Biology subjects

Chen, C.

Publications and source records attributed to Chen, C..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

Unlocking biological insight from single-cell data with an interpretable dual-stream foundation model

Deep learning foundation models are revolutionizing single-cell biology, yet learning holistic and discriminative representations from complex, high-dimensional data remains a central challenge. Although Transformer-based single-cell language models have shown significant progress, they typically rely on a single input-encoding scheme, a practice that results in the loss of critical gene expression information and hinders the effective learning of global cellular representations. To address these challenges, we introduce scDMC, an innovative single-cell Dual-stream Masked Contrastive pre-training framework designed to synergistically optimize information fidelity at both the gene and cellular levels. Pre-trained on only 2 million cells far fewer than the datasets used by mainstream models, scDMC sets a new state-of-the-art in multiple benchmark tasks, including cell annotation, clustering, and data integration. More importantly, we demonstrate that scDMC can uncover functional gene modules, infer cell-type-specific regulatory networks in a data-driven manner, and exhibits a high degree of biological interpretability.

bioinformatics↗

bioRxiv2025

A Novel 3D Visualization Method in Mice Identifies the Periportal Lamellar Complex (PLC) as a Key Regulator of Hepatic Ductal and Neuronal Branching Morphogenesis

The liver is a complex organ responsible for multiple functions, including metabolism, energy storage, detoxification, bile secretion, and immune regulation. Its highly organized vascular system plays a crucial role in maintaining functional zonation and tissue homeostasis. Within the liver, the hepatic artery, portal vein, hepatic vein, bile duct, and nerve networks intertwine to form an intricate three-dimensional architecture; however, traditional two-dimensional imaging fails to reveal their true spatial relationships, and current three-dimensional imaging methods remain insufficient to capture fine structural details. To achieve comprehensive visualization of these multi-ductal systems, we established a high-resolution three-dimensional imaging platform that combines multicolor perfusion of metallic compound nanoparticles (MCNPs) with an optimized tissue-clearing protocol (Liver-CUBIC), enabling simultaneous 3D reconstruction of the portal vein, hepatic artery, bile duct, and hepatic vein in mouse livers. Based on these data, we identified and defined a previously unrecognized structure located in the outer layer of the portal vein, termed the Periportal Lamellar Complex (PLC). The PLC encircles the portal vein between the vascular endothelium and the perisinusoidal region, exhibits low-permeability barrier characteristics, and contains a distinctive population of CD34Sca-1 endothelial cells. During liver fibrosis, the PLC extends from the portal vein toward the hepatic lobule, forming a structural scaffold that guides bile duct and nerve migration.

developmental biology↗

bioRxiv2025

Evolutionary convergence and trophic diversity in hot vent and cold seep shrimps showcase a continuum of symbiosis

Convergent evolution offers a powerful lens through which to examine the selective forces shaping life in extreme environments. In deep-sea hot vents and cold seeps, invertebrates have independently evolved symbioses with chemosynthetic bacteria, but repeated origins of such associations within a family remain rare. Here, we investigate the evolutionary emergence of chemosymbiosis in the shrimp family Alvinocarididae across 22 species collected globally. Electron microscopy identified a gradient of epibiotic bacterial colonization within the cephalothoracic cavity, ranging from absent to dense filamentous mats, suggesting distinct trophic strategies. Isotope and lipid trophic markers confirmed difference in reliance on chemosynthetic production among sympatric species with different bacterial colonization from a single vent. Phylogenetic analysis reveals at least two independent origins of chemosymbiosis, suggesting evolutionary convergence. Microhabitat association data further show that symbiotic phenotypes are most common in shrimps occupying the hottest, most geofluid-enriched microhabitats, though exceptions suggest contributions from additional ecological or physiological constraints. Our findings reveal many alvinocaridids as gradually evolving towards symbiosis, highlighting the importance of intermediate cases to understand the pathways to chemosymbiosis. This study contributes to a broader understanding of the predictability of evolutionary outcomes in distinct habitats such as vents, with broader implications for resilience of deep-sea ecosystems.

