovial microenvironment

ObjectiveDuring osteoarthritis (OA) progression, the synovial membrane undergoes profound structural and compositional remodeling and fibrosis. We sought to elucidate how evolving synovial microenvironmental mechanics during fibrotic remodeling influence cell behavior and drive the progression of synovial pathology. MethodsSkeletally-mature male C57BL/6J mice were subjected to destabilization of the medial meniscus (DMM). To control for surgical confounders, both sham-operated and unoperated mice were included, with evaluation at 4- and 8-weeks. Synovial micromechanics were quantified via atomic force microscopy (AFM). Single-cell RNA sequencing (scRNA-seq), RNA fluorescence in situ hybridization (FISH), and flow cytometry were employed to investigate cellular heterogeneity, spatial organization, and crosstalk within fibrotic and non-fibrotic synovial niches. ResultsProgressive fibrotic remodeling and marked matrix stiffening were observed in DMM-operated synovium but absent in sham- and un-operated controls. While both sham and DMM joints mounted an acute stromal and immune response to surgery, these changes resolved over time in sham conditions but persisted in DMM synovium. During disease progression, distinct functional subsets of synovial fibroblasts and immune cells emerged, with mechanosignalling pathways and distinct immune cell-fibroblast crosstalk robustly activated within DMM-induced fibrotic microenvironments. ConclusionThis study demonstrates the complex cellular dynamics and crosstalk that differentiate the evolution of the pathological synovial response in the fibrotic DMM condition relative to surgical sham controls. Our findings highlight mechanotransduction as a central mechanism driving OA synovial pathogenesis and underscore the utility of the DMM model as a platform to dissect the molecular underpinnings of synovial fibrosis.

bioengineering↗

bioRxiv2026

Reinnervation of Muscle Targets Enhances the Separability of Motor Unit Signals Following Peripheral Nerve Transfers

After amputation, advanced prosthetic limbs offer a promising means of restoring motor function. However, state-of-the-art prostheses often rely on aggregate electromyogram (EMG) signals to decode motor intention, which limits their ability to replicate natural limb movements. Decomposing EMG signals into individual motor unit components has shown potential for more natural control, but distinguishing between individual units can be challenging when nearby signals overlap. This study demonstrates that muscle target reinnervation surgeries can naturally increase physical separation between motor unit signals, thereby mitigating this overlap. Reinnervation of individual motor units is evaluated in a rodent hindlimb model after direct nerve-to-muscle implantation. Histological and electrophysiological analyses reveal that structural changes following reinnervation surgery result in beneficial motor unit signal changes, particularly improving spatial separation between motor unit signals compared to those in intact muscle. This spatial separation contributed to fewer instances of complex, overlapping signals in reinnervated muscle recordings. Motor unit signals were leveraged to provide a proof-of-concept of precise control of a virtual prosthesis for the first time after direct nerve-to-muscle implantation surgery. These findings highlight the potential of reinnervated muscle targets as key biological interfaces that facilitate motor unit separation, reducing the burden on decomposition algorithms and improving prosthetic control.

bioengineering↗

bioRxiv2026

MicroRNA Networks Driving Skeletal Aging and WNT Pathway Modulation

Cellular senescence is a key mechanism of skeletal aging in both physiological and accelerated conditions, such as radiotherapy. This study aimed to identify common differentially regulated microRNAs (miRs) across these contexts. We performed miR sequencing on three models: femurs from young (5-month-old) versus old (24-month-old) mice; focally radiated versus non-radiated femurs; and osteocytes from young versus old mice. Osteocytes were included in the comparison, as they have the longest lifespan in the mineralized bone matrix and they form 90-95% of all mesenchymal bone cell types. Among the three groups, miR-135a-5p and miR-671-5p were the common (i.e., shared) miRs that were downregulated, and miR-183-5p, a miR that regulates the WNT pathway, was the only shared upregulated miR, while miR-155-5p, a miR that regulates the Senescence-Associated Secretory Phenotype (SASP), was elevated in two conditions. The WNT-pathway has been positively associated with bone health and Sclerostin, a WNT-pathway inhibitor produced and secreted by osteocytes, has been implicated in accelerated skeletal deterioration following radiation. Thus, we used a neutralizing antibody to Sclerostin (Scl-Ab), to assess genes related to the WNT pathway and senescence, which are regulated by miR-183-5p and miR-155-5p, respectively. We further performed miR sequencing in radiated bones from mice treated with Scl-Ab and identified miR-133a-3p, a key miR that inhibits bone metabolism and function, which is upregulated in accelerated skeletal aging (i.e., focal radiation) downregulated by Scl-Ab. Overall, our study identifies potential regulatory gene pathways that modulate skeletal aging in the presence and absence of a WNT activator, Scl-Ab.

