Biology subjects

Lee, L.

Publications and source records attributed to Lee, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Two Pleckstrin homology domains scaffold SNAP-47-containing SNARE complexes

Long-term potentiation requires the regulated insertion of AMPA receptors into the postsynaptic membrane of neurons, a process mediated by a SNARE complex containing SNAP-47, syntaxin-3, and synaptobrevin-2. Compared to other SNAP proteins, SNAP-47 exhibits slower fusion kinetics and contains uncharacterized regions whose functions remain unclear. Here, we integrated biochemical approaches with artificial intelligence structure prediction tools and molecular dynamics to investigate the architecture of SNAP-47-containing SNARE complexes. AlphaFold3 predictions of the ternary SNAP-47-containing SNARE complex revealed one known Pleckstrin homology domain (PH1) and one previously unidentified PH domain (PH2), which we validated experimentally. BioEmu and molecular dynamics simulations indicated that PH1 and PH2 form a stable and energetically favorable interface. In this bound state, PH1 stably interacted with the SNARE coiled coil, and in silico acetylation at a lysine whose acetylation is known to impair SNAP-47 function disrupted this PH1-SNARE interface. AMPAR insertion via SNAP-47-containing SNARE complexes is triggered by the calcium sensor synaptotagmin, and we observed that PH1, PH2, and synaptotagmin-1 can simultaneously engage with the plasma membrane, consistent with a pro-fusion conformation. Together, we provide new mechanistic insight into how PH domains regulate SNAP-47-mediated membrane fusion during synaptic plasticity.

molecular biology↗

bioRxiv2026

Metabolic rewiring induces a viral mimicry-mediated quiescence in glioblastoma

Glioblastoma is a highly aggressive brain tumour driven by therapy-resistant glioblastoma stem cells (GSCs) that switch between dormant and proliferative states through poorly defined programs. In this study, we identify SAT1, encoding the rate-limiting polyamine-catabolic enzyme SSAT1, as enriched in quiescent GSCs, linking metabolic rewiring to dormancy. Pharmacologic induction of SSAT1 with the polyamine analogue N1,N11-Diethylnorspermine (DENSpm) triggers a chemoprotective, reversible growth arrest in patient-derived GSCs, independent of stemness, differentiation or senescence. SAT1-induced dormancy coincides with reduced eIF5A hypusination and global protein translation, and a marked rise in double-stranded RNA that activates type I interferon signalling. Knocking down the mitochondrial antiviral-signalling protein, essential for antiviral innate immunity, partially reverses this growth arrest, establishing viral mimicry as functionally required for dormancy. Single-cell and cohort analyses across GSCs and neural stem cells demonstrate that susceptibility to metabolically induced quiescence is set by an intrinsic inflammatory tone and lysosomal dependency, defining a context-dependent metabolic-immune axis which can be targeted to prevent GBM progression.

cancer biology↗

bioRxiv2026

Microglia drive demyelination via multiple sclerosis antibodies and BTK signaling

Microglia are the predominant immune cells in multiple sclerosis (MS) demyelinating lesions, where they phagocytose myelin, but whether they destroy myelin or merely scavenge its debris is unknown. Here, we explore whether pathogenic autoantibodies found in MS may induce the phagocytic destruction of myelin by microglia. Applying patient-derived, myelin-targeting antibodies to the mouse cortex, we developed an in vivo model of MS with focal demyelination that depended on epitope specificity and Fc gamma receptor and complement binding. Longitudinal monitoring of microglia-myelin interactions using in vivo two-photon microscopy revealed rapid microglial envelopment of intact myelin driving myelin loss, while single-cell RNA sequencing identified a demyelination-associated microglial signature. Parallel changes were observed in human MS lesions, where microglia enveloped intact myelin and similar genes were upregulated. Inhibition of Brutons tyrosine kinase (BTK) limited microglial transcriptional changes and prevented myelin loss following microglial envelopment. These findings directly implicate microglia in pathological myelin loss and support BTK inhibition as a therapeutic strategy to prevent demyelination by modulating microglia behavior.

