Biology subjects

Yu, H.

Publications and source records attributed to Yu, H..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

RNAi-based discrimination of exogenous DNA by mitotic heterochromatin in fission yeast

Various mechanisms protect prokaryotic cells from invasive exogenous (exo)DNA. However, these are rarely conserved in eukaryotes, where the existence of such processes remains elusive. Here, we uncover how fission yeast eliminates exoDNA through unequal partitioning. We show that intrinsic transcriptional features of plasmidial exoDNA produce small interfering (si)RNAs that recruit heterochromatin onto the plasmid. An active, heterochromatin-dependent clustering mechanism then causes its asymmetric partitioning during mitosis. The mitotic kinase Aurora B, which dissociates heterochromatin on segregating chromosomes, is distinctively hypoactive on plasmidial DNA, facilitating its unequal partitioning and, ultimately, elimination from the cell population. Thus, an interplay between RNAi-mediated exoDNA heterochromatinization and chromosomal phosphorylation enables fission yeast to discriminate self-from non-self-DNA, uncovering a hitherto undescribed cell-autonomous immune process in eukaryotic cells.

cell biology↗

bioRxiv2026

N-terminal Chirality and Sequence Variations Modulate the Conformational Landscape of Amyloid-beta 42

Amyloid beta (A{beta}), one of the hallmark proteins of Alzheimers Disease (AD), aggregates into plaques that are strongly linked to cognitive decline and neuronal death. Reducing its aggregation propensity may provide a strategy to slow the progression of AD. While chirality modulation has emerged as an innovative approach to disrupt this process, research has primarily focused on alterations at the C position, often overlooking the impact of the second chiral center, such as the C{beta} atom of Threonine. Furthermore, the underlying mechanisms governing these chiral effects remain elusive. Given the intrinsically disordered nature of the A{beta} peptide, we employed temperature-replica exchange molecular dynamics (T-REMD) simulations to explore its rugged conformational landscape. We considered sequence mutations (A2T, A2V), N-terminal chirality inversion of the first six residues (A2V1-6D and WT1-6D), and alteration of the second chiral center (C{beta}) of Threonine (A2TC{beta}). By analyzing the effect size and population change induced by these mutations and chiral modulation, we concluded that the modulation at the N-termini is not confined locally but also exerts specific effects on the central hydrophobic core (CHC) region. Inspection of their free energy landscape and representative structures reveals that the protective or pathogenic effects of these variants correlate with their similarity to the wild type (WT) ensemble. Beyond these static thermodynamics analyses, a direct connection to phase transitions was made by estimating heat capacity as a function of temperature. Both analyses predict that A2TC{beta} may exert a pathogenic effect, in contrast to the protective nature of A2T. These findings offer a deeper understanding of the effects of site-specific mutations and chirality and shed light on the development of advanced therapeutic strategies for AD.

biochemistry↗

bioRxiv2026

Interactome mapping in human excitatory neurons reveals novel risk genes and pathways in Alzheimer's disease