genomics↗

bioRxiv2025

Turning aging cells into a live vaccine: engineered senescent cancer cells with adjuvant celecoxib for immunotherapy

The immunoactivation effects of senescent tumor cells are a potential avenue for cancer therapy. They can act as antigen reservoirs for cancer vaccination, but how to maintain strong immunogenicity to induce a robust immunity is underexplored. In this study, we developed an engineered live vaccine composed of hydrogel-encapsulated senescent tumor cells and liposomal celecoxib (STCs+CLX-Lipo@Gel). This vaccine prolongs the in vivo persistence of senescent tumor cells and utilizes liposomal celecoxib (COX2 inhibitor) to promote the recruitment and maturation of dendritic cells (DC). Notably, a single dose can significantly delay melanoma growth by eliciting robust immunity. The vaccine extended the survival of mice with melanoma brain metastases. Moreover, this strategy also demonstrated high efficacy against orthotopic pancreatic tumors. This study presents a comprehensive strategy to boost the immunogenicity of whole-tumor-cell vaccines by leveraging senescent tumor cells and COX2 inhibition, with treatment efficacy in various tumor models. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/694320v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@f08fforg.highwire.dtl.DTLVardef@117d0aborg.highwire.dtl.DTLVardef@849665org.highwire.dtl.DTLVardef@adcf83_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic summary.C_FLOATNO Schematic illustration of the preparation of live-cell vaccines and the tumor-specific immune responses elicited by the vaccine. Created with BioRender.com. C_FIG

bioengineering↗

bioRxiv2025

Endothelial cell MHC molecules are necessary and sufficient to reject 3D-printed human skin grafts in an advanced human immune system mouse

Vascularized skins were 3D-printed using single donor human fibroblasts, pericytes, keratinocytes and endothelial cells (ECs), the latter either unmodified (WT-ECs) or deleted of MHC molecules (KO-ECs). Adult MISTRG6 immunodeficient mice neonatally inoculated with adult human hematopoietic stem cells (HSCs) received printed skin allogeneic to the HSCs and were boosted 3 weeks post-grafting with human peripheral blood mononuclear cells (PBMCs) autologous to the HSCs. HSC inoculation alone produced low levels of circulating human myeloid and lymphoid cells without affecting grafts; PBMC boosting dramatically increased circulating human CD4+ T cells and boosted CD8+ T cells only in mice with WT-EC grafts. These grafts became infiltrated by human macrophages, dendritic cells, CD4+ and CD8+ T cells, and showed evidence of rejection. Shared T cell clones were present in skin and spleen. KO-EC grafts had minimal infiltration of graft or spleen without rejection despite MHC molecule expression on other graft cell types.

immunology↗

bioRxiv2025

Deciphering the Antigenic Evolution of Seasonal Influenza A Viruses with PREDAC-Transformer: From Antigenic Clustering to Key Site Identification