neuroscience↗

bioRxiv2026

Glioblastoma Invasion Remodels Neural Circuits and Drives Persistent GABAergic Dysfunction in Human Brain Organoids

BackgroundGlioblastoma (GBM) is characterized by neurological dysfunction caused by tumor cells that interact with and alter neuronal circuits. However, the specific neuronal populations and molecular mechanisms most susceptible to GBM invasion remain poorly understood. MethodsWe created a human tumor-brain organoid model by combining U87 glioblastoma cells with iPSC-derived neural organoids. This system enabled us to study tumor-neural interactions over an extended period under standard temozolomide (TMZ) treatment. We used single-cell transcriptomics to monitor cell-type-specific responses. ResultsOur model recapitulated the diffuse infiltration observed in patients, leading to extensive structural remodeling and a profound loss of neuronal and glial populations. Single-cell analysis revealed that TMZ suppressed proliferative and biosynthetic programs but enriched for stress-responsive, mesenchymal-like, and therapy-adapted tumor states. Notably, GABAergic neurons exhibited the greatest transcriptional vulnerability, with [~]36% (7,499 of 20,659) of genes differentially expressed. Invasion triggered endoplasmic reticulum stress and shut down metabolic, respiratory, synaptic, and ion-homeostatic pathways. Crucially, SLC12A5-expressing GABAergic neurons plummeted from 31% to 12%, accompanied by a sharp decline in KCC2 protein expression. While TMZ partially rescued neuronal metabolic and electron transport chain function, it failed to restore SLC12A5/KCC2 expression or inhibitory signaling. ConclusionsGBM invasion leads to a continued imbalance of chloride in GABAergic networks, and this disruption remains even after undergoing tumor-targeted chemotherapy. This human iPSC-derived tumor-brain organoid platform provides a reliable and scalable system for studying complex tumor-neural interactions and exploring therapeutic approaches that aim to eliminate the tumor while preserving neural function.

cancer biology↗

bioRxiv2026

Beyond DNA barcodes: an open-source workflow for recovering and organizing barcoded vouchers for ecological and evolutionary research

1. Most species are neither discovered nor named, let alone included in analyses that require biological information such as trait measurements, images, ecological information and genome-scale data. Specimen-level DNA barcoding can help discover many of these species rapidly, but everything beyond discovery requires vouchers organized into putative species. Yet, existing barcoding workflows lack efficient techniques for voucher recovery, creating a post-barcoding bottleneck that limits the ability of converting barcoded specimens into biological knowledge. 2. Here we present a low-cost, open-source workflow consisting of two stages. The first safeguards barcoded specimens by separating them from DNA extracts and transferring them from microplates into ethanol-filled glass vials. The second converts the resulting voucher collection into a searchable physical resource by linking barcode-derived molecular Operational Taxonomic Unit (mOTU) assignments to vial positions and enabling specimens to be sorted into putative species either manually or automatically using a newly developed open-access robot (SORTER). 3. We evaluated the workflow using 2,024 insect specimens distributed across 21 96-well plates. For the first stage, DNA separation and specimen transfer required approximately 15 minutes per plate. For the second stage, MOTUmapper generated retrieval coordinates in a few seconds, after which the 2,024 vouchers belonging to the 452 putative species could be recovered manually in 5 days or with SORTER in 5 hours. Throughout both stages, specimen identities remained linked to barcode sequences, metadata and storage positions. 4. Vouchers are the Rosetta stones of biology because they connect different kinds of data to the same specimens. By safeguarding these vouchers and making them searchable, the workflow converts barcode projects from one-time molecular surveys into reusable resources for ecological and evolutionary research.

molecular biology↗

bioRxiv2026

Prostaglandin E2 facilitates reciprocal crosstalk between intestinal smooth muscle tissue and epithelium in tumor development