evolutionary biology↗

bioRxiv2025

Leucine-rich repeat kinase 2 impairs the release sites of Parkinson's disease vulnerable dopamine axons

The end-stage pathology of Parkinsons disease (PD) involves the loss of dopamine-producing neurons in the substantia nigra pars compacta (SNc). However, synaptic deregulation of these neurons begins much earlier. Understanding the mechanisms behind synaptic deficits is crucial for early therapeutic intervention, yet these remain largely unknown. In the SNc, different dopamine neuron subtypes show varying susceptibility patterns to PD, complicating our understanding. This study uses intersectional genetic mouse models to uncover synaptic perturbations in vulnerable dopamine neurons, focusing on the LRRK2 kinase, a protein closely linked to PD. Through a combination of immunofluorescence and advanced proximity labeling methods, we found higher LRRK2 expression in the most vulnerable dopamine neuron subclusters. High-resolution imaging revealed that pathogenic LRRK2 disrupts release sites in vulnerable dopamine axons, leading to decreased in vivo spontaneous and evoked striatal dopamine release in mice with LRRK2 mutations. Proteomic and biochemical analyses indicate that mutant LRRK2 increases the phosphorylation of RAB3 proteins, reducing their interactions with RIM1and RIM2 effector proteins and impacting their synaptic functions. Overall, this research highlights the cell-autonomous dysfunctions caused by mutant LRRK2 in neurons, which are primarily affected by the disease. It also provides a framework for future therapeutic strategies for early nigrostriatal synaptic deficits in PD.

neuroscience↗

bioRxiv2025

An Efficient Lasso Framework for Admixture-Aware Polygenic Scores

Polygenic scores (PGS) have promising clinical applications for risk stratification, disease screening, and personalized medicine. However, most PGS are trained on predominantly European ancestry cohorts and have limited portability to external populations. While cross-population PGS methods have demonstrated greater generalizability than single-ancestry PGS, they fail to properly account for individuals with recent admixture between continental ancestry groups. GAUDI is a recently proposed PGS method which overcomes this gap by leveraging local ancestry to estimate ancestry-specific effects, penalizing but allowing ancestry-differential effects. However, the modified fused LASSO approach used by GAUDI is computationally expensive and does not readily accommodate more than two-way admixture. To address these limitations, we introduce HAUDI, an efficient LASSO framework for admixed PGS construction. HAUDI re-parameterizes the GAUDI model as a standard LASSO problem, allowing for extension to multi-way admixture settings and far superior computational speed than GAUDI. In extensive simulations, HAUDI compares favorably to GAUDI while dramatically reducing computation time. In real data applications, HAUDI uniformly out-performs GAUDI across 18 clinical phenotypes, including total triglycerides (TG), C-reactive protein (CRP), and mean corpuscular hemoglobin concentration (MCHC), and shows substantial benefits over an ancestry-agnostic PGS for white blood cell count (WBC) and chronic kidney disease (CKD).

genomics↗

bioRxiv2025

REM Sleep Misfires: Intruding Delta Waves Forecast Tau, Amyloid, and Forgetting in Aging

Rapid Eye Movement (REM) sleep degrades with age, and more severely in Alzheimers disease (AD). REM sleep comprises about twenty percent of adult sleep, alternates between phasic and tonic periods, and includes delta waves (1-4Hz) in two forms: fast sawtooth waves and slower, NREM-like waves, whose expression dynamically varies across REM periods. Yet, the functional relevance of these REM sleep delta waves remains unknown. Here, using two independent cohorts, we show that aging is associated with a shift from fast sawtooth to slow NREM-like delta waves, particularly during phasic REM sleep--a period typically marked by high cortical activation. Beyond chronological age, this shift is associated with amyloid-beta and tau burden, suggesting that AD pathology disrupts REM-specific oscillatory patterns. Furthermore, this shift in REM oscillations is linked to impaired overnight memory consolidation, independent of NREM sleep quality. Moreover, variation in ApoE alleles, a major genetic risk factor for AD, was independently associated with a reduction in fast sawtooth wave density, thereby linking a genetic predisposition for AD to these specific REM microstructural changes. These findings identify a novel signature of memory decline in aging and implicate REM sleep as a distinct vulnerable substrate through which AD pathology may impair brain function.

