Biology subjects

Liu, H.

Publications and source records attributed to Liu, H..

At least 109 records · Page 6Linked to original sources

bioRxiv2026

Striatal FOXP2 is essential for stable vocal production in non-human primates

The transcription factor FOXP2 is the most well-known language-related gene in humans, yet its role in primate vocalization remains poorly understood. Here we report that knockdown of FOXP2 in the striatum markedly disrupts vocalization stability in the marmoset monkey, a valuable non-human primate model for studying vocal behavior. FOXP2 exhibited high expression in the marmoset striatum, especially during early development. Using the CRISPR-Cas12 system, we achieved specific in vivo editing of the FOXP2 gene and effective knockdown of FOXP2 protein expression in the marmoset striatum. Two neonatal marmosets received bilateral striatal injections of the gene-editing and control virus, respectively, and were raised together in the same family. In three such marmoset pairs, analysis of vocalizations recorded during 6-15 weeks post-injection revealed that striatal FOXP2 knockdown significantly altered vocal features and increased intra-individual variability in phee syllables--the most common marmoset vocalization, often produced repetitively as multi-syllable phee calls. Notably, in FOXP2-edited marmosets, acoustic alterations were minimal in the first syllable of phee calls but became progressively more pronounced in subsequent syllables, which exhibited a marked upward shift in the frequency spectrum over time with progressively steeper slopes. These temporal dynamics in vocal features reflect a reduction in the stability of continuous vocal production. In line with the known striatal functions in motor control, our findings provide the first evidence of FOXP2 in controlling vocalization in non-human primates, thereby opening new avenues for investigating the neural mechanisms underlying FOXP2 function.

neuroscience↗

bioRxiv2026

Axonal swelling as a neuron-specific compartment to sequester and expel misfolded proteins

Neurons are long-lived, highly specialized cells with extended neurites, requiring precise control of misfolded proteins over time and space. Yet, where misfolded proteins are directed and how quality-control pathways adapt during aging are still unresolved. Here, we identify a neuron-specific quality-control compartment that emerges in neurites as aggresome function declines with age, which we call SolAS (Soluble Misfolded Proteins-induced Axonal Swellings). These structures not only sequester misfolded proteins but also facilitate their clearance via microvesicles and exophers. During aging, neurite SolAS and soma aggresomes function hierarchically to maintain proteostasis, with aggresomes acting as the primary sequestration sites in young neurons and SolAS taking over this role as their function declines with age. This transition is driven by a shift from a ubiquitin-dominant to a SUMO-dominant balance. Moreover, solid pathogenic amyloids, such as GA50, can be converted into soluble forms and sequestered into SolAS via SUMO fusion, thereby reducing neurotoxicity. Our findings identify a previously unrecognized neuronal quality-control pathway critical for proteostasis during aging.

neuroscience↗

bioRxiv2026

Spatial Multi-Omics Reveals Extracellular Matrix Remodeling and VSMC Phenotypic Switching in Moyamoya Disease

