Biology subjects

Lu, G.

Publications and source records attributed to Lu, G..

At least 19 recordsLinked to original sources

bioRxiv2026

NeuroPack: Advanced Learnable Packaging Toolkit Towards Ultra-High Compression Ratio for Volumetric Neuroimaging

High-throughput 3D microscopic imaging generates brain-volume datasets at terabyte to petabyte scale, posing significant storage challenges for large-scale neuroimaging data. In this study, we introduce NeuroPack, a hyperprior-driven 3D deep-learning-based packaging toolkit specifically designed for compressing 3D microscopic volumes at the mesoscale. NeuroPack encodes a compact hyperprior stream that conditions its entropy model on local voxel-wise variance, adaptively allocating bits to preserve mesoscale anatomical details for an optimal rate-distortion balance. To ensure reproducible deployment across heterogeneous microscopy datasets and computing environments, NeuroPack implements model integerization for the hyperprior side-information pathway, whose hyper-decoder predicts the Gaussian mean and scale parameters used by the arithmetic coder. By replacing platform-dependent floating-point hyper-decoding with deterministic fixed-point integer convolutions, NeuroPack produces bit-exact entropy models across CPUs, GPUs, local workstations, and cloud servers, thereby preventing decoding drift caused by floating-point rounding, fused-multiply-add ordering, or library-specific kernels. This integerized design preserves rate-distortion behavior while maintaining efficient encoding and decoding for large anisotropic 3D microscopy volumes. Our method enables high-fidelity microscopy reconstruction at 100- to 1000-fold compression across diverse modalities and species. Quantitatively, NeuroPack delivers the strongest overall rate-distortion performance in both BD-PSNR and BD-MSSSIM, with average relative gains of 73.4% and 50.8%, respectively, over the best competing codec. Importantly, NeuroPack preserves image fidelity required for downstream morphological reconstruction and analysis, as validated by simultaneous human annotation of original and decompressed confocal whole-brain zebrafish microscopy images. Together, NeuroPack provides a learning-based compression framework explicitly tailored for microscopy data, establishing a scalable storage solution for data-intensive neuroimaging and AI-empowered biological discovery.

bioengineering↗

bioRxiv2026

Vascularized Organoids Emerge from a Heart-Foregut-like Intermediate Recapitulating Early Human Development

During early cardiogenesis, the heart regions lie in close contact with foregut endoderm, which supplies essential nutrients and signaling cues to orchestrate primitive heart tube assembly. Here, we show that self-organized heart/foregut like-structures emerge from human pluripotent stem cells (hPSCs). The initial heart/foregut-like structures, termed the Seed, are encased by surrounding supportive cells termed Soil, which provide a matrix microenvironment; the Seed progressively develops into chambered human cardiac organoids (hCOs) containing cardiomyocytes (CMs), epicardial cells, cardiac fibroblasts, and endothelial cells. Optimization of the induction system further enhanced hCO maturation and vascularization. Therefore, this Soil-Seed system provides a model to dissect human early heart/foregut self-organization.

developmental biology↗

bioRxiv2026

Role of Uridine Phosphorylase 1 (UPP1) in Pancreatic β-Cell Physiology and Its Dysregulation in Obesity and Type 2 Diabetes