neuroscience↗

bioRxiv2025

Dynamic representation of sound locations during task engagement in marmoset auditory cortex

In auditory cortex, neural responses to stimuli inside receptive fields (RFs) can be further facilitated by behavioral demands, such as attending to a spatial location. It is less clear how off-RF stimuli modulate neural responses and contribute to behavioral tasks. Our recent study revealed a particular form of location-specific facilitation evoked by repeated stimulation from an off-RF location, suggesting behavioral modulation of spatial RFs. To further explore this question, we trained marmosets to attend to sound locations that were either inside or outside the RFs of auditory cortical neurons. The majority of neurons showed increased firing rates at target locations inside their RFs. Interestingly, this increase also occurred outside the RFs, sometimes exceeding the responses at the RF center during passive listening. These task-related off-RF facilitation were much more common in the caudal area than in the rostral area and the primary auditory cortex. A normalization model reproduced the off-RF facilitation using widespread suppression. The models prediction was confirmed by experimental observations of widespread reductions in firing rate and hyperpolarized membrane potentials for off-RF stimuli. These results suggest that behavioral task demands recruit a broader range of neurons than those that are responsive to a target sound in the passive state.

neuroscience↗

bioRxiv2025

An Anterior Cingulate Cortex Neuronal Ensemble Controls Contextual Opioid Analgesic Tolerance

Opioids are first-line treatments for pain; however, tolerance leads to decreased efficacy and escalated dosing, increasing the risk of opioid use disorder and overdose. Despite well-established cellular and molecular adaptations, opioid analgesic tolerance can be rapidly reversed in settings where these drugs are not expected. The specific neuronal populations that orchestrate this expectation-based tolerance are not known. In this study, we used a contextual tolerance training method, whole-brain clearing, and immunostaining to identify brain regions involved in contextual tolerance and to pinpoint a neuronal ensemble in the anterior cingulate cortex (ACC) that is activated by contextual analgesic tolerance. We observed that calcium activity in principal neurons of the ACC is suppressed by fentanyl in opioid-naive mice and during contextual reversal, but not during contextual tolerance. Chemogenetic silencing of the ACC induced analgesic tolerance reversal in the opioid-associated context without affecting thermal nociception in opioid-free mice. Conversely, chemogenetic activation of the ACC contextual tolerance-active neuronal ensemble triggered analgesic tolerance in an unassociated context. This research highlights the role of ACC neuronal ensembles in mediating expectation-driven, contextual opioid analgesic tolerance without affecting basal nociception. Modulating ACC activity could provide a promising strategy to improve pain relief while maintaining the essential ability to detect harmful stimuli.