Seasonal influenza viruses undergo continuous antigenic drift due to mutations in the hemagglutinin (HA) protein, rendering vaccines ineffective and posing a significant global public health challenge. Existing computational models can predict antigenic relationships but generally lack interpretability, making it difficult to reveal the molecular determinants driving antigenic changes. To address this, we developed PREDAC-Transformer, an end-to-end deep learning framework that integrates sequence, physicochemical, and evolutionary features, and employs a self-attention mechanism to capture long-range dependencies relevant to antigenicity. More importantly, we introduce the integrated antigenicity score, which combines attention-based attribution with information-theoretic metrics to provide continuous quantification and ranking of the antigenic contributions of individual amino acid site. Our results demonstrate that PREDAC-Transformer not only significantly improves the accuracy of antigenic relationship prediction but also successfully recapitulates major historical antigenic cluster transitions. Using integrated antigenicity score, we systematically identified two classes of key sites: global key sites with sustained impact on antigenic evolution, and cluster-transition determining sites that drive cluster transitions. These sites include most canonical epitopes and reveal additional functional residues previously overlooked, which may influence immune escape via cooperative effects or glycosylation. Collectively, these findings advance our understanding of influenza antigenic evolution and provide novel insights for refining computational models. PREDAC-Transformer achieves high-precision prediction while attributing antigenic differences to individual residues, thereby linking viral genomic variation, antigenic change, and public health decision-making. This framework has the potential to reduce experimental burdens in influenza surveillance and assist in vaccine strain recommendation, thereby supporting global influenza control efforts.

bioinformatics↗

bioRxiv2025

Absolute hand determination of glycofibrils from natural sources in cryo-EM

Glycans are one of the four fundamental macromolecules that constitute life. However, compared with proteins and nucleic acids, our understanding of the structures and functional mechanisms of glycans remains limited. Moreover, it is generally challenging to obtain high-resolution three-dimensional structures of glycans. Recent studies have demonstrated the potential of the CryoSeek strategy in enabling high-throughput structural determination of glycans, thereby presenting novel avenues for their structural investigation. Meanwhhile, unlike proteins, near atomic resolution density maps of glycofibrils do not inherently facilitate the determination of absolute hand, which is a prerequisite for building atomic models of glycofibrils. Existing absolute hand determination methods have severe limitations in the cases of glycofibrils from natural sources. In this study, we introduce Ahaha, a straightforward and efficient method for determining such absolute hand in cryo-EM. With their absolute hand measured by Ahaha, we built atomic models of four glycofibrils derived from a natural water sample, facilitating the study of glycans. The online service of Ahaha is available at https://cryoseek.org/ahaha.

biophysics↗

bioRxiv2025

Integrative genomic and transcriptomic analyses uncover regulatory landscape of symbiotic nitrogen fixation in soybean natural population

Symbiotic nitrogen fixation (SNF) is a key trait in legume productivity, yet the genetic and regulatory basis underlying its natural variation remains poorly understood. Here, we integrated genome, transcriptome, and chromatin accessibility data from a soybean diversity panel comprising 380 accessions, including 108 wild and 272 cultivated lines. Genome-wide association studies (GWAS) detected multiple loci for SNF traits but with limited resolution due to polygenic architecture and environmental influences. Independent component analysis (ICA) identified 136 co-expression modules; ten ICs were strongly correlated with SNF phenotypes and enriched in circadian clock components (e.g., GmLHY1a/b), lipid metabolism, or defense signaling pathways. Transcriptome-wide association studies (TWAS) linked 1,453, 806, and 178 genes to NFP, NW, and NFE traits, respectively. Among TWAS hits, 185 transcription factors were identified, with 39.0% overlapping selective sweeps, suggesting regulatory evolution under domestication. To further dissect expression regulation, we performed eQTL mapping and detected 4,654 significant eQTLs, including 1,241 local (cis), 2,505 distal (trans), and 908 mixed. By integrating ATAC-seq data from sorted nodule nuclei, we found that eQTLs, particularly local eQTLs, are significantly enriched within open chromatin regions, indicating their regulatory potential. Notably, we validated the circadian clock gene GmLHY1b as a negative regulator of nodulation using CRISPR mutagenesis and CUT&Tag. Our integrative study provides comprehensive genomic and transcriptomic resources from a diverse soybean population, offering novel insights into SNF regulatory networks and a valuable foundation for future SNF research and soybean improvement.