Alzheimers disease (AD) is an irreversible neurodegenerative disease defined by its molecular hallmarks - amyloid beta peptide plaques and neurofibrillary Tau tangles. Despite significant progress that has been made in uncovering a large number of genetic risk factors through extensive genomic sequencing and genetic studies, the molecular mechanisms driving AD-associated pathology and cognitive decline remain poorly understood. Therefore, alongside the identification of more risk genes, it is also paramount to study how these genes function and influence each other within the cellular pathways and overall molecular networks in AD-relevant brain cell types. However, current human protein-protein interactome datasets were all generated in either yeast or generic human cell lines. Consequently, many important neuronal interactions, especially neuron-specific ones, have yet been discovered. To address this critical gap, we developed a highly scalable, high-quality interactome mapping pipeline in human excitatory neurons derived from induced pluripotent stem cells (iPSC), and generated a comprehensive, neuron-specific interactome map, named ADNeuronNet, for key AD risk genes. ADNeuronNet consists of 1,767 high-confidence interactions among 1,189 proteins and is the only dataset enriched with neuron-specific genes when compared to known protein interactions, including previous large-scale interactome maps, for the same baits in the literature. Within ADNeuronNet, we identified 1,375 novel interactions, many of which are likely neuron specific. For example, we identified a neuron-specific interactor, RIN2, for major AD risk factor BIN1 and confirmed RIN2s function in recruiting BIN1 to RAB5 positive early endosomes, a process that has been well-associated with AD etiology. Additionally, we performed quantitative interaction perturbation analyses on AD risk genes with AD-associated mutations or isoforms and identified significant changes in 99 protein interactions among 11 different protein variants. Finally, we found that subunits from the anaphase-promoting complex/cyclosome (APC/C), another novel BIN1 interactors identified by ADNeuronNet, mediated modulation of Tau-aggregation in neurons via regulation of APOE expression, uncovering a previously unrecognized BIN1-APC/C-APOE regulatory axis in AD pathobiology. In summary, these findings illustrate how our neuron-specific ADNeuronNet can be leveraged to uncover new risk gene candidates and cellular pathways that help advance our understanding of molecular mechanisms underlying AD etiology.

systems biology↗

bioRxiv2026

Development of a BM7G((TKO/hCD46/hCD55/hTHBD/hEPCR) Donor Pig with Endogenous Promoter-Driven Transgenes for Xenotransplantation

Xenotransplantation offers a potential solution to the organ shortage crisis. Multi-gene modification of pigs, such as knockout of three carbohydrate antigen-related genes and expression of immunoprotective proteins, can significantly improve xenograft survival. However, existing strategies face challenges: transposon-based transgenesis may lead to unstable expression, while exogenous promoters used in site-specific integration are susceptible to epigenetic silencing, hindering long-term stable expression. Therefore, developing a donor pig model capable of sustained multi-gene expression is critical. To address this, CRISPR-Cas9 was used to knockout three major glycan antigen genes to eliminate hyperacute rejection. Subsequently, four human protective genes were site-specifically integrated into the porcine Rosa26 safe-harbor locus, with expression driven by the endogenous Rosa26 promoter and the THBD core promoter for long-term stable and tissue-specific expression, and the selection marker was removed using Cre/loxP. Results showed complete absence of the three glycan antigens in BM7G pigs, while the four protective proteins were stably expressed in vascular endothelial cells and major organs. Among them, hCD55 and hCD46 were widely expressed, while hTHBD and hEPCR showed vascular-specific expression. In-vitro assays confirmed that BM7G porcine endothelial cells significantly reduced human antibody binding, effectively inhibited complement-dependent cytotoxicity, and decreased thrombin-antithrombin complex formation. In conclusion, by combining xenoantigen knockout with endogenous promoter-driven expression of multiple human protective genes, a seven-gene modified pig model with low immunogenicity and synergistic protective function was successfully constructed, providing an important donor resource for xenotransplantation preclinical research.

immunology↗

bioRxiv2026

Learning the All-Atom Equilibrium Distribution of Biomolecular Interactions at Scale

Biomolecular functions are governed by dynamic conformational ensembles rather than static structures. While models like AlphaFold have revolutionized static structure prediction, accurately capturing the equilibrium distribution of all-atom biomolecular interactions remains a significant challenge due to the high computational cost of molecular dynamics (MD). We present AnewSampling, a transferable generative foundation framework designed for the high-fidelity sampling of all-atom equilibrium distributions, which is the first model to faithfully reproduce MD at the all-atom level. It uses a quotient-space generative framework to ensure mathematical consistency and leverages the largest self-curated database of protein-ligand trajectories to date, with over 15 million conformations. Statistically, AnewSampling consistently outperforms all prior generative methods on the ATLAS monomer benchmark, and the all-atom capabilities of AnewSampling enable close statistical alignment with ground-truth MD for evaluating atomic biomolecular interactions in protein-ligand dynamics. Furthermore, AnewSampling successfully recovers coupled ligand and side-chain motions in CDK2 systems, overcoming a major sampling hurdle inherent to conventional MD. AnewSampling enables rapid exploration of conformational landscapes prior to intensive simulations, elucidating fundamental biophysical mechanisms and accelerating the broader design of functional biomolecules.

