Biology subjects

Wei, Y.

Publications and source records attributed to Wei, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

A gastric microbial chromatin remodeler drives gastric cancer progression and immune evasion by reprogramming the host epigenome

Emerging evidence highlights the crucial role of microbial communities in modulating cancer development and progression. In gastric cancer (GC), we identify Streptococcus anginosus (SA) as a tumor-resident oncobacterium that drives both tumor progression and immune evasion. We define a novel mechanism in which SA secretes extracellular vesicles (saEVs) that translocate the bacterial chromatin remodeler saSNF2 into host cell. There, saSNF2 partners with host transcription factor TEAD1--through its ATPase activity and participation in BAF complex assembly--to coordinately activate oncogenic transcription. This transkingdom interaction upregulates the palmitoyltransferase ZDHHC11, which in turn stabilizes PD-L1 via palmitoylation to establish an immunosuppressive niche, while also amplifying other TEAD1 target genes to fuel tumor progression. Functionally, saEVs promote tumor growth and limit CD8+ T-cell infiltration in vivo. Strikingly, pharmacological inhibition of ZDHHC11 reverses immune evasion and synergizes with anti-PD-1 checkpoint blockade. Our results establish SA as a multifaceted driver of GC and reveal the saSNF2-ZDHHC11 axis as a promising target to potentiate immunotherapy.

cancer biology↗

bioRxiv2025

Cross-species etiologically informed stratification enables T cell receptor-based diagnosis of Parkinson's Disease

BackgroundDeveloping peripheral blood-based diagnostic models for idiopathic Parkinsons disease (iPD), particularly those leveraging the T-cell receptor (TCR) repertoire, has long been considered infeasible because patient-derived TCRs appear to lack convergent sequence motifs. We reasoned that this apparent absence of shared TCR features likely reflects both insufficient sample sizes and unaccounted immune heterogeneity within the iPD population. MethodsWe reconstructed TCR repertoires from the two largest iPD cohorts currently available, anchoring them with three mechanistically distinct mouse models to stratify patients into model-anchored informed subtypes. Within these data-driven subtypes, we trained subtype-specific, multimodal multi-instance classifiers. ResultsWe demonstrated that iPD patients can be successfully stratified into model-anchored informed subtypes. Furthermore, the trained subtype-specific, multimodal multi-instance classifiers achieved an Area Under Curve (AUC) exceeding 0.8 for both subtypes. ConclusionsOur findings underscore the critical role of disease stratification in enabling TCR repertoire-based modeling in neurodegenerative diseases.

neuroscience↗

bioRxiv2025

Alveolar Type II Cell-derived MMP1high basal cells promote destructive microcysts in idiopathic pulmonary fibrosis.

Idiopathic Pulmonary Fibrosis (IPF) is a fatal lung disease characterized by progressive epithelial metaplasia and widespread fibrosis. Alveolar microcysts develop near terminal airways in IPF and are linked to poor outcome. Using HTII-280 as a short-term lineage marker of AT2-derived AT0 (SFTPC+/SCGB3A2+) and basaloid (KRT17) cells, together with organoids and spatial transcriptomics (Xenium), we highlight epithelial similarities between respiratory bronchioles (RBs) and alveolar microcysts both having AT0, SCGB3A2+, and basaloid/basal cells (BCs), albeit with expanded BCs in IPF microcysts. The AT0- and AT2-derived BCs strongly express the collagenase, matrix metalloproteinase protein-1, MMP1 in organoids -- mirroring in situ BCs lining IPF microcysts, but distinct from MMP1low BCs in large airways or normal lungs. Expression of MMP1 correlates with basal cell hypoxia pathway activity. MMP1high AT2-derived BCs and IPF BCs promoted type 1 collagen degradation ex vivo and in vivo after xenotransplantation, forming microcystic structures that were abrogated by concurrent MMP inhibitor treatment. Notably, a Frizzled 5 WNT agonist antibody reversed the MMP1high state of AT2-derived BCs, raising a possible therapeutic approach. These findings suggest AT2 transdifferentiation to basaloid/basal cells is uncommon in normal lungs but can expand as a potential source of alveolar destruction, likely contributing to the pernicious course of IPF.