neuroscience↗

bioRxiv2025

Aberrant recursive splicing in a human disease locus

Recursive splice sites are rare motifs postulated to facilitate splicing across massive introns and shape isoform diversity, especially for long, brain-expressed genes. The necessity of this unique mechanism remains unsubstantiated, as does the role of recursive splicing (RS) in human disease. From analyses of rare copy number variants (CNVs) from almost one million individuals, we previously identified large, heterozygous deletions eliminating an RS site (RS1) in the first intron of CADM2 that conferred substantial risk for attention deficit hyperactivity disorder (ADHD) and other neurobehavioral traits. CADM2 encodes a neuronally expressed cell adhesion molecule that has repeatedly been associated with ADHD and numerous similar traits. To explore the molecular impact of RS ablation in CADM2, we used CRISPR to model patient deletions and to target a smaller region ([~]500 base pairs) containing RS1 in both human induced neurons (iNs) and rats. Transcriptome analyses in unedited iNs provided a catalog of CADM2 transcripts, including novel transcripts that retained RS exons. Intriguingly, ablating RS1 altered the gradient of RNA abundance across the first intron of CADM2, decreased the level of CADM2 expression, and impacted transcript usage. Decreased CADM2 expression was reflected in reduced exon usage downstream of the RS1 site and global alteration to genes involved in neuronal processes including synapse and axon development. Given the scale of our analyses and the widespread association of CADM2 with neurobehavioral traits, we sought to validate these findings using in vivo models and found that rodent models harboring Cadm2 RS1 deletions exhibited significant changes in relevant behaviors and functional brain connectivity. In summary, our analyses demonstrate a functional role for RS as a noncoding regulatory mechanism in a gene associated with a spectrum of neuropsychiatric and behavioral traits. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/666599v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@171156borg.highwire.dtl.DTLVardef@13553baorg.highwire.dtl.DTLVardef@bee7forg.highwire.dtl.DTLVardef@156f19e_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

genomics↗

bioRxiv2025

MechanoAge, a machine learning platform to identify individuals susceptible to breast cancer based on mechanical properties of single cells

BackgroundExisting breast cancer risk models inadequately identify individuals at latent risk, particularly among women without known genetic mutations or family history. Risk is often underestimated or overestimated due to reliance on population-level data and neglect of cellular aging and mechanobiological alterations. MethodsWe profiled primary human mammary epithelial cells (HMECs) from women of varying ages and risk backgrounds using mechano-node-pore sensing (mechano-NPS), a high-throughput microfluidic platform that captures single-cell mechanical properties. Using machine learning, we developed a classifier, MechanoAge, to predict age-related mechanical phenotypes and introduce a novel index, mechano-RISQ, to quantify deviations linked to breast cancer risk. We further assessed the cytoskeletal protein keratin 14 (KRT14) as a molecular mediator of these mechanical states through overexpression and knockdown experiments. FindingsCells from younger women carrying BRCA1/2 mutations or with a family history of breast cancer exhibited accelerated mechanical aging compared to age-matched controls. Elevated mechano-RISQ scores reflected an increased proportion of cells with "older" mechanical profiles. KRT14 overexpression induced an aged mechanical phenotype in younger cells, while knockdown partially reversed this state in older cells. CyTOF profiling and modeling showed KRT14 modulation impacted protein expression signatures associated with aging and risk, particularly in luminal cells. InterpretationMechanical properties of breast epithelial cells reflect biologic aging and cancer susceptibility. Mechano-RISQ offers a new approach for identifying individuals at elevated risk, especially among average-risk populations, and may complement existing risk models by incorporating biophysical measures of epithelial aging.

cancer biology↗

bioRxiv2025

MOH: a novel multilayer multi-omics heterogeneous graph for single-cell clustering

Cell clustering is crucial in single-cell multi-omics research for identifying distinct cellular populations. Although there has been progress in integrating multi-omics data for clustering, combining more than two types of omics data remains challenging due to the diversity and heterogeneity of these datasets. Traditional approaches typically use heterogeneous graphs that integrate only two types of omics data, constructing graphs with genes and cells as nodes and a single type of edge representing their relationships. However, this method has limitations as it overlooks cell-cell interactions and struggles to capture complex cellular dynamics. Additionally, the graph structure must be redesigned whenever new omics data are introduced, limiting the scalability of these models. To address these issues, we introduce MOH, a novel single-cell clustering algorithm based on a multilayer multi-omics heterogeneous graph. MOH integrates three key single-cell omics types: scRNA-seq, scATAC-seq, and spatial transcriptomics. It constructs a multilayer heterogeneous graph to simultaneously extract and enhance representations from all three omics layers, incorporating both intra-layer and inter-layer edges to capture association and similarity relationships. This enriched representation leads to an accurate clustering results. Extensive experiments show that MOH outperforms six state-of-the-art methods on unsupervised clustering metrics, offering a precise and comprehensive analysis with consistent improvements across all evaluation criteria. Moreover, downstream analyses validate the results, revealing novel biological insights into immune disorder complications in cancer, cancer drug repurposing, and new signaling pathways, which merit further investigation and validation.