BackgroundMoyamoya disease (MMD) is a progressive cerebrovascular disorder characterized by steno-occlusive lesions and intimal hyperplasia. Although vascular smooth muscle cell (VSMC) phenotypic switching is implicated in its pathogenesis, the precise spatial interplay between extracellular matrix (ECM) remodeling and local metabolic alterations within the distinct vascular microenvironments remains unknown. MethodsSuperficial temporal artery (STA) samples from patients with MMD and controls were analyzed by histology, immunofluorescence, spatial transcriptomics, spatial proteomics, and spatial metabolomics. Single cell RNA sequencing was used to profile the cellular landscape of STA tissues. To functionally validate the identified pathway, human brain vascular smooth muscle cells (HBVSMCs) were stimulated with fibronectin 1 (FN1), and patient derived induced pluripotent stem cell smooth muscle cells (iPSC-SMCs) were generated for migration and protein expression assays following ITGA5 silencing or focal adhesion kinase (FAK) inhibition. ResultsMMD STA samples exhibited marked intimal hyperplasia with medial thinning and intimal accumulation of -SMA positive cells. Spatial transcriptomic and proteomic analyses identified an intimal remodeling program characterized by increased FN1, EFEMP1, fibronectin, ITGA5, and FAK, together with reduced MYH11. FN1 stimulation promoted smooth muscle cell migration, ECM associated protein expression, and FAK phosphorylation, whereas ITGA5 knockdown or FAK inhibition attenuated these effects. Patient derived MMD iPSC-SMCs showed similar abnormalities, including enhanced migration, increased FAK activation, reduced contractile markers, and increased ECM associated proteins. Spatial metabolomics and integrated multi-omics analyses further revealed that these changes were coupled to a metabolically depleted intimal niche enriched for reduced acyl-CoA related metabolites. ConclusionsIntegrated spatial multi-omics identifies coupled ECM remodeling and metabolic alteration in the hyperplastic intima of MMD. Within this context, the FN1-ITGA5-FAK axis emerges as a plausible mediator of smooth muscle remodeling that warrants further validation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/721225v1_ufig1.gif" ALT="Figure 1"> View larger version (90K): org.highwire.dtl.DTLVardef@3f6e19org.highwire.dtl.DTLVardef@554d49org.highwire.dtl.DTLVardef@451dd9org.highwire.dtl.DTLVardef@1aac1e9_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Parallel processing chains span cytoarchitectures to organize association cortex

Task fMRI1 and electrophysiology2 have revealed distributed, linked cortical patches with shared category preferences (e.g., faces, objects, places)1,3-5, smaller than cytoarchitectonic areas. Resting-state functional connectivity (RSFC) similarly showed that somato-cognitive action network (SCAN) nodes interleave with effectors (foot, hand, mouth), subdividing the precentral gyrus6. Here, using multiple precision functional mapping (PFM) modalities (RSFC, task, lags), we discovered that most of association cortex is organized like face processing and SCAN, with small, discrete patches interconnected into chains. Such patch-chains densely tile prefrontal cortex but are largely absent from primary cortex. Cortico-striatal connectivity is organized such that patches of the same chain connect to the same striatal location. Within chains, infra-slow fMRI signals are ordered in time. RSFC-defined chains align with task fMRI localizers (e.g., visual, motor, pain). Chains are absent at birth and emerge in the first year of life, suggesting their formation is at least partially experience-driven. Cytoarchitectonic areas are subdivided by patches, and patches in the same chain are distributed across different cytoarchitectures. Chains represent parallel ordered processing streams that are separated by information domain and behavioral goals, not cytoarchitectonics. Functional subdivision of architectonics into smaller patches, interlinked to form cross-architecture chains, enable greater parallelization and flexible specialization of processing.

neuroscience↗

bioRxiv2026

Cardiac oxidative stress monitoring enabled by hierarchical mechanical adaptation

Soft bioelectronics have advanced cardiac monitoring through electrophysiological tracking, yet this alone cannot resolve the metabolic pathology essential to surgical decision-making. However, real-time molecular sensing on beating hearts remains unresolved due to deformation-induced sensor failure and stress-induced metabolite artifacts. This challenge is exemplified by ischemia-reperfusion injury (IRI), a major cardiac surgery complication characterized by reactive oxidative species (ROS) bursts, where true pathological ROS signals being confounded by mechanotransduction-induced ROS artifacts. Herein, we propose an enzymatic cardiac oxidative stress biosensor (E-cardiac) with hierarchical mechanical adaptation: macro-scale biofluid-mediated contact, micro-scale fiber reorganization, and nano-scale enzymatic confinement within gold nanoarches dissipate interfacial stress. This produces ultrathin ([~]460 nm), soft (0.79 kPa) E-cardiac with robust electrochemical stability (100% strain), low detection limit (380 nM), rapid adhesion (<3 s), stable biosensing on beating heart, as well as minimal invasive deployment capability. Mechanical analysis and cellular studies confirm mitigated stress-induced ROS and absent PIEZO channel activation. Validated across cardiomyocytes, ex vivo tissues, multi-species ischemia models (mouse, rat, rabbit, pig), rat ischemia-reperfusion injury, and Langendorff hearts simulating graded perfusion deficits, E-cardiac quantitatively differentiates IRI severity (sham < ischemia < reperfusion) as well as detecting the "ECG blind window". The E-cardiac platform provides real-time metabolic feedback for surgical guidance during cardiac procedures, enabling timely intervention before irreversible damage.

