Biology subjects

Li, H.

Publications and source records attributed to Li, H..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

Uncovering key genes related to potato tuber starch concentration from the tuber bulking, maturation stage to storage

Potato is the worlds fourth major staple crop, and tuber starch is a critical dietary energy source and a food processing raw material. In this study, hybrid progenies of the high-starch cultivar Huasheng No.7 and China main commercial varieties were used as materials, high-throughput sequencing was performed on tuber samples at tuber bulking, maturation and storage stages. Combined with bioinformatics analysis, parent-progeny resequencing, SNP screening, the regulatory mechanism of tuber starch metabolism was explored. The results showed significant stage-specific transcriptional reprogramming in potato tubers: few differentially expressed genes (DEGs) were identified at tuber bulking and maturation stages, but massive transcriptional changes occurred during storage. XET family genes regulated cell wall remodeling and carbon translocation across all stages, and WRKY transcription factors specifically controlled starch homeostasis in stored tubers. The DEGs at different stage were induced by the SNPs from their parent, and the allele from the high-starch parent, Huasheng 7 may contribute the high-starch allele to the offsprings. One key gene, Soltu.DM.02G019910, which encoded {beta}-glucosidase, have a negatively relationship with tuber starch concentration. The low-starch potato breeding tubers shown higher significantly {beta}-glucosidase activity than high-starch breeding population at maturation stage. This study clarifies the molecular regulatory network of potato tuber starch metabolism and screens core regulatory genes from the tuber bulking stage to tuber storage, thereby providing theoretical support and genetic resources for molecular breeding of high-starch and storage-resistant potato varieties.

plant biology↗

bioRxiv2026

Hidden genetic diversity in 320 nearly-complete East Asian genome assemblies

East Asian populations, representing over 20% of the global population, remain critically underrepresented in human genomic studies, limiting our understanding of population-stratified genetic variation and its implications for health and disease. Here we present the first phase of the Asian Pan-Genome project (APG), comprising 320 nearly complete, fully phased haploid genome assemblies from 160 East Asian individuals. These assemblies achieve unprecedented quality, with an average contig N50 of 144.3 megabase pairs and an average quality value of 64.5. Leveraging these superior assemblies, we reveal previously uncharacterized diversity in human repeatome, including population-stratified patterns in centromere satellites and rDNA arrays. Compared to existing global human genome assemblies, the newly generated genomes supplement 152 million base pairs of novel sequences, 355 gene gains, 18,300 structural variation loci and 26 large euchromatic inversions missing from current human pangenomes. We perform population stratification analyses of structural variations, and further resolve the structural haplotypes of complex genomic regions such as Major Histocompatibility Complex and Survival Motor Neuron loci across global pangenomes, exemplifying tandem-duplicate and inversion-rich complex locus architectures in the human genome, respectively. This resource provides a critical foundation for human genetic studies, especially for East Asian populations, promoting more accurate variant discovery, reducing bias, and ultimately advancing the equity and efficacy of genomic medicine.