plant biology↗

bioRxiv2025

Senescent mast cells contribute to the progression of benign prostatic hyperplasia via SCF/c-KIT mediated endothelial-mesenchymal transition

Benign prostatic hyperplasia (BPH) is a common age-associated urological condition characterized by stromal expansion, but its cellular origins and regulatory mechanisms remain unclear. In this study, we identified endothelial-to-mesenchymal transition (EndMT) as a contributor to stromal cell accumulation in BPH. Using single-cell transcriptomic analysis, endothelial lineage tracing in mice, and validation in human samples, we showed that senescence-associated mast cells increased the expression of vascular endothelial growth factor A (VEGFA) and transforming growth factor-beta 1 (TGF-{beta}1) through the stem cell factor (SCF)/c-KIT-MAPK-JUND signaling pathway, thereby inducing EndMT in endothelial progenitor cells. Stromal fibroblasts express SCF, promoting mast cell activation and establishing a feedback loop that supports continued stromal proliferation. Intriguingly, inhibition of mast cell activation reduces EndMT and attenuates prostate enlargement in vivo. Thus, these findings revealed a senescence-linked immune-stromal interaction in the aging prostate and identify potential targets for therapeutic intervention in BPH.

cell biology↗

bioRxiv2025

Prg4+ fibro-adipogenic progenitors in muscle are crucial for bone fracture repair

Clinically, compromised fracture healing often occurs at sites with less muscle coverage and muscle flaps can provide the necessary healing environment for appropriate healing in severe bone loss. However, the underlying mechanisms are largely unknown. Here, we established a mouse reporter model for studying muscle cell contribution to bone fracture repair. Analyzing skeletal muscle scRNA-seq datasets revealed that Prg4 marks a fibro-adipogenic progenitor (FAP) subpopulation. In mice, Prg4+ cells were specifically located in the skeletal muscle, but not at the periosteum or inside cortical bone. These cells expressed FAP markers, responded to muscle injury, and became periosteal cells under normal and muscle injury conditions. Fracture fragmented muscle fibers, rapidly expanded Prg4+ FAPs at the injury site and promoted their migration into the fracture site. Later, they gave rise to many chondrocytes, osteoblasts, and osteocytes in the outer periphery of callus next to muscle. In repaired bones, the descendants of Prg4+ FAPs were detected as mesenchymal progenitors in the periosteum and osteocytes at the prior fracture site. A second fracture activated those cells and stimulated them to become osteoblasts in the inner part of callus. Importantly, ablation of Prg4+ FAPs impaired fracture healing and functional repair. In an intramembranous bone injury model (drill-hole), Prg4+ FAPs became periosteal cells, but their contribution to bone defect repair was significantly less than in fractures. Taken together, we demonstrate the critical role of FAPs in endochondral bone repair and uncover a novel mechanism by which mesenchymal progenitors transform from muscle to cortical bone. Significance statementFracture healing is often impaired in areas with less muscle coverage, but the mechanisms behind this are poorly understood. In this work, we uncovered a critical role of specific muscle cells, known as Prg4+ fibro-adipogenic progenitors (FAPs), in bone regeneration. Using mouse models, we show that these muscle-resident mesenchymal progenitors expand after bone injury, migrate to the fracture site, transform into various bone cells in the fracture callus, and eventually become bone surface progenitors after the bone is healed. This finding highlights the importance of muscle cells in endochondral fracture repair and reveals a novel crosstalk mechanism between muscle and bone tissues. Future studies targeting these muscle progenitor cells could develop new treatments for delayed and nonunion fractures.