Colorectal cancer arises from intestinal epithelial cells and is driven by the accumulation of aberrant signaling events that disrupt intestinal stem cell (ISC) homeostasis. While stromal regulation of the ISC niche is increasingly recognized, the contribution of the underlying/adjacent smooth muscle tissue (SMT) remains poorly characterized. In particular, the potential crosstalk between normal or tumoral epithelium and the SMT is largely unexplored. Here, we investigate the ability of the SMT in modulating normal and tumorigenic epithelial biology, and the impact of the tumoral epithelium on the underlying SMT. Mechanistically, by using imaging analyses, transcriptomics, and mass spectrometry, we identify the SMT-derived factor Prostaglandin E2 (PGE2) as the key driver of epithelial dedifferentiation, promoting YAP transcriptional activation, organoid enlargement, and spheroid morphology in intestinal epithelial organoids following SMT supernatant exposure. Conversely, we show that non-invasive tumoral epithelium induces significant changes in the underlying SMT. Tumor-associated SMT shows structural remodeling, inflammation, and reduced muscle fitness. Furthermore, we detected increased prostaglandin signaling, including upregulation of PGE2 synthase Ptgs1 (COX1), in the SMT underneath the epithelial tumor. Our results reveal a communication between the tumoral epithelium and the underlying SMT prior to metastasis, which could be a facilitating step for tumoral extramural progression. Taken together, these findings highlight a novel tumor-stroma interaction.

Molecular Biology↗

bioRxiv2026

Conserved structural features of the lncRNA HOTAIR in breast cancer cells

Long noncoding RNAs (lncRNAs) regulate diverse cellular processes and are frequently implicated in disease, but their functional mechanisms often remain elusive. One such lncRNA, HOTAIR (Hox transcript antisense intergenic RNA), is a [~]2.1 kb mammalian transcript whose overexpression promotes invasion and metastasis in breast cancer. However, the mechanisms by which HOTAIR influences gene regulation in cancer are poorly understood. To approach this problem through a structural lens, we determined the full-length in cellulo secondary structure of HOTAIR using chemical probing in a metastatic breast cancer cell line. The resulting structure shows that HOTAIR adopts a multidomain architecture and has local structural features unique to the cellular context. Comparison between in vitro and in cellulo chemical probing identifies regions of differential accessibility that may indicate context-dependent molecular interactions or folding. Conservation analyses further reveal that HOTAIR is conserved across primates with evidence of structural covariation in specific domains. Together, these results provide a roadmap for future mechanistic studies of structure-function relationships in HOTAIR and its contribution to gene regulation in cancer.

biochemistry↗

bioRxiv2026

Unified Transcriptome and Mechanics Map of the Intact Mammalian Preimplantation Embryo In Situ

The development and maintenance of multicellular tissues requires that cell states be closely coupled to their local environment, including geometric and mechanical cues. However, studying this coupling in intact tissues has been challenging, because existing measurement technologies cannot simultaneously assess mechanical properties and molecularly defined cell states. To address this gap, we introduce the Unified Transcriptome and Mechanics Map (UTMM), a method for concurrent measurement of the transcriptome and cytoplasmic stiffness (high-frequency elastic modulus) within intact 3D multicellular structures. UTMM relies on two innovations: (1) a targeted in situ RNA sequencing approach for intact 3D embryos (3DISS), and (2) a strategy that leverages high-frequency intracellular organelle fluctuations to infer cell-level stiffness in vivo. We applied UTMM to mouse embryos from the zygote through the morula stage to characterize how RNA expression and cytoplasmic stiffness become coupled during early lineage specification. Our data reveal that, in the early morula, transcriptional and morphological distinctions emerge between trophectoderm and inner cell mass (ICM) lineages, coinciding with a gradual decrease in cytoplasmic stiffness (softening) across all cells from the 2-cell through morula stages. Furthermore, we observe that early lineage biases align with differential mechanical properties, reflecting distinct emerging developmental programs. When we delayed this softening process via mechanical perturbation, embryonic progression was impeded, highlighting the functional importance of coordinated mechanical and transcriptional changes. Together, these results demonstrate UTMMs ability to bridge molecular and mechanical dynamics in multicellular systems, providing a powerful framework for investigating how biomechanical cues shape cell fate decisions in intact tissues. One Sentence SummaryJoint 3D in situ quantification of spatial transcriptome and cytoplasm mechanics in preimplantation mammalian embryos