bioengineering↗

bioRxiv2026

Specialised root hair cells facilitate rhizobial infection

Legumes establish symbiotic partnerships with soil bacteria that convert atmospheric nitrogen into plant-available forms. Symbiotic bacteria enter through root hairs following recognition by cell surface receptors that help identify compatible symbionts. However, many root hairs express these receptors, and it has long remained unclear why only a small fraction become infected. Here, we use single-cell transcriptomics to show that legumes pre-specify a rare root hair population for infection before bacterial contact. These susceptible root hairs represent less than one percent of the total, express infection-associated genes prior to encountering symbionts and are conserved in distantly related legumes. Their abundance is regulated by the hormone ethylene and correlates with infection capacity. Our findings reveal that root hair cells do not respond uniformly to symbionts but are instead transcriptionally specialised in advance to control infection entry points. This pre-specification provides a mechanism to balance symbiotic benefits against pathogen infection risks and may exemplify a more general strategy used by multicellular hosts to spatially restrict microbial access.

plant biology↗

bioRxiv2026

Designer indicators for two-photon recording of subthreshold voltage dynamics

Subthreshold voltage dynamics are critical for neuronal information integration, yet they remain understudied in vivo due to the limitations of current tools. While genetically encoded voltage indicators (GEVIs) offer a promising alternative, their application for deep-tissue recording using two-photon (2P) microscopy--a preferred method for deep-tissue recording--has been hindered by insufficient sensitivity for detecting millivolt-scale subthreshold signals. Here, we refined our multiparametric two-photon high-throughput screening platform to develop two novel GEVIs, JEDI3sub and JEDI3hyp, tailored explicitly for subthreshold voltage detection. Through fast 2P optical recording in awake, behaving mice, we demonstrated the superior sensitivity of JEDI3 indicators compared to JEDI-2P. We also showed that JEDI3sub can track population-level subthreshold optical tuning, while JEDI3hyp reliably captured subthreshold dynamics associated with sharp-wave ripple oscillations in hippocampal PV interneurons. Finally, JEDI3hyp facilitated extended imaging of brain-state-dependent, millivolt-scale subthreshold voltage changes across deep-layer somas, fine dendritic structures, and diverse cell types. By addressing the critical gap in 2P optical recording of subthreshold voltage dynamics, JEDI3 indicators open new avenues for studying neural information processing and its alterations in health and disease.

neuroscience↗

bioRxiv2026

A versatile, positive-going voltage indicator that enables accessible two-photon recordings in vivo

Genetically encoded voltage indicators (GEVIs) enable cell-type-specific optical readout of membrane potential, but two-photon (2P) spike detection has been hampered by low signal-to-noise and ultrafast off-kinetics, restricting use to specialized microscopes. We introduce FORCE1s, a green, positive-going GEVI engineered to make robust 2P voltage imaging broadly accessible. FORCE1s brightens from a dark baseline during depolarization, reports spikes with [~]100% {Delta}F/F in awake mice, and displays repolarization kinetics that are tuned for reliable spike detection at sub-kilohertz frame rates. As a result, FORCE1s supports spike-resolved multi-cell recordings on standard resonant-scanning microscopes, and further scales to larger fields of view and neuron counts on advanced modalities. FORCE1s also enables multiplexed voltage-neurotransmitter imaging and extended recordings in freely moving mice using a compact, affordable MEMS-based 2P miniscope. Together, these advances establish FORCE1s as a community-ready tool that democratizes deep-tissue voltage imaging across platforms and experimental contexts.