cell biology↗

bioRxiv2025

Discover the Maze-like Pathway for Glabridin Biosynthesis

Tailoring enzymes diversify plant metabolite scaffolds through complex, context-dependent modifications, generating maze-like biosynthetic networks that complicate metabolic pathway reconstruction. Here, we systematically deconstructed and reconstructed the biosynthetic network of glabridin, a valuable skin-whitening isoflavone from Glycyrrhiza. By integrating metabolic pathway mining with genome and 183 transcriptomes, we identified four functional routes among sixteen theoretical possibilities and uncovered a previously uncharacterized, ladder-like multi-route tailoring network. Reconstruction of such architecture in yeast revealed metabolic redundancy and interconnectivity confer unexpected robustness, enabling higher production efficiencies compared to a single-route design. Further modular engineering enabled the de novo biosynthesis of glabridin in yeast. Our work establishes a framework for reconstructing metabolic mazes and demonstrates that multi-route architectures can be harnessed to enhance the robustness and productivity of cell factories.

synthetic biology↗

bioRxiv2025

Cortical reactive microglia activate astrocytes, increasing neurodegeneration in human alcohol use disorder

Reactive microglia are associated with multiple brain diseases that may have specific disease phenotypes. Studies of human cortical microglia in alcohol use disorder (AUD) have characterized reactive microglial subtypes by transcriptome or histology. Preclinical studies have found proinflammatory signaling and microglia contribute to increases in alcohol drinking and preference, behaviors unique to AUD. This study of post-mortem human AUD combines microglial immunoreactivity (+IR) protein and changes in microglial gene expression (mRNA) in human orbital frontal cortex (OFC) in an effort to better characterize the reactive microglia associated with AUD. Since reactive microglia are linked to reactive astrocytes (GFAP+IR), oxidative DNA damage (8-hydroxy-2'-deoxyguanosine (8-OHdG+IR), and neurodegeneration (NeuN, MAP2+IR), we assessed these markers within the OFC. AUD reactive microglia were identified by increases in Iba1, CD11b (Mac1-OX42), CX3CR1, CSF1R, CD68, CCR2, P2RY12, SYK, and TFE3+IR in AUD OFC compared to control moderate drinkers. Tmem119+IR was decreased in AUD brain. Several of these microglial genes had parallel changes in +IR protein and mRNA. However, several microglial markers commonly used to identify reactive microglia did not show changes in mRNA, including Iba1, CD68, P2RY12, and CSF1R+IR. Overall, AUD microglia show increases in monocyte phagocytic markers, but not TREM2, DAP, or complement genes. Reactive microglial markers were highly correlated with reactive astrocyte GFAP+IR, oxidative stress 8-OHdG+IR, and loss of neurons (NeuN, MAP2+IR). Mediation analysis indicated reactive microglia contribute to both reactive astrocytes and oxidative stress, but only reactive astrocytes were found to significantly contribute to loss of neurons (NeuN+IR). These findings are supported by mouse studies finding chronic ethanol exposure increases reactive astrocytes and oxidative stress that is inhibited by DREADD blockade of microglial activation. Our findings support a distinct AUD reactive microglial phenotype that activates astrocytes, contributing to AUD neurodegeneration and possibly heavy drinking.

pharmacology and toxicology↗

bioRxiv2025

Deciphering the Sequence Basis and Application of Transcriptional Initiation Regulation in Plant Genomes Through Deep Learning

Transcription initiation is a critical regulatory step in plant gene expression, yet its sequence determinants remain largely elusive. Here we introduce GenoRetriever, an interpretable deep learning model that deciphers the sequence basis of transcriptional initiation regulation across plant genomes. Trained on STRIPE-seq data from 16 soybean tissues and six other crop species, GenoRetriever identifies 27 core sequence motifs that govern transcription start site (TSS) selection and usage. The model predicts TSS locations and usage levels with high accuracy, as validated by in silico motif insertions, saturation mutagenesis, and CRISPR-Cas9 promoter editing. It further reveals that 31.85% of natural variation between wild and domesticated soybean drives shifts in promoter motif usage during domestication, and uncovers lineage-specific motif effects between monocots and dicots. This interpretable model and its user-friendly web server for promoter analysis and design make GenoRetriever both a methodological innovation and practical tool for plant functional genomics and crop improvement.

plant biology↗