Aims/hypothesis Fasting plasma uridine concentrations are elevated in obese mice and in individuals with type 2 diabetes (T2D), suggesting that uridine may function as a metabolic signal that adjusts insulin secretion to changes in metabolic demand. Here, we tested this hypothesis by determining whether uridine potentiates glucose-stimulated insulin secretion (GSIS) in mouse and human islets and by identifying uridine phosphorylase 1 (UPP1), the principal enzyme responsible for systemic uridine catabolism, as a key mediator of this effect. Methods Whole-body Upp1 knockout (KO) and {beta}-cell-specific Upp1 knockout (KO{beta}) mice were used to determine the requirement for UPP1 in uridine-potentiated glucose-stimulated insulin secretion (GSIS) and glucose-stimulated MAPK activation. Leptin-deficient and diet-induced obese mouse models were used to assess the impact of obesity on uridine responsiveness. UPP1 protein abundance and subcellular localization were examined in islets from obese mice and human donors spanning a range of glycemic control. Integrated single-nucleus RNA sequencing and ATAC sequencing were performed on wild-type and Upp1 KO mouse islets to characterize {beta}-cell molecular remodeling associated with UPP1 deficiency and altered responses to uridine. Results Uridine potentiated GSIS in islets from chow-fed and high-fat diet-fed mice, but not in leptin-deficient obese mice. Uridine also potentiated GSIS in human islets, although this effect progressively declined with worsening glycemic control. In mouse islets, uridine potentiation was accompanied by transient activation of the MAPK pathway. Both uridine-potentiated GSIS and uridine-enhanced glucose-stimulated MAPK activation were abolished in islets from Upp1 KO and KO{beta} mice. The requirement for a transient MAPK signaling was further supported by pharmacological inhibition of MEK and constitutive activation of MEK1. Leptin-deficient islets exhibited impaired glucose-induced MAPK activation together with increased UPP1 protein expression. In human islets, UPP1 protein abundance positively correlated with donor HbA1c and displayed heterogeneous subcellular localization. Integrated single-nucleus multiomic analysis identified UPP1 as an important regulator of {beta}-cell identity, function, and transcriptional responses to uridine. Conclusions These findings establish UPP1 as a key regulator linking pyrimidine metabolism to {beta}-cell function and identify impaired uridine responsiveness as a potential contributor to and/or consequence of {beta}-cell dysfunction during the progression of T2D.

molecular biology↗

bioRxiv2026

Harmine Plus Exendin-4 Enhances Remission of Recent-Onset Type 1 Diabetes Following Anti-CD3 Therapy

Type 1 diabetes (T1D) results from autoimmune destruction of pancreatic {beta}-cells. While anti-CD3 therapy can delay disease progression and preserve residual {beta}-cell function, disease reversal will likely require both immune modulation and {beta}-cell regeneration. We found that the combination of harmine and exendin-4 (H+E) reduced inflammation-induced human {beta}-cell apoptosis, suppressed cytokine signaling and immunogenicity pathways, and improved {beta}-cell function. Although H+E alone did not reverse diabetes in NOD mice, low-dose anti-CD3 followed by H+E normalized blood glucose, increased insulin levels, improved glucose tolerance, expanded {beta}-cell mass, and enhanced diabetes remission. These effects were associated with reduced pro-inflammatory T-cell responses, increased regulatory T cells, and greater expression of exhaustion-related T-cell markers, without broad lymphocyte depletion. Similar immunomodulatory effects were observed in activated human PBMCs. Transcriptomic analyses identified the lncRNA SNHG6 as a key mediator of H+E action; SNHG6 protected {beta}-cells from cytokine-induced stress, apoptosis, and immunogenicity. Together, these findings demonstrate that H+E promotes {beta}-cell recovery and resilience while reducing {beta}-cell immunogenicity, enabling remission of recent-onset T1D when combined with anti-CD3 therapy. SNHG6 emerges as a novel regulator of {beta}-cell protection during inflammation.

cell biology↗

bioRxiv2026

Intranucleolar Invasion of Cajal Body Remnants Suppresses Ribosomal Biogenesis in cis and Telomerase Functions in trans

Cellular processes are compartmentalized within immiscible heterotypic condensates, yet the functional consequences of losing their physical segregation remain unclear. Here, we show that genetic inactivation of the RNA chaperone SMN forces the aberrant intermixing of the two most prominent nuclear condensates: nucleolus and Cajal Body (CB). Upon SMN depletion, CB components invade the nucleolus and undergo reduced mobility and solubility consistent with a liquid-to-gel-like hardening transition. The CB-scaffold coilin aberrantly enriches at the nucleolar FC/DFC boundary and occupies rDNA chromatin, thereby locally suppressing rRNA production. Concurrently, this sequestration globally impairs coilin targeting to snRNA/snoRNA loci and limits telomerase access to telomeres, reducing telomeric synthesis. Crucially, genetic coilin depletion alone alleviates this mistargeting and rescues these functional impairments across condensates. Our findings reveal an inter-condensate rheostat model in which the loss of CB-nucleolar immiscibility is directly sensed, communicated, and executed by CB remnants, thereby proportionally coupling the functional outputs of otherwise distinct RNPs essential for splicing, translation, and genomic integrity.