bioinformatics↗

bioRxiv2026

Ancestral secretory programs underlie the evolution of morphological innovations across Spiralia

Understanding how morphological innovation arise from ancestral genetic and cellular systems remains a major challenge in evolutionary biology. Molluscan shells represent one of the most diverse morphological novelties within Spiralia and have been central to the ecological and evolutionary diversification of molluscs. However, the cellular basis of shell formation and the evolutionary origin of shell-forming cell types remain poorly understood. Here, we present a single-cell transcriptomic atlas of the Pacific oyster (Crassostrea gigas) mantle and show that molluscan shell-forming cell types are evolutionarily recent innovations built upon ancestral epithelial secretory systems of spiralians. We identify five spatially segregated shell-forming epithelial cell types, and demonstrate that larval and adult shell-forming cells are developmentally independent and characterized by transcriptomes enriched for evolutionarily young genes. Cross-species cell-type comparisons further reveal that oyster shell-related genes are embedded within conserved epithelial and secretory programs across spiralians. Together, we propose that a substantial genetic foundation for shell formation was already present in the last common ancestor of Spiralia, and that molluscan shell diversity arose through repeated co-option of ancestral genetic programs coupled with novel genes. Our study provides a framework for understanding how ancient cellular architectures can be repeatedly reconfigured to generate morphological novelty during evolution.

evolutionary biology↗

bioRxiv2026

Presenilin 1 (PS1) located at mitochondrial inner membrane regulates mitochondrial cristae junction proteins arrangement and cristae formation in HEK293 cells

Presenilin 1 (PS1), a key pathogenic factor in familial Alzheimers disease, is implicated in regulation of mitochondrial functions, yet its precise sub-mitochondrial localization and underlying mechanisms remain poorly understood. In this study, we generated PS1 knockout (PS1 KO) cell lines to investigate the role of PS1 in mitochondrial structure and function. Our results demonstrated that PS1 is directly localized to the mitochondrial inner membrane. PS1 deficiency led to reduced ATP production, impaired mitochondrial respiration capacity, decreased mitochondrial membrane potential, disrupted Ca2+ homeostasis, and elevated reactive oxygen species (ROS) accumulation. Moreover, loss of PS1 caused abnormal mitochondrial cristae structure. Further analysis revealed that PS1 interacts with mitochondrial inner membrane proteins. Its absence promotes ATAD3A oligomerization and disrupts its arrangement at mitochondrial cristae junctions, leading to expansion of the mitochondria-associated membrane (MAM) and instability of mitochondrial DNA (mtDNA). Our findings demonstrate that PS1 acts as a central regulator of mitochondrial cristae morphogenesis by modulating protein interaction networks at cristae junctions, thereby illuminating fundamental molecular mechanisms contributing to mitochondrial dysfunctions in Alzheimers disease.

cell biology↗

bioRxiv2026

Porcine extended pluripotent stem cell-derived somite-like mesoderm cells with Dox-driven PAX7 are robust seed cell resource for facilitating production of cultured meat