bioinformatics↗

bioRxiv2025

Population genomics of the endangered scaly-foot snail defines conservation units amid deep-sea mining threats in Indian Ocean vents

Hydrothermal vents in the Indian Ocean face imminent deep-sea mining, yet lack baseline high-resolution connectivity data for their endemic fauna. We present the first population genomic study of the endangered scaly-foot snail (Chrysomallon squamiferum), an iconic species distributed across three vent biogeographic provinces. Analysing 125 individuals from eight vent fields using 14 million single-nucleotide polymorphisms, we identify five genetic groups that warrant recognition as evolutionarily significant units. Demographic modelling reveals critical contributions from extinct or unsampled phantom populations to the contemporary genetic structure. Together with physical ocean modelling, we show that the deep currents drive asymmetric south-to-north gene flows, while transform faults act as dispersal barriers. We propose Longqi-Duanqiao fields on the Southwest Indian Ridge and Wocan field on the Carlsberg Ridge as two isolated populations prioritised for protection. Given its exceptional adaptations, wide distribution, and public recognition, the scaly-foot snail is well-positioned to serve as both a flagship and umbrella species to ensure the survival of a broader suite of vent biodiversity. As the International Seabed Authority finalises its Mining Code in 2025, our findings provide essential genomic evidence to mitigate the impacts of mining on genetic diversity and inform transboundary conservation strategies for this vulnerable ecosystem.

ecology↗

bioRxiv2025

Liquid-Liquid Phase Separation of Sp100-HMG: Driving Biogenesis and Functional Diversity of PML Nuclear Bodies

Promyelocytic leukemia nuclear bodies (PML NBs) are membraneless organelles (0.1-1 m) integral to fundamental cellular processes, yet the molecular logic governing their hierarchical organization is unclear. Contrary to the classical "PML-sole-scaffold" model, we identify Sp100-HMG as the unique isoform that autonomously nucleates into liquid-like condensates. Our findings establish an "inside-out" assembly paradigm, where Sp100-HMG initiates a liquid core that recruits PML and other client proteins (DAXX, ATRX) through three distinct cooperative processes: I. Multimerization domain- and intrinsically disordered region (IDR)-mediated LLPS of Sp100-HMG, nucleating the core; II. C-terminal-dependent protein-protein interactions enriching client components; and III. SUMOylation-directed PML recruitment, facilitating the formation of a stabilizing peripheral shell. This assembly paradigm extends beyond Sp100-HMG, as evidenced by ZBTB16--a PML NB-associated oncoprotein implicated in acute promyelocytic leukemia -- adopting an analogous mechanism to organize PML-positive condensates. Using HEp-2 cells as a main model, we show this hierarchical assembly is critical for orchestrating transcriptional programs and cell-cycle dynamics. Together, our study defines a new biogenesis mode for PML-NBs, where a master liquid nucleator coordinates shell integrity and plasticity for nuclear homeostasis. Significance StatementPML nuclear bodies (PML NBs) serve as essential organizers of the cell nucleus, yet the assembly principles underlying their biogenesis and linking it to functional heterogeneity, spatial positioning, and compositional diversity remain elusive. This study overturns the long-standing "PML-centric" view by establishing an LLPS-driven, hierarchical "inside-out" assembly paradigm. We identify Sp100-HMG as a master liquid nucleator that initiates a core to organize the outer PML shell. This inner-core LLPS-driven assembly logic is shared by other PML NB-associated factors, such as the oncoprotein ZBTB16, providing a unified biophysical framework to explain the structural integrity and plasticity of nuclear condensates. Functionally, this organizational process is critical for shaping the compositional diversity and spatial specificity of PML bodies, thereby modulating transcriptional programs and cell-cycle dynamics in a context-dependent manner. These findings offer broad insights into how organized protein condensation sustains nuclear homeostasis and its dysfunction in diseases such as leukemia.