molecular biology↗

bioRxiv2026

SOX8-USP7-PGC-1α axis enhances thermogenesis in brown adipocytes

Obesity is one of the most prevalent diseases worldwide. Increasing thermogenesis to enhance energy expenditure has emerged as a promising therapeutic strategy. In an effort to identify new regulatory targets in thermogenic adipocytes, we found that SOX8 is correlated with obesity and serves as a novel marker of classical brown adipocytes in both humans and mice, upregulating during acute cold exposure. Functional studies further demonstrated that adipocyte-specific knockdown of SOX8 leads to obesity and metabolic dysfunction in mice. Mechanistically, SOX8 directly interacts with USP7 and stabilizes PGC-1 by reducing its K48-linked polyubiquitination. AAV-Rec2-mediated SOX8 overexpression initially enhanced energy expenditure, improved insulin sensitivity, and alleviated metabolic dysfunction in HFD-fed mice. However, prolonged SOX8 overexpression induced compensatory metabolic maladaptation, characterized by reduced energy expenditure, impaired glucose homeostasis, and mitochondrial structural disruption. These findings reveal a novel SOX8-USP7-PGC-1 regulatory axis in brown adipocytes, and reveal a previously unrecognized time-dependent effect of sustained thermogenic activation, highlighting SOX8 as a promising therapeutic target for obesity and metabolic syndrome.

cell biology↗

bioRxiv2026

Rice OsML1, a distant plant homologue of animal MD-2 protein, can also bind to and recognize bacterial LPS and co-triggers innate immunity

Lipopolysaccharides (LPSs) are pathogen-associated molecular patterns (PAMPs) of Gram-negative pathogenic bacteria recognized by plants, triggering typical pattern-triggered immunity (PTI) responses. However, a LPS sensing receptor for the recognition of plants remains largely undefined. A plant receptor for lipopolysaccharide (LPS) has not yet been identified. Here, we identify a plant protein, OsML1, with homologies to animal MD-2, which is capable of binding LPS. Furthermore, it may act as a molecular chaperone to assist CK1 in perceiving LPS signals. Our results show that OsML1 functions as an LPS-binding protein recognizing LPS and participates in downstream rice immune response activation. Structural modeling and sequence analysis revealed that OsML1 contains both a typical ML domain and a conserved three-dimensional {beta}-barrel structure as mammalian MD-2 proteins. Microscale thermophoresis assays confirmed that OsML1 binds LPS with high affinity. Functional analyses further demonstrated that OsML1 knockout plants show reduced resistance to the rice bacterial blight pathogen, as well as attenuated ROS bursts upon LPS treatments, whereas overexpression plants show enhanced immune responses. Metabolomic profiling indicated significant metabolic changes in OsML1 knockout plants, particularly in immune-related pathways involving lipids, amino acids, and antimicrobial compounds. OsML1 is consequently a structurally conserved and functional LPS-binding protein linking lipid metabolism, LPS perception, immune activation, and metabolic regulation. Phylogenetic and structural analyses revealed that OsML1 likely arose from a duplication of OsML2, forming an independently functional subgroup within the PITP family. Our study identifies OsML1 as a LPS recognition factor involved in LPS sensing and downstream ROS bursts activation, callose deposition, and broad-spectrum gene expression of resistance. These findings expand our knowledge of bacterial LPS perception and immune regulation in plants, offering novel targets and strategies for disease-resistant breeding.

plant biology↗

bioRxiv2026

Quantitative Neuropeptidomics Reveals Thermal Acclimation-Induced Remodeling of Peptidergic Signaling in the American Lobster Homarus americanus