cell biology↗

bioRxiv2025

An in situ generated CAR-M with IFNg and negative dominance Sirpa isoform augments hepatocellular carcinoma immunotherapy

Background and AimsChimeric antigen receptor (CAR) T cells have shown strong efficacy in hematological cancers but limited success in solid tumors. Macrophages, with their natural ability to infiltrate tumors, modulate immunity, and phagocytose cancer cells, offer a promising alternative when engineered with CARs. While studies have demonstrated the feasibility and anti-tumor activity of CAR macrophages (CAR-M), enhancing their persistence and phagocytic capacity remains a key challenge. Methods and ResultsBuilding on first-generation CD3{zeta}-based CAR-M, we developed a novel CAR targeting human GPC3, incorporating IFN-{gamma} and the extracellular domain of SIRP (SIRPECD) to improve CAR-M persistence and block the CD47-SIRP immune checkpoint. Following delivery via lipid nanoparticle-encapsulated mRNA (LNP-mRNA), the self-secreted IFN-{gamma} sustained M1 polarization through phospho-STAT1 activation. Meanwhile, the ectopically expressed SIRPECD competitively bound to CD47 on tumor cells, thereby blocking the endogenous SIRP-SHP2 interaction in a dominant-negative manner. This design enhanced pro-inflammatory activity and anti-tumor efficacy compared to CD3{zeta}-only CAR-M. Single-cell RNA sequencing and cellular analysis showed that in situ programmed CAR-M reprogrammed the tumor microenvironment toward inflammation in a murine HCC model. Moreover, CAR-M derived from human peripheral blood mononuclear cells (PBMCs) effectively phagocytosed human HCC organoids while sparing healthy tissues, indicating clinical potential. ConclusionsCollectively, our work presents a novel CAR design that enhances phagocytic function and sustains anti-tumor activity, offering a promising strategy for human solid tumor immunotherapy.

cancer biology↗

bioRxiv2025

Mapping the latent CRBN-molecular glue degrader interactome

Molecular glue degraders (MGDs) are a transformative modality in drug discovery. MGDs that work in concert with the E3 ligase CRL4CRBN can degrade a range of substrates through tailored MGDs. To explore CRL4CRBN reprogrammability, we tested whether reported CRBN-MGD substrates are part of a network of latent CRBN interactors, detectable with generic CRBN-MGDs. Leveraging highly parallel interaction measurement (GluePCA) between CRL4CRBN and human zinc-fingers (ZFs), we identified [~]210 ZFs bound to CRBN-pomalidomide, where top binders are already reported as degraded by dedicated MGDs. To map latent CRBN-MGDs interactions proteome-wide, and thus define the immediately accessible CRBN target space, we combined AI-derived protein surface queries (MaSIF-mimicry) with GluePCA. This pipeline identified 6 known and 43 novel CRBN-pomalidomide binders, thereby providing privileged starting points for MGD development. We expect this binding-focused, highly parallel workflow to be readily applicable to other MGD/E3 ligase systems, extending the target landscape of this emerging drug class.

molecular biology↗

bioRxiv2025

Cross-Species Cortical Geometry Reveals Conserved Gradients Across Primates and Human-Specific Expansion