neuroscience↗

bioRxiv2026

Periosteal and periarticular compartments house lymphatic vessels in bone

The anatomical localization of lymphatic vessels in bone remains controversial and has led to conflicting interpretations of skeletal lymphatic function. Here we assessed lymphatic identity and localization in bone using mouse genetic labeling, tissue clearance, and three-dimensional imaging. We analyzed long bones after extensive periosteum removal and identified Vegfr3+ blood vessels lacking Lyve1 expression within bone marrow, whereas Vegfr3+Lyve1+ lymphatic vessels were confined to residual periosteal regions. Genetic lineage tracing using Prox1-Cre/ER;mScarlet further confirmed that lymphatic vessels are absent from long bone marrow and restricted to periosteal compartments, particularly in fibrous but not cambial layers. Extending these analyses to the mandible, we observed Vegfr3+Lyve1+ lymphatic vessels localized to periarticular soft tissues surrounding the temporomandibular joint (TMJ), while mandibular bone marrow contained only Vegfr3+Lyve1- blood vessels and lacked Prox1 lineage-traced lymphatic vessels. Together, these findings establish that lymphatic vessels in bone are confined to periosteal and periarticular compartments and absent from bone marrow, providing a framework for interpreting lymphatic contributions to skeletal physiology and disease.

cell biology↗

bioRxiv2026

Photo-downregulation of SIRT4 mitigates aging in mice by enhancing H3K9ac via fatty acid metabolism

As organisms age, mitochondrial metabolic activity declines, and disrupted gene expression regulation mediated by histone acetylation induces the emergence of senescent physiological phenotypes in tissues. In this study, we found that periodic exposure to red light significantly increased histone H3 Lys9 acetylation (H3K9ac) levels in the tissues and organs of aged mice. Following red light exposure, silent information regulation factor 4 (SIRT4) protein levels in keratinocytes were notably reduced, whereas glycolysis, fatty acid metabolism, and the tricarboxylic acid (TCA) cycle were significantly activated in keratinocytes. The reduction in mitochondrial SIRT4 levels enhances the acetylation of mitochondrial metabolic proteins, particularly malonyl-CoA decarboxylase (MCD), a potent inhibitor of the key rate-limiting enzyme carnitine palmitoyltransferase 1A (CPT1A) in fatty acid oxidation. This process promotes mitochondrial fatty acid oxidation and TCA cycle. Additionally, the decrease in SIRT4 activates SIRT1 through feedback mechanisms, thereby alleviating its inhibition on PPAR- in senescent keratinocytes and comprehensively activating the expression of genes related to lipid metabolism. This lipid metabolism activation ultimately facilitates the accumulation of acetyl-CoA within keratinocytes, increases H3K9ac levels, and reshapes the expression patterns of senescence-related genes. Eventually, cellular aging is effectively mitigated by the synergistic regulation of metabolism, inflammation, and gene expression. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/717004v2_ufig1.gif" ALT="Figure 1"> View larger version (82K): org.highwire.dtl.DTLVardef@ba3865org.highwire.dtl.DTLVardef@1cc9a58org.highwire.dtl.DTLVardef@1a90e7borg.highwire.dtl.DTLVardef@1f5e88f_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical AbstractMechanism of anti-aging action of red light: Red light can reduce SIRT4 signalling in keratinocytes, thereby reactivating lipid metabolism and increasing levels of acetyl-CoA. This promotes histone acetylation, which in turn remodels the expression of age-related inflammatory factors and genes.

cell biology↗

bioRxiv2026

The senescence-inhibitory p53 isoform Δ133p53α represses the proinflammatory chemokine CXCL10 in progeria model mice and naturally aged mice