Cultured meat technology, with its significant advantages of shortening meat production cycles, reducing natural resource consumption, minimizing the risk of zoonotic disease transmission, and enabling precise control over nutritional composition and texture, offers a novel alternative source for human meat consumption. One of the major challenges to produce cultured meat in large scale is how to establish high.quality seed cells, which should have long term proliferative capacities and are able to differentiate into muscles efficienuy with simple procedures. Here, we first established an engineered porcine expanded potential stem cells (Tet-On-PAX7 EPSCs) containing Tet-On regulated PAX7 gene. Then the Tet-On-PAX7 EPSCs were induced to somite-liKe mesodermal cells. These somite-liKe mesodermal cells can be expanded over 1025-fold even after 40 passages in-vitro culture while retaining strong myogenic potential. The somite-like mesodermal cells treated with DOX for one day would differentiate into muscle stem cells (Muses), and the later were able to differentiate into muscles with an efficiency of up to 90% within just 7 days in 11-FSDeDa without Dox. Moreover, when somite-liKe mesodermal cells were seeded on patterned scaffolds, microcarrier scaffolds, or cultured in anchorage-independent suspension, they maintained high efficiency in muscle differentiation, confirming their potential to be used as seed cells for scaled cultured meat production.

developmental biology↗

bioRxiv2026

Cystinosin/Ers1 functions in redox homeostasis in the early secretory pathway

Cystinosis is an autosomal recessive inherited disorder caused by mutations in the CTNS gene, which encodes the highly conserved transmembrane protein cystinosin, a proton/cystine co-transporter at the lysosome membrane. However, reduction of cystine load in the lysosomes is insufficient to treat key disease symptoms, indicating that cystinosin performs additional disease-relevant functions. Here, we report that Ers1, the yeast homolog of cystinosin, localizes to and functions in the early secretory pathway. We provide evidence that Ers1 does not transport cystine. Ers1 genetically interacts with early secretory pathway recycling adaptors and redox-active Fe-S cluster-binding proteins. Notably, cystinosin-LKG, the extra-lysosomal localized splicing isoform of cystinosin, can functionally replace Ers1 in yeast. Collectively, our work uncovers a conserved role of cystinosin/Ers1 in the early secretory pathway, offering new molecular insights for understanding cystinosis pathology.

cell biology↗

bioRxiv2026

Heterozygote Advantage of a Single-Copy SNAP18 Truncation Allele Enables Dominant SCN Resistance and Yield Preservation in Soybean

Soybean cyst nematode (SCN, Heterodera glycines) is the most devastating pathogen threatening global soybean production. The long-term over-reliance on rhg1-a/b resistance has led to the rapid emergence of virulent SCN populations, creating an urgent demand for novel genetic resources to safeguard soybean yield. Here, we identified a rare gain-of-function allele, SNAP18lmm3, via map-based cloning of the lesion-mimic mutant (lmm3) in the SCN-susceptible Williams 82 (rhg1-c) background. This allele encodes a 24-amino-acid C-terminal truncation of SNAP18 and exhibits an unusual mixed dominance genetic profile: the autoimmune-related leaf lesion phenotype is recessive, whereas SCN resistance is dominant. Homozygous lmm3 plants suffer significant yield losses due to spontaneous cell death, but heterozygous (LMM3+/-) plants maintain normal growth, agronomic performance, and seed yield comparable to wild-type Williams 82 in SCN-free field environments. Critically, under artificial SCN inoculation in both field trials and controlled environments, LMM3+/- heterozygotes confer robust resistance, achieving a [~]4-fold yield advantage over SCN-infested Williams 82 and a [~]44% reduction in cyst formation relative to Williams 82. This resistance profile aligns with the broad-spectrum activity of the lmm3 homozygous mutant, supported by the conserved resistance mechanism of SNAP18lmm3. Transgenic expression of SNAP18lmm3 driven by the nematode-responsive HIP promoter (HIPpro) potently arrested nematode development at the J2 stage in transgenic hairy roots, as evidenced by the drastically reduced proportion of advanced-stage nematodes. Our findings establish SNAP18lmm3 as a potent, "plug-and-play" genetic resource that circumvents the limitations of traditional dosage-dependent resistance loci. This allele enables the development of high-yielding, SCN-resistant soybean cultivars through marker-assisted selection for the heterozygous state or precision genome editing, providing a practical solution for sustainable SCN management.