genomics↗

bioRxiv2026

Retinal electrical synapse plasticity is required for optimal visual performance

Most electrical synapses in the mammalian central nervous system are composed of Connexin 36 (Cx36). Electrical synapses are functionally plastic, changing their degree of coupling based on the activity of the cell or connected cells, or based on activation of neurotransmitter or neurohormone receptors. Plasticity can reach an extreme in which electrical synapses become functionally silent, which is a normal operational condition for some circuits. Cx36 coupling is regulated by phosphorylation, which opens the channels. In retinal circuits, Cx36 is often maintained in a poorly phosphorylated, poorly coupled state. We reasoned that phosphomimetic mutants of Cx36 could remain constitutively open and maintain circuits in a well-coupled state that will interrogate the need for plasticity. We developed a constitutively open Cx36 mutant by systematically replacing phosphorylatable residues that regulate coupling with acidic residues. Single mutants of serine 315 significantly modified functional regulation of coupling in HeLa cells, but mutation of four residues was required to produce a mutant that was constitutively open. This mutant, Cx36-S110D, T111E, S293D, S315D, called Cx36-DEDD, displayed high coupling in control conditions and only modest changes under phosphorylating and dephosphorylating conditions. We developed a conditional knockin mouse that expresses Cx36-DEDD and cytoplasmic tdTomato in cells that expressed Cre recombinase. When crossed with Six3-Cre mice, Cx36-DEDD expressed widely in the retina including in photoreceptors, bipolar, amacrine and ganglion cells. Rod-cone electrical coupling displayed the maximum of its physiological dynamic range, and photopic visual acuity and contrast sensitivity were significantly reduced in Cx36-DEDD homozygous animals. We conclude that reduction of coupling in some retinal circuits is required for optimal daylight vision. Significance StatementTwo types of synapses, chemical and electrical, work together throughout the central nervous system to perform neurological functions. While it is widely understood for chemical synapses that plasticity, changing the strength of synaptic connections, plays critical roles in many processes, this is far less understood for electrical synapses. By developing an electrical synapse protein mutant that locks channels in an open state, we have investigated retinal circuits that retain functional electrical synapses but lack their latitude for plasticity. This perturbation significantly compromises visual acuity and contrast sensitivity in the daylight, revealing that electrical synapse plasticity is necessary to tune retinal functions for optimal performance. Thus, electrical synapse plasticity along with chemical synapse plasticity is required for neural function.

neuroscience↗

bioRxiv2026

A highly Ca2+-permeable channelrhodopsin from the ancyromonad Nutomonas longa enables optogenetic control of Ca2+ signaling

Ca{superscript 2} is a ubiquitous regulator of cellular function, linking electrical activity to gene expression, secretion, metabolism, and synaptic plasticity. Yet, tools for its direct, time-resolved optical manipulation remain limited. Here, we report that NlCCR, a channelrhodopsin from Nutomonas longa, possesses high Ca{superscript 2} permeability, enabling precise optical control of Ca{superscript 2} signaling. Compared with CapChR2, the most potent engineered Ca{superscript 2}-conducting channelrhodopsin, NlCCR combines larger and faster photocurrents, higher Ca{superscript 2} permeability, weaker desensitization, and reduced inward rectification. Mutational analysis identified determinants of Ca{superscript 2} selectivity and further enhanced it by introducing carboxylate residues at the channels central gate. NlCCRs blue-shifted absorption (445 nm) minimized optical crosstalk with a red-shifted Ca{superscript 2} indicator, laying the groundwork for all-optical experiments. In mouse cortical pyramidal neurons, NlCCR enabled synaptic transmission independently of endogenous voltage-gated Ca{superscript 2} channels. These findings establish NlCCR as a broadly applicable tool for direct, temporally precise manipulation of Ca{superscript 2}-dependent signaling in living systems.

neuroscience↗

bioRxiv2026

Kruppel-like factors KLF5 & KLF8 emerge as master transcriptional regulators of Alzheimers disease, as revealed on cell fate regulomes in human brain organoids

In addition to the well described beta-amyloid plates accumulation and tau hyper-phosphorylation, Alzheimers disease (AD) is accompanied by major changes in gene expression. Herein, we aimed at revealing master transcription factors (TFs) responsible for gene expression changes during AD progression. For this, we have used human brain organoids (BORGs) harbouring AD-related genetic mutations (APP-Swedish, PSEN1-M146V), which were traced over multiple time-points by bulk and spatially-resolved transcriptomics. By reconstructing gene regulatory networks (GRNs) that recapitulate BORG development, we have identified a subset of 110 AD-specific master TFs, and for 75 of them we retrieved KLF5 and/or KLF8 binding motifs within their promoters. Furthermore, 64 of the AD-specific TFs found in BORGs are significantly over-expressed on AD human patients samples, confirming the relevance of these factors beyond the context of the familial genetic mutations. Finally, we have demonstrated that this AD-specific regulome is at least partially controlled by the aberrant CREB3L2-ATF4 heterodimer previously described as being induced by the beta-amyloid plates deposition. Overall, these findings reconstitute the regulome behind the progression of AD and highlights key TFs as potential druggable targets for the treatment of the disease.

systems biology↗

bioRxiv2026

A Novel Syngeneic Mouse Model to Study Immune Evasion in Head and Neck Squamous Cell Carcinoma