Global warming and rising ocean temperatures pose substantial challenges to marine ecosystems and crustacean populations. As an ectothermic species, the American lobster (Homarus americanus) relies on physiological and neurochemical mechanisms to maintain homeostasis under varying environmental conditions. To elucidate the role of neuropeptides in neuronal plasticity and systemic adaptation to temperature fluctuations, we employed a quantitative mass spectrometry-based approach to probe key neuropeptides involving thermal adaptation in four lobster neural tissues at three temperatures: 4 {degrees}C (cold), 11 {degrees}C (control), and 18 {degrees}C (warm). Peptidomic profiling revealed a global reduction in peptide abundance during cold exposure, alongside coordinated, tissue-specific reconfigurations of the neuropeptidome between experimental groups. Cold exposure led to a significant downregulation of RFamide, leucokinin, and pyrokinin peptides in the commissural ganglia, whereas B-type allatostatin (AST-B), natalisin, and RYamide peptides were drastically elevated in the brain of warm-acclimated animals, with comparatively fewer detectable peptide abundance changes in the sinus gland and the stomatogastric ganglion. Collectively, our findings elucidate neuropeptide signaling pathways underlying thermal tolerance and adaptive resilience in Homarus americanus, offering insights into the survival mechanism and neurochemical basis of neural circuits in response to thermal acclimation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/710231v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@a3d24borg.highwire.dtl.DTLVardef@1434aaaorg.highwire.dtl.DTLVardef@db11cforg.highwire.dtl.DTLVardef@6e5995_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Quantitative dissection of the metastatic cascade at single colony resolution

Metastasis is the leading cause of cancer-related deaths. However, the core determinants and mechanistic principles underlying the metastatic cascade remain elusive. Small cell lung cancer (SCLC) is a highly aggressive malignancy with exceptional metastatic potential and limited therapeutic options. Here, we present Metastasis Originated Barcode Sequencing (MOBA-seq), a high-throughput in vivo platform that systematically maps genetic regulators across the metastatic cascade at single-colony resolution. MOBA-seq integrates scalable barcode-based lineage tracing with a computational pipeline that quantitatively deconvolutes genotype-specific effects on metastatic seeding, dormancy, and clonal expansion across hundreds of thousands of metastatic events. Applying this approach to more than 400 candidate regulators of SCLC, we uncovered tissue-specific metastatic suppressors and universal metastatic essential genes. We identified metastatic seeding as the predominant determinant of metastasis. Comparative analysis across recipient mice of distinct genetic backgrounds further revealed that innate immune surveillance constrains metastatic progression by reducing metastatic seeding and enforcing dormancy, with additional modulation by sex and tissue context. We validated the frequently mutated gene CREBBP as a key metastasis suppressor whose loss enhances SCLC metastasis through both tumor-intrinsic and immune-modulatory mechanisms. This work establishes a scalable and quantitative platform for mapping the metastatic fitness landscape at single-colony resolution across hundreds of thousands of in vivo data points. Our approach offers a broadly applicable framework for dissecting the interactions between cancer-intrinsic and microenvironmental factors governing tumor initiation, progression, and therapeutic response.

cancer biology↗

bioRxiv2026

Molecular basis of BET family protein inhibition by four clinical-stage small-molecule inhibitor drugs

The bromodomain and extra-terminal (BET) family proteins are critical epigenetic readers involved in various diseases, making them attractive therapeutic targets. This study elucidates the molecular basis of inhibition by four clinical-stage BET inhibitors (ZEN-3694, INCB054329, PLX51107, and INCB057643) through detailed structural comparison and analysis. Using X-ray crystallography, we determined their complex structures with the second bromodomain of human BRD2 at 1.4-1.5 [A] resolution. All inhibitors occupy the conserved acetyl-lysine binding pocket via extensive hydrophobic interactions. This hydrophobic network is further coupled with hydrogen-bond contacts for inhibitor-binding stabilization. A common feature is the formation of at least one hydrogen bond with a conserved residue of N429. Notably, INCB057643 exhibits an enhanced polar network, forming additional hydrogen bonds with residues D377 and N429, which may contribute to its improved pharmacological profile. These structures reveal a shared competitive inhibition mechanism by occluding the acetyl-lysine binding site, providing a rational basis for their transcriptional repression and guiding future inhibitor design.