The primate cerebral cortex, characterized by its complex structural geometry, underlies advanced cognitive functions and represents a defining feature distinguishing primates from other mammals. However, cross-species patterns of cortical geometry and the links between human cortical geometry and transcriptional architecture remain poorly understood. We developed a geometry-based cross-species cortical alignment framework to systematically investigate the similarities and differences in structural connectivity and cortical expansion characteristics among macaques, chimpanzees, and humans, and additionally explored the transcriptional underpinnings of human cortical geometry. Our analysis revealed conserved spatial patterns of cortical geometric features across species, providing the foundation for constructing a cross-species structural common space to support the alignment framework. We found that primary sensory, somatomotor, and face-selective regions exhibited high structural connectivity similarity across species, whereas prefrontal and parietal association cortices displayed significant divergence. We also identified disproportionate cortical expansion in the default mode network, with a consistent expansion trend across different evolutionary lineages in primates. Furthermore, neuroimage-transcription analysis indicated that cortical geometric features were correlated with transcriptional profiles enriched in neurodevelopmental and connectivity-related pathways. These results highlight a conserved yet hierarchically differentiated organization of the cerebral cortex in primates, providing new insights into the biological basis of human brain evolution.

neuroscience↗

bioRxiv2025

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

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

neuroscience↗

bioRxiv2025

Enterococcus faecalis delivers Obg GTPase via extracellular vesicles to instigate mTOR activity and promote HCC tumorigenesis

Hepatocellular carcinoma (HCC) is a malignant tumor that has been associated with dysbiosis of the gut microbiota. However, how the gut microbiota plays an oncogenic role in HCC remains largely unknown. Here, we show that Enterococcus faecalis (E. faecalis) is highly enriched in liver tumor tissues and is positively correlated with pathogenesis of HCC. E. faecalis promotes liver cancer cell proliferation, protein translation, cell migration and tumorigenesis. Mechanistically, we found that EF-derived extracellular vesicles (EF-EVs) deliver EF-Obg GTPase to activate host mTOR, thereby promoting liver cancer progression. Intriguingly, the EF-Obg protein exerts its influence on the mTOR pathway via a Ras-like G domain involved in GTP binding. EF-Obg exhibits a striking homology with the G1 site of the G domain of Rheb, a key positive regulator of mTOR. Obg gene is critical for E. faecalis to activate mTOR to promote hepatocarcinogenesis based on an engineered obg knockdown strain by CRISPR interference experiment. Clinically, abundant EF-Obg protein expression is correlated with enhanced activation of mTOR, leading to poor overall survival in HCC patients. Significantly, treatment of mTOR inhibitor Everolimus confers effectiveness in EF-colonized liver cancer orthotopic model, suggesting that Everolimus therapeutic approach can be effective for liver cancer patients with enriched E. faecalis. Taken together, we provide mechanistic and functional evidence to verify a direct causal relationship between tumor-resident E. faecalis enrichment and liver carcinogenesis, revealing that EF-Obg functions as a previously unidentified cross-kingdom activator of mTOR to promote liver tumorigenesis.

cell biology↗

bioRxiv2025

CLOCK-dependent pathway in a single pair of LNd neurons instruct circadian-independent interval timing behavior.

Interval timing is a cognitive ability essential for behaviors such as mating, foraging, and decision-making, and it is distinct from circadian rhythm regulation. Despite the involvement of circadian clock genes in both interval timing and circadian rhythms, the mechanisms differentiating these functions remain unclear. Using Drosophila as a model, we demonstrate that the CLK/CYC heterodimer, but not PER/TIM, is essential for interval timing. Neuronal CLK/CYC expression is necessary and sufficient for sexual experience-dependent shorter mating duration (SMD) behavior. We identified that CLK/CYC expression in a single pair of ITP-positive LNd neurons is pivotal for SMD. These neurons are glutamatergic with output circuits to central brain regions. CLK variants lacking DNA binding motifs dissociate circadian rhythms from interval timing and sleep behaviors in these neurons. Our study uncovers a specialized circuit for interval timing and highlights the non-circadian functions of circadian clock genes. Statement of SignificanceThis study in Drosophila demonstrates that the CLK/CYC heterodimer is crucial for interval timing, distinct from circadian rhythm regulation. The research pinpoints a specific pair of neurons that are critical for shortened mating duration behavior, and it suggests that CLK variants can influence interval timing dissociation from circadian rhythm and sleep behaviors. HighlightsO_LICLK/CYC heterodimer are essential for interval timing. C_LIO_LISpecialized mechanism of interval timing behavior revealed. C_LIO_LIIdentified a pair of glutamatergic ITP-LNd neurons that independently regulate both interval timing and sleep. C_LIO_LIRevealed a novel mechanism by which CLK variants regulate sleep and interval timing. C_LI Graphical AbstractDifferent CLK/CYC mediate separate regulatory mechanism between circadian rhythm, sleep and interval timing in Drosophila melanogaster.