plant biology↗

bioRxiv2026

SNAP18 Truncation Triggers a Competitive Binding Switch Between NSF and ATG8f, Balancing Vesicular Trafficking and Autophagy for SCN Resistance in Soybean

Soybean cyst nematode (SCN, Heterodera glycines) poses the most devastating biotic threat to global soybean production. Traditional SCN resistance mediated by the Rhg1 locus predominantly relies on gene copy number expansion and elevated -SNAP protein dosage. Here, we report a novel resistance mechanism in a single-copy rhg1-c background, wherein a C-terminal 24-amino-acid truncation of SNAP18 (designated SNAP18lmm3) triggers a functional switch from vesicular trafficking to autophagic degradation. Biochemical assays and structural modeling demonstrate that this truncation severely impairs the canonical interaction between SNAP18 and N-ethylmaleimide-sensitive factor (NSF), disrupting SNARE complex recycling and inducing localized cytotoxicity. Concomitantly, the truncated SNAP18lmm3 exposes a binding interface for the autophagy-related protein ATG8f, routing the aberrant protein for selective autophagic clearance. This constitutively activated autophagic flux acts as a systemic detoxification system, preventing widespread cell death and ensuring normal plant growth under non-stressed conditions. Upon SCN infection, SNAP18lmm3 specifically hyper-accumulates within nematode-induced syncytia. This accumulation reaches levels fourfold higher than in adjacent cells, which overwhelms the local autophagic capacity and triggering targeted cell death that arrests nematode development. By elucidating this competitive molecular switch between NSF and ATG8f binding, our study establishes a "self-degrading toxin" model that resolves the inherent trade-off between plant growth and immunity. This work provides a new theoretical framework for engineering cellular homeostasis to enhance durable crop resistance against parasitic nematodes.

plant biology↗

bioRxiv2026

Cooperative and competitive interactions among transcription regulatory elements modulate transcription output

Transcription is modulated by interactions among transcription regulatory elements (TREs), including promoters and enhancers, but their underlying interaction specificities remain opaque. Here, we develop a Chromatin-Integrated, landing-pad-based Enhancer Reporter Assay, CIERA-seq, that interrogates regulatory interactions between target promoters and distal TREs in a controlled genomic and chromatin context. We find both promoter- and enhancer-TREs exhibit enhancer activities on target promoters with a specificity that depends on factors that TREs recruit. Promoters are generally enriched for factors involved in the core transcription process, whereas enhancers are enriched for pioneer factors and chromatin remodelers. Our CIERA-seq assays support a model where TREs activate target promoters constrained at different rate limiting steps in transcription by supplying complementary components of the transcription regulatory machinery. An orthogonal analysis using CRISPRi datasets shows that both promoters and enhancers can positively regulate expression of neighboring genes at their native loci. However, promoters are also more prone than enhancers to exhibit negative regulatory effects, a difference that may arise from competition for limiting transcriptional machinery. Together, these findings support a framework in which promoters and enhancers act as cooperative, or competitive, regulatory elements within local transcription hubs to modulate transcription outputs.