biophysics↗

bioRxiv2026

ATG-18 drives longevity in an HLH-30-dependent manner

Enhancing autophagy increases lifespan and healthspan in animal models, yet the precise molecular mechanisms underlying these effects are not fully understood. Here we show that overexpression of the essential autophagic gene atg-18 extends the lifespan of C. elegans. We describe a previously unknown, pleiotropic mechanism by which atg-18 impacts lysosomes and extends lifespan through the transcription factor hlh-30, the master regulator of lysosomal biogenesis. We show that, under stress conditions, HLH-30 requires atg-18 for nuclear translocation. Furthermore, atg-18 overexpression broadly improves health and stress resilience yet paradoxically increases early-life susceptibility to lethal heat stress. In contrast, enhances heat-stress survival a loss-of-function of function mutation in atg-18 enhances heat-stress survival, uncovering a temporal-specific effect of atg-18. These finding suggest an ATG-18--HLH-30 autophagy--lysosome pathway that plays a key role in lifespan and healthspan. Bulleted main discoveriesO_LIATG-18 overexpression increases C. elegans lifespan and plays an important role in resilience against starvation and heat stress. C_LIO_LIATG-18 is required for nuclear translocation of HLH-30 C_LIO_LIHLH-30 is required for ATG-18--mediated lifespan extension C_LIO_LIATG-18 positively regulates lysosomal biogenesis, suggesting a novel role as a molecular coordinator between autophagy and the lysosomal network. C_LI

molecular biology↗

bioRxiv2025

Mining of natural diversity enables efficient and expressible peptide asparaginyl ligases

Peptide asparaginyl ligases (PALs) are powerful tools for protein engineering but are limited by natural rarity and poor expression. We mined 23 cyclotide-rich Viola species, uncovering 29 new PALs that expanded the known repertoire to 47. A dual-objective screen identified VdiPAL1 as the best-performed natural PAL, with twice efficiency of wt-VyPAL2 and 12 mg L-1 soluble expression in E. coli. A broad P2 specificity including Trp/Ile/Leu/Phe/Tyr/Met was discovered across diverse PALs, which enables sequential click-compatible liposome dual-functionalization. 1.8L[A] crystal structure of VdiPAL1 reveals a pre-organized near-attack conformation (NAC), supported by constant-pH MD simulations linking pH-dependent reactivity to NAC geometry. Our homology- and structure-based design yielded VyOpt1, a quintuple mutant of VyPAL2 with over 24-fold improved expression via enhanced cap-domain foldability in a single design-test cycle. This work expands the PAL family and demonstrates a transferable cap-domain-based engineering strategy, highlighting natural diversity as a powerful driver of enzyme discovery and optimization. TOC summaryMining of cyclotide-rich Viola genus expanded the total number of natural peptide asparaginyl ligases (PALs) to 47, including the discovery of highly expressible VdiPAL1. Its high-resolution structure provided new insights for mechanism, and its sequence guided us to a generalized PAL engineering strategy, leading to 24-fold increment in VyPAL2 expression.

biochemistry↗

bioRxiv2025

Fungal Mst3-proteins are involved in fungal innate immunity needed for the recognition of bacteria surrounding the hyphae, as well as for plant pathogenicity

Fungal innate immunity overall responses are as fast as and resemble mammalian innate immunity. It does not, however, employ membrane toll-like receptors (TLRs), but should employ endocytosis of non-fungal molecular patterns recognized by nuclear-localizing receptors (NLR). Downstream, both types of receptors in mammals are Mammalian Ste20 kinases (MSTs). We identified single MST3 orthologs in the plant pathogens Fusarium graminearum (FgMST3) and Magnaporthe oryzae (MoMST3). We knocked out both genes and investigated mutants using a standard panel of tests for growth, development, and pathogenicity for each respective fungus. Both{Delta} FgMST3 and{Delta} MoMST3 strains showed reduced pathogenicity. The deletions negatively affected conidia production and conidia germination but had little effect on growth rate. However, the two mutants reacted differently to some stress treatments, such as Zn2+ and gentamicin. Furthermore, we constructed an innate immunity reporter system for F. graminearum based on a gene with fast responses to bacterial MAMPs to detect less than 4-hour responses to non-self-molecular patterns (NSMP) like bacterial outer membrane vesicles (OMVs) as well as trace levels of sucrose, as a plant NSMP. The reporter gene responses to OMVs of MST3 mutant strains were severely reduced. Our results suggest that both MoMst3 and FgMst3 are involved in fungal innate immunity downstream of unknown NLR proteins, motivating studies to try to identify genes for the NLR-like receptors. Finding such and investigating how they work and vary between fungal species and strains should be useful for understanding fungal biotic interactions with viruses, bacteria, plants, and animals.