animal behavior and cognition↗

bioRxiv2025

Predicting the unseen: a diffusion-based debiasing framework for transcriptional response prediction at single-cell resolution

Predicting cellular responses to genetic perturbations is critical for advancing our understanding of gene regulation. While single-cell CRISPR perturbation assays such as Perturb-seq provide direct measurements of gene function, the scale of these experiments is limited by cost and feasibility. This motivates the development of computational approaches that can accurately infer responses to unmeasured perturbations from related experimental data. We introduce dbDiffusion, a generative framework that integrates diffusion models with classifier-free guidance derived from perturbation information, operating in latent space through a variational autoencoder (VAE). Diffusion models are probabilistic generative models that approximate data distributions by reversing a Markovian diffusion process, progressively denoising Gaussian noise into structured outputs. By exploiting biological similarities in gene expression profiles and relationships among perturbations, dbDiffusion enables the conditional generation of gene expressions for previously unobserved perturbations. In contrast to competing approaches, dbDiffusion does not rely on LLM or foundation models, which have been found to yield unsatisfactory results. Rather, it leverages embeddings derived from measured perturbations to generalize to unseen pertur-bations, effectively transferring information across related experimental conditions. In benchmarking against state-of-the-art methods on Perturb-seq datasets, dbDiffusion demonstrates superior accuracy in predicting perturbation responses. A methodological innovation of dbDiffusion is the integration of prediction-powered inference, which corrects for biases inherent in generative models and enables statistically rigorous downstream tasks, including identification of differentially expressed genes. By combining deep generative modeling with principled inference, dbDiffusion establishes a scalable computational framework for predicting and analyzing transcriptomic perturbation responses, significantly extending the utility of Perturb-seq experiments.

genomics↗

bioRxiv2025

TREM2 macrophages are associated with enhanced response to PD-1 blockade in human hepatocellular carcinoma

Macrophages are known to dampen tumor immunity. However, identifying druggable targets that modulate these cells to improve existing immunotherapies has been limited by a dearth of studies identifying macrophages that associate with pathological response to immune checkpoint blockade. To fulfill this unmet clinical need, we leveraged transcriptional and spatial profiling of specimens collected from a Phase II clinical trial studying neoadjuvant PD-1 blockade in patients with hepatocellular carcinoma (HCC). We determined that the intratumoral abundance of TREM2-expressing macrophages and serological levels of soluble TREM2 are elevated in patients who responded to PD-1 blockade, compared to non-responders. We validated these findings in a second HCC cohort and in the IMbrave150 trial. These highlight the robust potential for TREM2 macrophages to predict therapeutic responses of HCC to immunotherapy. Therefore, our study provides a novel basis for the use of TREM2 macrophages to strategize treatment for patients with HCC to maximize therapeutic benefit.

immunology↗

bioRxiv2025

Broad brain biodistribution conferred by an AAV to restore TDP-43 function mitigates Frontotemporal Demenia-like deficits