cell biology↗

bioRxiv2025

A trade-off mechanism underpins the evolution of a young two-gene sex-determining system in plants

Sexual systems in animals and plants are remarkably diverse, with dioecy having evolved independently in numerous lineages. In plants, dioecy often evolved more recently than in the best-studied animal systems, making plants especially important for understanding how separate sexes evolved independently from functionally hermaphrodite ancestors. Despite long-standing theories of developmental trade-offs in sex allocation, the underlying genetic mechanisms remain elusive. Here, we show that the XY sex determination system in the dioecious plant species Eurycorymbus cavaleriei in Sapindaceae involves two Y-linked mutations that act jointly within the developmental male-female trade-off: YUN{Delta}, a truncated allele that lowers the dosage of the D-class MADS-box gene YUN, and SUNMAO, a novel sRNA locus that silences the X-linked SUN allele. In females, SUN stabilizes the HD-ZIP transcription factor KUN, which is a known sex determinant in another dioecious plant, thereby promoting femaleness by increasing YUN expression; loss of SUN expression, together with the effect of YUN{Delta}, shifts development toward males. Two interlocking regulatory loops in this "SKY" module (SUN-KUN-YUN) fine-tunes YUN dosage. This dioecious system in E. cavaleriei likely evolved by sequential mutations in genes acting in the predicted male-female trade-off system, with their close linkage reflecting a translocation, and later recombination-suppressing inversions.

plant biology↗

bioRxiv2025

Inertial sensing of water content in tumor spheroids

Cellular water content governs the concentration of all biomolecules inside a cell, thereby influencing the physical and functional properties of the cell. However, measurements of water content in physiologically relevant cell culture models remain largely unavailable, particularly in 3D models such as tumor spheroids and organoids. Here, we achieve such measurements using a commercially available, industrial-grade, steel tube. The steel tube functions as a mechanical resonator that inertially senses the buoyant mass of particles. For microgram-scale particles [≥]400 {micro}m in diameter, we achieve <1% precision error in buoyant mass with a 5-minute acquisition interval. By sequentially measuring the buoyant mass of individual, glioblastoma patient-derived tumor spheroids in media of different densities and cell permeabilities, we determine the absolute and fractional (v/v) water content of the spheroids, along with their dry mass, volume, and density properties. We achieve ~0.4% precision error in fractional water content with a throughput of 3 spheroids per hour. This enables us to detect both inter-spheroid variability in fractional water content and acute responses to kinase inhibition. Overall, we establish a simple and accessible technique for quantifying water content in living 3D cell culture models, opening new avenues for studying biophysical regulation in multicellular systems.

bioengineering↗

bioRxiv2025

An open-source pipeline for calcium imaging and all-optical physiology in human stem cell-derived neurons

High-throughput profiling of neuronal activity at single-cell resolution is essential for advancing our understanding of brain function, enabling large-scale functional screens, and modeling neurological disorders. However, existing approaches are limited by scalability, manual data processing, and variability, thus restricting their ability to detect disease-associated phenotypes. Here, we present a scalable, open-source platform that integrates optogenetic stimulation, calcium imaging, automated data acquisition, and a fully integrated analysis pipeline. By combining spontaneous and evoked activity profiling, the system enables robust quantification of dynamic neuronal responses across hundreds of stem cell-derived human neurons and multiple timepoints, facilitating phenotyping at both cellular and network levels. We validated the platform by recapitulating established activity phenotypes in neurodevelopmental disorders including CDKL5 Deficiency Disorder and SSADH deficiency. In addition, we generated CRISPR-Cas9 knock-in human induced pluripotent stem cell (hiPSC) lines stably expressing the genetically encoded calcium indicator GCaMP6s to model network dysfunction in Tuberous Sclerosis Complex (TSC). Using this system, we further demonstrated functional rescue of the altered neuronal activity observed in the TSC following pharmacological intervention. By linking single-cell dynamics to population-level phenotypes, this framework provides a powerful and broadly applicable tool for disease modeling, mechanistic studies, and therapeutic screening across a range of neurological disorders.