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, and patient outcomes have remained largely unchanged despite advances in multimodal therapy. Immune checkpoint inhibitors (ICIs), which block the PD-1/PD-L1 axis to restore T cell-mediated anti-tumor immunity, have emerged as a promising treatment strategy. However, response rates remain below 20% in HNSCC, underscoring the need to better understand mechanisms of immune evasion within the tumor microenvironment. Syngeneic mouse models are essential for studying tumor-immune interactions, yet currently available HNSCC models are limited. Here, we report the development of a novel FVB/NJ-derived syngeneic HNSCC model generated from 7,12-dimethylbenz(a)anthracene (DMBA)-induced primary on floor of mouth/buccal tumors, designated FMOC1, FMOC2, and FMOC3 (FVB/NJ Mouse Oral Cancer). In vitro, all FMOC cell lines exhibited robust proliferative capacity with distinct proliferation kinetics. In vivo, all FMOC cell lines exhibited characteristic HNSCC histopathology, including cytokeratin 5 positivity, and were tumorigenic in immunodeficient NCG mice; however, in syngeneic immunocompetent mice, only FMOC1 demonstrated sustained tumor growth at orthotopic and flank sites, whereas FMOC2 and FMOC3 tumors underwent spontaneous regression within 2 weeks, indicating differential immune-dependent tumorigenicity among the lines. Consistent with this, depletion of CD4+ and/or CD8+ T cells restored tumor growth in FMOC2 and FMOC3 models, indicating a critical role for T cell-mediated immunity in tumor suppression. Notably, FMOC1 tumors were responsive to anti-PD-L1 and anti-CTLA-4 therapy, supporting their utility for evaluating immunotherapeutic strategies. Collectively, these findings establish the FMOC model as a novel and versatile platform to study tumor-immune interactions and immune evasion mechanisms in HNSCC, with potential applications in preclinical immunotherapy development.

cancer biology↗

bioRxiv2026

Engineering Oncolytic Measles Virus with MG53 Couples Pyroptotic Tumor Killing with Immune Microenvironment Remodeling to Enhance Checkpoint Immunotherapy in Non-small Cell Lung Cancer

Lung cancer is the leading cause of cancer-related mortality worldwide, with only approximately 30% of patients benefiting from current immune checkpoint immunotherapy. Oncolytic virotherapy offers a promising strategy to overcome this resistance; however, achieving both potent tumor cytotoxicity and robust antitumor immune activation remains a major challenge. Here, we engineered oncolytic measles virus expressing the tumor suppressor MG53 (TRIM72), designated rMeV-MG53, and evaluated its therapeutic potential against non-small cell lung cancer (NSCLC). rMeV-MG53 retained replication kinetics comparable to parental MeV while driving significantly greater cytotoxicity than an unarmed control in NSCLC cells. Mechanistically, MG53 arming amplified caspase-3-dependent apoptosis and potentiated Gasdermin E (GSDME) cleavage, engaging GSDME-mediated pyroptosis as a key tumor-killing mechanism; pharmacological inhibition confirmed caspase-dependent apoptosis as the initiating event leading to pyroptosis, while excluding necroptosis and ferroptosis as significant contributors to rMeV-MG53-induced cytotoxicity. MG53 overexpression induced an intrinsic pro-inflammatory transcriptional signature enriched for TNF, NF-{kappa}B, and IL-17 signaling, and rMeV-MG53 elicited significantly stronger type I interferon and pro-inflammatory cytokine induction than the unarmed control. In an immunocompetent, MeV-permissive syngeneic NSCLC model, intratumoral rMeV-MG53 achieved superior tumor growth inhibition, amplified caspase-3/GSDME pyroptosis, selectively upregulated Cxcl10, Ifng, and Il1b, and drove robust CD8 T-cell and Granzyme B effector infiltration. This immune remodeling was accompanied by compensatory PD-L1 upregulation, and combining rMeV-MG53 with anti-PD-L1 blockade achieved the strongest tumor suppression of all treatment groups. These findings establish MG53-armed oncolytic MeV as a strategy coupling GSDME-mediated pyroptosis with antitumor immune remodeling to sensitize immune-resistant NSCLC to checkpoint immunotherapy.