TDP-43 dysfunction is an early pathogenic determinant of frontotemporal lobar degeneration with TDP-43 pathology (FTLD-TDP), a devastating disorder currently without effective therapy. Here, we exploit a blood-brain-barrier (BBB)-permeable AAV (AAV-PHP.eB) that confers broad brain biodistribution to restore TDP-43 function in a TDP-43 deficient model (CamKIIa-CreER;Tardbp mice) that mimics the early stage of TDP-43 dysfunction occurring in FTLD-TDP. Intracerebroventricular delivery by AAV-PHP.eB of CTR, our previously characterized splicing repressor, revealed its accumulation in [~]40% of adult hippocampal neurons. Remarkably, treatment of adult CamKIIa-CreER;Tardbpf/fmice with AAV-PHP.eB-CTR restored TDP-43 function, attenuated neuronal aberrant activity and memory deficits, and rescued neuron loss. Importantly, we showed that TDP-43s autoregulatory element restricts CTR expression to a physiological range. No overt phenotype was observed after long-term exposure to AAV-PHP.eB-CTR in aged mice, highlighting a favorable safety profile for this gene therapy. These results validate that BBB-crossing AAVs can deliver CTR with a biodistribution in the adult brain that is broad enough to rescue FTD-like phenotypes, supporting clinical testing of this gene therapy for FTLD-TDP.

neuroscience↗

bioRxiv2025

Multigram-scale stereoselective synthesis of neurosteroid isomers by gut microbial isolates using plant biomass-derived medium

Neurosteroids are vital therapeutics for mood disorders, with FDA-approved allopregnanolone (Zulresso) for postpartum depression and zuranolone for major depressive disorder representing breakthrough treatments. However, current production methods rely on costly animal-derived sources or non-stereoselective chemical synthesis that require extensive chiral purification steps. Here, we present a sustainable microbial platform utilizing gut bacteria and a completely plant-based medium for stereoselective neurosteroid biosynthesis. Through bioinformatics- and structural biology-guided screening of more than 3000 bacterial isolates, we identified three anaerobic gut strains exhibiting distinct stereospecificities: Holdemania filiformis produces isopregnanolone (3{beta}-hydroxy-5-pregnan-20-one), Clostridium innocuum generates epipregnanolone (3{beta}-hydroxy-5{beta}-pregnan-20-one), and Hungatella effluvii synthesizes pregnanolone (3-hydroxy-5{beta}-pregnan-20-one). We developed Molasses-Okara Medium (MOM), a fully plant-derived composite medium combining sugarcane molasses with enzymatically hydrolyzed okara devoid of animal-derived components. In multigram batch whole-cell biotransformation trials using MOM, we achieved >95% progesterone conversion into target neurosteroid isomers. The inherent stereoselectivity of these whole-cell biotransformations bypasses downstream chiral chromatographic separation, enabling pharmaceutical-grade product recovery through a simple open-column purification. Compared to using peptone-yeast-glucose media for whole-cell biotransformation, MOM reduced production costs by 90% and carbon footprint by 95% that embodies sustainable bioeconomy principles in pharmaceutical biotechnology. Technology Readiness BoxWe argue that this gut microbiota-derived neurosteroid bioproduction technology has reached a Technology Readiness Level (TRL) of 4, having been validated in laboratory environments with the demonstrated multigram-scale synthesis of high-purity neurosteroids. The platform integrates stereoselective bacterial isolates (Holdemania filiformis, Clostridium innocuum, and Hungatella effluvii) with a sustainable plant-based fermentation medium (molasses-okara medium), achieving >90% progesterone conversion efficiency, >99.9% stereochemical purity, and the successful production of 0.7-0.9 g of neurosteroids per gram of progesterone across multiple 1 L fed-batch fermentations. Compared with conventional chemical synthesis approaches that require expensive chiral catalysts and multi-step purification, this microbial platform offers inherent stereoselectivity while eliminating animal-derived media components. Despite these advantages, several challenges remain for industrial implementation, including scale-up validation beyond laboratory conditions, optimization of anaerobic bioprocess control at pilot scale, and ensuring consistent performance under variable industrial feedstock conditions. Addressing these issues will require pilot-scale demonstration (10-50 L bioreactors), process robustness validation, and supply chain development for plant-based feedstocks. Regulatory pathway development will also be essential for pharmaceutical applications, particularly establishing precedents for gut microbiota-derived therapeutic compounds under existing cGMP frameworks HighlightsO_LIIdentification of gut bacteria for stereoselective synthesis of neurosteroid isomers (isopregnanolone, epipregnanolone, pregnanolone) with >99% chiral purity C_LIO_LISustainable plant biomass-based medium replacing animal-derived components for whole-cell progesterone biotransformation C_LIO_LIMulti-gram scale production of progestogenic neurosteroids and one-step-open-column purification bypassing chiral chromatographic separation C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/671209v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@11147b0org.highwire.dtl.DTLVardef@1799d64org.highwire.dtl.DTLVardef@14c33deorg.highwire.dtl.DTLVardef@1e14e21_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