developmental biology↗

bioRxiv2026

Convergence on BRAF and MAPK Signaling in Glioma Development in a P53-ENU model

Pediatric high-grade gliomas (HGGs) are aggressive and lethal brain tumors that account for 15- 20% of all pediatric central nervous system (CNS) malignancies and remain largely incurable. These tumors, despite having mutational targets that activate MAPK signaling, are frequently resistant to targeted therapies in their malignant states, but often show responses when they are in lower grade form. These findings suggest a need to identify and intercept early tumorigenic events that arise in earlier tumor developmental stages. To investigate the molecular events in glioma progression, we developed and characterized a NestinCre/+;Trp53fl/fl mouse model combined with in utero exposure to the classic chemical mutagen N-ethyl-N-nitrosourea (ENU). This model mimics the context of genetic predisposition paired with an environmental genotoxic insult, and mice with loss of TRP53 in early neural precursors who are exposed to ENU at embryonic day 13.5 reproducibly develop HGGs postnatally that retain features of the human tumors. By sampling discrete lesions at premalignant, early, and late stages, we observed progressive increases in genetic complexity, stemness features, and immune signatures across tumor evolution. Notably, a recurrent Braf mutation emerged in a majority of early lesions and persisted in advanced tumors, consistent with the occurrence of BRAFV600E mutations in human gliomas that arise in children and undergo transition from lower grade to higher grade stages. Additional components of the RAS-RAF-MAPK signaling cascade, including Kras, Nras and Nf1 were found to be mutated at the late tumor stage, indicating convergent activation of this pathway in this model. Cell lines derived from early lesions responded to BRAF inhibitors, but cells from endpoint tumors were less responsive. Together, this model reveals aspects of the molecular and cellular evolution of glioma development in vivo, and identifies RAS-MAPK signaling as a critical molecular bottleneck selected for the ENU-induced mutations. This genetic-environmental model may be valuable to understanding key determinants of glioma initiation and progression, and for evaluating new therapies that limit MAPK signaling.

cancer biology↗

bioRxiv2026

A CRISPR-Based Humanized Model Reveals Cooperative Role of STAG2 Loss in Familial GATA2-Deficient MDS Progression

Myelodysplastic syndrome (MDS) is a heterogeneous myeloid malignancy driven by hematopoietic stem cell dysfunction, leading to ineffective hematopoiesis and cytopenias. Familial GATA2 deficiency is the most common cause of Myelodysplastic syndrome in adolescents, with progression often accelerated by co-occurring mutations, notably STAG2 loss-of-function. Using CRISPR/Cas9-mediated genome engineering in primary human fetal liver-derived hematopoietic stem cells and xenotransplantation in mice, we modeled GATA2-deficient Myelodysplastic syndrome with acquired STAG2 loss to investigate disease initiation and progression. While GATA2 deficiency alone had minimal short-term impact in our model, combined GATA2 and STAG2 loss increased hematopoietic stem cell maintenance and self-renewal, induced a myeloid-lineage bias, and expanded primitive progenitors. Single-cell transcriptional profiling revealed upregulation of stemness genes and inflammatory pathways. This humanized model faithfully recapitulates high-risk GATA2-deficient Myelodysplastic syndrome, providing mechanistic insight into how cooperative mutations drive stem cell expansion, inflammatory signaling, and myeloid skewing. Visual Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/702879v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1972beforg.highwire.dtl.DTLVardef@1c57886org.highwire.dtl.DTLVardef@16bd582org.highwire.dtl.DTLVardef@8e728a_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LIHumanized model of familial GATA2-deficiency requires the loss of STAG2 for progression to an MDS disease phenotype C_LIO_LIGATA2-ko+STAG2-ko increase HSC self-renewal, induce a myeloid-lineage bias, and trigger an inflammatory transcriptional program C_LI

cancer biology↗

bioRxiv2026

Prioritizing Neuroactive Ligands Using Motif-Guided Virtual Discovery and Zebrafish Profiling