molecular biology↗

bioRxiv2026

Harnessing Tumor-Specific Transcript Diversity Uncovers a Shared Neoantigen Reservoir for Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is refractory to immunotherapy due to its immunologically cold microenvironment and the scarcity of mutation-derived neoantigens. Here, we introduce NeoAPP, a computational tool designed to systematically decode neoantigens arising from tumor-specific transcripts (TSTs) generated by transcriptional dysregulation. Multi-cohort transcriptomic profiling of 413 PDAC samples using NeoAPP reveal a median of 351 neoantigens per sample derived from 56 neoantigen-encoding TSTs (neoTSTs), surpassing mutation-derived counterparts in both abundance and patient coverage. Mechanistic analyses show that non-canonical splicing junction and transposable element activation drive neoantigen generation, while FOXA2-regulated promoter usage constitutes a potential major source of neoTSTs. Tumor-derived neoTSTs are also detected in extracellular vesicles and cancer-associated fibroblasts, implicating stromal crosstalk in immune modulation. Vaccination with neoTSTs induce CD8+ T cell responses in HLA-A*02:01/A*11:01 transgenic mice and suppressed tumor growth in syngeneic PDAC models. Collectively, this work establishes TST-derived neoantigens as a dominant and therapeutically actionable antigen reservoir in PDAC, advancing a transcriptome-guided framework for neoantigen discovery with potential to overcome immune resistance in low-mutation cancers. Abstract Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/705024v1_ufig1.gif" ALT="Figure 1"> View larger version (71K): org.highwire.dtl.DTLVardef@82ff31org.highwire.dtl.DTLVardef@401342org.highwire.dtl.DTLVardef@b0771corg.highwire.dtl.DTLVardef@15c03ef_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Accurate strand-specific long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution

Recent advances in long-read transcriptome sequencing enable high-throughput profiling of full-length RNA isoforms in bulk, single-cell, and single-nucleus samples. However, long-read datasets typically contain a mixture of complete and partial transcripts, leading to pervasive ambiguity in read-to-isoform assignment and complicating accurate isoform identification and quantification, particularly in the absence of reliable reference annotations. These challenges are further amplified in single-cell and single-nucleus samples, where coverage is sparse and transcriptional heterogeneity is high. Here, we present the Long Read Alignment Assembler (LRAA), a unified and versatile computational framework for isoform identification and quantification from long-read RNA sequencing data across bulk, single-cell, and single-nucleus transcriptomic samples. LRAA combines splice-graph based structural modeling with expectation maximization based optimization to probabilistically resolve ambiguous read assignments and improve isoform abundance estimation. The framework supports quantification-only, reference-guided, and fully reference-free (de novo) modes of analysis within a single methodological paradigm. We benchmarked LRAA using both simulated and genuine long-read datasets spanning sequencing standards and whole transcriptomes. Central to this evaluation is a novel benchmarking strategy based on Multiplexed Overexpression of Regulatory Factors (MORFs), which provides biologically expressed, barcoded isoforms with unambiguous read-level ground truth. Across all benchmarks, including MORFs, synthetic spike-ins, and whole-transcriptome datasets, LRAA consistently outperformed state-of-the-art methods in isoform identification accuracy, sensitivity, and expression quantification. Finally, we demonstrate the biological utility of LRAA by resolving cell-type-specific isoform usage across peripheral blood immune cell populations and by detecting a pathogenic cryptic isoform of STMN2 with associated transcriptional changes in single-nucleus RNA-seq data from frontal cortex tissue of an individual with frontotemporal dementia (FTD). Together, these results establish LRAA as a robust and general solution for resolving transcript diversity in complex biological systems, from development to disease.

bioinformatics↗

bioRxiv2026

Rapid peripheral reprogramming of myelinated afferents drives human hyperalgesia

A small burn can render a large area of skin painfully tender. This widespread hyperalgesia protects injured tissue and is typically attributed to altered spinal cord mechanisms. Whether peripheral sensory afferents directly interact to contribute to hyperalgesia remains unclear. Using single-unit microneurography, we recorded cutaneous afferents before and after inducing localized TRPV1-mediated inflammatory flare. This triggered minutes-scale reweighting of transcriptomically defined TRPV1- afferents, with divergent effects among myelinated (A{beta}-range) classes: tactile receptors showed reduced responsiveness, whereas mechano-nociceptors underwent sensitization. These changes paralleled diminished tactile sensitivity and intensified mechanical pain. Recruitment of mechanically silent branches in A{beta}-range mechano-nociceptors produced wide-field amplification of peripheral nociceptive signaling beyond the inflamed site. These findings suggest that rapid peripheral crosstalk from TRPV1+ afferents reprograms TRPV1- A{beta}-afferents and drives human hyperalgesia.