immunology↗

bioRxiv2025

Lipid Metabolism Remodeling in Human Cardiomyocyte Differentiation and Maturation

During cardiac development, metabolic remodeling is characterized by a transition from glycolysis-dependent energy production to reliance on fatty acid oxidation. Lipids function as essential energy substrates and structural components throughout cardiac formation and maturation. However, the dynamic changes in endogenous lipid species during human cardiac development remain incompletely elucidated. In this study, we delineated distinct lipidomic profiles of human embryonic stem cells (ESCs), mesoderm (MES), cardiac progenitors (CPCs), immature cardiomyocytes (CMs), and mature CMs derived from ESCs using high-performance liquid chromatography (HPLC). Notably, ceramide concentrations peaked at the CPC stage, suggesting a pivotal role in mediating the MES-to-CPCs transition. Concurrently, lipid metabolites including GM3, phosphatidylcholine (PC), lysophosphatidylcholine (LPC), and lysophosphatidic acid (LPA) were significantly upregulated in mature CMs. Integrative transcriptomic and chromatin accessibility analyses further refined the landscape of lipid remodeling during CM differentiation. Functional assays demonstrated that LPA enhances the stability of the beating rhythm in CPCs, while both PC and LPA facilitate CM maturation. Collectively, our findings establish a comprehensive and dynamic lipidomic atlas of human cardiogenesis, providing a novel framework to advance the understanding of lipid-mediated regulatory mechanisms in human heart development.

developmental biology↗

bioRxiv2025

Protectin D1/GPR37 signaling enhances macrophage-dependent efferocytosis to attenuate experimental abdominal aortic aneurysm formation

Abdominal aortic aneurysms (AAAs) are chronic inflammatory vascular disorders characterized by progressive aortic dilation and destruction of the vascular wall, often culminating in rupture. Current management is limited to surgical repair, with no approved targeted pharmacologic therapies. In this study, we investigated the immunomodulatory role of Protectin D1 (PD1), a specialized pro-resolving lipid mediator, through G-protein-coupled receptor 37 (GPR37) signaling on macrophages in mitigating AAA progression and preventing aortic rupture. Single cell-RNA sequencing analysis of human tissue demonstrated significant differences in PD1/GPR37 axis-related genes in macrophages in AAAs compared to control aortic tissue. Using an established murine AAA model, PD1 administration significantly attenuated aortic diameter, pro-inflammatory cytokine and matrix metalloproteinase (MMP2) expression, as well as maintained aortic morphology in a GPR37-dependent manner. Importantly, PD1 treatment prevented preformed AAA progression to aortic rupture in another preclinical elastase+BAPN model of aortic rupture, by attenuating aortic diameter, tissue inflammation as well as decreasing macrophage infiltration, preserving elastin integrity, and restoring smooth muscle -actin expression in the aortic wall. Mechanistically, PD1 enhanced macrophage efferocytosis of apoptotic vascular smooth muscle cells in the murine aortic tissue as well as in isolated macrophages via GPR37-dependent manner and attenuated the inflammatory paracrine secretion of macrophage-specific paracrine release of TNF- and IL-{beta}. These findings suggest that PD1/GPR37 signaling on macrophages promotes inflammation-resolution by enhancing efferocytosis of apoptotic SMCs conferring protection against aortic inflammation and remodeling to mitigate AAA formation and rupture. Significance StatementThis study elucidates the protective role of specialized proresolving lipid mediator, Protectin D1, by activating macrophages via GPR37 receptors, to enhance the clearance of apoptotic smooth muscle cells to mitigate aortic inflammation and vascular remodeling during abdominal aortic aneurysm formation. We observed that several key inflammation related genes were associated with PD1/GPR37-dependent signaling in macrophages of human AAAs. Detailed analysis in experimental models delineated the signaling pathway where upregulating macrophage-dependent efferocytosis via immunomodulation by Protectin D1 attenuated aortic inflammation and remodeling, indicating a potential mechanism for therapeutic intervention in the pathobiology of AAAs to prevent aortic rupture.