Virtual screening of ultra-large chemical libraries is a highly effective strategy for early-stage drug discovery. However, these pipelines often yield thousands of molecules that pass computational filters, and in silico-derived interaction energies do not consistently predict experimental efficacy. Furthermore, many high-affinity hits do not necessarily function effectively in an organism with tissues, barriers, and extensive off-target possibilities. A major hurdle in drug discovery is the prioritization of top candidates for rodent testing. Here, we introduce Rosetta Engine for Anchoring Ligands with a Motif ("REAL-M"), a novel computational screening algorithm that uses structural interaction data from the Protein Data Bank (PDB) to guide ligand placement and selection. Using the hypocretin receptor as a test case for this computational pipeline, 28 of 30 predicted antagonists significantly blocked binding of the cognate peptide agonist in a PRESTO-Tango cell-based reporter assay, including six chemically diverse molecules with comparable efficacy to preexisting antagonists. Three of the six molecules significantly mitigated hypocretin-induced larval zebrafish hyperactivity. Secondary testing with a zebrafish hcrtr2 null mutant ensured that behavioral phenotypes were not due to off-target interactions, which we did observe with preexisting antagonists. This pipeline is readily adaptable to the thousands of zebrafish proteins with highly conserved binding pockets.

pharmacology and toxicology↗

bioRxiv2026

Common Genetic Variants of The Cardiac Sodium Channel Alter Patient Response to Class 1b Antiarrhythmics

Several common variants have been identified in SCN5A, which encodes the cardiac sodium channel -subunit Nav1.5 and is targeted by class I antiarrhythmics. Lidocaine and its analog mexiletine both have a primary amine that blocks Na+ current. While lidocaine is highly effective in terminating ventricular tachycardia after acute myocardial infarction, mexiletine has been shown to prevent arrhythmia induction in only [~]20% of patients. The factors underlying this inconsistent drug response are unclear. Here, we use cardiomyocytes that are derived from induced pluripotent stem cells to observe that a common polymorphism in the SCN5A gene, S1103Y, exhibits an altered pharmacological response to mexiletine, with enhanced use-dependent and tonic block of peak sodium current. In addition, an unexpected increase in late sodium current causes action potential prolongation. This paradoxical proarrhythmic phenotype shifts the paradigm of conventional antiarrhythmic therapy with mexiletine, suggesting that background variants may alter pharmacological responses leading to unanticipated consequences. Our results suggest that the unique genetic background of patients should inform therapeutic approaches to treat and prevent arrhythmias associated with common cardiac pathologies.

physiology↗

bioRxiv2025

Integrative Taxonomy: From FASTA Pain to Species Gain with the interactive ''IntegraTax''

Here we present IntegraTax, a tool for analysing and managing taxonomic projects that combine DNA data with other evidence such as morphology to arrive at integrative species boundaries. IntegraTax visualizes genetic clusters through single-linkage clustering ("Objective Clustering") and provides an interactive browser interface that allows users to record taxonomic decisions regarding species limits. Projects can be saved at any stage, thus allowing continuous tracking of annotations and taxonomic decisions across many sessions. A typical IntegraTax session starts with a set of sequences that are visualized as a cluster fusion diagram revealing the genetic distances between the sequences and clusters. Users can define an "instability zone" to distinguish clusters that are clearly distinct, likely representing separate species, from those whose status is uncertain based on genetic data alone. Based on the instability zone setting, IntegraTax then suggests which and how many specimens should be studied with a second source of data to validate species hypotheses. This process is facilitated by an interactive html environment that enables detailed specimen-level annotations. For example, a taxonomist can label which specimens have been studied, which clusters have been validated as species, and which species can be identified. By combining clustering, intuitive visualization, and easy annotation in one interactive framework, IntegraTax treats species hypotheses as annotated objects that can be inspected, revised, and exported at any stage, with documentation of examined specimens. It simultaneously allows researchers to manage taxonomy projects with tens of thousands of specimens and hundreds of species. This will become increasingly important as taxonomists start resolving the species boundaries of the millions of undescribed species particularly within hyperdiverse dark taxa.