MORC2 Mediates Transcriptional Regulation Through Liquid-Liquid Phase Separation and DNA Binding

MORC2 is a chromatin-associated ATPase essential for transcriptional silencing and genome stability, yet the biophysical principles governing its regulatory activity remain elusive. Here, we demonstrate that full-length MORC2 undergoes biomolecular condensation to form dynamic nuclear assemblies, a process fundamentally required for its repressor function. Endogenous MORC2 forms discrete, dynamic condensates in neurons from EGFP-MORC2 knock-in mice, supporting the physiological relevance of these assemblies in vivo. Mechanistically, a 3.1 [A] crystal structure of coiled-coil 3 (CC3) identifies a dimeric scaffold that serves as a structural hub, while multivalent sticker interactions between an intrinsically disordered region (IDR) and a newly defined IDR-binding domain (IBD) drive condensation. We show that DNA acts as a molecular scaffold that triggers MORC2 condensation, which in turn allosterically stimulates its ATPase activity. Critically, by employing a "killswitch" strategy to decouple assembly from internal fluidity, we reveal that only dynamic MORC2 condensates--not static aggregates or condensation-deficient mutants--can restore transcriptional repression in MORC2-knockout cells. Furthermore, pathogenic variants linked to CMT2Z and SMA differentially perturb these material properties and enzymatic turnover, providing a mechanistic link between condensate dysregulation and human neuropathies. Together, our findings establish a DNA-templated condensation mechanism for MORC2 and provide a molecular framework for understanding how the material state of chromatin-associated machinery dictates gene regulation and disease pathogenesis

cell biology↗

bioRxiv2025

Bottlebrush Polymer Conjugates for Enhanced Antisense Oligonucleotide Therapy in Myotonic Dystrophy Type 1

Oligonucleotides are a promising genetic medicine for myotonic dystrophy type 1 (DM1), the most common adult-onset muscular dystrophy. However, poor muscle distribution of nucleic acid drugs after systemic administration has hindered drug development, and no curative treatment exists. Additionally, DM1 pathology requires drug localization to the nucleus, where pathogenic mutant RNA is trapped, posing challenges after endocytosis and endosomal escape. Here, we show that a locked nucleic acid oligonucleotide targeting mutant CUGexp RNA tracts, conjugated to a bottlebrush polymer, exhibited improved muscle distribution and potent correction of DM1-associated splicing at low nanomolar doses in a DM1 mouse model. Significant improvements in myotonia, body weight, and grip strength were observed. The conjugates were well tolerated after 12 weeks of weekly intravenous dosing. These results suggest that bottlebrush polymer bioconjugates may overcome key limitations of traditional antisense drugs for muscular dystrophies, with the potential as potent, durable, and cost-efficient DM1 therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/668589v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@e3961corg.highwire.dtl.DTLVardef@194225dorg.highwire.dtl.DTLVardef@5c470dorg.highwire.dtl.DTLVardef@3cc46a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Membrane Tethering of Honeybee Antimicrobial Peptides in Drosophila Enhances Pathogen Defense at the Cost of Stress-Induced Host Vulnerability