immunology↗

bioRxiv2025

Human Organoids Reveal PTEN-driven Mesendoderm Specification via Retinoic Acid Signaling Suppression

During early embryogenesis, epiblast cells ingress through the primitive streak (PS) and commit to a mesendoderm (MES) fate, giving rise to both mesodermal and endodermal lineages. Despite advancements in human organoid technology for modeling pre-implantation blastocyst stage, robust systems that accurately recapitulate MES specification and PS formation during the post-implantation stage remain limited. Here, we show that human induced pluripotent stem cells can be used to generate three-dimensional MES organoids that faithfully mimic in vivo human MES specification, particularly from the anterior PS. We demonstrate that MES organoid formation is dependent on PTEN expression and that loss of PTEN severely impairs the formation of mesoderm and definitive endoderm derivatives arising from MES organoids. To elucidate the molecular mechanisms underlying these defects, we conducted an integrative multi-omics analysis, including transcriptome, chromatin accessibility profiling, metabolism, and phosphoproteomics, on wild-type and PTEN-/-MES cells. These analyses revealed that PTEN suppresses retinoic acid (RA) signaling during MES lineage commitment. Furthermore, we identified the RA-degrading enzyme CYP26A1 as a downstream effector of PTEN. Notably, while excessive RA induced by PTEN ablation is detrimental to MES cell generation, physiological levels of RA are necessary. Collectively, our human MES organoids offer a valuable model for dissecting early human development, and our findings identify PTEN as a key regulator of MES fate commitment through inhibition of RA signaling.

developmental biology↗

bioRxiv2025

Viral tRNA-like structure hijacks host ribosomes for poly(A)-independent translation

Positive-sense RNA viruses often use 3' tRNA-like structures (TLSs) instead of poly(A) tails to capture the host translation machinery. While TLSs resemble canonical tRNAs and engage host factors, their ability to directly recruit ribosomes has remained unresolved. Here, we present cryo-electron microscopy snapshots of the histidine-accepting TLS (TLSHis) from tobacco mosaic virus bound to the 60S subunit, the 80S ribosome, and the 80S-tRNAiMet initiation complex. Across these states, TLSHis is consistently anchored to the L1 stalk of 60S, even under cycloheximide treatment, yet remains dynamic on the 40S subunit. Structural analysis shows that TLSHis transitions from the E-site to an adjacent Z-site to accommodate initiator tRNA. Functional assays show that TLSHis preferentially associates with ribosomal subunits over polysomes and can substitute for a poly(A) tail to promote robust cap-dependent translation. Together, these findings reveal how a viral tRNA mimic hijacks host ribosomes to promote poly(A)-independent translation.

molecular biology↗

bioRxiv2025

Nutrient excess remodels islet autonomic innervation via pancreatic schwann cells

Nutrient excess results in short- and long-term adaptations in the structure and function of metabolic organs, such as pancreatic islets. Pancreatic innervation contributes to islet architecture and function in many species, including humans, but little is known about its adaptation to over-nutrition. Here, we use 3D imaging to show that short-term high fat diet rapidly remodels islet sympathetic innervation while long-term high fat diet results in islet-specific cholinergic neuropathy. Using highly targeted, organ- and circuit-specific approaches, we demonstrate that remodeling of pancreatic innervation contributes to impaired glycemic control with short- and long-term nutrient excess. Counteracting the nutrient-induced changes in sympathetic and parasympathetic inputs to the pancreas using neuromodulation and repurposed FDA-approved approaches, we can significantly improve glycemic control even with long-term high fat diet. Finally, we identify islet Schwann cells as a source of the neurotrophic factor, S100b, contributing to rapid sympathetic hyperinnervation with short-term overnutrition. Our findings reveal novel adaptations in islet innervation contributing to nutrition-mediated metabolic dysfunction that can be ameliorated by targeting pancreatic neural circuits.

physiology↗