Aims{Delta}133p53 is a naturally occurring isoform of the human p53 protein that inhibits p53-mediated cellular senescence. We previously reported that transgenic expression of this senescence-inhibitory p53 isoform counteracts aging-associated pathological changes in progeria model mice (heterozygous LmnaG609G/+). The anti-aging effect of {Delta}133p53 was attributed in part to reduced levels of the proinflammatory cytokine IL-6. This study aims to comprehensively profile {Delta}133p53-induced changes in cytokines and chemokines. MethodsA Luminex-based multiplex quantitative assay was performed using mouse serum samples from transgenic {Delta}133p53-expressing LmnaG609G/+ mice and non-expressing controls. Quantitative RT-PCR and RNA in situ hybridization assays were used to assess Cxcl10 expression in mouse tissues. In addition, gene expression datasets from human tissues were analyzed. ResultsWe confirmed {Delta}133p53-mediated repression of serum IL-6 levels. We also found that {Delta}133p53 reduced serum levels of CXCL1, IL-1, and CXCL10. We further characterized CXCL10, which has not previously been associated with progeria in mice or humans. Consistent with reduced serum CXCL10 levels, both young (15-week-old) and old (10-month-old) {Delta}133p53-expressing LmnaG609G/+ mice showed reduced Cxcl10 expression in the liver, spleen, and brain, major organs that produce CXCL10, compared with age-matched non-expressing controls. In naturally aged wild-type mice (2 years old), transgenic {Delta}133p53 expression also significantly repressed Cxcl10 expression in the spleen and brain. An inverse association between CXCL10 and {Delta}133p53 levels was observed in human spleen tissues, suggesting physiological relevance to human aging. ConclusionCXCL10, a proinflammatory chemokine elevated in both accelerated and natural aging, is a potential target of the anti-inflammatory activity of {Delta}133p53.

physiology↗

bioRxiv2026

Seeded aggregation of ANXA11 induces prion-like propagation, TDP-43 co-pathology and nucleocytoplasmic transport defects

Mutations in ANXA11 cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), yet the mechanisms linking ANXA11 dysfunction to neurodegeneration remain poorly defined. Recent cryo-EM studies revealed heteromeric ANXA11-TDP-43 filaments in patient brains, suggesting a direct pathological connection between these two ALS-associated proteins. However, whether ANXA11 possesses intrinsic amyloidogenic properties and how its aggregation relates to TDP-43 proteinopathy remain unknown. Here, we demonstrate that ANXA11 undergoes liquid-liquid phase separation and subsequently matures into amyloid fibrils through a liquid-to-solid phase transition. ANXA11 fibrils exhibit prion-like properties, including self-templating seeding activity and intercellular propagation in human iPSC-derived neurons. Strikingly, ANXA11 fibrils induces pathological conversion of TDP-43, including hyperphosphorylation, accumulation in detergent-insoluble fractions, and formation of cytoplasmic aggregates. TurboID proximity-labeling proteomics further revealed aggregation-dependent enrichment of nuclear pore complex and nucleocytoplasmic transport factors in the ANXA11 aggregate-proximal proteome. Consistently, ANXA11 aggregation was associated with nuclear envelope abnormalities, altered nucleoporin distribution, impaired mRNA export, and progressive neuronal toxicity in iPSC-derived neurons. Together, these findings establish ANXA11 as an intrinsically amyloidogenic, phase-transition-competent protein whose seeded assemblies propagate between cells, induce TDP-43 co-pathology, and are linked to nucleocytoplasmic transport defects and neuronal injury, thereby providing a mechanistic framework for ANXA11-associated ALS/FTD pathogenesis. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/713853v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@1aaad3org.highwire.dtl.DTLVardef@c51d5eorg.highwire.dtl.DTLVardef@10b2891org.highwire.dtl.DTLVardef@1945575_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIANXA11 undergoes liquid-liquid phase separation and matures into amyloid fibrils through a liquid-to-solid phase transition. C_LIO_LIANXA11 fibrils supports homotypic seeding and propagate within SH-SY5Y cells and iPSC-derived neurons. C_LIO_LIANXA11 fibrils induce TDP-43 pathological conversion, including phosphorylation and accumulation in insoluble aggregates. C_LIO_LIANXA11 aggregation is associated with nuclear pore complex remodeling, impaired mRNA export, and neuronal toxicity. C_LI In BriefANXA11 undergoes phase separation and matures into prion-like amyloid fibrils through a liquid-to-solid transition. These seeded assemblies propagate between cells and human neurons, induce TDP-43 pathological conversion, and are associated with remodeling of nuclear pore complexes, impaired mRNA export, and progressive neuronal toxicity. ANXA11 forms seeded amyloid assemblies that spread between cells, induce TDP-43 pathology, and disrupt nucleocytoplasmic transport.

neuroscience↗

bioRxiv2026

A Dynamic Oligomerization Network Coordinates Hemagglutinin-Mediated Membrane Fusion on Influenza Virions