immunology↗

bioRxiv2026

Tumor-derived stearic acid induces macrophage Egr2 signaling to suppress anti-tumor immunity in breast cancer

BackgroundMacrophages in breast cancer are highly heterogeneous and targeting both tissue-resident and bone marrow-derived macrophages represents a high-potential strategy in breast cancer immunotherapy. MethodsMyeloid-specific Egr2 knockout (KO) mice were used to determine roles of macrophage Egr2 signaling in tumor progression and anti-tumor immune responses. RNA-seq analysis and Flow cytometry were used to examine regulation of Egr2 in tumor-associated macrophages (TAMs) and fatty acid-stimulated macrophages. Tumor cell and macrophage admixture study was used to evaluate effects of fatty acid educated macrophages on anti-tumor responses. ResultsHere we showed that early growth response 2 (Egr2) was highly expressed in mammary tissue macrophages and recruited macrophages upon tumor progression. Depletion of Egr2 in myeloid cells significantly decreased the immunosuppressive function of polarized M2-like macrophages and TAMs. Tumor progression was delayed in myeloid cell Egr2 knockout mice, which was associated with enhanced function of effector CD8+ T cells and NK cells. Mechanistically, we showed that retinol and nicotinamide metabolism in TAMs were impaired after Egr2 depletion. Further, tumor cell-derived stearic acid (SA) was identified as an important fatty acid inducing Egr2 expression. SA stimulation induced macrophage-mediated immunosuppression in an Egr2 dependent manner. Addition of oleic acid (OA) uniquely repressed SA-induced Egr2 expression and immunosuppressive activity in macrophages. ConclusionsOur study thus uncovers a novel SA-Egr2 pathway driving macrophage immunosuppression and novel molecular mechanism of OA mediated anti-tumor effect. WHAT IS ALREADY KNOWN ON THIS TOPICLipid-associated macrophages (LAMs) accumulate lipids and promote immune suppression, tumor growth and metastasis in breast cancers. Fatty acids play a dual, complex role in tumor immunity, acting as both pro-tumorigenic and anti-tumorigenic effects. However, molecular mechanisms underlying fatty acid modulated macrophages and their roles in tumor remain not fully elucidated. WHAT THIS STUDY ADDSWe demonstrate that Egr2 is essential for the immunosuppressive function of IL-4 polarized M2-like macrophages and TAMs. Tumor cell-derived stearic acid (SA) was identified as an important fatty acid inducing Egr2 expression and immunosuppression in macrophages. Adding oleic acid (OA) uniquely repressed SA-induced Egr2 expression and immunosuppression. HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYSA-Egr2 axis is a novel pathway driving macrophage immunosuppression. OA treatment enhances macrophage anti-tumor immunity via inhibiting Egr2 signaling and immunosuppression. The data supports the notion that diets enriched in OA may have potential for prevention and suppression of breast cancer.

immunology↗

bioRxiv2026

Interpretable Local-to-Global Estimation of Brain Aging Speed From Morphological Changes Using Longitudinal Structural MRI Data

Accurate characterization of brain aging is essential for understanding cognitive decline and assessing the risk of neurodegenerative disease. Brain age estimated from cross-sectional MRI provides a snapshot of brain health relative to chronological age, and the derived brain age delta has emerged as a promising biomarker. However, brain age delta reflects cumulative effects at a single time point and fails to capture ongoing aging dynamics. Longitudinal approaches address this limitation by estimating age differences between scan pairs to derive aging speed. Nevertheless, existing methods primarily rely on intensity or texture differences between image pairs, overlook the spatial heterogeneity of aging processes, and provide limited interpretability. To overcome these limitations, we propose a novel framework that estimates brain aging speed from longitudinal deformation fields obtained via diffeomorphic registration. Instead of solely generating a single global estimate, our method produces patch-wise local aging predictions and adaptively integrates them into a unified global prediction, improving both predictive performance and interpretability. Evaluated on large-scale datasets, our approach achieves superior accuracy compared with existing methods and enhances the identification of abnormal aging patterns in diseased populations. Code is available at https://github.com/Kateridge/Morphology-AgingSpeed.