zoology↗

bioRxiv2025

CREG1 promotes autophagy and protects the heart against nutritional stress-induced injury and age-associated hypertrophy, fibrosis and diastolic dysfunction

BackgroundCellular repressor of E1A-stimulated genes 1 (CREG1) is an evolutionarily conserved endolysosomal glycoprotein that enhances lysosomal biogenesis and autophagy, suppresses proliferation, and promotes differentiation. A prior gene targeting strategy that produced truncated N-terminal fragments resulted in embryonic lethality, limiting the ability to assess the physiological role of complete CREG1 loss. We hypothesized that CREG1 regulates cardiac autophagy, thereby maintaining cardiac structure and function under both physiological and stress conditions. MethodsWe generated true Creg1 knockout (KO) mice by deleting the entire open reading frame and established a gain-of-function model by inserting human CREG1 into the Rosa26 locus. Cardiac structure and function were assessed in global and cardiomyocyte-specific Creg1 knockout (cmCreg1KO) and knock-in (cmCREG1KI) mice. Autophagy was evaluated using biochemical assays, immunofluorescence, electron microscopy, and the CAG-EGFP-RFP-LC3 reporter analysis. ResultsGlobal Creg1 knockout mice developed progressive cardiac hypertrophy, fibrosis, and diastolic dysfunction at [~]80 weeks of age. At younger ages, CREG1 deficiency increased susceptibility to nutritional stress, resulting in mitochondrial damage and myofiber disruption in cardiomyocytes. cmCreg1KO mice exhibited dilated cardiomyopathy, left atrial thrombosis, and lethality around 50 weeks of age; however, interpretation of disease severity is confounded by Myh6-Cre-associated cardiotoxicity, which may mask additional pathogenic effects attributable to CREG1 loss. In contrast, cmCREG1KI mice demonstrated enhanced exercise capacity under nutritional stress. Mechanistically, CREG1 was localized to endolysosomal and autophagosomal compartments. Loss of CREG1 impaired autophagy flux and mitophagy, likely due to defective autophagosome membrane expansion and degradation. In contrast, CREG1 overexpression enhanced autophagy in cardiomyocytes. ConclusionsCREG1 is a key regulator of cardiac autophagy, protecting the heart against nutritional stress-induced injury and age-associated cardiac hypertrophy, fibrosis, and diastolic dysfunction. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/687936v1_ufig1.gif" ALT="Figure 1000"> View larger version (60K): org.highwire.dtl.DTLVardef@1b9fc05org.highwire.dtl.DTLVardef@150e48aorg.highwire.dtl.DTLVardef@1cc47adorg.highwire.dtl.DTLVardef@75ed53_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Autoantibody origins in lupus and in relapse post CAR-T therapy

Anti-CD19 chimeric antigen receptor (CAR)-T therapy induces profound remissions in lupus by depleting B cells, challenging the longstanding view that treatment-resistant disease is sustained by long-lived plasma cells. Additionally, emerging relapses highlight the need to understand how pathogenic autoantibodies arise. Using molecular antibody tagging in mice with human monogenic lupus variants, we reveal that autoantibody-producing cell cohorts are long-lived but plasma cells are short-lived, requiring continuous replenishment from proliferating precursors. The spleen acts as a major plasma cell reservoir, with perivascular localization conserved in mice and lupus patients. Relapse after anti-CD19 CAR-T occurred through newly-generated B cells rather than treatment-resistant clones. Plasma cell depletion by anti-BCMA CAR-T failed to eliminate some precursors that become autoantibody-secreting. These findings demonstrate that continuous B cell-to-plasma cell differentiation, not intrinsic plasma cell longevity, sustains pathogenic antibody responses in lupus, supporting a potential benefit of adjunctive therapies after CAR-T, particularly in genetically predisposed patients.

immunology↗

bioRxiv2025

Automated Specimen Triage for Dark Taxa: Deep Learning Enables Orientation, Sex Identification, and Anatomical Segmentation from Robotic Imaging