Influenza A virus (IAV) entry is mediated by the trimeric glycoprotein hemagglutinin (HA), which undergoes low-pH-triggered conformational rearrangements to drive membrane fusion. Although biochemical and biophysical studies have long suggested that HA trimers function cooperatively, the structural basis for this cooperativity on intact virions has remained unclear. Here, using cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), we determine the in situ structure of prefusion HA on native virions at 3.58 [A] resolution, enabling atomic modeling of membrane-anchored HA. We show that neighbouring HA trimers engage in lateral interactions mediated by HA1 subunits, assembling into flexible dimeric, pentameric, and hexameric organizations that form locally ordered lattices on the viral surface. A 6.0 [A] reconstruction of the HA-dimer reveals the molecular interfaces underlying these assemblies. Disruption of the dominant HA1-HA1 interaction markedly impairs viral entry and slows membrane fusion kinetics. Together, these findings define a virion-level mechanism for coordinated HA activation and establish a structural framework for understanding cooperative membrane fusion by class-I viral fusion proteins.

biophysics↗

bioRxiv2026

Coronavirus envelope protein drives iron sensing disorder by hijacking the TAp73-FDXR axis

Iron overload is increasingly recognized as a critical contributor to coronavirus pathogenesis1, yet the underlying induction mechanisms remain unclear. Here, we uncover a fundamental pathway by which coronavirus drives IRP1 RNA-binding activity to induce iron accumulation2 via targeting the TAp73-FDXR axis. Specifically, coronavirus infection represses transcription of FDXR (encoding the key rate-limiting enzyme in host iron-sulfur cluster synthesis3), thereby impairing host iron-sulfur cluster generation to trigger the functional conversion of the cytosolic aconitase 1 (ACO1) into iron-regulatory protein 1 (IRP1)4, ultimately leading to the hosts persistently false perception of iron deficiency. We identify TAp73 as the primary transcription factor governing FDXR expression, and demonstrate that the coronavirus envelope protein (CoV-E) orchestrates TAp73 nuclear export. Subsequently, CoV-E binds TAp73 through a critical valine residue within its C-terminal PBM domain, inducing the K48-linked ubiquitination and proteasomal degradation of TAp73. Furthermore, we developed a CoV-E-targeting molecule, DPTP-FC, which blocks CoV-E-TAp73 interaction via forming steric hindrance and effectively alleviates iron accumulation and tissue damage caused by PEDV, PDCoV, and SARS-CoV-2 infection. Our study reveals the central role of the TAp73-FDXR axis in CoV-induced iron accumulation, highlighting CoV-E as an attractive antiviral target and DPTP-FC as a promising therapeutic candidate.

microbiology↗

bioRxiv2026

Paternal behavior is controlled by preoptic Trpc5 neurons

Male parenting behavior is highly conserved and activated only after offspring are born. Here we show that the behavioral switch from infanticide in virgin male mice to caregiving in wild-type sires is associated with enhanced expression and activation of Transient receptor potential channel 5 (Trpc5) in estrogen receptor (Esr1)-expressing neurons in the hypothalamic medial preoptic area (MPOA). While selective deletion of Trpc5 from Esr1MPOA neurons diminishes paternal behavior in sires, overexpression of Trpc5 in these neurons converts the otherwise infanticidal virgin males to exhibit care to pups. Mechanistically, Trpc5-dependent changes in neuronal excitability underlie fatherhood-associated Esr1MPOA neuron plasticity. Notably, Trpc5 overexpression also enhances escape behavior and elicits exploratory diving behavior, suggesting that these neurons control a broader adaptive parenting response in males. These findings establish a Trpc5-dependent MPOA neural signal as a critical regulator of paternal behavior.

neuroscience↗

bioRxiv2026

HViLM: A Foundation Model for Viral Genomics Enables Multi-Task Prediction of Pathogenicity, Transmissibility, and Host Tropism