neuroscience↗

bioRxiv2026

Whole-genome resequencing identified loci underwent divergent selection and improved local adaptability in groundnut (Arachis hypogaea)

There is an urgent need to expand groundnut genomics knowledge base to improve yield and adaptability in the target environments. Whole-genome sequencing can discover selective sweeps in the genomic regions distinguishing adaptive from non-adaptive germplasm within target environments. When combined with genome-wide association studies (GWAS), this approach can reveal genes underpinning local adaptability and yield advantage. The objective of this study was to establish a genome-wide quantitative framework form identifying genomic regions under selection, with a particular focus on narrowing down regions associated with important yield and adaptive traits. Moreover, validation of elite haplotype distributions in an independent fully sequenced groundnut panel. A panel of 197 groundnut accessions was subjected to whole-genome sequencing and phenotypic evaluation to dissect the collection into adaptive and non-adaptive subsets to uncover the genomic regions under selection. This was then combined with GWAS to uncover genetic variants governing agronomic traits associated with yield and adaptability. The stringent single and multi-trait analysis identified 60 loci for 12 agronomic traits, of which seven loci controlled multiple yield related traits and were pleiotropic. Within our diversity panel, 48 genomic regions showed signs of selection. Among these selective sweeps, six positively selected loci were co-localized with trait associated loci. A large genomic region on chr2 spanning [~]78 Mb was under divergent selection and harbored genes underpinning yield and 20-pod length. A F-box transcription factor, Arahy.37HYKA, on chr9, and an alanine transferase protein gene, Arahy.E9MTVL, on chr12 carried peak SNPs associated with yield and related traits. We further cross-validated our results in another groundnut355 panel, where the corresponding genes within LD blocks showed significant effects on HKW, pod length and pod weight. The genomic resources developed here provide a high-resolution variation map to delineate the genes underpinning yield and developmental traits in groundnut, improved our understanding of the genetic basis of important agronomic traits, and provide a valuable resource for further functional genomics studies and groundnut improvement programs.

genomics↗

bioRxiv2026

Discovering Heterogeneous Neurodegenerative Disease Patterns From MRI Data for Improved Prediction

Neurodegenerative diseases exhibit substantial heterogeneity, complicating both diagnosis and prognosis. Identifying clinically meaningful subtypes is crucial for understanding disease mechanisms and can also improve diagnostic precision and prognostic accuracy. Existing subtyping approaches primarily rely on unsupervised learning of patient data for capturing inter-individual variability, often failing to uncover subtypes that are informative for diagnosis or prognosis. To address this limitation, we propose a novel mixture-of-experts (MoE) framework that integrates predictive modeling with subtype identification. Unlike traditional subtyping methods, our approach learns a router to assign individuals to specialized expert networks, each corresponding to a distinct subtype, to improve predictive accuracy. This MoE framework ensures that the discovered subtypes are not only statistically distinct but also clinically informative. We evaluate the framework on a real-world dataset of mild cognitive impairment (MCI) subjects and a semi-simulated dataset, demonstrating superior performance for predicting MCI subjects progression to Alzheimers disease while identifying distinct clinically meaningful MCI subtypes. Code is available at https://github.com/Kateridge/MoESubtyping.

neuroscience↗

bioRxiv2026

A superfolding sfPepper enables superresolution and single-molecule RNA imaging in live cells

Fluorescent RNAs (FRs) have emerged as powerful tools for the visualization of RNA in live cells. However, the poor folding of FRs is a major limiting factor in many advanced RNA imaging applications. Here, we describe a novel strategy to significantly increase the folding efficiency of FRs. By introducing a stabilizing stem and performing targeted mutagenesis at key junction regions, we develop a superfolder variant of the Pepper aptamer, termed sfPepper, that exhibits a striking twofold increase in folding efficiency compared with Pepper under physiological conditions. sfPepper exhibits much improved thermostability and reduced ion dependence and, most importantly, is substantially brighter than Pepper in live cells. sfPepper enables robust imaging of diverse noncoding RNAs and messenger RNAs with increased signal-to-background ratios and stimulated emission depletion (STED) superresolution imaging of CUG trinucleotide repeat-containing toxic RNAs. Remarkably, only four sfPepper repeats facilitate sensitive single-molecule mRNA tracking, revealing dynamic heterogeneity among ER-associated mRNA molecules. Together, this study establishes an efficient strategy for improving FR folding and offers a powerful tool for fluorescently labelling RNAs in live cells.