Robotic specimen processing is transforming biodiversity discovery by replacing labor-intensive handling with scalable systems that can simultaneously generate high-quality specimen images. We demonstrate that these images can be leveraged by deep learning to efficiently extract key biological information and guide targeted specimen processing. Using a model dark taxon, the Phoridae (Diptera), the workflow performs three core tasks: sex identification, specimen orientation classification, and anatomical segmentation. Sex identification allows selective retention of diagnostically informative specimens, avoiding wasted effort on non-diagnostic individuals. Orientation classification enables specimens in the desired orientation to proceed immediately, while suboptimally oriented specimens can be repositioned for informative processing. Anatomical segmentation allows targeted processing of specimens displaying diagnostic characters or targeted analysis of specific anatomical regions in subsequent workflow steps. Comparative analysis of model architectures shows task-specific selection is crucial: a Convolutional Neural Network achieved an accuracy of 0.94 for orientation, a Vision Transformer achieved 0.88 for sex, and a U-Net precisely segmented nine anatomical regions with a mean IoU of 0.78. These results demonstrate that robotic imaging combined with deep learning provides a validated foundation for high-throughput, targeted specimen processing, maximising efficiency and utility for taxonomic and trait-based analyses, and supporting scalable, sustainable biodiversity workflows.

bioinformatics↗

bioRxiv2025

Programmed meiotic errors facilitate dichotomous sperm production in the silkworm, Bombyx mori

The goal of meiosis is typically to produce haploid gametes (eggs or sperm). Failure to do so is catastrophic for fertility and offspring health. However, Lepidopteran (moths and butterflies) males produce two morphs of sperm: nucleated (eupyrene) sperm which fertilize the egg, and anucleated (apyrene) sperm, both of which are essential for fertilization. The meiotic differences in the two types of spermatogenesis have not been well characterized, and our knowledge of the molecular differences between eupyrene and apyrene spermatogenesis are extremely limited in all systems. The only factor identified as being required for apyrene spermatogenesis is Sex-lethal (Sxl). Here, we show through cytological analysis of early meiotic events that there are several key differences in the genesis of apyrene sperm and eupyrene sperm. Specifically, apyrene spermatocytes fail to condense and pair their chromosomes during meiotic prophase I. In addition, telomeres do not attach to the nuclear envelope. Due to these differences, full-length synaptonemal complex does not form. RNA sequencing of both eupyrene- and apyrene-producing testes revealed distinct changes in transcriptional programs, including down-regulation of a myriad of meiotic genes and cell cycle checkpoint factors during apyrene meiosis. By comparing wild-type and Sxl-knockout apyrene testes, we found that Sxl is not required for the changes in the expression of the meiotic genes but instead plays a role in checkpoint inactivation to allow this error-prone meiosis to proceed. Together, our findings reveal significant insights into two converging molecular pathways that promote the formation of dimorphic sperm in Lepidoptera.

genetics↗

bioRxiv2025

MYD88 mutations in clonal hematopoiesis promote inflammation and hematopoietic stem cell expansion

Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by expansion of mutant hematopoietic stem and progenitor cells (HSPCs) and an increased risk of chronic diseases and cancers. While mutations in DNMT3A, TET2, and ASXL1 are common in CHIP, the contribution of less frequent gene mutations is not well understood. Here, we report MYD88 mutations, including lymphoma-associated and novel variants in blood cells of the general population and newly diagnosed solid cancer patients. MYD88 CHIP mutations in HSPCs activate NF-{kappa}B, indicating a gain-of-function activity. Modeling MYD88 CHIP in mice, Myd88L252P (equivalent of human L265P) expression resulted in a competitive fitness advantage of HSPCs. Myd88L252P HSPCs exhibit a myeloid cell bias and inflammation, leading to hematologic disease. Single-cell RNA sequencing indicated that Myd88L252P expands distinct hematopoietic and immune cell clusters and activates immune-related pathways in HSPCs. An IRAK1/4 inhibitor suppressed MYD88-dependent NF-{kappa}B activation and reversed Myd88L252P cell expansion. Overall, MYD88 mutations contribute to CHIP by inducing innate immune pathways in HSPCs and inflammatory disease.

cancer biology↗