neuroscience↗

bioRxiv2025

Hybrid peptide DNA nanomaterials enable potent and broad-spectrum virus neutralization

The continued emergence of antigenic drift and drug-resistant viral strains highlights the need for antiviral strategies that deliver robust efficacy, broad subtype coverage, and minimal off-target toxicity. We demonstrate a potent and broad-spectrum strategy that employs hybrid biomaterials of Urumin (a host defense peptide) and a honeycomb (HC) DNA origami through spatially organized multivalent presentation for enhanced antiviral efficacy. Molecular dynamics simulations reveal that Urumin penetrates and destabilizes the hemagglutinin (HA) trimer core, disrupting influenza A viral (IAV) entry. Arranging Urumin in trimeric clusters on the HC enables potent multivalent binding to trimeric HAs on IAV, enhancing antiviral efficacy at nanomolar concentrations, [~]1,000-fold more effective than free Urumin. In vitro assays confirm HC-Urumin outperforms free Urumin in blocking viral entry and preserving cell viability in more IAV subtypes. In vivo studies show that compared to free Urumin, HC-Urumin treatment reduces disease severity, preserves physiological behavior, and decreases mortality in infected mice, while maintaining virus-specific adaptive immune responses without altering humoral immunity. Our study offers an advanced and effective materials platform and strategy for broad-spectrum, low-dose intervention against human and animal IAVs, which can be adapted to combat other viruses by patterning corresponding host defense peptides on custom designed DNA nanostructures.

bioengineering↗

bioRxiv2025

Super-pangenome analysis of 3562 human and animal papillomavirus isolates illuminates their genome and pathogenicity evolution

Papillomaviruses (PVs) are groups of ubiquitous DNA viruses infecting a wide range of vertebrate hosts, including human. The infection of some human PVs (i.e., HPVs) are strongly associated with cancers, but it remains elusive how such pathogenicity evolved at the genomic level. Here we performed a super-pangenome analysis on a compendium of well-curated 3562 human and animal PV genomes. We found their global genomic diversity being strongly associated with their body sites and tissue origins, but not with their host, geographical, or disease specificity. By reconciling time-resolved phylogenies of PVs and their hosts, we revealed a high-resolution view on how virus-host cospeciation, horizontal host switches, and duplication/loss turnovers collectively shaped the evolution of PVs. We identified key selection-driven mutations that defined the genus-specific divergence of PVs, with those underlying the rise of Alpha-PVs highly enriched in the N-terminal domain of E1 gene. Especially, we identified a group of risk-defining variant sites showing contrasting genotypes between low-risk and high-risk HPVs. With four independent PV genome cohorts, we further validated their high sensitivity and specificity on HPV risk classification even at single site level, underscoring their application values in large-scale HPV screening tests. Finally, with cervical and oropharyngeal cancer patient cohorts assembled by this study, we also evaluated the prognostic value of specific HPV16 variants in predicting patient survival. Taken together, such illumination on the genome and pathogenicity evolution of PVs paves the road for better prevention, control, and treatment of PV-related cancers. Significance statementPapillomaviruses (PVs) are ancient and widespread DNA viruses co-evolved with many vertebrate hosts, including human. Some human PVs (e.g., HPV16 and HPV18) bear strong association with cancers, raising a pressing public health challenge. A better understanding of how such pathogenicity evolved holds the key in addressing this challenge. Here we systematically investigated the genomic and evolutionary diversity of PVs via a pangenome study on over 3500 human and animal PV isolates, which revealed key selection-driven mutations shaping their genome and pathogenicity evolution. With independently acquired HPV-associated cancer cohorts, we further demonstrated how some of these important HPV variants can serve as clinically informative predictive and prognostic biomarkers. Such comprehensive characterization on PVs genome diversity, pathogenicity evolution, and clinical implication paves the road for better prevention, control, and treatment of PV-related cancers.

genomics↗