molecular biology↗

bioRxiv2026

A multi-agent workflow converts CAR-T patient evidence into experimentally testable hypotheses

Clinical studies of chimeric antigen receptor (CAR)-T therapy generate diverse molecular and clinical evidence that remains fragmented across publications, public repositories and patient-derived datasets, limiting systematic therapeutic discovery. Here we present BioPathfinder, an evidence-guided multi-agent workflow for closed-loop biomedical discovery. BioPathfinder constructs a provenance-aware knowledge resource linking publications with patient single-cell RNA sequencing (scRNA-seq) datasets and clinical metadata, and uses role-specialized large language model agents to generate, review and prioritize diverse, falsifiable and dataset-aware mechanistic hypotheses for computational and experimental validation. Applied to a curated corpus of CAR-T-treated patient studies and matched scRNA-seq datasets, BioPathfinder identified candidate mechanisms underlying CAR-T persistence, dysfunction and therapeutic resistance. The workflow prioritized the hypothesis that genes associated with an NK-like transition programme could be targeted to reduce CAR-T exhaustion and improve persistence. Analysis of patient scRNA-seq datasets showed enrichment of this programme in exhausted post-infusion CAR-T cells. Virtual perturbation prioritized transition-associated receptor genes, including KLRC1, KLRD1 and KLRG1, and expert review selected KLRC1, encoding NKG2A, for experimental validation. In vitro and in vivo chronic-stimulation models showed that NKG2A marked activated, exhaustion-associated CD8 CAR-T cells, whereas NKG2A blockade enhanced antitumour activity and persistence-associated functional readouts in vivo. BioPathfinder establishes a generalizable framework that transforms fragmented clinical single-cell evidence into experimentally validated therapeutic hypotheses, providing a scalable strategy for AI-guided biomedical discovery. HIGHLIGHTSO_LIBioPathfinder integrates fragmented CAR-T clinical studies, patient scRNA-seq datasets and metadata into a provenance-aware evidence resource for AI-guided hypothesis discovery. C_LIO_LIA multi-agent workflow generates, critiques and prioritizes diverse, falsifiable, dataset-aware mechanisms underlying CAR-T persistence, dysfunction and therapeutic resistance. C_LIO_LIBioPathfinder prioritizes KLRC1/NKG2A as a therapeutic target, and experimental validation demonstrates that NKG2A blockade enhances CAR-T persistence and antitumour function. C_LI

bioengineering↗

bioRxiv2026

Multidimensional atlas of RNA-regulated proteins revealed by RNA-dependent thermal proteome profiling

RNA and proteins interact pervasively in cellular processes, yet the functional relevance of most RNA-binding proteins remains unknown. To address this, we developed RNA-dependent thermal proteome profiling (RTPP), a method that identifies RNA-regulated proteins (RRPs) by detecting changes in a proteins structural stability upon RNA binding, without requiring crosslinking or enrichment. Applying RTPP in HEK293T cells revealed 1,664 RRPs, including 257 previously undetected RNA-binding "orphans". One such orphan, SGK3, binds the lncRNA CASC15, facilitating its PtdIns(3)P binding, endosomal recruitment and kinase activity. We further generated a tissue-specific RRP atlas, identifying interactions unique to particular organs, including hippocampus-specific RRPs dysregulated in Alzheimers disease. Integrating RTPP with proximity labeling resolved RNA-binding heterogeneities across subcellular compartments. Live-cell RNase treatment also uncovered proteins associated with cell surface RNA, revealing that RO60 form nanoscale clusters with glycoRNA. RTPP provides a powerful approach to decipher functional RNA-protein interactions across multiple biological dimensions.