neuroscience↗

bioRxiv2026

Molecular basis of enfumafungin inhibition and resistance in Candida glabrata β-1,3-Glucan synthase FKS1

{beta}-1,3-Glucan synthase FKS1 is essential for fungal cell wall biogenesis and serves as a validated target of widely prescribed antifungal drugs. However, the molecular mechanism of pathogenic FKS1, its modes of inhibition, and the associated resistance mechanisms remain elusive, hindering the antifungal development. Here, we focus on Candida glabrata FKS1, a clinically relevant target frequently linked to antifungal resistance. We present cryo-EM structures of C. glabrata FKS1 in multiple detergent environments and in complex with the triterpenoid antifungal enfumafungin. Integrated functional studies revealed a key catalytic residue within the conserved ED motif and uncovered structural adaptations to different membrane-mimetic environments, rationalizing FKS1s sensitivity to its surrounding membrane context. Enfumafungin binds at the extracellular membrane leaflet of cgFKS1 transmembrane domain, engaging a convex surface separated from the cytosolic active site, consistent with its role as a non-competitive inhibitor. Further analyses identified key enfumafungin-binding residues from TM5-TM6 and elucidated the molecular basis of drug resistance in C. glabrata. Collectively, these findings establish a mechanistic framework for pathogenic FKS1 function and inhibition and provide a molecular basis for the rational design of next-generation antifungal therapeutics.

microbiology↗

bioRxiv2026

The endoderm cell trajectory of urochordate Styela clava reveals the dual developmental origin and evolution of digestive tract

The digestive system exhibits extensive diversity in developmental mechanisms and morphology across metazoans, yet the evolutionary origins underlying its organ differentiation remain unclear. Here, single-cell RNA sequencing was employed to investigate endodermal cell lineage specification during metamorphosis in the urochordate Styela clava, a newly established model for chordate evolution. By profiling 26,099 cells across five stages, we identified 21 major cell clusters and reconstructed the endodermal differentiation trajectories. Our analysis reveals two larval endodermal progenitor populations with distinct differentiation potentials. Pseudotime and RNA velocity analyses indicate that these progenitors give rise to stomach and intestinal lineages, respectively. Cross-species comparisons reveal putative homologous relationships between ascidian endodermal lineages and mouse definitive and visceral endodermal lineages, suggesting dual origins of digestive tract in chordates. We also identified conserved TGF-{beta} and FGF regulatory programs in digestive organ patterning and highlight earlier fate restriction of stomach and intestinal progenitors in ascidians compared to vertebrates. These findings provide insights into how chordate digestive organs evolved from ancestral endodermal patterning programs.

evolutionary biology↗

bioRxiv2026

Asymmetric partition of the O-GlcNAcome in mitosis ensures binary cell fate decision

Many cellular components undergo biased segregation during stem cell division, but whether such order extends to the proteome has remained unknown. Using our real-time O-GlycoTracer, we find that O-GlcNAcylated proteins (the O-GlcNAcome) segregate asymmetrically during Drosophila neuroblast mitosis, predisposing the two daughters to distinct fates. The daughter that preserves stem cell identity inherits most of the O-GlcNAcome. This asymmetric partition requires putative O-GlcNAc readers, notably 14-3-3 proteins. We further identify the nuclear pore complex (NPC) as a major O-GlcNAc substrate in neuroblasts; Nup153, located in the nuclear basket, shows O-GlcNAc-dependent biased inheritance. Perturbing multiple steps in this segregation pathway disrupts neuroblast differentiation, reduces brain size, and causes adult learning deficits. These findings reveal a coordinated O-GlcNAc-driven mechanism for proteome-level asymmetric inheritance during neural stem cell division, with implications for neurodevelopmental disorders linked to OGT or 14-3-3 mutations.

cell biology↗