MotivationThe emergence of novel viral pathogens poses critical threats to global health, yet current computational approaches for viral risk assessment are predominantly virus-specific and require extensive retraining for each new threat. Computational methods for rapid characterization of emerging viruses across multiple epidemiologically relevant dimensions--pathogenicity, host tropism, and transmissibility--are urgently needed to inform public health responses and guide experimental prioritization. ResultsWe present HViLM (Human Virome Language Model), the first foundation model for panviral genomic analysis through continued pre-training of DNABERT-2 on 5 million non-redundant viral sequences (MMseqs2-clustered from 25 million chunks at 80% identity) spanning 9,000 species across 45+ viral families from the VIRION database. We introduce the Human Virome Understanding Evaluation (HVUE) benchmark comprising seven curated datasets across three prediction tasks: pathogenicity classification, host tropism prediction, and transmissibility assessment. Through parameter-efficient fine-tuning with LoRA, HViLM achieves state-of-the-art performance with average accuracies of 95.32% for pathogenicity, 96.25% for host tropism, and 97.36% for transmissibility assessment. The model demonstrates robust cross-family generalization, substantially outperforming sequence-similarity baselines and general genomic foundation models. Attention-based interpretability analysis reveals that HViLM captures biologically meaningful pathogenicity determinants through molecular mimicry of host regulatory elements, including convergent evolution of eight independent sequences targeting Interferon Regulatory Factor 1 (Irf1) for immune evasion. AvailabilityThe HVUE benchmark datasets, training scripts, and complete implementation are publicly available at https://github.com/duttaprat/HViLM. Pre-trained HViLM-base model weights and fine-tuned task-specific variants are available on Hugging Face at https://huggingface.co/duttaprat/HViLM-base. Supplementary informationSupplementary data are available online.

bioinformatics↗

bioRxiv2026

ISPpu10 is a structure-gated bridge RNA recombinase that drives safe, large-scale genomic plasticity

IS110 elements employ bridge RNA to direct target site recognition, yet whether additional layers of specificity exist beyond RNA-DNA base pairing is unknown. Here we identified ISPpu10, an IS110 element in Pseudomonas putida that is associated with >100-kb segmental amplifications during adaptive laboratory evolution. All insertions mapped to multiple identical copies of a single conserved intergenic sequence harboring a GC-rich 5' extension that forms a stem-loop. Systematic mismatch and compensatory substitution scanning revealed a sequence-structure dual-match logic: base pairing between the bridge RNA and target DNA serves as an RNA-guided match, whereas the target-encoded stem-loop provides an additional specificity determinant. Transplanting this stem-loop into Escherichia coli targets improved on-target integration and reduced genome-wide off-target insertion, establishing the stem-loop as a portable structural gate. These findings reveal a structural recognition layer beyond base-pairing, suggesting how bacteria reconcile transposition with genome integrity and offering a strategy for precise genome editing.

microbiology↗

bioRxiv2026

Functional impact of PCSK9 variants on LDL uptake in a knockout hepatic model

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a central regulator of low-density lipoprotein (LDL) cholesterol metabolism, yet the functional consequences of many clinically observed PCSK9 variants remain unknown. To establish a rigorous system for quantitative variant assessment, we generated a PCSK9 knockout (KO) HepG2 cell line through CRISPR/Cas9-mediated deletion of exons 2-8, effectively removing both the prodomain and catalytic regions required for PCSK9 function. This null background enabled systematic functional mapping of wild-type (WT) PCSK9 and multiple clinically relevant variants representing well-characterized, recurrent, and previously understudied alleles. Functional assays revealed pronounced heterogeneity among variant activities. The classical gain-of-function (GOF) variants D374Y and R496W exhibited robust suppression of LDL uptake, whereas A443T--an infrequently reported and previously uncharacterized variant--demonstrated a loss-of-function (LOF)-like phenotype with significantly enhanced LDL uptake. Additional poorly characterized variants, including V4I, R104C/V114A, and R496W/N425S, displayed minimal functional profiles, providing novel mechanistic insights. Surface LDL receptor (LDLR) levels generally correlated with LDL uptake but revealed unique patterns for specific variants. This KO-based rescue system provides a high-resolution framework for mechanistic classification of both established and poorly characterized PCSK9 variants, bridging the gap between genetic discovery and functional interpretation while supporting precision lipid-lowering strategies.

biochemistry↗