molecular biology↗

bioRxiv2026

A DNA-scaffolded Retron Ring Mediates Antiphage Immunity

Retrons are a diverse family of bacterial defence systems that couple reverse transcriptase (RT) activity to antiphage immunity by producing multicopy single-stranded DNA (msDNA). Yet, the molecular mechanisms by which most systems detect infection and execute immunity remain unknown. Here, we define the structure, immune sensing and effector mechanisms of retron type IX, composed of an RT, a non-coding RNA, a tandem KH-HTH subunit and a HEPN RNase effector. Retron IX confers robust protection against diverse bacteriophages. Cryo-EM and biochemical analyses reveal a supramolecular ring assembly composed of 8-10 repeating modules, spanning up to 230 [A] in diameter. Within this assembly, the msDNA scaffolds the outer rim inhibiting the HEPN ribonuclease in a catalytically poised state, with the active site occluded within the inner layer. We identify a phage-encoded PD-(D/E)XK nuclease as the immune trigger that cleaves the exposed msDNA stem-loop, leading to ring disassembly and HEPN effector release. Upon activation, the HEPN ribonucleases cleave tRNAs indiscriminately, inducing dormancy and blocking phage propagation. Our findings unveil how ring-shaped higher-order assembly controls enzymatic activities while allowing signal-specific activation and establish the ncRNA as an evolvable scaffold underlying the remarkable structural and defensive diversity of bacterial retron immune complexes.

microbiology↗

bioRxiv2026

Epstein-Barr virus transformation creates a methionine-dependent ferroptosis vulnerability in B cells

Epstein-Barr virus (EBV) causes over 200,000 cancers annually, including immunoblastic lymphomas in immunosuppressed hosts. Most transformed cells arrest, yet survive when deprived of the essential amino acid methionine. We instead find that EBV transformed lymphoblastoid cell lines (LCLs), which model the EBV latency III program-driven B-cell lymphoproliferative diseases of immunosuppressed hosts, rapidly die upon methionine restriction. Methionine restriction elevated LCL lipid reactive oxygen species and triggered ferroptosis. Whereas methionine restriction hypomethylates the EBV genome and triggers viral reactivation in latency I Burkitt cells by lowering the cellular methylation potential, the LCL latency III program instead redirected methionine toward redox defense, without altering the SAM/SAH ratio. Stable-isotope tracing revealed that latency III strongly induces transsulfuration, synthesizing cysteine de novo to support glutathione pools. The EBV oncoprotein LMP2A, which mimics B-cell receptor signaling, supported newly infected human B cell cystathionine-{beta}-synthase and cystathionine-{gamma}-lyase expression and methionine dependence, phenocopied by immunoglobulin crosslinking. In vivo, dietary methionine restriction impaired LCL xenograft outgrowth and depleted tumor cystine. Combined methioninase and cyst(e)inase administration blocked both cysteine sources, collapsed tumor glutathione levels, and triggered ferroptosis. Our results define methionine metabolism as a targetable ferroptosis vulnerability of EBV-transformed B cells. HighlightsO_LIMethionine restriction triggers EBV-transformed lymphoblastoid B cell ferroptosis C_LIO_LIEBV latency III induces transsulfuration to sustain LCL cysteine and glutathione C_LIO_LIMethioninase or dietary methionine restriction strongly impair LCL growth in vivo C_LIO_LIMethioninase plus cyst(e)inase collapses xenograft GSH levels and drives ferroptosis C_LI

biochemistry↗

bioRxiv2026

Discrete depolarisations of chordotonal organ neurons propagate toward the soma and are independent of the sensory TRP channels NompC and Nanchung-Inactive.