Antimicrobial peptides (AMPs) represent a promising alternative to conventional antibiotics in combating multidrug-resistant pathogens, yet their clinical translation is hindered by proteolytic instability, cytotoxicity, and poor bioavailability. Here, we demonstrate that glycosylphosphatidylinositol (GPI)-mediated membrane tethering of honeybee defensin1 (Def1) in Drosophila melanogaster enhances its antimicrobial efficacy by [~]100-fold compared to secreted or untethered forms, while preserving physiological and behavioral integrity under baseline conditions. Using a genetically engineered Drosophila model, we expressed three Def1 variants: native (Def1), secreted (s-Def1), and membrane-tethered (t-Def1). Flies expressing t-Def1 exhibited superior bacterial clearance of Pseudomonas aeruginosa and improved survival post-infection, with no adverse effects on locomotion, courtship, or sleep architecture. However, under stress paradigms--including sleep deprivation and dextran sulfate sodium (DSS)-induced gut injury--t-Def1 exacerbated intestinal barrier dysfunction, as evidenced by elevated Smurf phenotype incidence, highlighting a trade-off between antimicrobial potency and epithelial vulnerability. Our work establishes Drosophila as a powerful platform for dissecting AMP mechanisms and engineering spatially targeted therapies, offering translational insights for pollinator health and human infectious disease management. These results advocate for iterative refinement of membrane-anchoring strategies to balance therapeutic efficacy with host safety, advancing the development of next-generation AMPs with minimized off-target effects.

biochemistry↗

bioRxiv2025

Learning the native-like codons with a 5'UTR and secondary RNA structure aided species-informed transformer model

Efficient protein expression across heterologous hosts remains a major challenge in synthetic biology, largely due to species-specific differences in codon usage and regulatory sequence context. A key difficulty lies in reconstructing the codon landscape of the target expression system within a foreign host with a native-like codon preference. To address this, we present TransCodon, a Transformer-based deep learning model that leverages both 5 untranslated regions (5UTRs) and coding sequences (CDS), along with explicit species identifiers and RNA secondary structure information, to learn nuanced codon usage patterns across diverse organisms. By incorporating multisource genomic data and modeling sequence dependencies in a masked language modeling paradigm, TransCodon effectively captures both local and global determinants of codon preference. Our experiments demonstrate that integrating species-level information during training significantly improves the models ability to predict optimal synonymous codons when considering different evaluation metrics. More importantly it identifies native-like codons with less divergence from natural sequences compared to other methods. Besides, TransCodon could capture more low-frequency codons which are often omitted by other deep learning-based methods. The results thus indicate that TransCodon as a robust codon language model has the potential for generating native-like CDS with high translational efficiency in target hosts.

bioinformatics↗

bioRxiv2025

Cell layer-specific modification of cell wall is associated with exo-mesocarp split in pistachio (Pistacia vera L.)

Pistachio (Pistacia vera) is a drought and salinity-tolerant perennial whose fruit features a fleshy exo-mesocarp, or "hull," that protects the kernel. Hull development and degradation are key to kernel quality, yet the anatomy and mechanisms driving hull breakdown during late-stage development remain largely unknown. Here, we show that the hull contains anatomically distinct layers of hypodermal parenchyma and filler parenchyma. Using a combination of transcriptome analyses and immunohistochemistry, we show that changes in pectin associated gene expression and modification of this polysaccharide are involved in hull cell size increase, loss of cell-cell adhesion, and softening. Anatomical analysis shows that filler parenchyma expands during late-stage hull development while hypodermal parenchyma remains constant in size. Field data suggest that irrigation and humidity affect pistachio hull split, implicating a role for water status in cell expansion. In summary, the complex interplay between molecular, cellular, and environmental changes suggests that cell layer-specific modifications of the cell wall are linked to exo-mesocarp splitting, forming a model for understanding the mechanism of fruit split during ripening in non-berry fruit crops. HighlightCell-layer specific modifications of the cell wall are associated with cell expansion and loss of cell-cell adhesion, leading to hull split during late-stage pistachio fruit development.

plant biology↗