The electrophysiological process of auditory transduction in insects remains largely conjecture due to the unknown role of ion channels localised to the cilia, but experimental evidence supports either NompC or Nan-Iav as the auditory mechanotransduction ion channel. Here, we knocked down two key genes that code for the two candidate sound-activated ion channels using dsRNA-mediated RNA interference. We measured sound-evoked activity of the auditory nerve and intracellular electrical currents from the ciliated ending of individual auditory receptors. We found that the sound-evoked nerve activity was reduced in nompC, nan and ift88 knockdown. Using whole-cell patch clamp recordings we found that nompC and nan knockdown resulted in reduced sound-evoked transduction current. Stochastic depolarisations hypothesised to be mediated from one of the candidate mechanotransduction ion channels, either NompC or Nan-Iav, where not affected by knockdown of either channel. The discrete depolarisations are therefore mediated through another unidentified ion channel. We test the hypothesis that discrete depolarisations are graded action potentials that travel toward the soma through noise analysis of the transduction current and analysis of discrete depolarisations to voltage-steps. As a positive control we also knocked down ift88, a protein essential for transporting proteins, including ion channels, along the cilium and found both the transduction current and the discrete depolarisations decreased. Key pointsO_LIInjection of dsRNA decreased RNA of nompC and nan C_LIO_LISound-evoked nerve activity is reduced for RNAi-mediated knockdown of nompC and nan C_LIO_LINompC and Nan both contribute to the transduction current C_LIO_LIThe stochastic discrete depolarisations are not due to NompC or Nan-Iav ion channel but to a third unidentified ion channel. C_LIO_LINoise analysis of the transduction current and the discrete depolarisations suggests they are graded action potentials that travel in the direction of the soma. C_LIO_LIKnockdown of ift88 reduced both the transduction current and discrete depolarisations. C_LI Significance StatementInsects are important to understand, economically, agriculturally and medically. However, we still do not understand fundamental aspects of how insects detect their own body movements, vibrations and sound. These senses are detected by insect chordotonal organs, specialised miniaturised mechanoreceptors that convert movements into electrical signals through specialised ion channels. Previous experimental work has advocated either NompC or Nan-Iav as the mechanosensitive ion channel. Here, for the first time, we reduced the expression of both nompC and nan and measured the sound-evoked transduction current directly from neurons in a specialised auditory chordotonal organ. In contradiction to previous studies, we show that both ion channels contribute to the transduction current and find that electrical signals termed "discrete depolarisations" travel toward the soma.

neuroscience↗

bioRxiv2026

A Variant-Resistant Linear Epitope in the SARS-CoV-2 Nucleocapsid Protein for Antigen Detection

We previously generated a mouse monoclonal antibody, N179, against the SARS-CoV-2 nucleocapsid (N) protein and developed a colloidal gold-based immunochromatographic test strip. This assay achieved a detection limit of 2 ng/mL and displayed 98% concordance with RT-qPCR results. However, the precise epitope recognized by mAb N179 had not been defined. Using a panel of GST-fused N protein truncation fragments, we mapped the linear B-cell epitope recognized by mAb N179 to the flexible C-terminal tail of the N protein by Western blotting and ELISA. The minimal binding motif required for mAb N179 recognition was identified as 390QTVTLL395. Multiple sequence alignment of 11 representative SARS-CoV-2 lineages, including Alpha, Beta, Gamma, Delta, and Omicron subvariants BA.1, BA.2, and BA.3.2, revealed that this epitope was completely conserved across all variants analyzed. Stringent local pairwise alignment analysis using EMBOSS WATER further showed that the 390QTVTLL395 motif achieved a perfect 6/6 match exclusively in SARS-CoV-2; no identical sequence was detected in the seven common human coronaviruses, four influenza viruses, or five bat coronaviruses examined. Structural prediction analyses indicated that this region is surface-exposed and possesses a strong linear B-cell epitope propensity. Together, these findings identify 390QTVTLL395 as a specific molecular signature of SARS-CoV-2 among the viruses analyzed. Our results provide an epitope-level explanation for the sustained diagnostic reliability of the mAb N179-based assay against emerging variants, clarify the molecular basis for its lack of cross-reactivity, and may inform the rational design of SARS-CoV-2 diagnostics targeting conserved, mutation-resistant epitopes. ImportanceWe identified the exact nucleocapsid protein epitope recognized by monoclonal antibody N179, a diagnostic antibody used in a colloidal gold rapid assay. The identified 390QTVTLL395 motif at residues 390 to 395 was conserved among the SARS-CoV-2 variants analyzed and was not present as an identical continuous sequence in the related respiratory viruses examined. This work supports precise epitope mapping as a useful strategy for evaluating and revalidating diagnostic antibodies as respiratory viruses evolve.

microbiology↗